Diff of the two buildlogs: -- --- b1/build.log 2024-12-23 21:59:54.383275887 +0000 +++ b2/build.log 2024-12-23 22:02:17.916764841 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 23 09:56:39 -12 2024 -I: pbuilder-time-stamp: 1734990999 +I: Current time: Tue Dec 24 12:00:10 +14 2024 +I: pbuilder-time-stamp: 1734991210 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/13000/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 23 22:00 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='9fb0d42981b8426ba609d8f2b2aa6ee6' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='13000' - PS1='# ' - PS2='> ' + INVOCATION_ID=f9ffa6695f9e4a208afa014b68765574 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=19956 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5G0qSGoZ/pbuilderrc_ffwG --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5G0qSGoZ/b1 --logfile b1/build.log ruby-bio_2.0.5-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5G0qSGoZ/pbuilderrc_wxns --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5G0qSGoZ/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32a 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/13000/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -86,7 +118,7 @@ Depends: debhelper-compat (= 13), gem2deb, ruby-libxml, ruby-test-unit, docbook-to-man, rdtool dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19694 files and directories currently installed.) +(Reading database ... 19681 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -258,10 +290,10 @@ Get: 137 http://deb.debian.org/debian unstable/main armhf ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 138 http://deb.debian.org/debian unstable/main armhf rdtool all 0.6.38-4.1 [44.5 kB] Get: 139 http://deb.debian.org/debian unstable/main armhf ruby-libxml armhf 5.0.3-1+b1 [72.1 kB] -Fetched 43.5 MB in 1s (34.6 MB/s) +Fetched 43.5 MB in 4s (11.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19694 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19681 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.8-3) ... Selecting previously unselected package libexpat1:armhf. @@ -274,7 +306,7 @@ Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20014 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20001 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_armhf.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. @@ -336,7 +368,7 @@ Unpacking libpython3-stdlib:armhf (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21077 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21064 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_armhf.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package sgml-base. @@ -726,8 +758,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Dec 23 21:58:22 UTC 2024. -Universal Time is now: Mon Dec 23 21:58:22 UTC 2024. +Local time is now: Mon Dec 23 22:01:02 UTC 2024. +Universal Time is now: Mon Dec 23 22:01:02 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -853,7 +885,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable @@ -1110,4392 +1146,4392 @@ Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: - test_db_ids: .: (0.001751) - test_dbs: .: (0.000732) - test_go_ids: .: (0.000645) - test_go_terms: .: (0.000668) - test_parser: .: (0.001119) - test_set_date: .: (0.000632) - test_set_desc: .: (0.000657) - test_to_str: .: (0.000705) + test_db_ids: .: (0.001589) + test_dbs: .: (0.000711) + test_go_ids: .: (0.000482) + test_go_terms: .: (0.000497) + test_parser: .: (0.000929) + test_set_date: .: (0.000558) + test_set_desc: .: (0.000534) + test_to_str: .: (0.000521) Bio::FuncTestCommandBackports: - test_mktmpdir_with_block: .: (0.001916) - test_mktmpdir_without_block: .: (0.001740) - test_remove_entry_secure: .: (0.001020) + test_mktmpdir_with_block: .: (0.001981) + test_mktmpdir_without_block: .: (0.001403) + test_remove_entry_secure: .: (0.000939) Bio::FuncTestCommandCallMisc1: - test_call_command: .: (0.004193) - test_call_command_fork: .: (0.000466) - test_call_command_open3: .: (0.004249) - test_call_command_popen: .: (0.003432) + test_call_command: .: (0.007278) + test_call_command_fork: .: (0.000381) + test_call_command_open3: .: (0.010842) + test_call_command_popen: .: (0.005011) Bio::FuncTestCommandCallSimple: - test_call_command: .: (0.003546) - test_call_command_fork: .: (0.000398) - test_call_command_open3: .: (0.003414) - test_call_command_popen: .: (0.003260) + test_call_command: .: (0.005415) + test_call_command_fork: .: (0.000424) + test_call_command_open3: .: (0.005450) + test_call_command_popen: .: (0.005900) Bio::FuncTestCommandCallWithSpace: - test_call_command: .: (0.003871) - test_call_command_fork: .: (0.000400) - test_call_command_open3: .: (0.003736) - test_call_command_popen: .: (0.003244) + test_call_command: .: (0.005660) + test_call_command_fork: .: (0.000376) + test_call_command_open3: .: (0.005248) + test_call_command_popen: .: (0.004795) Bio::FuncTestCommandChdir: - test_call_command_chdir: .: (0.003586) - test_call_command_fork_chdir: .: (0.000794) - test_call_command_popen_chdir: .: (0.003205) - test_query_command_chdir: .: (0.003110) - test_query_command_fork_chdir: .: (0.000746) - test_query_command_popen_chdir: .: (0.002892) + test_call_command_chdir: .: (0.003229) + test_call_command_fork_chdir: .: (0.000759) + test_call_command_popen_chdir: .: (0.003022) + test_query_command_chdir: .: (0.002757) + test_query_command_fork_chdir: .: (0.000718) + test_query_command_popen_chdir: .: (0.003078) Bio::FuncTestCommandQuery: - test_query_command: .: (0.006664) - test_query_command_fork: .: (0.002275) - test_query_command_open3: .: (0.006194) - test_query_command_popen: .: (0.005740) + test_query_command: .: (0.007444) + test_query_command_fork: .: (0.003331) + test_query_command_open3: .: (0.007828) + test_query_command_popen: .: (0.007587) Bio::FuncTestCommandTmpdir: - test_close!: .: (0.001922) - test_initialize: .: (0.001046) - test_path: .: (0.000858) - test_path_after_close: .: (0.001203) + test_close!: .: (0.001845) + test_initialize: .: (0.000842) + test_path: .: (0.000788) + test_path_after_close: .: (0.001044) Bio::FuncTestSequenceOutputEMBL: - test_output_embl: .: (0.032142) - test_output_fasta: .: (0.020533) + test_output_embl: .: (0.023497) + test_output_fasta: .: (0.014900) Bio::NCBIDB::TestCommon: - test_acc_version: .: (0.000915) - test_accession: .: (0.000656) - test_accessions: .: (0.000560) - test_comment: .: (0.000472) - test_common_name: .: (0.000593) - test_definition: .: (0.000645) - test_features: .: (0.000934) - test_gi: .: (0.000574) - test_keywords: .: (0.000603) - test_locus: .: (0.000387) - test_nid: .: (0.000514) - test_organism: .: (0.000556) - test_origin: .: (0.000626) - test_references: .: (0.001489) - test_segment: .: (0.000623) - test_source: .: (0.000862) - test_taxonomy: .: (0.000579) - test_version: .: (0.000621) - test_versions: .: (0.000532) + test_acc_version: .: (0.000869) + test_accession: .: (0.000519) + test_accessions: .: (0.000515) + test_comment: .: (0.000395) + test_common_name: .: (0.000444) + test_definition: .: (0.000516) + test_features: .: (0.000695) + test_gi: .: (0.000422) + test_keywords: .: (0.000477) + test_locus: .: (0.000300) + test_nid: .: (0.000383) + test_organism: .: (0.000445) + test_origin: .: (0.000497) + test_references: .: (0.001051) + test_segment: .: (0.000504) + test_source: .: (0.000725) + test_taxonomy: .: (0.000455) + test_version: .: (0.000491) + test_versions: .: (0.000381) Bio::TestAA: - test_13: .: (0.000620) - test_1n: .: (0.000338) - test_name2one: .: (0.000459) - test_name2three: .: (0.000493) - test_one2name: .: (0.000347) - test_one2three: .: (0.000349) - test_three2name: .: (0.000311) - test_three2one: .: (0.000427) - test_to_1_1: .: (0.000311) - test_to_1_3: .: (0.000381) - test_to_1_name: .: (0.000405) - test_to_3_1: .: (0.000320) - test_to_3_3: .: (0.000330) - test_to_3_name: .: (0.000380) - test_to_re: .: (0.000425) + test_13: .: (0.000636) + test_1n: .: (0.000297) + test_name2one: .: (0.000404) + test_name2three: .: (0.000332) + test_one2name: .: (0.000273) + test_one2three: .: (0.000259) + test_three2name: .: (0.000271) + test_three2one: .: (0.000318) + test_to_1_1: .: (0.000255) + test_to_1_3: .: (0.000394) + test_to_1_name: .: (0.000312) + test_to_3_1: .: (0.000277) + test_to_3_3: .: (0.000303) + test_to_3_name: .: (0.000419) + test_to_re: .: (0.000348) Bio::TestAAConstants: - test_bio_aminoacid: .: (0.000677) + test_bio_aminoacid: .: (0.000599) Bio::TestAAindex: - test_api: .: (0.000522) - test_auto_aax1: .: (0.000684) - test_auto_aax2: .: (0.000645) + test_api: .: (0.000431) + test_auto_aax1: .: (0.000653) + test_auto_aax2: .: (0.000516) Bio::TestAAindex1: - test_author: .: (0.000984) - test_comment: .: (0.000667) - test_correlation_coefficient: .: (0.001306) - test_dblinks: .: (0.000656) - test_definition: .: (0.000645) - test_entry_id: .: (0.000627) - test_index: .: (0.000974) - test_journal: .: (0.000715) - test_title: .: (0.000665) + test_author: .: (0.000756) + test_comment: .: (0.000600) + test_correlation_coefficient: .: (0.001293) + test_dblinks: .: (0.000590) + test_definition: .: (0.000503) + test_entry_id: .: (0.000506) + test_index: .: (0.000803) + test_journal: .: (0.000590) + test_title: .: (0.000506) Bio::TestAAindex2: - test_access_A_R: .: (0.002341) - test_access_R_A: .: (0.001960) - test_author: .: (0.000690) - test_cols: .: (0.000623) - test_comment: .: (0.000652) - test_dblinks: .: (0.000649) - test_definition: .: (0.000659) - test_entry_id: .: (0.000647) - test_journal: .: (0.000705) - test_matrix: .: (0.001991) - test_matrix_1_2: .: (0.001903) - test_matrix_2_2: .: (0.001918) - test_matrix_A_R: .: (0.001962) - test_matrix_R_A: .: (0.001909) - test_matrix_determinant: .: (0.012130) - test_matrix_rank: .: (0.011854) - test_matrix_transpose: .: (0.002270) - test_rows: .: (0.000632) - test_title: .: (0.020444) + test_access_A_R: .: (0.001935) + test_access_R_A: .: (0.001393) + test_author: .: (0.000637) + test_cols: .: (0.000554) + test_comment: .: (0.000512) + test_dblinks: .: (0.000432) + test_definition: .: (0.000458) + test_entry_id: .: (0.000519) + test_journal: .: (0.000540) + test_matrix: .: (0.001423) + test_matrix_1_2: .: (0.001339) + test_matrix_2_2: .: (0.001375) + test_matrix_A_R: .: (0.001432) + test_matrix_R_A: .: (0.001407) + test_matrix_determinant: .: (0.008047) + test_matrix_rank: .: (0.007867) + test_matrix_transpose: .: (0.001705) + test_rows: .: (0.000475) + test_title: .: (0.015671) Bio::TestAAindexConstant: - test_delimiter: .: (0.000711) - test_tagsize: .: (0.000345) + test_delimiter: .: (0.000556) + test_tagsize: .: (0.000225) Bio::TestAbif: - test_complement: .: (0.019563) - test_seq: .: (0.018082) - test_to_biosequence: .: (0.019430) + test_complement: .: (0.015456) + test_seq: .: (0.014314) + test_to_biosequence: .: (0.015511) Bio::TestActsLikeMap: - test_mixin: .: (0.000887) + test_mixin: .: (0.000769) Bio::TestActsLikeMapAndMarker: - test_mixin: .: (0.000878) + test_mixin: .: (0.000704) Bio::TestActsLikeMarker: - test_mixin: .: (0.000664) + test_mixin: .: (0.000460) Bio::TestAlignment: - test_add_seq_no_key: .: (0.000795) - test_add_seq_using_seq_with_aaseq_method: .: (0.000410) - test_add_seq_using_seq_with_definition_method: .: (0.000333) - test_add_seq_using_seq_with_entry_id_method: .: (0.000357) - test_add_seq_using_seq_with_naseq_method: .: (0.000389) - test_add_seq_using_seq_with_seq_method: .: (0.000397) - test_consensus_iupac_gap_modes: .: (0.001140) - test_consensus_iupac_missing_char: .: (0.000539) - test_consensus_iupac_missing_char_option: .: (0.000603) - test_consensus_iupac_no_gaps: .: (0.000773) - test_consensus_iupac_of_ambiguous_bases: .: (0.001198) - test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.014476) - test_consensus_opt_gap_mode: .: (0.001689) - test_consensus_opt_missing_char: .: (0.000685) - test_consensus_string_no_gaps: .: (0.000712) - test_consensus_threshold_four_sequences: .: (0.001533) - test_consensus_threshold_two_sequences: .: (0.001051) - test_convert_match: .: (0.000838) - test_convert_unmatch: .: (0.000475) - test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000504) - test_convert_unmatch_different_match_char: .: (0.000427) - test_convert_unmatch_multiple_sequences: .: (0.000995) - test_default_gap_char: .: (0.000275) - test_default_gap_regexp_matches_default_gap_char: .: (0.000290) - test_default_missing_char: .: (0.000272) - test_each_site_equal_length: .: (0.000468) - test_each_site_unequal_length: .: (0.000507) - test_equals: .: (0.000551) - test_match_line_protein: .: (0.001208) - test_normalizebang_extends_sequences_with_gaps: .: (0.000465) - test_seq_length_is_max_seq_length: .: (0.002244) - test_seq_length_when_one_sequence: .: (0.000309) - test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000297) - test_seqclass_when_seqclass_set: .: (0.000313) - test_seqclass_when_sequence_used: .: (0.000297) - test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000294) - test_set_and_get_gap_char: .: (0.000315) - test_store_cannot_override_key: .: (0.000297) - test_store_with_default_keys_and_user_defined_keys: .: (0.000316) - test_store_with_nil_key_uses_next_number_for_key: .: (0.000297) + test_add_seq_no_key: .: (0.000569) + test_add_seq_using_seq_with_aaseq_method: .: (0.000367) + test_add_seq_using_seq_with_definition_method: .: (0.000279) + test_add_seq_using_seq_with_entry_id_method: .: (0.000339) + test_add_seq_using_seq_with_naseq_method: .: (0.000308) + test_add_seq_using_seq_with_seq_method: .: (0.000765) + test_consensus_iupac_gap_modes: .: (0.000830) + test_consensus_iupac_missing_char: .: (0.000454) + test_consensus_iupac_missing_char_option: .: (0.000431) + test_consensus_iupac_no_gaps: .: (0.000588) + test_consensus_iupac_of_ambiguous_bases: .: (0.000755) + test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.010034) + test_consensus_opt_gap_mode: .: (0.001286) + test_consensus_opt_missing_char: .: (0.000538) + test_consensus_string_no_gaps: .: (0.000546) + test_consensus_threshold_four_sequences: .: (0.001115) + test_consensus_threshold_two_sequences: .: (0.000769) + test_convert_match: .: (0.000656) + test_convert_unmatch: .: (0.000361) + test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000408) + test_convert_unmatch_different_match_char: .: (0.000328) + test_convert_unmatch_multiple_sequences: .: (0.000772) + test_default_gap_char: .: (0.000223) + test_default_gap_regexp_matches_default_gap_char: .: (0.000235) + test_default_missing_char: .: (0.000220) + test_each_site_equal_length: .: (0.000358) + test_each_site_unequal_length: .: (0.000348) + test_equals: .: (0.000444) + test_match_line_protein: .: (0.000935) + test_normalizebang_extends_sequences_with_gaps: .: (0.000333) + test_seq_length_is_max_seq_length: .: (0.000407) + test_seq_length_when_one_sequence: .: (0.000236) + test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000243) + test_seqclass_when_seqclass_set: .: (0.000244) + test_seqclass_when_sequence_used: .: (0.000230) + test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000255) + test_set_and_get_gap_char: .: (0.000228) + test_store_cannot_override_key: .: (0.000248) + test_store_with_default_keys_and_user_defined_keys: .: (0.000257) + test_store_with_nil_key_uses_next_number_for_key: .: (0.000296) Bio::TestAlignmentEnumerableExtension: - test_alignment_collect: .: (0.000632) - test_alignment_concat: .: (0.000435) - test_alignment_length: .: (0.000267) - test_alignment_lstrip!: .: (0.000497) - test_alignment_lstrip_nil: .: (0.000345) - test_alignment_normalize!: .: (0.000279) - test_alignment_rstrip!: .: (0.000473) - test_alignment_rstrip_nil: .: (0.000352) - test_alignment_site: .: (0.000445) - test_alignment_slice: .: (0.000295) - test_alignment_strip!: .: (0.000600) - test_alignment_strip_nil: .: (0.000376) - test_alignment_subseq: .: (0.000395) - test_alignment_window: .: (0.000296) - test_collect_each_site: .: (0.000395) - test_consensus_each_site_default: .: (0.000462) - test_consensus_each_site_gap_mode_1: .: (0.000441) - test_consensus_each_site_gap_mode_minus1: .: (0.000517) - test_consensus_iupac: .: (0.001593) - test_consensus_string_default: .: (0.000441) - test_consensus_string_half: .: (0.000456) - test_convert_match: .: (0.000365) - test_convert_unmatch: .: (0.000329) - test_each_seq: .: (0.000334) - test_each_site: .: (0.000512) - test_each_site_step: .: (0.000383) - test_each_window: .: (0.000468) - test_match_line: .: (0.002933) - test_match_line_amino: .: (0.003679) - test_match_line_nuc: .: (0.000523) - test_private_alignment_site: .: (0.000317) - test_remove_all_gaps!: .: (0.000855) - test_seqclass: .: (0.000288) - test_seqclass=: .: (0.000423) - test_seqclass_default: .: (0.000262) + test_alignment_collect: .: (0.000543) + test_alignment_concat: .: (0.000328) + test_alignment_length: .: (0.000234) + test_alignment_lstrip!: .: (0.000371) + test_alignment_lstrip_nil: .: (0.000279) + test_alignment_normalize!: .: (0.000238) + test_alignment_rstrip!: .: (0.000795) + test_alignment_rstrip_nil: .: (0.000274) + test_alignment_site: .: (0.000355) + test_alignment_slice: .: (0.000235) + test_alignment_strip!: .: (0.000430) + test_alignment_strip_nil: .: (0.000289) + test_alignment_subseq: .: (0.000306) + test_alignment_window: .: (0.000229) + test_collect_each_site: .: (0.000312) + test_consensus_each_site_default: .: (0.000331) + test_consensus_each_site_gap_mode_1: .: (0.000355) + test_consensus_each_site_gap_mode_minus1: .: (0.000348) + test_consensus_iupac: .: (0.001101) + test_consensus_string_default: .: (0.000354) + test_consensus_string_half: .: (0.000328) + test_convert_match: .: (0.000290) + test_convert_unmatch: .: (0.000294) + test_each_seq: .: (0.000269) + test_each_site: .: (0.000392) + test_each_site_step: .: (0.000304) + test_each_window: .: (0.000362) + test_match_line: .: (0.002132) + test_match_line_amino: .: (0.002477) + test_match_line_nuc: .: (0.000394) + test_private_alignment_site: .: (0.000292) + test_remove_all_gaps!: .: (0.000600) + test_seqclass: .: (0.000250) + test_seqclass=: .: (0.000286) + test_seqclass_default: .: (0.000204) Bio::TestAlignmentMultiFastaFormat: - test_alignment: .: (0.008967) - test_determine_seq_method: .: (0.005295) - test_entries: .: (0.001041) + test_alignment: .: (0.006531) + test_determine_seq_method: .: (0.003811) + test_entries: .: (0.000768) Bio::TestAlignmentOutput: - test_avoid_same_name: .: (0.000753) - test_avoid_same_name_numbering: .: (0.000429) - test_clustal_have_same_name_true: .: (0.000373) - test_have_same_name_false: .: (0.000340) + test_avoid_same_name: .: (0.000616) + test_avoid_same_name_numbering: .: (0.000357) + test_clustal_have_same_name_true: .: (0.000265) + test_have_same_name_false: .: (0.000257) Bio::TestAlignmentPropertyMethods: - test_gap_char=: .: (0.001234) - test_gap_char_default: .: (0.000320) - test_gap_char_never_nil: .: (0.000308) - test_gap_regexp: .: (0.000303) - test_gap_regexp=: .: (0.000319) - test_gap_regexp_never_nil: .: (0.000290) - test_get_all_property_default: .: (0.000317) - test_get_all_property_nodefault: .: (0.000332) - test_is_gap_default_false: .: (0.000308) - test_is_gap_default_true: .: (0.000311) - test_is_gap_nodefault_false: .: (0.000308) - test_is_gap_nodefault_true: .: (0.000307) - test_missing_char=: .: (0.000304) - test_missing_char_default: .: (0.000296) - test_missing_char_never_nil: .: (0.000285) - test_seqclass=: .: (0.000355) - test_seqclass_default: .: (0.000314) - test_seqclass_never_nil: .: (0.000305) - test_set_all_property: .: (0.000331) + test_gap_char=: .: (0.000859) + test_gap_char_default: .: (0.000301) + test_gap_char_never_nil: .: (0.000256) + test_gap_regexp: .: (0.000248) + test_gap_regexp=: .: (0.000257) + test_gap_regexp_never_nil: .: (0.000236) + test_get_all_property_default: .: (0.000244) + test_get_all_property_nodefault: .: (0.000260) + test_is_gap_default_false: .: (0.000249) + test_is_gap_default_true: .: (0.000249) + test_is_gap_nodefault_false: .: (0.000298) + test_is_gap_nodefault_true: .: (0.000249) + test_missing_char=: .: (0.000242) + test_missing_char_default: .: (0.000242) + test_missing_char_never_nil: .: (0.000233) + test_seqclass=: .: (0.000578) + test_seqclass_default: .: (0.000247) + test_seqclass_never_nil: .: (0.000233) + test_set_all_property: .: (0.000290) Bio::TestAlignmentSite: - test_consensus_iupac: .: (0.001625) - test_consensus_string_50percent: .: (0.000324) - test_consensus_string_50percent_nil: .: (0.000311) - test_consensus_string_default: .: (0.000259) - test_consensus_string_default_nil: .: (0.000268) - test_has_gap_false: .: (0.000266) - test_has_gap_true: .: (0.000254) - test_match_line_amino_100percent: .: (0.000363) - test_match_line_amino_missing: .: (0.001008) - test_match_line_amino_strong: .: (0.000402) - test_match_line_amino_weak: .: (0.000452) - test_match_line_nuc_100percent: .: (0.000357) - test_match_line_nuc_missing: .: (0.000360) - test_remove_gaps!: .: (0.000310) - test_remove_gaps_bang_not_removed: .: (0.000249) + test_consensus_iupac: .: (0.001204) + test_consensus_string_50percent: .: (0.000260) + test_consensus_string_50percent_nil: .: (0.000245) + test_consensus_string_default: .: (0.000211) + test_consensus_string_default_nil: .: (0.000219) + test_has_gap_false: .: (0.000226) + test_has_gap_true: .: (0.000223) + test_match_line_amino_100percent: .: (0.000293) + test_match_line_amino_missing: .: (0.000733) + test_match_line_amino_strong: .: (0.000298) + test_match_line_amino_weak: .: (0.000325) + test_match_line_nuc_100percent: .: (0.000264) + test_match_line_nuc_missing: .: (0.000262) + test_remove_gaps!: .: (0.000278) + test_remove_gaps_bang_not_removed: .: (0.000209) Bio::TestAtomFinder: - test_atoms: .: (0.048287) - test_each_atom: .: (0.000660) - test_find_atom: .: (0.000542) + test_atoms: .: (0.033524) + test_each_atom: .: (0.000480) + test_find_atom: .: (0.000453) Bio::TestBioFastaDefline: - test_acc_version: .: (0.001215) - test_accession: .: (0.001211) - test_accessions: .: (0.001060) - test_description: .: (0.000870) - test_descriptions: .: (0.000925) - test_entry_id: .: (0.000887) - test_get: .: (0.001057) - test_get_all_by_type: .: (0.000920) - test_get_by_type: .: (0.000969) - test_gi: .: (0.000828) - test_id_strings: .: (0.001710) - test_locus: .: (0.000872) - test_method_missing: .: (0.001060) - test_to_s: .: (0.000999) - test_words: .: (0.002005) + test_acc_version: .: (0.000950) + test_accession: .: (0.000885) + test_accessions: .: (0.000849) + test_description: .: (0.000672) + test_descriptions: .: (0.000655) + test_entry_id: .: (0.000586) + test_get: .: (0.000717) + test_get_all_by_type: .: (0.000583) + test_get_by_type: .: (0.000611) + test_gi: .: (0.000578) + test_id_strings: .: (0.001143) + test_locus: .: (0.000565) + test_method_missing: .: (0.000761) + test_to_s: .: (0.000705) + test_words: .: (0.001359) Bio::TestBioGOOntology: - test_dag_edit_format_parser: .: (0.002305) - test_goid2term: .: (0.001063) - test_parse_goids: .: (0.001021) + test_dag_edit_format_parser: .: (0.001781) + test_goid2term: .: (0.000740) + test_parse_goids: .: (0.000737) Bio::TestBioGenBank: - test_basecount: .: (0.000976) - test_circular: .: (0.000749) - test_classification: .: (0.000898) - test_date: .: (0.000644) - test_date_modified: .: (0.001685) - test_division: .: (0.000661) - test_each_cds_feature: .: (0.002062) - test_each_cds_qualifiers: .: (0.002214) - test_each_gene: .: (0.002128) - test_entry_id: .: (0.000715) - test_length: .: (0.000780) - test_locus_circular: .: (0.000841) - test_locus_class: .: (0.001001) - test_locus_date: .: (0.000776) - test_locus_division: .: (0.000793) - test_locus_entry_id: .: (0.000803) - test_locus_length: .: (0.000768) - test_locus_natype: .: (0.000809) - test_locus_strand: .: (0.000766) - test_natype: .: (0.000717) - test_seq: .: (0.000835) - test_seq_len: .: (0.000858) - test_strand: .: (0.000771) - test_strandedness: .: (0.000710) - test_to_biosequence: .: (0.005719) + test_basecount: .: (0.000800) + test_circular: .: (0.000521) + test_classification: .: (0.000710) + test_date: .: (0.000499) + test_date_modified: .: (0.001318) + test_division: .: (0.000519) + test_each_cds_feature: .: (0.001541) + test_each_cds_qualifiers: .: (0.001641) + test_each_gene: .: (0.001564) + test_entry_id: .: (0.000543) + test_length: .: (0.000577) + test_locus_circular: .: (0.000642) + test_locus_class: .: (0.000752) + test_locus_date: .: (0.000607) + test_locus_division: .: (0.000584) + test_locus_entry_id: .: (0.000620) + test_locus_length: .: (0.000660) + test_locus_natype: .: (0.000650) + test_locus_strand: .: (0.000599) + test_natype: .: (0.000543) + test_seq: .: (0.000686) + test_seq_len: .: (0.000628) + test_strand: .: (0.000672) + test_strandedness: .: (0.000559) + test_to_biosequence: .: (0.004099) Bio::TestBioGenPept: - test_circular: .: (0.000912) - test_date: .: (0.000563) - test_dbsource: .: (0.014118) - test_division: .: (0.000669) - test_entry_id: .: (0.000573) - test_length: .: (0.000578) - test_locus: .: (0.000611) - test_seq: .: (0.000660) - test_seq_len: .: (0.000591) + test_circular: .: (0.000773) + test_date: .: (0.000441) + test_dbsource: .: (0.011220) + test_division: .: (0.000609) + test_entry_id: .: (0.000516) + test_length: .: (0.000477) + test_locus: .: (0.000477) + test_seq: .: (0.000499) + test_seq_len: .: (0.000492) Bio::TestBioKEGGGENES_b0529: - test_aalen: .: (0.001031) - test_aaseq: .: (0.001229) - test_chromosome: .: (0.000694) - test_codon_usage: .: (0.000965) - test_cu_list: .: (0.000575) - test_dblinks_as_hash: .: (0.000768) - test_dblinks_as_strings: .: (0.000702) - test_definition: .: (0.000663) - test_division: .: (0.000591) - test_eclinks: .: (0.001181) - test_entry: .: (0.000624) - test_entry_id: .: (0.000631) - test_gbposition: .: (0.000635) - test_gene: .: (0.000655) - test_genes: .: (0.000644) - test_keggclass: .: (0.000692) - test_keggclasses: .: (0.000762) - test_locations: .: (0.000901) - test_motifs_as_hash: .: (0.001233) - test_motifs_as_strings: .: (0.000603) - test_name: .: (0.000662) - test_names_as_array: .: (0.000684) - test_new: .: (0.000595) - test_ntlen: .: (0.000816) - test_ntseq: .: (0.000949) - test_organism: .: (0.000579) - test_orthologs_as_hash: .: (0.000638) - test_orthologs_as_strings: .: (0.000693) - test_pathway: .: (0.000664) - test_pathway_after_pathways_as_strings: .: (0.000893) - test_pathway_before_pathways_as_strings: .: (0.000819) - test_pathways_as_hash: .: (0.000663) - test_pathways_as_strings: .: (0.000626) - test_position: .: (0.000611) - test_structure: .: (0.000899) + test_aalen: .: (0.000897) + test_aaseq: .: (0.000603) + test_chromosome: .: (0.000928) + test_codon_usage: .: (0.000809) + test_cu_list: .: (0.000473) + test_dblinks_as_hash: .: (0.000576) + test_dblinks_as_strings: .: (0.000463) + test_definition: .: (0.000528) + test_division: .: (0.000500) + test_eclinks: .: (0.000536) + test_entry: .: (0.000959) + test_entry_id: .: (0.000516) + test_gbposition: .: (0.000552) + test_gene: .: (0.000549) + test_genes: .: (0.000548) + test_keggclass: .: (0.000620) + test_keggclasses: .: (0.000658) + test_locations: .: (0.000796) + test_motifs_as_hash: .: (0.001006) + test_motifs_as_strings: .: (0.000561) + test_name: .: (0.000522) + test_names_as_array: .: (0.000580) + test_new: .: (0.000544) + test_ntlen: .: (0.000735) + test_ntseq: .: (0.000807) + test_organism: .: (0.000482) + test_orthologs_as_hash: .: (0.000525) + test_orthologs_as_strings: .: (0.000910) + test_pathway: .: (0.000572) + test_pathway_after_pathways_as_strings: .: (0.000747) + test_pathway_before_pathways_as_strings: .: (0.000634) + test_pathways_as_hash: .: (0.000501) + test_pathways_as_strings: .: (0.000489) + test_position: .: (0.000471) + test_structure: .: (0.000505) Bio::TestBioKEGGGENOME_T00005: - test_chromosomes: .: (0.003503) - test_comment: .: (0.001233) - test_data_source: .: (0.001070) - test_definition: .: (0.001061) - test_disease: .: (0.001006) - test_entry_id: .: (0.001271) - test_lineage: .: (0.001159) - test_nalen: .: (0.001008) - test_name: .: (0.000987) - test_new: .: (0.000981) - test_num_gene: .: (0.001276) - test_num_rna: .: (0.000971) - test_original_databases: .: (0.001016) - test_original_db: .: (0.001110) - test_plasmids: .: (0.001204) - test_references: .: (0.007346) - test_statistics: .: (0.001561) - test_taxid: .: (0.001140) - test_taxonomy: .: (0.001111) + test_chromosomes: .: (0.002660) + test_comment: .: (0.001036) + test_data_source: .: (0.000772) + test_definition: .: (0.000767) + test_disease: .: (0.000765) + test_entry_id: .: (0.000991) + test_lineage: .: (0.000824) + test_nalen: .: (0.000836) + test_name: .: (0.000765) + test_new: .: (0.000830) + test_num_gene: .: (0.000986) + test_num_rna: .: (0.000918) + test_original_databases: .: (0.000839) + test_original_db: .: (0.000858) + test_plasmids: .: (0.000963) + test_references: .: (0.005419) + test_statistics: .: (0.001180) + test_taxid: .: (0.000988) + test_taxonomy: .: (0.000949) Bio::TestBioKEGGGENOME_T00070: - test_chromosomes: .: (0.001252) - test_comment: .: (0.000764) - test_data_source: .: (0.001015) - test_definition: .: (0.000721) - test_disease: .: (0.000699) - test_entry_id: .: (0.000682) - test_lineage: .: (0.000783) - test_nalen: .: (0.000645) - test_name: .: (0.000665) - test_new: .: (0.000643) - test_num_gene: .: (0.001078) - test_num_rna: .: (0.000729) - test_original_databases: .: (0.000633) - test_original_db: .: (0.000661) - test_plasmids: .: (0.000961) - test_references: .: (0.001069) - test_statistics: .: (0.000660) - test_taxid: .: (0.001146) - test_taxonomy: .: (0.000745) + test_chromosomes: .: (0.001097) + test_comment: .: (0.001075) + test_data_source: .: (0.000612) + test_definition: .: (0.000667) + test_disease: .: (0.000527) + test_entry_id: .: (0.000505) + test_lineage: .: (0.000558) + test_nalen: .: (0.000509) + test_name: .: (0.000542) + test_new: .: (0.000495) + test_num_gene: .: (0.000812) + test_num_rna: .: (0.000567) + test_original_databases: .: (0.000549) + test_original_db: .: (0.000505) + test_plasmids: .: (0.000710) + test_references: .: (0.000777) + test_statistics: .: (0.000499) + test_taxid: .: (0.000910) + test_taxonomy: .: (0.000599) Bio::TestBioKEGGPATHWAY_ec00072: - test_compounds_as_hash: .: (0.000978) - test_compounds_as_strings: .: (0.000592) - test_dblinks_as_hash: .: (0.000547) - test_dblinks_as_strings: .: (0.000569) - test_description: .: (0.000603) - test_diseases_as_hash: .: (0.000549) - test_diseases_as_strings: .: (0.000530) - test_entry_id: .: (0.001278) - test_enzymes_as_strings: .: (0.000808) - test_genes_as_hash: .: (0.000609) - test_genes_as_strings: .: (0.000532) - test_keggclass: .: (0.000614) - test_ko_pathway: .: (0.000593) - test_modules_as_hash: .: (0.000615) - test_modules_as_strings: .: (0.000551) - test_name: .: (0.000643) - test_new: .: (0.000565) - test_organism: .: (0.000563) - test_orthologs_as_hash: .: (0.001256) - test_orthologs_as_strings: .: (0.000789) - test_pathways_as_hash: .: (0.000577) - test_pathways_as_strings: .: (0.000547) - test_reactions_as_hash: .: (0.000539) - test_reactions_as_strings: .: (0.000548) - test_references: .: (0.000536) - test_rel_pathways_as_hash: .: (0.000684) - test_rel_pathways_as_strings: .: (0.000590) + test_compounds_as_hash: .: (0.000772) + test_compounds_as_strings: .: (0.000453) + test_dblinks_as_hash: .: (0.000449) + test_dblinks_as_strings: .: (0.000398) + test_description: .: (0.000483) + test_diseases_as_hash: .: (0.000413) + test_diseases_as_strings: .: (0.000375) + test_entry_id: .: (0.000950) + test_enzymes_as_strings: .: (0.000699) + test_genes_as_hash: .: (0.000416) + test_genes_as_strings: .: (0.000394) + test_keggclass: .: (0.000457) + test_ko_pathway: .: (0.000406) + test_modules_as_hash: .: (0.000416) + test_modules_as_strings: .: (0.000452) + test_name: .: (0.000440) + test_new: .: (0.000471) + test_organism: .: (0.000434) + test_orthologs_as_hash: .: (0.000929) + test_orthologs_as_strings: .: (0.000629) + test_pathways_as_hash: .: (0.000449) + test_pathways_as_strings: .: (0.000436) + test_reactions_as_hash: .: (0.000400) + test_reactions_as_strings: .: (0.000382) + test_references: .: (0.000390) + test_rel_pathways_as_hash: .: (0.000471) + test_rel_pathways_as_strings: .: (0.000504) Bio::TestBioKEGGPATHWAY_hsa00790: - test_compounds_as_hash: .: (0.001411) - test_compounds_as_strings: .: (0.001418) - test_dblinks_as_hash: .: (0.000636) - test_dblinks_as_strings: .: (0.000599) - test_description: .: (0.000624) - test_diseases_as_hash: .: (0.000648) - test_diseases_as_strings: .: (0.000668) - test_entry_id: .: (0.000643) - test_enzymes_as_strings: .: (0.000577) - test_genes_as_hash: .: (0.001247) - test_genes_as_strings: .: (0.000809) - test_keggclass: .: (0.000657) - test_ko_pathway: .: (0.000630) - test_modules_as_hash: .: (0.000641) - test_modules_as_strings: .: (0.000646) - test_name: .: (0.000646) - test_new: .: (0.000606) - test_organism: .: (0.000675) - test_orthologs_as_hash: .: (0.000878) - test_orthologs_as_strings: .: (0.000644) - test_pathways_as_hash: .: (0.000655) - test_pathways_as_strings: .: (0.000599) - test_reactions_as_hash: .: (0.000572) - test_reactions_as_strings: .: (0.000573) - test_references: .: (0.000586) - test_rel_pathways_as_hash: .: (0.000691) - test_rel_pathways_as_strings: .: (0.000702) + test_compounds_as_hash: .: (0.001186) + test_compounds_as_strings: .: (0.001059) + test_dblinks_as_hash: .: (0.000536) + test_dblinks_as_strings: .: (0.000476) + test_description: .: (0.000527) + test_diseases_as_hash: .: (0.000484) + test_diseases_as_strings: .: (0.000445) + test_entry_id: .: (0.000503) + test_enzymes_as_strings: .: (0.000450) + test_genes_as_hash: .: (0.000884) + test_genes_as_strings: .: (0.000587) + test_keggclass: .: (0.000484) + test_ko_pathway: .: (0.000471) + test_modules_as_hash: .: (0.000493) + test_modules_as_strings: .: (0.000490) + test_name: .: (0.000538) + test_new: .: (0.000472) + test_organism: .: (0.000508) + test_orthologs_as_hash: .: (0.000672) + test_orthologs_as_strings: .: (0.000610) + test_pathways_as_hash: .: (0.000477) + test_pathways_as_strings: .: (0.000461) + test_reactions_as_hash: .: (0.000429) + test_reactions_as_strings: .: (0.000423) + test_references: .: (0.000417) + test_rel_pathways_as_hash: .: (0.000586) + test_rel_pathways_as_strings: .: (0.000492) Bio::TestBioKEGGPATHWAY_ko00312: - test_compounds_as_hash: .: (0.000846) - test_compounds_as_strings: .: (0.001109) - test_dblinks_as_hash: .: (0.000522) - test_dblinks_as_strings: .: (0.000572) - test_description: .: (0.000558) - test_diseases_as_hash: .: (0.000507) - test_diseases_as_strings: .: (0.000502) - test_entry_id: .: (0.000595) - test_enzymes_as_strings: .: (0.000507) - test_genes_as_hash: .: (0.000548) - test_genes_as_strings: .: (0.000489) - test_keggclass: .: (0.000559) - test_ko_pathway: .: (0.000537) - test_modules_as_hash: .: (0.000512) - test_modules_as_strings: .: (0.001224) - test_name: .: (0.000669) - test_new: .: (0.000511) - test_organism: .: (0.000539) - test_orthologs_as_hash: .: (0.000699) - test_orthologs_as_strings: .: (0.000579) - test_pathways_as_hash: .: (0.000576) - test_pathways_as_strings: .: (0.000512) - test_reactions_as_hash: .: (0.000496) - test_reactions_as_strings: .: (0.000492) - test_references: .: (0.000518) - test_rel_pathways_as_hash: .: (0.001310) - test_rel_pathways_as_strings: .: (0.000522) + test_compounds_as_hash: .: (0.000701) + test_compounds_as_strings: .: (0.000508) + test_dblinks_as_hash: .: (0.000381) + test_dblinks_as_strings: .: (0.000400) + test_description: .: (0.000426) + test_diseases_as_hash: .: (0.000386) + test_diseases_as_strings: .: (0.000374) + test_entry_id: .: (0.000425) + test_enzymes_as_strings: .: (0.000371) + test_genes_as_hash: .: (0.000365) + test_genes_as_strings: .: (0.000379) + test_keggclass: .: (0.000421) + test_ko_pathway: .: (0.000413) + test_modules_as_hash: .: (0.000376) + test_modules_as_strings: .: (0.000879) + test_name: .: (0.000612) + test_new: .: (0.000420) + test_organism: .: (0.000459) + test_orthologs_as_hash: .: (0.000504) + test_orthologs_as_strings: .: (0.000428) + test_pathways_as_hash: .: (0.000402) + test_pathways_as_strings: .: (0.000378) + test_reactions_as_hash: .: (0.000390) + test_reactions_as_strings: .: (0.000422) + test_references: .: (0.000448) + test_rel_pathways_as_hash: .: (0.000602) + test_rel_pathways_as_strings: .: (0.000476) Bio::TestBioKEGGPATHWAY_map00030: - test_compounds_as_hash: .: (0.000846) - test_compounds_as_strings: .: (0.000604) - test_dblinks_as_hash: .: (0.000610) - test_dblinks_as_strings: .: (0.000625) - test_description: .: (0.000928) - test_diseases_as_hash: .: (0.000606) - test_diseases_as_strings: .: (0.001131) - test_entry_id: .: (0.000775) - test_enzymes_as_strings: .: (0.000568) - test_genes_as_hash: .: (0.000568) - test_genes_as_strings: .: (0.000564) - test_keggclass: .: (0.000682) - test_ko_pathway: .: (0.000642) - test_modules_as_hash: .: (0.000841) - test_modules_as_strings: .: (0.001044) - test_name: .: (0.000698) - test_new: .: (0.000582) - test_organism: .: (0.000678) - test_orthologs_as_hash: .: (0.000572) - test_orthologs_as_strings: .: (0.000566) - test_pathways_as_hash: .: (0.000601) - test_pathways_as_strings: .: (0.000619) - test_reactions_as_hash: .: (0.000561) - test_reactions_as_strings: .: (0.000817) - test_references: .: (0.001883) - test_rel_pathways_as_hash: .: (0.000748) - test_rel_pathways_as_strings: .: (0.000694) + test_compounds_as_hash: .: (0.000836) + test_compounds_as_strings: .: (0.000514) + test_dblinks_as_hash: .: (0.000686) + test_dblinks_as_strings: .: (0.000564) + test_description: .: (0.000784) + test_diseases_as_hash: .: (0.000536) + test_diseases_as_strings: .: (0.000931) + test_entry_id: .: (0.000763) + test_enzymes_as_strings: .: (0.000624) + test_genes_as_hash: .: (0.000511) + test_genes_as_strings: .: (0.000540) + test_keggclass: .: (0.000634) + test_ko_pathway: .: (0.000614) + test_modules_as_hash: .: (0.000769) + test_modules_as_strings: .: (0.000839) + test_name: .: (0.000753) + test_new: .: (0.000549) + test_organism: .: (0.000683) + test_orthologs_as_hash: .: (0.000497) + test_orthologs_as_strings: .: (0.000700) + test_pathways_as_hash: .: (0.000823) + test_pathways_as_strings: .: (0.000637) + test_reactions_as_hash: .: (0.000662) + test_reactions_as_strings: .: (0.000821) + test_references: .: (0.001754) + test_rel_pathways_as_hash: .: (0.000784) + test_rel_pathways_as_strings: .: (0.000750) Bio::TestBioKeggDRUG: - test_activity: .: (0.000953) + test_activity: .: (0.001221) + test_comment: .: (0.000946) + test_dblinks_as_hash: .: (0.001167) + test_dblinks_as_strings: .: (0.000933) + test_entry_id: .: (0.000852) + test_formula: .: (0.000808) + test_kcf: .: (0.000741) + test_mass: .: (0.000679) + test_name: .: (0.000773) + test_names: .: (0.001052) + test_pathways_as_hash: .: (0.000740) + test_pathways_as_strings: .: (0.000594) + test_products: .: (0.000872) + test_remark: .: (0.000702) +Bio::TestBioKeggGLYCAN: test_comment: .: (0.000903) - test_dblinks_as_hash: .: (0.000836) - test_dblinks_as_strings: .: (0.000693) - test_entry_id: .: (0.000646) - test_formula: .: (0.000647) - test_kcf: .: (0.000605) - test_mass: .: (0.000649) - test_name: .: (0.000815) - test_names: .: (0.001030) + test_composition: .: (0.000708) + test_compounds: .: (0.000622) + test_dblinks_as_hash: .: (0.001122) + test_dblinks_as_strings: .: (0.000646) + test_entry_id: .: (0.000674) + test_enzymes: .: (0.000641) + test_kcf: .: (0.000526) + test_keggclass: .: (0.000557) + test_mass: .: (0.000610) + test_name: .: (0.000565) + test_orthologs_as_hash: .: (0.000992) + test_orthologs_as_strings: .: (0.000680) test_pathways_as_hash: .: (0.000707) - test_pathways_as_strings: .: (0.000643) - test_products: .: (0.000825) - test_remark: .: (0.000711) -Bio::TestBioKeggGLYCAN: - test_comment: .: (0.000963) - test_composition: .: (0.000735) - test_compounds: .: (0.000687) - test_dblinks_as_hash: .: (0.001341) - test_dblinks_as_strings: .: (0.000753) - test_entry_id: .: (0.000686) - test_enzymes: .: (0.000732) - test_kcf: .: (0.000590) - test_keggclass: .: (0.000652) - test_mass: .: (0.000659) - test_name: .: (0.000670) - test_orthologs_as_hash: .: (0.001232) - test_orthologs_as_strings: .: (0.000726) - test_pathways_as_hash: .: (0.000688) - test_pathways_as_strings: .: (0.000628) - test_reactions: .: (0.000647) - test_references: .: (0.000797) - test_remark: .: (0.000628) + test_pathways_as_strings: .: (0.000538) + test_reactions: .: (0.000596) + test_references: .: (0.000643) + test_remark: .: (0.000552) Bio::TestBioKeggGLYCAN_G01366: - test_comment: .: (0.000812) - test_composition: .: (0.001052) - test_compounds: .: (0.000603) - test_dblinks_as_hash: .: (0.000651) - test_dblinks_as_strings: .: (0.000535) - test_entry_id: .: (0.000554) - test_enzymes: .: (0.000529) - test_kcf: .: (0.000536) - test_keggclass: .: (0.000553) - test_mass: .: (0.000547) - test_name: .: (0.000529) - test_orthologs_as_hash: .: (0.000525) - test_orthologs_as_strings: .: (0.000980) - test_pathways_as_hash: .: (0.000594) - test_pathways_as_strings: .: (0.000494) - test_reactions: .: (0.000530) - test_references: .: (0.000495) - test_remark: .: (0.000560) + test_comment: .: (0.000863) + test_composition: .: (0.000931) + test_compounds: .: (0.000541) + test_dblinks_as_hash: .: (0.000671) + test_dblinks_as_strings: .: (0.000519) + test_entry_id: .: (0.000512) + test_enzymes: .: (0.000510) + test_kcf: .: (0.000458) + test_keggclass: .: (0.000510) + test_mass: .: (0.000559) + test_name: .: (0.000514) + test_orthologs_as_hash: .: (0.000476) + test_orthologs_as_strings: .: (0.000604) + test_pathways_as_hash: .: (0.000462) + test_pathways_as_strings: .: (0.000434) + test_reactions: .: (0.000448) + test_references: .: (0.000452) + test_remark: .: (0.000456) Bio::TestBioKeggPathway_rn00250: - test_compounds_as_hash: .: (0.001366) - test_compounds_as_strings: .: (0.000814) - test_dblinks_as_hash: .: (0.001128) - test_dblinks_as_strings: .: (0.000605) - test_description: .: (0.000670) - test_diseases_as_hash: .: (0.000662) - test_diseases_as_strings: .: (0.000622) - test_entry_id: .: (0.000662) - test_enzymes_as_strings: .: (0.000586) - test_genes_as_hash: .: (0.000631) - test_genes_as_strings: .: (0.000578) - test_keggclass: .: (0.000637) - test_ko_pathway: .: (0.001093) - test_modules_as_hash: .: (0.000862) - test_modules_as_strings: .: (0.000708) - test_name: .: (0.000658) - test_new: .: (0.000620) - test_organism: .: (0.000660) - test_orthologs_as_hash: .: (0.000587) - test_orthologs_as_strings: .: (0.000631) - test_pathways_as_hash: .: (0.000644) - test_pathways_as_strings: .: (0.001013) - test_reactions_as_hash: .: (0.001328) - test_reactions_as_strings: .: (0.000977) - test_references: .: (0.001258) - test_rel_pathways_as_hash: .: (0.001116) - test_rel_pathways_as_strings: .: (0.000844) + test_compounds_as_hash: .: (0.001195) + test_compounds_as_strings: .: (0.000696) + test_dblinks_as_hash: .: (0.000947) + test_dblinks_as_strings: .: (0.000531) + test_description: .: (0.000555) + test_diseases_as_hash: .: (0.000558) + test_diseases_as_strings: .: (0.000523) + test_entry_id: .: (0.000663) + test_enzymes_as_strings: .: (0.000578) + test_genes_as_hash: .: (0.000533) + test_genes_as_strings: .: (0.000508) + test_keggclass: .: (0.000563) + test_ko_pathway: .: (0.000899) + test_modules_as_hash: .: (0.000718) + test_modules_as_strings: .: (0.000744) + test_name: .: (0.000712) + test_new: .: (0.000600) + test_organism: .: (0.000606) + test_orthologs_as_hash: .: (0.000647) + test_orthologs_as_strings: .: (0.000535) + test_pathways_as_hash: .: (0.000605) + test_pathways_as_strings: .: (0.000929) + test_reactions_as_hash: .: (0.001157) + test_reactions_as_strings: .: (0.000898) + test_references: .: (0.006631) + test_rel_pathways_as_hash: .: (0.001052) + test_rel_pathways_as_strings: .: (0.000705) Bio::TestBioLITDB: - test_author: .: (0.000960) - test_entry_id: .: (0.000579) - test_field: .: (0.000576) - test_journal: .: (0.000596) - test_keyword: .: (0.001325) + test_author: .: (0.000816) + test_entry_id: .: (0.000536) + test_field: .: (0.000586) + test_journal: .: (0.000515) + test_keyword: .: (0.001096) test_reference: .: (0.001063) - test_title: .: (0.000631) - test_volume: .: (0.000604) + test_title: .: (0.000611) + test_volume: .: (0.000513) Bio::TestBioNBRF: - test_aalen: .: (0.000822) - test_aaseq: .: (0.000468) - test_entry: .: (0.000427) - test_length: .: (0.000442) - test_nalen: .: (0.000575) - test_naseq: .: (0.000515) - test_seq: .: (0.001058) - test_seq_class: .: (0.000535) - test_to_nbrf: .: (0.000490) + test_aalen: .: (0.000877) + test_aaseq: .: (0.000531) + test_entry: .: (0.000421) + test_length: .: (0.000424) + test_nalen: .: (0.000548) + test_naseq: .: (0.000913) + test_seq: .: (0.000620) + test_seq_class: .: (0.000458) + test_to_nbrf: .: (0.000499) Bio::TestBioTreeOutputPrivate: - test_to_newick_format_label: .: (0.000924) - test_to_newick_format_leaf: .: (0.000829) - test_to_newick_format_leaf_NHX: .: (0.000533) + test_to_newick_format_label: .: (0.000921) + test_to_newick_format_leaf: .: (0.000699) + test_to_newick_format_leaf_NHX: .: (0.000465) Bio::TestBl2seqReport: - test_db_len: .: (0.001725) - test_db_num: .: (0.001911) - test_new: .: (0.000765) - test_undefed_methods: .: (0.002725) - test_undefed_methods_for_iteration: .: (0.002512) + test_db_len: .: (0.001541) + test_db_num: .: (0.001516) + test_new: .: (0.000827) + test_undefed_methods: .: (0.002080) + test_undefed_methods_for_iteration: .: (0.002026) Bio::TestBl2seqReportConstants: - test_rs: .: (0.000620) + test_rs: .: (0.000515) Bio::TestBl2seqReportHit: - test_empty_hits: .: (0.001711) - test_hits: .: (0.000816) + test_empty_hits: .: (0.001585) + test_hits: .: (0.000754) Bio::TestBlast: - test_blast_reports_format0: .: (0.014165) - test_blast_reports_format0_with_block: .: (0.001841) - test_blast_reports_format7: .: (0.041135) - test_blast_reports_format7_with_block: .: (0.039006) - test_blast_reports_format7_with_parser: .: (0.039028) - test_blast_reports_format7_with_parser_with_block: .: (0.046071) - test_blast_reports_format8: .: (0.002406) - test_blast_reports_format8_with_block: .: (0.001433) - test_blast_reports_format8_with_parser: .: (0.000741) - test_blast_reports_format8_with_parser_with_block: .: (0.000698) - test_blast_reports_xml: .: (0.037587) - test_blast_reports_xml_with_block: .: (0.037518) - test_blastll: .: (0.000520) - test_db: .: (0.000470) - test_exec_genomenet: .: (0.000429) - test_exec_local: .: (0.000398) - test_exec_ncbi: .: (0.000397) - test_filter: .: (0.000437) - test_format: .: (0.000511) - test_make_command_line: .: (0.001483) - test_make_command_line_2: .: (0.001069) - test_matrix: .: (0.000462) - test_new: .: (0.000762) - test_new_opt_string: .: (0.001154) - test_option: .: (0.000510) - test_option_set: .: (0.000729) - test_option_set_m0: .: (0.000673) - test_options: .: (0.000455) - test_output: .: (0.000481) - test_parse_result: .: (0.064823) - test_parser: .: (0.007868) - test_program: .: (0.000492) - test_query: .: (0.000425) - test_self_local: .: (0.000672) - test_self_remote: .: (0.009087) - test_server: .: (0.000540) + test_blast_reports_format0: .: (0.011264) + test_blast_reports_format0_with_block: .: (0.001754) + test_blast_reports_format7: .: (0.029819) + test_blast_reports_format7_with_block: .: (0.028566) + test_blast_reports_format7_with_parser: .: (0.027617) + test_blast_reports_format7_with_parser_with_block: .: (0.035656) + test_blast_reports_format8: .: (0.002234) + test_blast_reports_format8_with_block: .: (0.001472) + test_blast_reports_format8_with_parser: .: (0.000871) + test_blast_reports_format8_with_parser_with_block: .: (0.000707) + test_blast_reports_xml: .: (0.027425) + test_blast_reports_xml_with_block: .: (0.027365) + test_blastll: .: (0.000662) + test_db: .: (0.000672) + test_exec_genomenet: .: (0.000556) + test_exec_local: .: (0.000519) + test_exec_ncbi: .: (0.000448) + test_filter: .: (0.000418) + test_format: .: (0.000744) + test_make_command_line: .: (0.001404) + test_make_command_line_2: .: (0.001013) + test_matrix: .: (0.000458) + test_new: .: (0.000708) + test_new_opt_string: .: (0.000600) + test_option: .: (0.000464) + test_option_set: .: (0.000677) + test_option_set_m0: .: (0.000554) + test_options: .: (0.000393) + test_output: .: (0.000387) + test_parse_result: .: (0.049167) + test_parser: .: (0.006601) + test_program: .: (0.000576) + test_query: .: (0.000476) + test_self_local: .: (0.000649) + test_self_remote: .: (0.007675) + test_server: .: (0.000498) Bio::TestBlastNCBIOptions: - test_add_options: .: (0.009950) - test_delete: .: (0.001093) - test_equal_equal: .: (0.010687) - test_get: .: (0.001120) - test_make_command_line_options: .: (0.000929) - test_normalize!: .: (0.008445) - test_parse: .: (0.000740) - test_set: .: (0.010257) + test_add_options: .: (0.008096) + test_delete: .: (0.000948) + test_equal_equal: .: (0.008825) + test_get: .: (0.001033) + test_make_command_line_options: .: (0.000939) + test_normalize!: .: (0.007043) + test_parse: .: (0.000628) + test_set: .: (0.008353) Bio::TestBlastReport: - test_db: .: (0.063136) - test_db_len: .: (0.038491) - test_db_num: .: (0.038251) - test_each_hit: .: (0.037621) - test_each_iteration: .: (0.039298) - test_eff_space: .: (0.037744) - test_entrez_query: .: (0.036926) - test_entropy: .: (0.036518) - test_expect: .: (0.036610) - test_filter: .: (0.038233) - test_gap_extend: .: (0.037589) - test_gap_open: .: (0.036937) - test_hits: .: (0.036472) - test_hsp_len: .: (0.036366) - test_inclusion: .: (0.039037) - test_iterations: .: (0.037190) - test_kappa: .: (0.036787) - test_lambda: .: (0.036376) - test_matrix: .: (0.036291) - test_message: .: (0.038830) - test_parameters: .: (0.037413) - test_pattern: .: (0.036702) - test_program: .: (0.037149) - test_query_def: .: (0.036586) - test_query_id: .: (0.038553) - test_query_len: .: (0.036922) - test_reference: .: (0.036492) - test_sc_match: .: (0.036604) - test_sc_mismatch: .: (0.036243) - test_statistics: .: (0.038767) - test_version: .: (0.036810) + test_db: .: (0.046278) + test_db_len: .: (0.027841) + test_db_num: .: (0.027587) + test_each_hit: .: (0.027350) + test_each_iteration: .: (0.030841) + test_eff_space: .: (0.028639) + test_entrez_query: .: (0.026866) + test_entropy: .: (0.026484) + test_expect: .: (0.028567) + test_filter: .: (0.028301) + test_gap_extend: .: (0.027087) + test_gap_open: .: (0.028176) + test_hits: .: (0.027569) + test_hsp_len: .: (0.026631) + test_inclusion: .: (0.028835) + test_iterations: .: (0.026983) + test_kappa: .: (0.027027) + test_lambda: .: (0.026722) + test_matrix: .: (0.026894) + test_message: .: (0.028747) + test_parameters: .: (0.027038) + test_pattern: .: (0.026904) + test_program: .: (0.026378) + test_query_def: .: (0.026863) + test_query_id: .: (0.028424) + test_query_len: .: (0.026805) + test_reference: .: (0.026547) + test_sc_match: .: (0.026734) + test_sc_mismatch: .: (0.026544) + test_statistics: .: (0.028141) + test_version: .: (0.030004) Bio::TestBlastReportDefault: - test_db: .: (0.001691) - test_db_len: .: (0.001551) - test_db_num: .: (0.001286) - test_each_hit: .: (0.001136) - test_each_iteration: .: (0.001053) - test_eff_space: .: (0.001394) - test_entropy: .: (0.001176) - test_expect: .: (0.001316) - test_gap_extend: .: (0.001589) - test_gap_open: .: (0.001374) - test_gapped_entropy: .: (0.001181) - test_gapped_kappa: .: (0.001130) - test_gapped_lambda: .: (0.001154) - test_hits: .: (0.001139) - test_iterations: .: (0.001035) - test_kappa: .: (0.001160) - test_lambda: .: (0.001326) - test_matrix: .: (0.001294) - test_message: .: (0.001078) - test_pattern: .: (0.001046) - test_program: .: (0.001079) - test_query_def: .: (0.001197) - test_query_len: .: (0.001102) - test_reference: .: (0.015222) - test_sc_match: .: (0.001609) - test_sc_mismatch: .: (0.001324) - test_version: .: (0.001069) + test_db: .: (0.001584) + test_db_len: .: (0.001554) + test_db_num: .: (0.001212) + test_each_hit: .: (0.001200) + test_each_iteration: .: (0.001032) + test_eff_space: .: (0.001196) + test_entropy: .: (0.001049) + test_expect: .: (0.001056) + test_gap_extend: .: (0.001076) + test_gap_open: .: (0.001191) + test_gapped_entropy: .: (0.001124) + test_gapped_kappa: .: (0.001037) + test_gapped_lambda: .: (0.000983) + test_hits: .: (0.000921) + test_iterations: .: (0.000977) + test_kappa: .: (0.001009) + test_lambda: .: (0.000927) + test_matrix: .: (0.001118) + test_message: .: (0.001124) + test_pattern: .: (0.000915) + test_program: .: (0.000951) + test_query_def: .: (0.000970) + test_query_len: .: (0.000896) + test_reference: .: (0.001014) + test_sc_match: .: (0.001107) + test_sc_mismatch: .: (0.001016) + test_version: .: (0.000902) Bio::TestBlastReportHit: - test_Hit_accession: .: (0.036629) - test_Hit_bit_score: .: (0.036302) - test_Hit_definition: .: (0.040328) - test_Hit_evalue: .: (0.037486) - test_Hit_hit_id: .: (0.038069) - test_Hit_hsps: .: (0.036874) - test_Hit_identity: .: (0.036470) - test_Hit_lap_at: .: (0.038411) - test_Hit_len: .: (0.036598) - test_Hit_midline: .: (0.036658) - test_Hit_num: .: (0.036324) - test_Hit_overlap: .: (0.037832) - test_Hit_query_def: .: (0.037264) - test_Hit_query_end: .: (0.037172) - test_Hit_query_id: .: (0.038653) - test_Hit_query_len: .: (0.037569) - test_Hit_query_seq: .: (0.040178) - test_Hit_query_start: .: (0.037885) - test_Hit_taeget_def: .: (0.037048) - test_Hit_target_end: .: (0.037403) - test_Hit_target_id: .: (0.036838) - test_Hit_target_len: .: (0.039885) - test_Hit_target_seq: .: (0.037685) - test_Hit_target_start: .: (0.037081) + test_Hit_accession: .: (0.026498) + test_Hit_bit_score: .: (0.026080) + test_Hit_definition: .: (0.029452) + test_Hit_evalue: .: (0.026495) + test_Hit_hit_id: .: (0.027593) + test_Hit_hsps: .: (0.026947) + test_Hit_identity: .: (0.026800) + test_Hit_lap_at: .: (0.028102) + test_Hit_len: .: (0.026323) + test_Hit_midline: .: (0.026083) + test_Hit_num: .: (0.026292) + test_Hit_overlap: .: (0.027592) + test_Hit_query_def: .: (0.026993) + test_Hit_query_end: .: (0.026421) + test_Hit_query_id: .: (0.026203) + test_Hit_query_len: .: (0.026246) + test_Hit_query_seq: .: (0.028217) + test_Hit_query_start: .: (0.026568) + test_Hit_taeget_def: .: (0.025941) + test_Hit_target_end: .: (0.026249) + test_Hit_target_id: .: (0.026087) + test_Hit_target_len: .: (0.027917) + test_Hit_target_seq: .: (0.026343) + test_Hit_target_start: .: (0.026034) Bio::TestBlastReportHitDefault: - test_Hit_bit_score: .: (0.001788) - test_Hit_definition: .: (0.001247) - test_Hit_evalue: .: (0.001194) - test_Hit_hsps: .: (0.001144) - test_Hit_identity: .: (0.001244) - test_Hit_lap_at: .: (0.001914) - test_Hit_len: .: (0.001204) - test_Hit_midline: .: (0.001621) - test_Hit_overlap: .: (0.001187) - test_Hit_query_end: .: (0.001573) - test_Hit_query_seq: .: (0.001623) - test_Hit_query_start: .: (0.001927) - test_Hit_taeget_def: .: (0.001179) - test_Hit_target_end: .: (0.001585) - test_Hit_target_id: .: (0.001160) - test_Hit_target_len: .: (0.001163) - test_Hit_target_seq: .: (0.001553) - test_Hit_target_start: .: (0.001905) + test_Hit_bit_score: .: (0.001711) + test_Hit_definition: .: (0.001190) + test_Hit_evalue: .: (0.001289) + test_Hit_hsps: .: (0.001069) + test_Hit_identity: .: (0.001141) + test_Hit_lap_at: .: (0.001417) + test_Hit_len: .: (0.001037) + test_Hit_midline: .: (0.001308) + test_Hit_overlap: .: (0.001197) + test_Hit_query_end: .: (0.001366) + test_Hit_query_seq: .: (0.001249) + test_Hit_query_start: .: (0.001250) + test_Hit_taeget_def: .: (0.000972) + test_Hit_target_end: .: (0.001164) + test_Hit_target_id: .: (0.001570) + test_Hit_target_len: .: (0.001119) + test_Hit_target_seq: .: (0.001296) + test_Hit_target_start: .: (0.001242) Bio::TestBlastReportHitMulti: - test_Hit_accession: .: (0.114075) - test_Hit_bit_score: .: (0.114151) - test_Hit_definition: .: (0.110279) - test_Hit_evalue: .: (0.112830) - test_Hit_hit_id: .: (0.112748) - test_Hit_hsps: .: (0.109608) - test_Hit_identity: .: (0.112510) - test_Hit_lap_at: .: (0.112893) - test_Hit_len: .: (0.109160) - test_Hit_midline: .: (0.112367) - test_Hit_num: .: (0.115175) - test_Hit_overlap: .: (0.111744) - test_Hit_query_def: .: (0.110700) - test_Hit_query_end: .: (0.116051) - test_Hit_query_id: .: (0.111965) - test_Hit_query_len: .: (0.110779) - test_Hit_query_seq: .: (0.114992) - test_Hit_query_start: .: (0.113910) - test_Hit_taeget_def: .: (0.109990) - test_Hit_target_end: .: (0.113282) - test_Hit_target_id: .: (0.113584) - test_Hit_target_len: .: (0.110391) - test_Hit_target_seq: .: (0.113633) - test_Hit_target_start: .: (0.115526) + test_Hit_accession: .: (0.078623) + test_Hit_bit_score: .: (0.078036) + test_Hit_definition: .: (0.076853) + test_Hit_evalue: .: (0.079385) + test_Hit_hit_id: .: (0.083153) + test_Hit_hsps: .: (0.075745) + test_Hit_identity: .: (0.079802) + test_Hit_lap_at: .: (0.079403) + test_Hit_len: .: (0.075605) + test_Hit_midline: .: (0.078658) + test_Hit_num: .: (0.079082) + test_Hit_overlap: .: (0.077336) + test_Hit_query_def: .: (0.076815) + test_Hit_query_end: .: (0.079196) + test_Hit_query_id: .: (0.081422) + test_Hit_query_len: .: (0.082682) + test_Hit_query_seq: .: (0.081686) + test_Hit_query_start: .: (0.081690) + test_Hit_taeget_def: .: (0.077537) + test_Hit_target_end: .: (0.080169) + test_Hit_target_id: .: (0.079000) + test_Hit_target_len: .: (0.078154) + test_Hit_target_seq: .: (0.078883) + test_Hit_target_start: .: (0.081494) Bio::TestBlastReportHitMultiREXML: - test_Hit_accession: .: (0.112215) - test_Hit_bit_score: .: (0.109934) - test_Hit_definition: .: (0.112872) - test_Hit_evalue: .: (0.112089) - test_Hit_hit_id: .: (0.108640) - test_Hit_hsps: .: (0.112258) - test_Hit_identity: .: (0.112490) - test_Hit_lap_at: .: (0.108065) - test_Hit_len: .: (0.112144) - test_Hit_midline: .: (0.113142) - test_Hit_num: .: (0.109957) - test_Hit_overlap: .: (0.109108) - test_Hit_query_def: .: (0.111742) - test_Hit_query_end: .: (0.111458) - test_Hit_query_id: .: (0.107971) - test_Hit_query_len: .: (0.111201) - test_Hit_query_seq: .: (0.111898) - test_Hit_query_start: .: (0.107715) - test_Hit_taeget_def: .: (0.111305) - test_Hit_target_end: .: (0.112053) - test_Hit_target_id: .: (0.109900) - test_Hit_target_len: .: (0.108911) - test_Hit_target_seq: .: (0.111201) - test_Hit_target_start: .: (0.111081) + test_Hit_accession: .: (0.079929) + test_Hit_bit_score: .: (0.080439) + test_Hit_definition: .: (0.081916) + test_Hit_evalue: .: (0.080539) + test_Hit_hit_id: .: (0.076491) + test_Hit_hsps: .: (0.081699) + test_Hit_identity: .: (0.081711) + test_Hit_lap_at: .: (0.077176) + test_Hit_len: .: (0.080180) + test_Hit_midline: .: (0.081748) + test_Hit_num: .: (0.081619) + test_Hit_overlap: .: (0.078302) + test_Hit_query_def: .: (0.082821) + test_Hit_query_end: .: (0.082389) + test_Hit_query_id: .: (0.078044) + test_Hit_query_len: .: (0.081219) + test_Hit_query_seq: .: (0.081145) + test_Hit_query_start: .: (0.079604) + test_Hit_taeget_def: .: (0.078999) + test_Hit_target_end: .: (0.080946) + test_Hit_target_id: .: (0.081695) + test_Hit_target_len: .: (0.076486) + test_Hit_target_seq: .: (0.082918) + test_Hit_target_start: .: (0.081514) Bio::TestBlastReportHitREXML: - test_Hit_accession: .: (0.036502) - test_Hit_bit_score: .: (0.036548) - test_Hit_definition: .: (0.036697) - test_Hit_evalue: .: (0.038569) - test_Hit_hit_id: .: (0.037059) - test_Hit_hsps: .: (0.036592) - test_Hit_identity: .: (0.037245) - test_Hit_lap_at: .: (0.038026) - test_Hit_len: .: (0.037497) - test_Hit_midline: .: (0.036782) - test_Hit_num: .: (0.036475) - test_Hit_overlap: .: (0.036270) - test_Hit_query_def: .: (0.039079) - test_Hit_query_end: .: (0.037067) - test_Hit_query_id: .: (0.036591) - test_Hit_query_len: .: (0.036503) - test_Hit_query_seq: .: (0.038142) - test_Hit_query_start: .: (0.037856) - test_Hit_taeget_def: .: (0.036550) - test_Hit_target_end: .: (0.036453) - test_Hit_target_id: .: (0.036286) - test_Hit_target_len: .: (0.038408) - test_Hit_target_seq: .: (0.036922) - test_Hit_target_start: .: (0.036493) + test_Hit_accession: .: (0.026622) + test_Hit_bit_score: .: (0.026681) + test_Hit_definition: .: (0.028744) + test_Hit_evalue: .: (0.029877) + test_Hit_hit_id: .: (0.028243) + test_Hit_hsps: .: (0.026534) + test_Hit_identity: .: (0.027830) + test_Hit_lap_at: .: (0.028468) + test_Hit_len: .: (0.027039) + test_Hit_midline: .: (0.028321) + test_Hit_num: .: (0.026665) + test_Hit_overlap: .: (0.026608) + test_Hit_query_def: .: (0.029590) + test_Hit_query_end: .: (0.026432) + test_Hit_query_id: .: (0.030053) + test_Hit_query_len: .: (0.026444) + test_Hit_query_seq: .: (0.029085) + test_Hit_query_start: .: (0.027230) + test_Hit_taeget_def: .: (0.026464) + test_Hit_target_end: .: (0.028415) + test_Hit_target_id: .: (0.026346) + test_Hit_target_len: .: (0.028593) + test_Hit_target_seq: .: (0.026448) + test_Hit_target_start: .: (0.027474) Bio::TestBlastReportHitTabular: - test_Hit_accession: .: (0.001052) - test_Hit_bit_score: .: (0.000572) - test_Hit_definition: .: (0.000514) - test_Hit_evalue: .: (0.000519) - test_Hit_hit_id: .: (0.000527) - test_Hit_hsps: .: (0.000538) - test_Hit_identity: .: (0.000526) - test_Hit_lap_at: .: (0.000518) - test_Hit_len: .: (0.000830) - test_Hit_midline: .: (0.000501) - test_Hit_num: .: (0.000512) - test_Hit_overlap: .: (0.000545) - test_Hit_query_def: .: (0.000530) - test_Hit_query_end: .: (0.000507) - test_Hit_query_id: .: (0.000504) - test_Hit_query_len: .: (0.000518) - test_Hit_query_seq: .: (0.000488) - test_Hit_query_start: .: (0.000498) - test_Hit_taeget_def: .: (0.000494) - test_Hit_target_end: .: (0.000500) - test_Hit_target_id: .: (0.000487) - test_Hit_target_len: .: (0.000492) - test_Hit_target_seq: .: (0.000537) - test_Hit_target_start: .: (0.000569) + test_Hit_accession: .: (0.000966) + test_Hit_bit_score: .: (0.000816) + test_Hit_definition: .: (0.000618) + test_Hit_evalue: .: (0.000563) + test_Hit_hit_id: .: (0.000568) + test_Hit_hsps: .: (0.000525) + test_Hit_identity: .: (0.000514) + test_Hit_lap_at: .: (0.000571) + test_Hit_len: .: (0.000446) + test_Hit_midline: .: (0.000411) + test_Hit_num: .: (0.000473) + test_Hit_overlap: .: (0.000418) + test_Hit_query_def: .: (0.000493) + test_Hit_query_end: .: (0.000417) + test_Hit_query_id: .: (0.000692) + test_Hit_query_len: .: (0.000556) + test_Hit_query_seq: .: (0.000414) + test_Hit_query_start: .: (0.000470) + test_Hit_taeget_def: .: (0.000420) + test_Hit_target_end: .: (0.000391) + test_Hit_target_id: .: (0.000593) + test_Hit_target_len: .: (0.000478) + test_Hit_target_seq: .: (0.000480) + test_Hit_target_start: .: (0.000399) Bio::TestBlastReportHsp: - test_Hsp_align_len: .: (0.036917) - test_Hsp_bit_score: .: (0.039962) - test_Hsp_density: .: (0.037236) - test_Hsp_evalue: .: (0.036773) - test_Hsp_gaps: .: (0.037027) - test_Hsp_hit_frame: .: (0.038078) - test_Hsp_hit_from: .: (0.037728) - test_Hsp_hit_to: .: (0.036767) - test_Hsp_hseq: .: (0.036693) - test_Hsp_identity: .: (0.036731) - test_Hsp_midline: .: (0.038797) - test_Hsp_mismatch_count: .: (0.037202) - test_Hsp_num: .: (0.036513) - test_Hsp_pattern_from: .: (0.036895) - test_Hsp_pattern_to: .: (0.038452) - test_Hsp_percent_identity: .: (0.037487) - test_Hsp_positive: .: (0.036539) - test_Hsp_qseq: .: (0.036723) - test_Hsp_query_frame: .: (0.036717) - test_Hsp_query_from: .: (0.038584) - test_Hsp_query_to: .: (0.036931) - test_Hsp_score: .: (0.036623) + test_Hsp_align_len: .: (0.026787) + test_Hsp_bit_score: .: (0.030946) + test_Hsp_density: .: (0.027255) + test_Hsp_evalue: .: (0.027509) + test_Hsp_gaps: .: (0.026982) + test_Hsp_hit_frame: .: (0.028690) + test_Hsp_hit_from: .: (0.028699) + test_Hsp_hit_to: .: (0.026671) + test_Hsp_hseq: .: (0.028421) + test_Hsp_identity: .: (0.027811) + test_Hsp_midline: .: (0.029164) + test_Hsp_mismatch_count: .: (0.026776) + test_Hsp_num: .: (0.027091) + test_Hsp_pattern_from: .: (0.026507) + test_Hsp_pattern_to: .: (0.029010) + test_Hsp_percent_identity: .: (0.027249) + test_Hsp_positive: .: (0.028868) + test_Hsp_qseq: .: (0.026828) + test_Hsp_query_frame: .: (0.028596) + test_Hsp_query_from: .: (0.027203) + test_Hsp_query_to: .: (0.026847) + test_Hsp_score: .: (0.027121) Bio::TestBlastReportHspDefault: - test_Hsp_align_len: .: (0.001681) - test_Hsp_bit_score: .: (0.001170) - test_Hsp_evalue: .: (0.001181) - test_Hsp_gaps: .: (0.001241) - test_Hsp_hit_frame: .: (0.001162) - test_Hsp_hit_from: .: (0.001912) - test_Hsp_hit_to: .: (0.001537) - test_Hsp_hseq: .: (0.001586) - test_Hsp_identity: .: (0.001161) - test_Hsp_midline: .: (0.001614) - test_Hsp_percent_identity: .: (0.001205) - test_Hsp_positive: .: (0.001149) - test_Hsp_qseq: .: (0.002129) - test_Hsp_query_frame: .: (0.001160) - test_Hsp_query_from: .: (0.001553) - test_Hsp_query_to: .: (0.001524) - test_Hsp_score: .: (0.001189) + test_Hsp_align_len: .: (0.001615) + test_Hsp_bit_score: .: (0.001237) + test_Hsp_evalue: .: (0.001129) + test_Hsp_gaps: .: (0.001162) + test_Hsp_hit_frame: .: (0.001187) + test_Hsp_hit_from: .: (0.001404) + test_Hsp_hit_to: .: (0.001459) + test_Hsp_hseq: .: (0.001617) + test_Hsp_identity: .: (0.001144) + test_Hsp_midline: .: (0.001412) + test_Hsp_percent_identity: .: (0.001177) + test_Hsp_positive: .: (0.001139) + test_Hsp_qseq: .: (0.001448) + test_Hsp_query_frame: .: (0.001153) + test_Hsp_query_from: .: (0.001922) + test_Hsp_query_to: .: (0.001434) + test_Hsp_score: .: (0.001145) Bio::TestBlastReportHspMulti: - test_Hsp_align_len: .: (0.111269) - test_Hsp_bit_score: .: (0.113540) - test_Hsp_density: .: (0.108138) - test_Hsp_evalue: .: (0.116721) - test_Hsp_gaps: .: (0.117176) - test_Hsp_hit_frame: .: (0.115934) - test_Hsp_hit_from: .: (0.113442) - test_Hsp_hit_to: .: (0.117027) - test_Hsp_hseq: .: (0.117058) - test_Hsp_identity: .: (0.114871) - test_Hsp_midline: .: (0.113385) - test_Hsp_mismatch_count: .: (0.116476) - test_Hsp_num: .: (0.116095) - test_Hsp_pattern_from: .: (0.114035) - test_Hsp_pattern_to: .: (0.114079) - test_Hsp_percent_identity: .: (0.116134) - test_Hsp_positive: .: (0.115949) - test_Hsp_qseq: .: (0.111794) - test_Hsp_query_frame: .: (0.115186) - test_Hsp_query_from: .: (0.116250) - test_Hsp_query_to: .: (0.114931) - test_Hsp_score: .: (0.112079) + test_Hsp_align_len: .: (0.080301) + test_Hsp_bit_score: .: (0.084889) + test_Hsp_density: .: (0.082173) + test_Hsp_evalue: .: (0.081859) + test_Hsp_gaps: .: (0.083462) + test_Hsp_hit_frame: .: (0.081607) + test_Hsp_hit_from: .: (0.080287) + test_Hsp_hit_to: .: (0.082792) + test_Hsp_hseq: .: (0.082311) + test_Hsp_identity: .: (0.081319) + test_Hsp_midline: .: (0.080221) + test_Hsp_mismatch_count: .: (0.082619) + test_Hsp_num: .: (0.082208) + test_Hsp_pattern_from: .: (0.079997) + test_Hsp_pattern_to: .: (0.082145) + test_Hsp_percent_identity: .: (0.093960) + test_Hsp_positive: .: (0.087220) + test_Hsp_qseq: .: (0.077474) + test_Hsp_query_frame: .: (0.079973) + test_Hsp_query_from: .: (0.081028) + test_Hsp_query_to: .: (0.082433) + test_Hsp_score: .: (0.080010) Bio::TestBlastReportHspMultiREXML: - test_Hsp_align_len: .: (0.115673) - test_Hsp_bit_score: .: (0.116108) - test_Hsp_density: .: (0.114699) - test_Hsp_evalue: .: (0.111377) - test_Hsp_gaps: .: (0.115304) - test_Hsp_hit_frame: .: (0.115387) - test_Hsp_hit_from: .: (0.113222) - test_Hsp_hit_to: .: (0.112317) - test_Hsp_hseq: .: (0.114875) - test_Hsp_identity: .: (0.114577) - test_Hsp_midline: .: (0.112958) - test_Hsp_mismatch_count: .: (0.111874) - test_Hsp_num: .: (0.114744) - test_Hsp_pattern_from: .: (0.114915) - test_Hsp_pattern_to: .: (0.110297) - test_Hsp_percent_identity: .: (0.115574) - test_Hsp_positive: .: (0.115199) - test_Hsp_qseq: .: (0.114412) - test_Hsp_query_frame: .: (0.110616) - test_Hsp_query_from: .: (0.115811) - test_Hsp_query_to: .: (0.214874) - test_Hsp_score: .: (0.114734) + test_Hsp_align_len: .: (0.085072) + test_Hsp_bit_score: .: (0.082929) + test_Hsp_density: .: (0.079695) + test_Hsp_evalue: .: (0.112961) + test_Hsp_gaps: .: (0.081698) + test_Hsp_hit_frame: .: (0.083392) + test_Hsp_hit_from: .: (0.091056) + test_Hsp_hit_to: .: (0.129317) + test_Hsp_hseq: .: (0.091536) + test_Hsp_identity: .: (0.089128) + test_Hsp_midline: .: (0.111372) + test_Hsp_mismatch_count: .: (0.091201) + test_Hsp_num: .: (0.087254) + test_Hsp_pattern_from: .: (0.100112) + test_Hsp_pattern_to: .: (0.090154) + test_Hsp_percent_identity: .: (0.083873) + test_Hsp_positive: .: (0.084157) + test_Hsp_qseq: .: (0.091840) + test_Hsp_query_frame: .: (0.081642) + test_Hsp_query_from: .: (0.084752) + test_Hsp_query_to: .: (0.211525) + test_Hsp_score: .: (0.084152) Bio::TestBlastReportHspREXML: - test_Hsp_align_len: .: (0.038525) - test_Hsp_bit_score: .: (0.038002) - test_Hsp_density: .: (0.037833) - test_Hsp_evalue: .: (0.036909) - test_Hsp_gaps: .: (0.039801) - test_Hsp_hit_frame: .: (0.038296) - test_Hsp_hit_from: .: (0.037816) - test_Hsp_hit_to: .: (0.037459) - test_Hsp_hseq: .: (0.037559) - test_Hsp_identity: .: (0.039368) - test_Hsp_midline: .: (0.038058) - test_Hsp_mismatch_count: .: (0.037520) - test_Hsp_num: .: (0.037171) - test_Hsp_pattern_from: .: (0.036952) - test_Hsp_pattern_to: .: (0.040033) - test_Hsp_percent_identity: .: (0.037974) - test_Hsp_positive: .: (0.037577) - test_Hsp_qseq: .: (0.036933) - test_Hsp_query_frame: .: (0.038087) - test_Hsp_query_from: .: (0.039497) - test_Hsp_query_to: .: (0.038569) - test_Hsp_score: .: (0.037039) + test_Hsp_align_len: .: (0.028078) + test_Hsp_bit_score: .: (0.027040) + test_Hsp_density: .: (0.026643) + test_Hsp_evalue: .: (0.027117) + test_Hsp_gaps: .: (0.028937) + test_Hsp_hit_frame: .: (0.027356) + test_Hsp_hit_from: .: (0.027598) + test_Hsp_hit_to: .: (0.026720) + test_Hsp_hseq: .: (0.028567) + test_Hsp_identity: .: (0.049484) + test_Hsp_midline: .: (0.035219) + test_Hsp_mismatch_count: .: (0.028643) + test_Hsp_num: .: (0.028379) + test_Hsp_pattern_from: .: (0.033552) + test_Hsp_pattern_to: .: (0.038199) + test_Hsp_percent_identity: .: (0.035741) + test_Hsp_positive: .: (0.028242) + test_Hsp_qseq: .: (0.032870) + test_Hsp_query_frame: .: (0.029834) + test_Hsp_query_from: .: (0.044044) + test_Hsp_query_to: .: (0.055162) + test_Hsp_score: .: (0.036289) Bio::TestBlastReportHspTabular: - test_Hsp_align_len: .: (0.001539) - test_Hsp_bit_score: .: (0.000726) - test_Hsp_density: .: (0.000571) - test_Hsp_evalue: .: (0.000564) - test_Hsp_gaps: .: (0.000545) - test_Hsp_hit_frame: .: (0.000538) - test_Hsp_hit_from: .: (0.000537) - test_Hsp_hit_to: .: (0.000528) - test_Hsp_hseq: .: (0.000539) - test_Hsp_identity: .: (0.000514) - test_Hsp_midline: .: (0.000511) - test_Hsp_mismatch_count: .: (0.000516) - test_Hsp_num: .: (0.000524) - test_Hsp_pattern_from: .: (0.000541) - test_Hsp_pattern_to: .: (0.000930) - test_Hsp_percent_identity: .: (0.000628) - test_Hsp_positive: .: (0.000533) - test_Hsp_qseq: .: (0.000532) - test_Hsp_query_frame: .: (0.000535) - test_Hsp_query_from: .: (0.000570) - test_Hsp_query_to: .: (0.000517) - test_Hsp_score: .: (0.000518) + test_Hsp_align_len: .: (0.000844) + test_Hsp_bit_score: .: (0.000327) + test_Hsp_density: .: (0.000333) + test_Hsp_evalue: .: (0.000302) + test_Hsp_gaps: .: (0.000300) + test_Hsp_hit_frame: .: (0.000281) + test_Hsp_hit_from: .: (0.000273) + test_Hsp_hit_to: .: (0.000406) + test_Hsp_hseq: .: (0.000269) + test_Hsp_identity: .: (0.000254) + test_Hsp_midline: .: (0.000256) + test_Hsp_mismatch_count: .: (0.000384) + test_Hsp_num: .: (0.000263) + test_Hsp_pattern_from: .: (0.000230) + test_Hsp_pattern_to: .: (0.000231) + test_Hsp_percent_identity: .: (0.000252) + test_Hsp_positive: .: (0.000236) + test_Hsp_qseq: .: (0.000233) + test_Hsp_query_frame: .: (0.000232) + test_Hsp_query_from: .: (0.000236) + test_Hsp_query_to: .: (0.000433) + test_Hsp_score: .: (0.000272) Bio::TestBlastReportIteration: - test_hits: .: (0.037364) - test_message: .: (0.037264) - test_num: .: (0.040284) - test_statistics: .: (0.038415) + test_hits: .: (0.027119) + test_message: .: (0.035934) + test_num: .: (0.032312) + test_statistics: .: (0.029654) Bio::TestBlastReportIterationDefault: - test_hits: .: (0.001834) - test_message: .: (0.001110) - test_num: .: (0.001079) + test_hits: .: (0.005025) + test_message: .: (0.001477) + test_num: .: (0.001352) Bio::TestBlastReportIterationMulti: - test_each: .: (0.112432) - test_hits: .: (0.111372) - test_message: .: (0.113481) - test_num: .: (0.110157) - test_query_def: .: (0.113040) - test_query_id: .: (0.113659) - test_query_len: .: (0.109025) - test_statistics: .: (0.112403) + test_each: .: (0.092384) + test_hits: .: (0.079665) + test_message: .: (0.146036) + test_num: .: (0.080664) + test_query_def: .: (0.090861) + test_query_id: .: (0.088058) + test_query_len: .: (0.094942) + test_statistics: .: (0.086821) Bio::TestBlastReportIterationMultiREXML: - test_each: .: (0.114454) - test_hits: .: (0.108716) - test_message: .: (0.112504) - test_num: .: (0.113508) - test_query_def: .: (0.108699) - test_query_id: .: (0.112601) - test_query_len: .: (0.113285) - test_statistics: .: (0.109003) + test_each: .: (0.092164) + test_hits: .: (0.112291) + test_message: .: (0.090015) + test_num: .: (0.090446) + test_query_def: .: (0.079500) + test_query_id: .: (0.081269) + test_query_len: .: (0.087645) + test_statistics: .: (0.096333) Bio::TestBlastReportIterationREXML: - test_hits: .: (0.039752) - test_message: .: (0.038083) - test_num: .: (0.037506) - test_statistics: .: (0.036815) + test_hits: .: (0.032223) + test_message: .: (0.029647) + test_num: .: (0.029691) + test_statistics: .: (0.045757) Bio::TestBlastReportIterationTabular: - test_hits: .: (0.001119) - test_message: .: (0.000567) - test_num: .: (0.000548) - test_statistics: .: (0.000551) + test_hits: .: (0.001112) + test_message: .: (0.000562) + test_num: .: (0.000855) + test_statistics: .: (0.000624) Bio::TestBlastReportMulti: - test_db: .: (0.113732) - test_db_len: .: (0.111952) - test_db_num: .: (0.110954) - test_each_hit: .: (0.113758) - test_each_iteration: .: (0.111790) - test_eff_space: .: (0.110429) - test_entropy: .: (0.113067) - test_expect: .: (0.111120) - test_filter: .: (0.109589) - test_gap_extend: .: (0.112836) - test_gap_open: .: (0.111936) - test_hits: .: (0.109717) - test_hsp_len: .: (0.112956) - test_iterations: .: (0.112592) - test_kappa: .: (0.109173) - test_lambda: .: (0.112314) - test_matrix: .: (0.112985) - test_message: .: (0.108438) - test_parameters: .: (0.113040) - test_pattern: .: (0.113609) - test_program: .: (0.108858) - test_query_def: .: (0.111145) - test_query_id: .: (0.113146) - test_query_len: .: (0.109882) - test_reference: .: (0.109624) - test_reports: .: (0.112613) - test_statistics: .: (0.111880) - test_version: .: (0.108781) + test_db: .: (0.093017) + test_db_len: .: (0.182124) + test_db_num: .: (0.122127) + test_each_hit: .: (0.183419) + test_each_iteration: .: (0.131454) + test_eff_space: .: (0.104726) + test_entropy: .: (0.090161) + test_expect: .: (0.148301) + test_filter: .: (0.100466) + test_gap_extend: .: (0.092989) + test_gap_open: .: (0.089632) + test_hits: .: (0.085018) + test_hsp_len: .: (0.084007) + test_iterations: .: (0.083613) + test_kappa: .: (0.079956) + test_lambda: .: (0.082047) + test_matrix: .: (0.084560) + test_message: .: (0.079077) + test_parameters: .: (0.084125) + test_pattern: .: (0.086078) + test_program: .: (0.081123) + test_query_def: .: (0.118941) + test_query_id: .: (0.085104) + test_query_len: .: (0.090669) + test_reference: .: (0.099158) + test_reports: .: (0.085665) + test_statistics: .: (0.080869) + test_version: .: (0.078075) Bio::TestBlastReportMultiREXML: - test_db: .: (0.113810) - test_db_len: .: (0.113532) - test_db_num: .: (0.108996) - test_each_hit: .: (0.111621) - test_each_iteration: .: (0.113463) - test_eff_space: .: (0.109812) - test_entropy: .: (0.108917) - test_expect: .: (0.111542) - test_filter: .: (0.111264) - test_gap_extend: .: (0.107860) - test_gap_open: .: (0.111185) - test_hits: .: (0.112226) - test_hsp_len: .: (0.110138) - test_iterations: .: (0.109167) - test_kappa: .: (0.111926) - test_lambda: .: (0.111348) - test_matrix: .: (0.108127) - test_message: .: (0.110686) - test_parameters: .: (0.112596) - test_pattern: .: (0.110757) - test_program: .: (0.109088) - test_query_def: .: (0.110475) - test_query_id: .: (0.111511) - test_query_len: .: (0.110912) - test_reference: .: (0.112853) - test_reports: .: (0.115942) - test_statistics: .: (0.115274) - test_version: .: (0.113571) + test_db: .: (0.080934) + test_db_len: .: (0.086827) + test_db_num: .: (0.079794) + test_each_hit: .: (0.079263) + test_each_iteration: .: (0.083161) + test_eff_space: .: (0.079098) + test_entropy: .: (0.080908) + test_expect: .: (0.083306) + test_filter: .: (0.084376) + test_gap_extend: .: (0.085649) + test_gap_open: .: (0.087434) + test_hits: .: (0.089648) + test_hsp_len: .: (0.090250) + test_iterations: .: (0.083352) + test_kappa: .: (0.091002) + test_lambda: .: (0.089723) + test_matrix: .: (0.083225) + test_message: .: (0.087308) + test_parameters: .: (0.087971) + test_pattern: .: (0.086937) + test_program: .: (0.085260) + test_query_def: .: (0.088454) + test_query_id: .: (0.087284) + test_query_len: .: (0.083079) + test_reference: .: (0.082287) + test_reports: .: (0.086600) + test_statistics: .: (0.084684) + test_version: .: (0.083117) Bio::TestBlastReportREXML: - test_db: .: (0.039592) - test_db_len: .: (0.038501) - test_db_num: .: (0.037708) - test_each_hit: .: (0.039722) - test_each_iteration: .: (0.040576) - test_eff_space: .: (0.039049) - test_entrez_query: .: (0.037967) - test_entropy: .: (0.037461) - test_expect: .: (0.041086) - test_filter: .: (0.038056) - test_gap_extend: .: (0.037665) - test_gap_open: .: (0.037985) - test_hits: .: (0.040507) - test_hsp_len: .: (0.038424) - test_inclusion: .: (0.037652) - test_iterations: .: (0.037833) - test_kappa: .: (0.040366) - test_lambda: .: (0.038381) - test_matrix: .: (0.038146) - test_message: .: (0.037692) - test_parameters: .: (0.040286) - test_pattern: .: (0.038550) - test_program: .: (0.037776) - test_query_def: .: (0.037592) - test_query_id: .: (0.050676) - test_query_len: .: (0.039283) - test_reference: .: (0.038061) - test_sc_match: .: (0.037570) - test_sc_mismatch: .: (0.038009) - test_statistics: .: (0.041945) - test_version: .: (0.039402) + test_db: .: (0.029313) + test_db_len: .: (0.028775) + test_db_num: .: (0.027941) + test_each_hit: .: (0.029408) + test_each_iteration: .: (0.028667) + test_eff_space: .: (0.032287) + test_entrez_query: .: (0.048617) + test_entropy: .: (0.027283) + test_expect: .: (0.028646) + test_filter: .: (0.026555) + test_gap_extend: .: (0.026490) + test_gap_open: .: (0.027240) + test_hits: .: (0.028489) + test_hsp_len: .: (0.027061) + test_inclusion: .: (0.026676) + test_iterations: .: (0.026721) + test_kappa: .: (0.028862) + test_lambda: .: (0.027044) + test_matrix: .: (0.026921) + test_message: .: (0.026860) + test_parameters: .: (0.028723) + test_pattern: .: (0.027275) + test_program: .: (0.027002) + test_query_def: .: (0.027123) + test_query_id: .: (0.028331) + test_query_len: .: (0.027936) + test_reference: .: (0.026955) + test_sc_match: .: (0.027186) + test_sc_mismatch: .: (0.027033) + test_statistics: .: (0.028993) + test_version: .: (0.027155) Bio::TestBlastReportTabular: - test_db: .: (0.001441) - test_db_len: .: (0.000688) - test_db_num: .: (0.000583) - test_each_hit: .: (0.000591) - test_each_iteration: .: (0.000610) - test_eff_space: .: (0.000620) - test_entrez_query: .: (0.000603) - test_entropy: .: (0.000559) - test_expect: .: (0.000575) - test_filter: .: (0.000549) - test_gap_extend: .: (0.000557) - test_gap_open: .: (0.000553) - test_hits: .: (0.000578) - test_hsp_len: .: (0.000585) - test_inclusion: .: (0.001191) - test_iterations: .: (0.000773) - test_kappa: .: (0.000579) - test_lambda: .: (0.000571) - test_matrix: .: (0.000638) - test_message: .: (0.000589) - test_parameters: .: (0.000583) - test_pattern: .: (0.000612) - test_program: .: (0.000554) - test_query_def: .: (0.000588) - test_query_id: .: (0.000566) - test_query_len: .: (0.000555) - test_reference: .: (0.000583) - test_sc_match: .: (0.000619) - test_sc_mismatch: .: (0.000560) - test_statistics: .: (0.000791) - test_version: .: (0.000578) + test_db: .: (0.000780) + test_db_len: .: (0.000448) + test_db_num: .: (0.000601) + test_each_hit: .: (0.000377) + test_each_iteration: .: (0.000353) + test_eff_space: .: (0.000338) + test_entrez_query: .: (0.000349) + test_entropy: .: (0.000339) + test_expect: .: (0.000338) + test_filter: .: (0.000338) + test_gap_extend: .: (0.000371) + test_gap_open: .: (0.000340) + test_hits: .: (0.000382) + test_hsp_len: .: (0.000356) + test_inclusion: .: (0.000344) + test_iterations: .: (0.000770) + test_kappa: .: (0.000494) + test_lambda: .: (0.000429) + test_matrix: .: (0.000354) + test_message: .: (0.000341) + test_parameters: .: (0.000368) + test_pattern: .: (0.000345) + test_program: .: (0.000333) + test_query_def: .: (0.000355) + test_query_id: .: (0.000340) + test_query_len: .: (0.000320) + test_reference: .: (0.000325) + test_sc_match: .: (0.000341) + test_sc_mismatch: .: (0.000316) + test_statistics: .: (0.000349) + test_version: .: (0.000766) Bio::TestChain: - test_aaseq: .: (0.001069) - test_addLigand: .: (0.000498) - test_addResidue: .: (0.000514) - test_atom_seq: .: (0.000562) - test_comp: .: (0.000574) - test_each: .: (0.000497) - test_each_heterogen: .: (0.000482) - test_each_residue: .: (0.000515) - test_get_heterogen_by_id: .: (0.000525) - test_get_residue_by_id: .: (0.000464) - test_inspect: .: (0.000560) - test_rehash: .: (0.000957) - test_rehash_heterogens: .: (0.000475) - test_rehash_residues: .: (0.000464) - test_square_brace: .: (0.000503) - test_to_s: .: (0.000529) + test_aaseq: .: (0.000837) + test_addLigand: .: (0.000284) + test_addResidue: .: (0.000255) + test_atom_seq: .: (0.000313) + test_comp: .: (0.000367) + test_each: .: (0.000301) + test_each_heterogen: .: (0.000288) + test_each_residue: .: (0.000279) + test_get_heterogen_by_id: .: (0.000269) + test_get_residue_by_id: .: (0.000261) + test_inspect: .: (0.000323) + test_rehash: .: (0.000271) + test_rehash_heterogens: .: (0.000246) + test_rehash_residues: .: (0.000647) + test_square_brace: .: (0.000277) + test_to_s: .: (0.000264) Bio::TestChainFinder: - test_chains: .: (0.000938) - test_each_chain: .: (0.000526) - test_find_chain: .: (0.000485) + test_chains: .: (0.000505) + test_each_chain: .: (0.000230) + test_find_chain: .: (0.000208) Bio::TestClustalWReport::TestClustalWReport: - test_alignment: .: (0.026302) - test_header: .: (0.002374) - test_match_line: .: (0.001736) - test_sequence0: .: (0.002428) - test_sequence1: .: (0.001855) + test_alignment: .: (0.017971) + test_header: .: (0.001671) + test_match_line: .: (0.001077) + test_sequence0: .: (0.001723) + test_sequence1: .: (0.001266) Bio::TestClustalWReport::TestClustalWReportSeqnos: - test_alignment: .: (0.026175) - test_header: .: (0.003190) - test_match_line: .: (0.002303) - test_sequence0: .: (0.002384) - test_sequence1: .: (0.002647) + test_alignment: .: (0.018168) + test_header: .: (0.001824) + test_match_line: .: (0.001834) + test_sequence0: .: (0.001519) + test_sequence1: .: (0.001748) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: - test_alignment: .: (0.037606) - test_header: .: (0.003312) - test_match_line: .: (0.001925) - test_sequence0: .: (0.001876) - test_sequence1: .: (0.002056) + test_alignment: .: (0.024935) + test_header: .: (0.002391) + test_match_line: .: (0.001259) + test_sequence0: .: (0.001230) + test_sequence1: .: (0.001398) Bio::TestCodonTable: - test_Tables: .: (0.000783) - test_accessor: .: (0.000544) - test_definition: .: (0.000409) - test_each: .: (0.000452) - test_revtrans: .: (0.000669) - test_self_accessor: .: (0.000444) - test_self_copy: .: (0.002077) - test_set_accessor: .: (0.257068) - test_start: .: (0.000466) - test_start_codon?: .: (0.000422) - test_stop: .: (0.000365) - test_stop_codon?: .: (0.000401) - test_table: .: (0.000370) + test_Tables: .: (0.000473) + test_accessor: .: (0.000248) + test_definition: .: (0.000163) + test_each: .: (0.000198) + test_revtrans: .: (0.000316) + test_self_accessor: .: (0.000171) + test_self_copy: .: (0.001413) + test_set_accessor: .: (0.168113) + test_start: .: (0.000251) + test_start_codon?: .: (0.000289) + test_stop: .: (0.000223) + test_stop_codon?: .: (0.000248) + test_table: .: (0.000215) Bio::TestCodonTableConstants: - test_Definitions: .: (0.000827) - test_Starts: .: (0.000402) - test_Tables: .: (0.000331) - test_stops: .: (0.000370) + test_Definitions: .: (0.000476) + test_Starts: .: (0.000373) + test_Tables: .: (0.000213) + test_stops: .: (0.000316) Bio::TestColorScheme: - test_buried: .: (0.002834) + test_buried: .: (0.001898) Bio::TestCommand: - test_command_constants: .: (0.000761) - test_escape_shell: .: (0.000577) - test_escape_shell_unix: .: (0.000467) - test_escape_shell_windows: .: (0.000465) - test_make_cgi_params_by_array_of_array: .: (0.001012) - test_make_cgi_params_by_array_of_hash: .: (0.001057) - test_make_cgi_params_by_array_of_string: .: (0.000570) - test_make_cgi_params_by_hash_in_string: .: (0.001355) - test_make_cgi_params_by_hash_in_symbol: .: (0.001412) - test_make_cgi_params_by_string: .: (0.000542) - test_make_command_line: .: (0.000466) - test_make_command_line_unix: .: (0.000452) - test_make_command_line_windows: .: (0.000459) - test_safe_command_line_array: .: (0.000485) - test_safe_command_line_array_passthrough: .: (0.000444) + test_command_constants: .: (0.000459) + test_escape_shell: .: (0.000326) + test_escape_shell_unix: .: (0.000274) + test_escape_shell_windows: .: (0.000435) + test_make_cgi_params_by_array_of_array: .: (0.000653) + test_make_cgi_params_by_array_of_hash: .: (0.000616) + test_make_cgi_params_by_array_of_string: .: (0.000351) + test_make_cgi_params_by_hash_in_string: .: (0.000855) + test_make_cgi_params_by_hash_in_symbol: .: (0.001119) + test_make_cgi_params_by_string: .: (0.000367) + test_make_command_line: .: (0.000311) + test_make_command_line_unix: .: (0.000263) + test_make_command_line_windows: .: (0.000269) + test_safe_command_line_array: .: (0.000292) + test_safe_command_line_array_passthrough: .: (0.000286) Bio::TestContingencyTable: - test_lite_example: .: (0.498895) + test_lite_example: .: (0.341833) Bio::TestDB: - test_entry_id: .: (0.000872) - test_exists: .: (0.000401) - test_fetch: .: (0.000532) - test_get: .: (0.000377) - test_open: .: (0.000345) - test_tags: .: (0.000339) + test_entry_id: .: (0.000598) + test_exists: .: (0.000194) + test_fetch: .: (0.000346) + test_get: .: (0.000222) + test_open: .: (0.000217) + test_tags: .: (0.000212) Bio::TestDataType: - test_const_like_method: .: (0.001479) - test_pdb_achar: .: (0.000733) - test_pdb_atom: .: (0.000677) - test_pdb_character: .: (0.000666) - test_pdb_date: .: (0.000825) - test_pdb_idcode: .: (0.000675) - test_pdb_integer: .: (0.000367) - test_pdb_list: .: (0.000394) - test_pdb_lstring: .: (0.000656) - test_pdb_real: .: (0.000549) - test_pdb_resudue_name: .: (0.000700) - test_pdb_slist: .: (0.000411) - test_pdb_string: .: (0.000695) - test_pdb_stringrj: .: (0.000427) - test_pdb_symop: .: (0.000731) - test_specification_list: .: (0.000436) + test_const_like_method: .: (0.000951) + test_pdb_achar: .: (0.000467) + test_pdb_atom: .: (0.000411) + test_pdb_character: .: (0.000398) + test_pdb_date: .: (0.000391) + test_pdb_idcode: .: (0.000538) + test_pdb_integer: .: (0.000194) + test_pdb_list: .: (0.000271) + test_pdb_lstring: .: (0.000395) + test_pdb_real: .: (0.000331) + test_pdb_resudue_name: .: (0.000463) + test_pdb_slist: .: (0.000253) + test_pdb_string: .: (0.000411) + test_pdb_stringrj: .: (0.000237) + test_pdb_symop: .: (0.000395) + test_specification_list: .: (0.000267) Bio::TestEMBL: - test_ac: .: (0.001640) - test_accession: .: (0.001219) - test_cc: .: (0.000996) - test_de: .: (0.001152) - test_division: .: (0.005385) - test_dr: .: (0.001073) - test_dt: .: (0.001126) - test_dt_created: .: (0.001089) - test_dt_iterator: .: (0.001087) - test_dt_updated: .: (0.001495) - test_each_cds: .: (0.001591) - test_each_gene: .: (0.001586) - test_entry: .: (0.001508) - test_fh: .: (0.001108) - test_ft: .: (0.001602) - test_ft_accessor: .: (0.001525) - test_ft_iterator: .: (0.001877) - test_id_line: .: (0.001155) - test_id_line_data_class: .: (0.001199) - test_id_line_division: .: (0.001391) - test_id_line_entry_name: .: (0.001171) - test_id_line_iterator: .: (0.001186) - test_id_line_molecule_type: .: (0.001156) - test_id_line_sequence_length: .: (0.001189) - test_kw: .: (0.001147) - test_molecule: .: (0.001168) - test_oc: .: (0.001343) - test_og: .: (0.001032) - test_os: .: (0.001192) - test_ref: .: (0.001443) - test_references: .: (0.001822) - test_seq: .: (0.001797) - test_sequence_length: .: (0.001172) - test_sq: .: (0.001171) - test_sq_get: .: (0.001344) - test_sv: .: (0.001095) - test_version: .: (0.001124) + test_ac: .: (0.001145) + test_accession: .: (0.000882) + test_cc: .: (0.000675) + test_de: .: (0.000755) + test_division: .: (0.000856) + test_dr: .: (0.000908) + test_dt: .: (0.000786) + test_dt_created: .: (0.000744) + test_dt_iterator: .: (0.000750) + test_dt_updated: .: (0.001073) + test_each_cds: .: (0.001172) + test_each_gene: .: (0.001038) + test_entry: .: (0.001036) + test_fh: .: (0.000802) + test_ft: .: (0.001064) + test_ft_accessor: .: (0.001042) + test_ft_iterator: .: (0.001330) + test_id_line: .: (0.000803) + test_id_line_data_class: .: (0.000805) + test_id_line_division: .: (0.000953) + test_id_line_entry_name: .: (0.000808) + test_id_line_iterator: .: (0.000808) + test_id_line_molecule_type: .: (0.000819) + test_id_line_sequence_length: .: (0.000967) + test_kw: .: (0.000787) + test_molecule: .: (0.000866) + test_oc: .: (0.000878) + test_og: .: (0.000693) + test_os: .: (0.000763) + test_ref: .: (0.001004) + test_references: .: (0.001264) + test_seq: .: (0.001383) + test_sequence_length: .: (0.000863) + test_sq: .: (0.000752) + test_sq_get: .: (0.000738) + test_sv: .: (0.000880) + test_version: .: (0.000710) Bio::TestEMBL89: - test_ac: .: (0.001468) - test_accession: .: (0.001373) - test_cc: .: (0.000971) - test_de: .: (0.001098) - test_division: .: (0.001177) - test_dr: .: (0.000963) - test_dt: .: (0.001280) - test_dt_created: .: (0.001078) - test_dt_iterator: .: (0.000973) - test_dt_updated: .: (0.001012) - test_each_cds: .: (0.001741) - test_each_gene: .: (0.001391) - test_entry: .: (0.001244) - test_fh: .: (0.001021) - test_ft: .: (0.001714) - test_ft_accessor: .: (0.001431) - test_ft_iterator: .: (0.001501) - test_id_line: .: (0.001198) - test_id_line_data_class: .: (0.001280) - test_id_line_division: .: (0.001137) - test_id_line_entry_name: .: (0.001111) - test_id_line_iterator: .: (0.001091) - test_id_line_molecule_type: .: (0.001499) - test_id_line_sequence_length: .: (0.001158) - test_id_line_sequence_version: .: (0.001125) - test_kw: .: (0.001140) - test_molecule: .: (0.001129) - test_oc: .: (0.001634) - test_og: .: (0.000996) - test_os: .: (0.001112) - test_ref: .: (0.001381) - test_references: .: (0.002150) - test_seq: .: (0.001840) - test_sequence_length: .: (0.001265) - test_sq: .: (0.001622) - test_sq_get: .: (0.001157) - test_sv: .: (0.001184) - test_version: .: (0.001234) + test_ac: .: (0.000932) + test_accession: .: (0.000666) + test_cc: .: (0.000746) + test_de: .: (0.000636) + test_division: .: (0.000723) + test_dr: .: (0.000567) + test_dt: .: (0.000614) + test_dt_created: .: (0.000706) + test_dt_iterator: .: (0.000555) + test_dt_updated: .: (0.000548) + test_each_cds: .: (0.000954) + test_each_gene: .: (0.001012) + test_entry: .: (0.000703) + test_fh: .: (0.000563) + test_ft: .: (0.000912) + test_ft_accessor: .: (0.001052) + test_ft_iterator: .: (0.000892) + test_id_line: .: (0.000640) + test_id_line_data_class: .: (0.000614) + test_id_line_division: .: (0.000893) + test_id_line_entry_name: .: (0.000676) + test_id_line_iterator: .: (0.000628) + test_id_line_molecule_type: .: (0.000609) + test_id_line_sequence_length: .: (0.000603) + test_id_line_sequence_version: .: (0.000942) + test_kw: .: (0.000626) + test_molecule: .: (0.000664) + test_oc: .: (0.000726) + test_og: .: (0.000856) + test_os: .: (0.000817) + test_ref: .: (0.000839) + test_references: .: (0.001029) + test_seq: .: (0.001563) + test_sequence_length: .: (0.000708) + test_sq: .: (0.000662) + test_sq_get: .: (0.000597) + test_sv: .: (0.001020) + test_version: .: (0.000753) Bio::TestEMBLAPI: - test_ac: .: (0.000949) - test_accessions: .: (0.000610) + test_ac: .: (0.000553) + test_accessions: .: (0.000286) Bio::TestEMBLCommon: - test_ac: .: (0.000952) - test_accession: .: (0.000376) - test_accessions: .: (0.000371) - test_de: .: (0.000360) - test_definition: .: (0.000399) - test_description: .: (0.000355) - test_dr: .: (0.000371) - test_keywords: .: (0.000344) - test_kw: .: (0.000346) - test_oc: .: (0.000359) - test_og: .: (0.000354) - test_os: .: (0.000348) - test_ref: .: (0.000414) - test_references: .: (0.000349) + test_ac: .: (0.000347) + test_accession: .: (0.000166) + test_accessions: .: (0.000170) + test_de: .: (0.000159) + test_definition: .: (0.000312) + test_description: .: (0.000167) + test_dr: .: (0.000162) + test_keywords: .: (0.000154) + test_kw: .: (0.000162) + test_oc: .: (0.000164) + test_og: .: (0.000160) + test_os: .: (0.000152) + test_ref: .: (0.000158) + test_references: .: (0.000162) Bio::TestEMBLDB: - test_fetch: .: (0.001144) - test_p_entry2hash: .: (0.000396) + test_fetch: .: (0.000499) + test_p_entry2hash: .: (0.000154) Bio::TestEMBLToBioSequence: - test_classification: .: (0.009207) - test_date_created: .: (0.001606) - test_date_modified: .: (0.001449) - test_definition: .: (0.001230) - test_division: .: (0.001301) - test_entry_id: .: (0.001313) - test_entry_version: .: (0.001241) - test_features: .: (0.001725) - test_keywords: .: (0.001185) - test_molecule_type: .: (0.001908) - test_primary_accession: .: (0.001211) - test_references: .: (0.002034) - test_release_created: .: (0.001882) - test_release_modified: .: (0.001453) - test_secondary_accessions: .: (0.001219) - test_sequence_version: .: (0.001362) - test_species: .: (0.012784) - test_topology: .: (0.001368) + test_classification: .: (0.006199) + test_date_created: .: (0.001194) + test_date_modified: .: (0.000835) + test_definition: .: (0.000711) + test_division: .: (0.000771) + test_entry_id: .: (0.000780) + test_entry_version: .: (0.001070) + test_features: .: (0.001079) + test_keywords: .: (0.000717) + test_molecule_type: .: (0.000791) + test_primary_accession: .: (0.001168) + test_references: .: (0.001292) + test_release_created: .: (0.000741) + test_release_modified: .: (0.001080) + test_secondary_accessions: .: (0.000829) + test_sequence_version: .: (0.000868) + test_species: .: (0.009833) + test_topology: .: (0.000877) Bio::TestEMBLToBioSequenceRoundTrip: - test_classification: .: (0.052678) - test_date_created: .: (0.058691) - test_date_modified: .: (0.009254) - test_definition: .: (0.009435) - test_division: .: (0.009501) - test_entry_id: .: (0.008637) - test_entry_version: .: (0.008890) - test_features: .: (0.009257) - test_keywords: .: (0.008779) - test_molecule_type: .: (0.008303) - test_primary_accession: .: (0.008390) - test_references: .: (0.009399) - test_release_created: .: (0.008500) - test_release_modified: .: (0.008178) - test_secondary_accessions: .: (0.009034) - test_sequence_version: .: (0.008457) - test_species: .: (0.008923) - test_topology: .: (0.008141) + test_classification: .: (0.039791) + test_date_created: .: (0.043631) + test_date_modified: .: (0.006602) + test_definition: .: (0.006765) + test_division: .: (0.006505) + test_entry_id: .: (0.006448) + test_entry_version: .: (0.005866) + test_features: .: (0.006571) + test_keywords: .: (0.006222) + test_molecule_type: .: (0.005622) + test_primary_accession: .: (0.006025) + test_references: .: (0.006483) + test_release_created: .: (0.005685) + test_release_modified: .: (0.006038) + test_secondary_accessions: .: (0.006222) + test_sequence_version: .: (0.005897) + test_species: .: (0.006066) + test_topology: .: (0.005835) Bio::TestFasta: - test_db: .: (0.000804) - test_format: .: (0.000416) - test_format_arg_integer: .: (0.000424) - test_format_arg_str: .: (0.000396) - test_ktup: .: (0.000387) - test_matrix: .: (0.000376) - test_option: .: (0.000518) - test_options: .: (0.000428) - test_output: .: (0.000336) - test_program: .: (0.000366) - test_server: .: (0.000369) + test_db: .: (0.000945) + test_format: .: (0.000266) + test_format_arg_integer: .: (0.000268) + test_format_arg_str: .: (0.000244) + test_ktup: .: (0.000236) + test_matrix: .: (0.000236) + test_option: .: (0.000328) + test_options: .: (0.000250) + test_output: .: (0.000208) + test_program: .: (0.000309) + test_server: .: (0.000238) Bio::TestFastaDeflineEmb: - test_acc_version: .: (0.000799) - test_accession: .: (0.000489) - test_accessions: .: (0.000461) - test_description: .: (0.000418) - test_descriptions: .: (0.001040) - test_entry_id: .: (0.000431) - test_get_all_by_type: .: (0.000474) - test_gi: .: (0.000433) - test_id_strings: .: (0.000575) - test_list_ids: .: (0.000418) - test_locus: .: (0.000442) - test_words: .: (0.000589) + test_acc_version: .: (0.000531) + test_accession: .: (0.000275) + test_accessions: .: (0.000284) + test_description: .: (0.000254) + test_descriptions: .: (0.000248) + test_entry_id: .: (0.000707) + test_get_all_by_type: .: (0.000272) + test_gi: .: (0.000338) + test_id_strings: .: (0.000366) + test_list_ids: .: (0.000262) + test_locus: .: (0.000275) + test_words: .: (0.000361) Bio::TestFastaDeflineGI1: - test_acc_version: .: (0.000790) - test_accession: .: (0.000480) - test_accessions: .: (0.000494) - test_description: .: (0.000444) - test_descriptions: .: (0.000483) - test_emb: .: (0.000488) - test_entry_id: .: (0.000439) - test_get_all_by_type: .: (0.001141) - test_get_emb: .: (0.000486) - test_gi: .: (0.000464) - test_id_strings: .: (0.000602) - test_list_ids: .: (0.000465) - test_locus: .: (0.000554) - test_words: .: (0.000591) + test_acc_version: .: (0.000497) + test_accession: .: (0.000294) + test_accessions: .: (0.000294) + test_description: .: (0.000263) + test_descriptions: .: (0.000342) + test_emb: .: (0.000298) + test_entry_id: .: (0.000268) + test_get_all_by_type: .: (0.000302) + test_get_emb: .: (0.000799) + test_gi: .: (0.000284) + test_id_strings: .: (0.000368) + test_list_ids: .: (0.000278) + test_locus: .: (0.000282) + test_words: .: (0.000440) Bio::TestFastaDeflineGI2: - test_acc_version: .: (0.000740) - test_accession: .: (0.000464) - test_accessions: .: (0.000437) - test_description: .: (0.000416) - test_descriptions: .: (0.000450) - test_entry_id: .: (0.000414) - test_get_all_by_type: .: (0.000412) - test_gi: .: (0.000412) - test_id_strings: .: (0.001267) - test_list_ids: .: (0.000509) - test_locus: .: (0.000430) - test_sp: .: (0.000456) - test_words: .: (0.000518) + test_acc_version: .: (0.000529) + test_accession: .: (0.000291) + test_accessions: .: (0.000273) + test_description: .: (0.000247) + test_descriptions: .: (0.000258) + test_entry_id: .: (0.000253) + test_get_all_by_type: .: (0.000255) + test_gi: .: (0.000264) + test_id_strings: .: (0.000430) + test_list_ids: .: (0.000740) + test_locus: .: (0.000310) + test_sp: .: (0.000284) + test_words: .: (0.000316) Bio::TestFastaDeflineGIMultiple: - test_acc_version: .: (0.000912) - test_accession: .: (0.000568) - test_accessions: .: (0.000600) - test_description: .: (0.000537) - test_descriptions: .: (0.000554) - test_entry_id: .: (0.000579) - test_get_all_by_type: .: (0.000532) - test_gi: .: (0.000540) - test_id_strings: .: (0.000915) - test_list_ids: .: (0.000558) - test_locus: .: (0.006929) - test_words: .: (0.000980) + test_acc_version: .: (0.000568) + test_accession: .: (0.000366) + test_accessions: .: (0.000421) + test_description: .: (0.000332) + test_descriptions: .: (0.000337) + test_entry_id: .: (0.000335) + test_get_all_by_type: .: (0.000278) + test_gi: .: (0.000274) + test_id_strings: .: (0.000613) + test_list_ids: .: (0.000279) + test_locus: .: (0.000276) + test_words: .: (0.000626) Bio::TestFastaDeflineSce: - test_acc_version: .: (0.000837) - test_accession: .: (0.000554) - test_accessions: .: (0.000514) - test_description: .: (0.000509) - test_descriptions: .: (0.000508) - test_entry_id: .: (0.000481) - test_get_all_by_type: .: (0.000502) - test_gi: .: (0.001249) - test_id_strings: .: (0.000761) - test_list_ids: .: (0.000502) - test_locus: .: (0.000514) - test_words: .: (0.000730) + test_acc_version: .: (0.000508) + test_accession: .: (0.000256) + test_accessions: .: (0.000247) + test_description: .: (0.000238) + test_descriptions: .: (0.000242) + test_entry_id: .: (0.000237) + test_get_all_by_type: .: (0.000240) + test_gi: .: (0.000307) + test_id_strings: .: (0.000935) + test_list_ids: .: (0.000258) + test_locus: .: (0.000229) + test_words: .: (0.000375) Bio::TestFastaDeflineSimple: - test_acc_version: .: (0.000724) - test_accession: .: (0.000417) - test_accessions: .: (0.000426) - test_description: .: (0.000406) - test_descriptions: .: (0.000462) - test_entry_id: .: (0.000388) - test_get_all_by_type: .: (0.000383) - test_gi: .: (0.000435) - test_id_strings: .: (0.000487) - test_list_ids: .: (0.000422) - test_locus: .: (0.000390) - test_words: .: (0.000466) + test_acc_version: .: (0.000402) + test_accession: .: (0.000192) + test_accessions: .: (0.000182) + test_description: .: (0.000180) + test_descriptions: .: (0.000250) + test_entry_id: .: (0.000179) + test_get_all_by_type: .: (0.000184) + test_gi: .: (0.000182) + test_id_strings: .: (0.000288) + test_list_ids: .: (0.000178) + test_locus: .: (0.000173) + test_words: .: (0.000205) Bio::TestFastaDeflineSwissProt: - test_acc_version: .: (0.000776) - test_accession: .: (0.000505) - test_accessions: .: (0.000452) - test_description: .: (0.000425) - test_descriptions: .: (0.000428) - test_entry_id: .: (0.000416) - test_get: .: (0.000459) - test_get_all_by_type: .: (0.000453) - test_id_strings: .: (0.001315) - test_list_ids: .: (0.000455) - test_locus: .: (0.000460) - test_sp: .: (0.000453) - test_words: .: (0.000627) + test_acc_version: .: (0.000415) + test_accession: .: (0.000218) + test_accessions: .: (0.000233) + test_description: .: (0.000197) + test_descriptions: .: (0.000191) + test_entry_id: .: (0.000190) + test_get: .: (0.000213) + test_get_all_by_type: .: (0.000230) + test_id_strings: .: (0.000819) + test_list_ids: .: (0.000219) + test_locus: .: (0.000189) + test_sp: .: (0.000209) + test_words: .: (0.000321) Bio::TestFastaDeflineTrembl: - test_acc_version: .: (0.000754) - test_accession: .: (0.000498) - test_accessions: .: (0.000478) - test_description: .: (0.000421) - test_descriptions: .: (0.000411) - test_entry_id: .: (0.000400) - test_get: .: (0.000433) - test_get_all_by_type: .: (0.000412) - test_id_strings: .: (0.001417) - test_list_ids: .: (0.000440) - test_locus: .: (0.000432) - test_tr: .: (0.000488) - test_words: .: (0.000764) + test_acc_version: .: (0.000467) + test_accession: .: (0.000212) + test_accessions: .: (0.000206) + test_description: .: (0.000214) + test_descriptions: .: (0.000195) + test_entry_id: .: (0.000187) + test_get: .: (0.000206) + test_get_all_by_type: .: (0.000187) + test_id_strings: .: (0.000371) + test_list_ids: .: (0.000583) + test_locus: .: (0.000216) + test_tr: .: (0.000256) + test_words: .: (0.000382) Bio::TestFastaFirstName: - test_first_name1: .: (0.000735) - test_first_name_multi_identifier: .: (0.000422) - test_first_name_single_worded_defintion: .: (0.000433) - test_no_definition: .: (0.000395) - test_space_before_first_name: .: (0.000431) - test_tabbed_defintion: .: (0.000396) + test_first_name1: .: (0.000451) + test_first_name_multi_identifier: .: (0.000192) + test_first_name_single_worded_defintion: .: (0.000178) + test_no_definition: .: (0.000177) + test_space_before_first_name: .: (0.000186) + test_tabbed_defintion: .: (0.000178) Bio::TestFastaFormat: - test_aalen: .: (0.001521) - test_aaseq: .: (0.000757) - test_acc_version: .: (0.000570) - test_accession: .: (0.000544) - test_accessions: .: (0.000556) - test_data: .: (0.000406) - test_definition: .: (0.000426) - test_entry: .: (0.000402) - test_entry_id: .: (0.000522) - test_entry_overrun: .: (0.000400) - test_first_name: .: (0.000417) - test_gi: .: (0.000533) - test_identifiers: .: (0.000598) - test_length: .: (0.000426) - test_query: .: (0.000474) - test_seq: .: (0.000440) + test_aalen: .: (0.000415) + test_aaseq: .: (0.000209) + test_acc_version: .: (0.000879) + test_accession: .: (0.000452) + test_accessions: .: (0.000323) + test_data: .: (0.000190) + test_definition: .: (0.000190) + test_entry: .: (0.000198) + test_entry_id: .: (0.000334) + test_entry_overrun: .: (0.000193) + test_first_name: .: (0.000201) + test_gi: .: (0.000305) + test_identifiers: .: (0.000272) + test_length: .: (0.000220) + test_query: .: (0.000245) + test_seq: .: (0.000208) Bio::TestFastaFormatConst: - test_delimiter: .: (0.000912) + test_delimiter: .: (0.000421) Bio::TestFastaFormatKeggGenesAA: - test_acc_version: .: (0.000856) - test_data: .: (0.000423) - test_definition: .: (0.000420) - test_entry: .: (0.000472) - test_entry_id: .: (0.000569) - test_first_name: .: (0.000424) + test_acc_version: .: (0.000503) + test_data: .: (0.000198) + test_definition: .: (0.000188) + test_entry: .: (0.000190) + test_entry_id: .: (0.000268) + test_first_name: .: (0.000251) Bio::TestFastaFormatKeggGenesNT: - test_nalen: .: (0.000747) - test_naseq: .: (0.000430) - test_naseq_class: .: (0.000449) + test_nalen: .: (0.000456) + test_naseq: .: (0.000212) + test_naseq_class: .: (0.000210) Bio::TestFastaFormatSwissProt: - test_locus: .: (0.000760) + test_locus: .: (0.000486) Bio::TestFastaInitialize: - test_new_1: .: (0.002314) - test_option: .: (0.000392) - test_option_backward_compatibility: .: (0.000480) + test_new_1: .: (0.001359) + test_option: .: (0.000232) + test_option_backward_compatibility: .: (0.000236) Bio::TestFastaNumericFormat: - test_arg: .: (0.000850) - test_data: .: (0.000512) - test_definition: .: (0.000400) - test_each: .: (0.000501) - test_entry: .: (0.000392) - test_entry_id: .: (0.000485) - test_length: .: (0.000536) - test_to_biosequence: .: (0.002771) + test_arg: .: (0.000467) + test_data: .: (0.000304) + test_definition: .: (0.000178) + test_each: .: (0.000255) + test_entry: .: (0.000184) + test_entry_id: .: (0.000225) + test_length: .: (0.000254) + test_to_biosequence: .: (0.001994) Bio::TestFastaQuery: - test_query: .: (0.000672) - test_self_local: .: (0.000291) - test_self_parser: .: (0.000283) - test_self_remote: .: (0.000285) + test_query: .: (0.000319) + test_self_local: .: (0.000111) + test_self_parser: .: (0.000108) + test_self_remote: .: (0.000120) Bio::TestFastacmd: - test_database: .: (0.000675) - test_fastacmd: .: (0.000411) - test_methods: .: (0.000445) + test_database: .: (0.000334) + test_fastacmd: .: (0.000157) + test_methods: .: (0.000226) Bio::TestFastq::TestFastq_error_diff_ids: - test_validate_format: .: (0.002504) + test_validate_format: .: (0.001582) Bio::TestFastq::TestFastq_error_double_qual: - test_validate_format: .: (0.001672) + test_validate_format: .: (0.001098) Bio::TestFastq::TestFastq_error_double_seq: - test_validate_format: .: (0.001488) + test_validate_format: .: (0.000907) Bio::TestFastq::TestFastq_error_long_qual: - test_validate_format: .: (0.001523) + test_validate_format: .: (0.000961) Bio::TestFastq::TestFastq_error_no_qual: - test_validate_format: .: (0.002272) + test_validate_format: .: (0.001448) Bio::TestFastq::TestFastq_error_qual_del: - test_validate_format: .: (0.001742) + test_validate_format: .: (0.000888) Bio::TestFastq::TestFastq_error_qual_escape: - test_validate_format: .: (0.001503) + test_validate_format: .: (0.000955) Bio::TestFastq::TestFastq_error_qual_null: - test_validate_format: .: (0.002142) + test_validate_format: .: (0.001314) Bio::TestFastq::TestFastq_error_qual_space: - test_validate_format: .: (0.001712) + test_validate_format: .: (0.000957) Bio::TestFastq::TestFastq_error_qual_tab: - test_validate_format: .: (0.001481) + test_validate_format: .: (0.000951) Bio::TestFastq::TestFastq_error_qual_unit_sep: - test_validate_format: .: (0.001590) + test_validate_format: .: (0.000883) Bio::TestFastq::TestFastq_error_qual_vtab: - test_validate_format: .: (0.001504) + test_validate_format: .: (0.001418) Bio::TestFastq::TestFastq_error_short_qual: - test_validate_format: .: (0.001554) + test_validate_format: .: (0.000975) Bio::TestFastq::TestFastq_error_spaces: - test_validate_format: .: (0.003492) + test_validate_format: .: (0.002412) Bio::TestFastq::TestFastq_error_tabs: - test_validate_format: .: (0.003900) + test_validate_format: .: (0.002363) Bio::TestFastq::TestFastq_error_trunc_at_plus: - test_validate_format: .: (0.001640) + test_validate_format: .: (0.000928) Bio::TestFastq::TestFastq_error_trunc_at_qual: - test_validate_format: .: (0.001956) + test_validate_format: .: (0.001041) Bio::TestFastq::TestFastq_error_trunc_at_seq: - test_validate_format: .: (0.001505) + test_validate_format: .: (0.000893) Bio::TestFastq::TestFastq_illumina_full_range: - test_error_probabilities_as_illumina: .: (0.016120) - test_error_probabilities_as_sanger: .: (0.017378) - test_error_probabilities_as_solexa: .: (0.023978) - test_quality_scores_as_illumina: .: (0.001281) - test_quality_scores_as_sanger: .: (0.001034) - test_quality_scores_as_solexa: .: (0.001232) - test_validate_format: .: (0.001851) + test_error_probabilities_as_illumina: .: (0.010999) + test_error_probabilities_as_sanger: .: (0.011342) + test_error_probabilities_as_solexa: .: (0.011717) + test_quality_scores_as_illumina: .: (0.006215) + test_quality_scores_as_sanger: .: (0.000742) + test_quality_scores_as_solexa: .: (0.000859) + test_validate_format: .: (0.001227) Bio::TestFastq::TestFastq_longreads_original_sanger: - test_definition: .: (0.003774) - test_entry_id: .: (0.003589) - test_error_probabilities: .: (0.415071) - test_nalen: .: (0.003418) - test_naseq: .: (0.003252) - test_quality_scores: .: (0.005349) - test_quality_string: .: (0.002923) - test_roundtrip: .: (0.447729) - test_seq: .: (0.002901) - test_sequence_string: .: (0.002981) - test_to_biosequence: .: (0.422877) - test_to_biosequence_and_output: .: (0.014669) - test_to_s: .: (0.003012) - test_validate_format: .: (0.003177) - test_validate_format_with_array: .: (0.002885) + test_definition: .: (0.002647) + test_entry_id: .: (0.002476) + test_error_probabilities: .: (0.279616) + test_nalen: .: (0.002514) + test_naseq: .: (0.002371) + test_quality_scores: .: (0.003905) + test_quality_string: .: (0.002110) + test_roundtrip: .: (0.323826) + test_seq: .: (0.002409) + test_sequence_string: .: (0.002074) + test_to_biosequence: .: (0.282847) + test_to_biosequence_and_output: .: (0.010160) + test_to_s: .: (0.002095) + test_validate_format: .: (0.002517) + test_validate_format_with_array: .: (0.002255) Bio::TestFastq::TestFastq_mask: - test_mask_20: .: (0.001520) - test_mask_20_with_empty_string: .: (0.001125) - test_mask_20_with_longer_string: .: (0.001514) - test_mask_20_with_x: .: (0.001192) - test_mask_60: .: (0.001390) + test_mask_20: .: (0.001100) + test_mask_20_with_empty_string: .: (0.000665) + test_mask_20_with_longer_string: .: (0.001248) + test_mask_20_with_x: .: (0.000907) + test_mask_60: .: (0.001055) Bio::TestFastq::TestFastq_sanger_full_range: - test_error_probabilities_as_illumina: .: (0.022150) - test_error_probabilities_as_sanger: .: (0.025207) - test_error_probabilities_as_solexa: .: (0.024380) - test_quality_scores_as_illumina: .: (0.001904) - test_quality_scores_as_sanger: .: (0.001109) - test_quality_scores_as_solexa: .: (0.001453) - test_validate_format: .: (0.001880) + test_error_probabilities_as_illumina: .: (0.015093) + test_error_probabilities_as_sanger: .: (0.017324) + test_error_probabilities_as_solexa: .: (0.016921) + test_quality_scores_as_illumina: .: (0.001492) + test_quality_scores_as_sanger: .: (0.000955) + test_quality_scores_as_solexa: .: (0.001114) + test_validate_format: .: (0.001471) Bio::TestFastq::TestFastq_solexa_full_range: - test_error_probabilities_as_illumina: .: (0.017433) - test_error_probabilities_as_sanger: .: (0.106866) - test_error_probabilities_as_solexa: .: (0.034209) - test_quality_scores_as_illumina: .: (0.001624) - test_quality_scores_as_sanger: .: (0.002038) - test_quality_scores_as_solexa: .: (0.000944) - test_validate_format: .: (0.001808) + test_error_probabilities_as_illumina: .: (0.012339) + test_error_probabilities_as_sanger: .: (0.081351) + test_error_probabilities_as_solexa: .: (0.024968) + test_quality_scores_as_illumina: .: (0.001444) + test_quality_scores_as_sanger: .: (0.001683) + test_quality_scores_as_solexa: .: (0.000886) + test_validate_format: .: (0.001511) Bio::TestFeature: - test_append: .: (0.000785) - test_append_nil: .: (0.000436) - test_assoc: .: (0.000464) - test_each: .: (0.000390) - test_feature: .: (0.000377) - test_locations: .: (0.001098) - test_new: .: (0.000397) - test_position: .: (0.000419) - test_qualifiers: .: (0.000380) + test_append: .: (0.000730) + test_append_nil: .: (0.000417) + test_assoc: .: (0.000481) + test_each: .: (0.000902) + test_feature: .: (0.000399) + test_locations: .: (0.000542) + test_new: .: (0.000408) + test_position: .: (0.000399) + test_qualifiers: .: (0.000406) Bio::TestFeatures: - test_append: .: (0.000865) - test_arg: .: (0.000445) - test_each: .: (0.000454) - test_features: .: (0.000440) + test_append: .: (0.000879) + test_arg: .: (0.000448) + test_each: .: (0.000437) + test_features: .: (0.000446) Bio::TestFlatFile::TestDefaultAutoDetect: - test_aaindex1: .: (0.003318) - test_aaindex2: .: (0.000942) - test_blast: .: (0.000621) - test_blastxml: .: (0.001495) - test_embl: .: (0.000782) - test_embl_oldrelease: .: (0.000727) - test_fastaformat: .: (0.001090) - test_fastanumericformat: .: (0.000596) - test_fastq: .: (0.000649) - test_genbank: .: (0.000662) - test_genpept: .: (0.000722) - test_hmmer: .: (0.000690) - test_maxml_cluster: .: (0.008146) - test_maxml_sequence: .: (0.000471) - test_medline: .: (0.000557) - test_prosite: .: (0.006869) + test_aaindex1: .: (0.002869) + test_aaindex2: .: (0.000841) + test_blast: .: (0.000725) + test_blastxml: .: (0.001472) + test_embl: .: (0.000912) + test_embl_oldrelease: .: (0.000781) + test_fastaformat: .: (0.001037) + test_fastanumericformat: .: (0.000573) + test_fastq: .: (0.000692) + test_genbank: .: (0.000663) + test_genpept: .: (0.000741) + test_hmmer: .: (0.003678) + test_maxml_cluster: .: (0.005929) + test_maxml_sequence: .: (0.000333) + test_medline: .: (0.000382) + test_prosite: .: (0.006642) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. -.: (0.007038) - test_transfac: .: (0.004195) +.: (0.005960) + test_transfac: .: (0.003827) Bio::TestFlatFile::TestFlatFileClassMethod: - test_auto_0arg: .: (0.000832) - test_auto_1arg_filename: .: (0.001222) - test_auto_1arg_io: .: (0.001499) - test_auto_1arg_io_with_block: .: (0.001996) - test_auto_1arg_with_block: .: (0.001782) - test_auto_2arg_filename_mode: .: (0.001068) - test_auto_2arg_filename_mode_with_block: .: (0.002508) - test_auto_3arg: .: (0.001033) - test_auto_3arg_with_block: .: (0.001856) - test_foreach: .: (0.001542) - test_new_2arg_class: .: (0.001195) - test_new_2arg_nil: .: (0.001131) - test_open_0arg: .: (0.000489) - test_open_1arg_class: .: (0.000440) - test_open_1arg_filename: .: (0.001009) - test_open_1arg_io: .: (0.000970) - test_open_1arg_io_with_block: .: (0.001944) - test_open_1arg_nil: .: (0.000454) - test_open_1arg_with_block: .: (0.002483) - test_open_2arg_autodetect: .: (0.001008) - test_open_2arg_autodetect_io: .: (0.000966) - test_open_2arg_autodetect_io_with_block: .: (0.001927) - test_open_2arg_autodetect_with_block: .: (0.001729) - test_open_2arg_class: .: (0.000617) - test_open_2arg_class_io: .: (0.001251) - test_open_2arg_class_io_with_block: .: (0.001470) - test_open_2arg_class_with_block: .: (0.001469) - test_open_2arg_filename_mode: .: (0.001018) - test_open_2arg_filename_mode_with_block: .: (0.002344) - test_open_3arg: .: (0.001918) - test_open_3arg_with_block: .: (0.004360) - test_open_4arg: .: (0.004497) - test_to_a: .: (0.001513) + test_auto_0arg: .: (0.000666) + test_auto_1arg_filename: .: (0.001676) + test_auto_1arg_io: .: (0.001240) + test_auto_1arg_io_with_block: .: (0.001482) + test_auto_1arg_with_block: .: (0.001374) + test_auto_2arg_filename_mode: .: (0.000762) + test_auto_2arg_filename_mode_with_block: .: (0.001825) + test_auto_3arg: .: (0.000765) + test_auto_3arg_with_block: .: (0.001254) + test_foreach: .: (0.001056) + test_new_2arg_class: .: (0.000444) + test_new_2arg_nil: .: (0.001122) + test_open_0arg: .: (0.000322) + test_open_1arg_class: .: (0.000274) + test_open_1arg_filename: .: (0.000717) + test_open_1arg_io: .: (0.000748) + test_open_1arg_io_with_block: .: (0.001352) + test_open_1arg_nil: .: (0.000296) + test_open_1arg_with_block: .: (0.001858) + test_open_2arg_autodetect: .: (0.000789) + test_open_2arg_autodetect_io: .: (0.000766) + test_open_2arg_autodetect_io_with_block: .: (0.001481) + test_open_2arg_autodetect_with_block: .: (0.001471) + test_open_2arg_class: .: (0.000514) + test_open_2arg_class_io: .: (0.001088) + test_open_2arg_class_io_with_block: .: (0.001389) + test_open_2arg_class_with_block: .: (0.001092) + test_open_2arg_filename_mode: .: (0.000938) + test_open_2arg_filename_mode_with_block: .: (0.001417) + test_open_3arg: .: (0.001915) + test_open_3arg_with_block: .: (0.003156) + test_open_4arg: .: (0.003342) + test_to_a: .: (0.001450) Bio::TestFlatFile::TestFlatFileFastaFormat: - test_autodetect: .: (0.001438) - test_close: .: (0.000534) - test_dbclass: .: (0.000508) - test_dbclass_eq: .: (0.000602) - test_dbclass_nil: .: (0.001287) - test_each: .: (0.000911) - test_each_entry: .: (0.001243) - test_ended_pos: .: (0.000827) - test_entry_pos_flag: .: (0.000594) - test_entry_raw: .: (0.001026) - test_eof?: .: (0.000929) - test_next_entry: .: (0.001199) - test_path: .: (0.000521) - test_pos: .: (0.001409) - test_raw: .: (0.001060) - test_rewind: .: (0.000748) - test_start_pos: .: (0.000797) - test_start_pos_ended_pos_not_recorded: .: (0.000860) - test_to_io: .: (0.000564) + test_autodetect: .: (0.001091) + test_close: .: (0.000467) + test_dbclass: .: (0.000427) + test_dbclass_eq: .: (0.000818) + test_dbclass_nil: .: (0.000664) + test_each: .: (0.000938) + test_each_entry: .: (0.001048) + test_ended_pos: .: (0.000664) + test_entry_pos_flag: .: (0.000484) + test_entry_raw: .: (0.000848) + test_eof?: .: (0.000724) + test_next_entry: .: (0.000876) + test_path: .: (0.000797) + test_pos: .: (0.000717) + test_raw: .: (0.000995) + test_rewind: .: (0.000692) + test_start_pos: .: (0.000685) + test_start_pos_ended_pos_not_recorded: .: (0.000747) + test_to_io: .: (0.000457) Bio::TestFlatFile::TestFlatFileWithCustomClass: - test_simpleformat: .: (0.000921) - test_simpleformat2: .: (0.000682) + test_simpleformat: .: (0.000794) + test_simpleformat2: .: (0.000514) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: - test_close: .: (0.000723) - test_eof_false_after_prefetch: .: (0.001033) - test_eof_false_first: .: (0.000482) - test_eof_true: .: (0.000607) - test_getc: .: (0.000493) - test_getc_after_prefetch: .: (0.000427) - test_gets: .: (0.000427) - test_gets_equal_prefetch_gets: .: (0.000464) - test_gets_paragraph_mode: .: (0.000578) - test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000906) - test_gets_paragraph_mode_within_buffer: .: (0.001016) - test_gets_rs: .: (0.000548) - test_gets_rs_equal_prefetch_gets: .: (0.000612) - test_gets_rs_within_buffer: .: (0.001436) - test_pos: .: (0.000524) - test_pos=: .: (0.000475) - test_prefetch_buffer: .: (0.000469) - test_prefetch_gets: .: (0.000499) - test_prefetch_gets_with_arg: .: (0.000503) - test_rewind: .: (0.000408) - test_skip_spaces: .: (0.000454) - test_to_io: .: (0.000432) - test_ungetc: .: (0.000451) - test_ungetc_after_prefetch: .: (0.000530) - test_ungets: .: (0.000518) + test_close: .: (0.000578) + test_eof_false_after_prefetch: .: (0.000980) + test_eof_false_first: .: (0.000420) + test_eof_true: .: (0.000481) + test_getc: .: (0.000349) + test_getc_after_prefetch: .: (0.000327) + test_gets: .: (0.000335) + test_gets_equal_prefetch_gets: .: (0.000377) + test_gets_paragraph_mode: .: (0.000484) + test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000777) + test_gets_paragraph_mode_within_buffer: .: (0.000820) + test_gets_rs: .: (0.000442) + test_gets_rs_equal_prefetch_gets: .: (0.000524) + test_gets_rs_within_buffer: .: (0.001219) + test_pos: .: (0.000466) + test_pos=: .: (0.000392) + test_prefetch_buffer: .: (0.000353) + test_prefetch_gets: .: (0.000402) + test_prefetch_gets_with_arg: .: (0.000454) + test_rewind: .: (0.000350) + test_skip_spaces: .: (0.000375) + test_to_io: .: (0.000377) + test_ungetc: .: (0.000366) + test_ungetc_after_prefetch: .: (0.000474) + test_ungets: .: (0.000626) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: - test_self_for_io: .: (0.000763) - test_self_open_file: .: (0.001054) - test_self_open_file_with_block: .: (0.000609) + test_self_for_io: .: (0.000673) + test_self_open_file: .: (0.000403) + test_self_open_file_with_block: .: (0.000944) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: - test_parse_file_open_arg_int_opt: .: (0.000718) - test_parse_file_open_arg_int_perm: .: (0.000374) - test_parse_file_open_arg_int_perm_opt: .: (0.000371) - test_parse_file_open_arg_integer: .: (0.000401) - test_parse_file_open_arg_nil: .: (0.000334) - test_parse_file_open_arg_opt: .: (0.000448) - test_parse_file_open_arg_opt_with_integer_mode: .: (0.000400) - test_parse_file_open_arg_str: .: (0.000383) - test_parse_file_open_arg_str_opt: .: (0.000443) - test_parse_file_open_arg_str_perm: .: (0.000386) - test_parse_file_open_arg_str_perm_opt: .: (0.000398) - test_parse_file_open_arg_str_with_enc: .: (0.000417) - test_parse_file_open_arg_str_with_ext_enc: .: (0.000392) - test_parse_file_open_mode_integer: .: (0.000337) - test_parse_file_open_mode_nil: .: (0.000468) - test_parse_file_open_mode_str: .: (0.000435) - test_parse_file_open_mode_str_with_enc: .: (0.000385) - test_parse_file_open_mode_str_with_ext_enc: .: (0.000378) + test_parse_file_open_arg_int_opt: .: (0.000487) + test_parse_file_open_arg_int_perm: .: (0.000172) + test_parse_file_open_arg_int_perm_opt: .: (0.000169) + test_parse_file_open_arg_integer: .: (0.000165) + test_parse_file_open_arg_nil: .: (0.000263) + test_parse_file_open_arg_opt: .: (0.000293) + test_parse_file_open_arg_opt_with_integer_mode: .: (0.000615) + test_parse_file_open_arg_str: .: (0.000328) + test_parse_file_open_arg_str_opt: .: (0.000325) + test_parse_file_open_arg_str_perm: .: (0.000210) + test_parse_file_open_arg_str_perm_opt: .: (0.000250) + test_parse_file_open_arg_str_with_enc: .: (0.000212) + test_parse_file_open_arg_str_with_ext_enc: .: (0.000264) + test_parse_file_open_mode_integer: .: (0.000237) + test_parse_file_open_mode_nil: .: (0.000656) + test_parse_file_open_mode_str: .: (0.004595) + test_parse_file_open_mode_str_with_enc: .: (0.000362) + test_parse_file_open_mode_str_with_ext_enc: .: (0.000266) Bio::TestFlatFileSplitter::TestTemplate: - test_dbclass: .: (0.000688) - test_entry: .: (0.000413) - test_entry_ended_pos: .: (0.000437) - test_entry_pos_flag: .: (0.000428) - test_entry_start_pos: .: (0.000388) - test_get_entry: .: (0.000492) - test_rewind: .: (0.000405) - test_skip_leader: .: (0.000429) - test_stream: .: (0.000406) - test_stream_pos: .: (0.000953) + test_dbclass: .: (0.000520) + test_entry: .: (0.000292) + test_entry_ended_pos: .: (0.000257) + test_entry_pos_flag: .: (0.000295) + test_entry_start_pos: .: (0.000253) + test_get_entry: .: (0.000393) + test_rewind: .: (0.000302) + test_skip_leader: .: (0.000292) + test_stream: .: (0.000244) + test_stream_pos: .: (0.000291) Bio::TestFlatFileSplitter::TestDefault: - test_delimiter: .: (0.000728) - test_delimiter_overrun: .: (0.000367) - test_entry: .: (0.000515) - test_entry_ended_pos: .: (0.000473) - test_entry_ended_pos_default_nil: .: (0.000434) - test_entry_start_pos: .: (0.000434) - test_entry_start_pos_default_nil: .: (0.000451) - test_get_entry: .: (0.000774) - test_get_parsed_entry: .: (0.000747) - test_header: .: (0.000376) - test_skip_leader: .: (0.000505) - test_skip_leader_without_header: .: (0.000549) + test_delimiter: .: (0.000535) + test_delimiter_overrun: .: (0.000246) + test_entry: .: (0.000324) + test_entry_ended_pos: .: (0.000318) + test_entry_ended_pos_default_nil: .: (0.000270) + test_entry_start_pos: .: (0.000230) + test_entry_start_pos_default_nil: .: (0.000201) + test_get_entry: .: (0.000445) + test_get_parsed_entry: .: (0.000491) + test_header: .: (0.000241) + test_skip_leader: .: (0.000269) + test_skip_leader_without_header: .: (0.000337) Bio::TestFlatFileSplitter::TestLineOriented: - test_dbclass: .: (0.001050) - test_entry_ended_pos: .: (0.000741) - test_entry_start_pos: .: (0.000748) - test_flag_to_fetch_header: .: (0.000725) - test_get_entry: .: (0.000881) - test_get_parsed_entry: .: (0.001352) - test_rewind: .: (0.000816) - test_skip_leader: .: (0.000506) + test_dbclass: .: (0.000694) + test_entry_ended_pos: .: (0.000963) + test_entry_start_pos: .: (0.000447) + test_flag_to_fetch_header: .: (0.000427) + test_get_entry: .: (0.000667) + test_get_parsed_entry: .: (0.000609) + test_rewind: .: (0.000565) + test_skip_leader: .: (0.000297) Bio::TestGCGMsf: - test_alignment: .: (0.002756) - test_checksum: .: (0.001141) - test_compcheck: .: (0.000848) - test_date: .: (0.000758) - test_description: .: (0.000730) - test_entry_id: .: (0.000706) - test_gap_length_weight: .: (0.000748) - test_gap_weight: .: (0.000759) - test_heading: .: (0.000698) - test_length: .: (0.000695) - test_seq_type: .: (0.000838) - test_symbol_comparison_table: .: (0.000773) - test_validate_checksum: .: (0.004573) + test_alignment: .: (0.002065) + test_checksum: .: (0.000547) + test_compcheck: .: (0.000484) + test_date: .: (0.000502) + test_description: .: (0.000465) + test_entry_id: .: (0.000776) + test_gap_length_weight: .: (0.000538) + test_gap_weight: .: (0.000463) + test_heading: .: (0.000465) + test_length: .: (0.000426) + test_seq_type: .: (0.000430) + test_symbol_comparison_table: .: (0.000399) + test_validate_checksum: .: (0.003508) Bio::TestGFF: - test_record_class: .: (0.002005) - test_records: .: (0.001024) + test_record_class: .: (0.000960) + test_records: .: (0.000584) Bio::TestGFF2: - test_const_version: .: (0.001574) - test_gff_version: .: (0.001163) - test_metadata: .: (0.001762) - test_metadata_size: .: (0.001206) - test_records_size: .: (0.001136) - test_to_s: .: (0.002007) + test_const_version: .: (0.001046) + test_gff_version: .: (0.001279) + test_metadata: .: (0.000841) + test_metadata_size: .: (0.000828) + test_records_size: .: (0.000787) + test_to_s: .: (0.001683) Bio::TestGFF2ComplexAttributes: - test_attributes_case1: .: (0.000865) - test_attributes_case2: .: (0.000613) - test_attributes_incompatible_backslash_semicolon: .: (0.000722) + test_attributes_case1: .: (0.000492) + test_attributes_case2: .: (0.000299) + test_attributes_incompatible_backslash_semicolon: .: (0.000376) Bio::TestGFF2MetaData: - test_data: .: (0.000618) - test_directive: .: (0.000342) - test_parse: .: (0.000390) + test_data: .: (0.000340) + test_directive: .: (0.000218) + test_parse: .: (0.000244) Bio::TestGFF2Record: - test_attribute: .: (0.001343) - test_attribute_nonexistent: .: (0.000963) - test_attributes: .: (0.000884) - test_attributes_to_hash: .: (0.000936) - test_comment_only?: .: (0.000811) - test_delete_attribute: .: (0.000904) - test_delete_attribute_multiple: .: (0.001528) - test_delete_attribute_multiple2: .: (0.000988) - test_delete_attribute_multiple_nil: .: (0.000899) - test_delete_attribute_nil: .: (0.000880) - test_delete_attribute_nonexistent: .: (0.000895) - test_delete_attributes: .: (0.001433) - test_delete_attributes_multiple: .: (0.000910) - test_delete_attributes_nonexistent: .: (0.000852) - test_end: .: (0.000820) - test_eqeq: .: (0.001873) - test_eqeq_false: .: (0.002043) - test_feature: .: (0.000763) - test_frame: .: (0.000770) - test_get_attribute: .: (0.001006) - test_get_attribute_nonexistent: .: (0.000792) - test_get_attributes: .: (0.001569) - test_get_attributes_nonexistent: .: (0.000781) - test_replace_attributes: .: (0.000930) - test_replace_attributes_multiple_multiple_over: .: (0.000962) - test_replace_attributes_multiple_multiple_same: .: (0.000999) - test_replace_attributes_multiple_multiple_two: .: (0.000888) - test_replace_attributes_multiple_single: .: (0.001470) - test_replace_attributes_nonexistent: .: (0.000874) - test_replace_attributes_nonexistent_multiple: .: (0.000923) - test_replace_attributes_single_multiple: .: (0.000916) - test_score: .: (0.000752) - test_self_parse: .: (0.002231) - test_seqname: .: (0.000816) - test_set_attribute: .: (0.000857) - test_set_attribute_multiple: .: (0.001059) - test_set_attribute_nonexistent: .: (0.000914) - test_sort_attributes_by_tag!: .: (0.001095) - test_sort_attributes_by_tag_bang_test2: .: (0.001104) - test_sort_attributes_by_tag_bang_with_block: .: (0.001028) - test_source: .: (0.000843) - test_start: .: (0.000777) - test_strand: .: (0.000792) - test_to_s: .: (0.002006) + test_attribute: .: (0.007956) + test_attribute_nonexistent: .: (0.000598) + test_attributes: .: (0.001252) + test_attributes_to_hash: .: (0.000669) + test_comment_only?: .: (0.000564) + test_delete_attribute: .: (0.000623) + test_delete_attribute_multiple: .: (0.001032) + test_delete_attribute_multiple2: .: (0.000741) + test_delete_attribute_multiple_nil: .: (0.000584) + test_delete_attribute_nil: .: (0.000594) + test_delete_attribute_nonexistent: .: (0.000499) + test_delete_attributes: .: (0.001028) + test_delete_attributes_multiple: .: (0.000621) + test_delete_attributes_nonexistent: .: (0.000571) + test_end: .: (0.000528) + test_eqeq: .: (0.001221) + test_eqeq_false: .: (0.001517) + test_feature: .: (0.000511) + test_frame: .: (0.000523) + test_get_attribute: .: (0.000694) + test_get_attribute_nonexistent: .: (0.000543) + test_get_attributes: .: (0.001024) + test_get_attributes_nonexistent: .: (0.000514) + test_replace_attributes: .: (0.000591) + test_replace_attributes_multiple_multiple_over: .: (0.000606) + test_replace_attributes_multiple_multiple_same: .: (0.000684) + test_replace_attributes_multiple_multiple_two: .: (0.000582) + test_replace_attributes_multiple_single: .: (0.000999) + test_replace_attributes_nonexistent: .: (0.000569) + test_replace_attributes_nonexistent_multiple: .: (0.000608) + test_replace_attributes_single_multiple: .: (0.000502) + test_score: .: (0.000413) + test_self_parse: .: (0.001451) + test_seqname: .: (0.000419) + test_set_attribute: .: (0.000530) + test_set_attribute_multiple: .: (0.000567) + test_set_attribute_nonexistent: .: (0.000485) + test_sort_attributes_by_tag!: .: (0.000667) + test_sort_attributes_by_tag_bang_test2: .: (0.000662) + test_sort_attributes_by_tag_bang_with_block: .: (0.000609) + test_source: .: (0.000418) + test_start: .: (0.000406) + test_strand: .: (0.000934) + test_to_s: .: (0.000791) Bio::TestGFF2RecordEmpty: - test_comment: .: (0.000766) - test_comment_eq: .: (0.000389) - test_comment_only?: .: (0.000390) - test_comment_only_false: .: (0.000378) - test_to_s: .: (0.000389) - test_to_s_not_empty: .: (0.000591) + test_comment: .: (0.000451) + test_comment_eq: .: (0.000189) + test_comment_only?: .: (0.000177) + test_comment_only_false: .: (0.000176) + test_to_s: .: (0.000189) + test_to_s_not_empty: .: (0.000318) Bio::TestGFF3: - test_const_version: .: (0.002465) - test_gff_version: .: (0.001670) - test_records: .: (0.002535) - test_sequence_regions: .: (0.001686) - test_sequences: .: (0.002285) - test_to_s: .: (0.002963) + test_const_version: .: (0.001776) + test_gff_version: .: (0.001040) + test_records: .: (0.001578) + test_sequence_regions: .: (0.001104) + test_sequences: .: (0.001409) + test_to_s: .: (0.002338) Bio::TestGFF3MetaData: - test_data: .: (0.001111) - test_directive: .: (0.000355) - test_parse: .: (0.000394) + test_data: .: (0.000423) + test_directive: .: (0.000155) + test_parse: .: (0.000192) Bio::TestGFF3Record: - test_attributes: .: (0.001152) - test_end: .: (0.000745) - test_feature: .: (0.000748) - test_frame: .: (0.000781) - test_id: .: (0.001246) - test_score: .: (0.000718) - test_seqname: .: (0.000739) - test_source: .: (0.000771) - test_start: .: (0.000799) - test_strand: .: (0.001248) - test_to_s: .: (0.001209) - test_to_s_attr_order_changed: .: (0.001411) + test_attributes: .: (0.000663) + test_end: .: (0.000413) + test_feature: .: (0.000422) + test_frame: .: (0.000438) + test_id: .: (0.000401) + test_score: .: (0.000419) + test_seqname: .: (0.000388) + test_source: .: (0.000431) + test_start: .: (0.000395) + test_strand: .: (0.000817) + test_to_s: .: (0.000700) + test_to_s_attr_order_changed: .: (0.000857) Bio::TestGFF3RecordEscape: - test_escape: .: (0.000829) - test_escape_attribute: .: (0.000586) - test_escape_seqid: .: (0.000577) - test_unescape: .: (0.000530) + test_escape: .: (0.000490) + test_escape_attribute: .: (0.000247) + test_escape_seqid: .: (0.000473) + test_unescape: .: (0.000330) Bio::TestGFF3RecordGap: - test___scan_gap: .: (0.001783) - test_eqeq: .: (0.000689) - test_new_from_sequences_na: .: (0.000704) - test_new_from_sequences_na_aa: .: (0.001012) - test_new_from_sequences_na_aa_boundary_gap: .: (0.001388) - test_new_from_sequences_na_aa_example: .: (0.001048) - test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000952) - test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.001364) - test_process_sequences_na: .: (0.000869) - test_process_sequences_na_aa: .: (0.000724) - test_process_sequences_na_aa_reverse_frameshift: .: (0.000736) - test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000723) - test_process_sequences_na_aa_tooshort: .: (0.000992) - test_process_sequences_na_tooshort: .: (0.000851) - test_to_s: .: (0.001113) + test___scan_gap: .: (0.001174) + test_eqeq: .: (0.000388) + test_new_from_sequences_na: .: (0.000390) + test_new_from_sequences_na_aa: .: (0.000644) + test_new_from_sequences_na_aa_boundary_gap: .: (0.000833) + test_new_from_sequences_na_aa_example: .: (0.000625) + test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000532) + test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000498) + test_process_sequences_na: .: (0.003004) + test_process_sequences_na_aa: .: (0.000415) + test_process_sequences_na_aa_reverse_frameshift: .: (0.000373) + test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000696) + test_process_sequences_na_aa_tooshort: .: (0.000793) + test_process_sequences_na_tooshort: .: (0.001194) + test_to_s: .: (0.000607) Bio::TestGFF3RecordMisc: - test_attributes_none: .: (0.000847) - test_attributes_one: .: (0.000472) - test_attributes_with_escaping: .: (0.000533) - test_id_multiple: .: (0.000813) - test_id_multiple2: .: (0.000765) - test_id_replace: .: (0.000543) - test_id_set: .: (0.001265) - test_initialize_9: .: (0.000374) - test_phase: .: (0.000542) - test_score: .: (0.000519) - test_to_s_void: .: (0.000467) + test_attributes_none: .: (0.000681) + test_attributes_one: .: (0.000416) + test_attributes_with_escaping: .: (0.000419) + test_id_multiple: .: (0.000682) + test_id_multiple2: .: (0.000585) + test_id_replace: .: (0.000530) + test_id_set: .: (0.000532) + test_initialize_9: .: (0.000366) + test_phase: .: (0.000702) + test_score: .: (0.000336) + test_to_s_void: .: (0.000240) Bio::TestGFF3RecordTarget: - test_end: .: (0.000716) - test_parse: .: (0.000620) - test_start: .: (0.000440) - test_strand: .: (0.000406) - test_target_id: .: (0.000419) - test_to_s: .: (0.000617) + test_end: .: (0.000498) + test_parse: .: (0.000355) + test_start: .: (0.000199) + test_strand: .: (0.000200) + test_target_id: .: (0.000209) + test_to_s: .: (0.000341) Bio::TestGFF3SequenceRegion: - test_end: .: (0.001291) - test_parse: .: (0.000719) - test_seqid: .: (0.000452) - test_start: .: (0.000404) - test_to_s: .: (0.000603) + test_end: .: (0.000457) + test_parse: .: (0.001054) + test_seqid: .: (0.000233) + test_start: .: (0.000203) + test_to_s: .: (0.000324) Bio::TestGFFRecord: - test_attributes: .: (0.000820) - test_comment: .: (0.000455) - test_end: .: (0.000444) - test_feature: .: (0.000452) - test_frame: .: (0.000458) - test_score: .: (0.000429) - test_seqname: .: (0.000912) - test_source: .: (0.000459) - test_start: .: (0.000441) - test_strand: .: (0.000438) + test_attributes: .: (0.000494) + test_comment: .: (0.000226) + test_end: .: (0.000250) + test_feature: .: (0.000225) + test_frame: .: (0.000216) + test_score: .: (0.000223) + test_seqname: .: (0.000212) + test_source: .: (0.000585) + test_start: .: (0.000281) + test_strand: .: (0.000215) Bio::TestGFFRecordConstruct: - test_add_seqname: .: (0.000734) + test_add_seqname: .: (0.000437) Bio::TestGeneAssociation: - test_aspect: .: (0.000727) - test_assigned_by: .: (0.000437) - test_date: .: (0.000455) - test_db: .: (0.000420) - test_db_object_id: .: (0.000416) - test_db_object_name: .: (0.000448) - test_db_object_symbol: .: (0.000405) - test_db_object_synonym: .: (0.000774) - test_db_object_type: .: (0.000421) - test_db_reference: .: (0.000501) - test_evidence: .: (0.000419) - test_goid: .: (0.000464) - test_parser: .: (0.001490) - test_qualifier: .: (0.000489) - test_taxon: .: (0.000438) - test_to_str: .: (0.000451) - test_with: .: (0.000852) + test_aspect: .: (0.000464) + test_assigned_by: .: (0.000219) + test_date: .: (0.000525) + test_db: .: (0.000225) + test_db_object_id: .: (0.000208) + test_db_object_name: .: (0.000242) + test_db_object_symbol: .: (0.000203) + test_db_object_synonym: .: (0.000211) + test_db_object_type: .: (0.000203) + test_db_reference: .: (0.000556) + test_evidence: .: (0.000238) + test_goid: .: (0.000230) + test_parser: .: (0.001337) + test_qualifier: .: (0.000328) + test_taxon: .: (0.000293) + test_to_str: .: (0.000285) + test_with: .: (0.000256) Bio::TestGenscanReport: - test_date_run: .: (0.002484) - test_gccontent: .: (0.001975) - test_genscan_version: .: (0.002664) - test_isochore: .: (0.001941) - test_length: .: (0.002600) - test_matrix: .: (0.001903) - test_predictions_size: .: (0.001963) - test_query_name: .: (0.002634) - test_time: .: (0.001944) + test_date_run: .: (0.002403) + test_gccontent: .: (0.001464) + test_genscan_version: .: (0.001441) + test_isochore: .: (0.001940) + test_length: .: (0.001369) + test_matrix: .: (0.002583) + test_predictions_size: .: (0.001372) + test_query_name: .: (0.001889) + test_time: .: (0.001373) Bio::TestGenscanReportExon: - test_acceptor_score: .: (0.002712) - test_donor_score: .: (0.001911) - test_exon_type: .: (0.001965) - test_exon_type_long: .: (0.002344) - test_first: .: (0.001849) - test_initiation_score: .: (0.002154) - test_last: .: (0.009236) - test_number: .: (0.002076) - test_p_value: .: (0.002448) - test_phase: .: (0.002046) - test_range: .: (0.002082) - test_score: .: (0.002233) - test_strand: .: (0.001932) - test_t_score: .: (0.002238) - test_termination_score: .: (0.001850) + test_acceptor_score: .: (0.001734) + test_donor_score: .: (0.001730) + test_exon_type: .: (0.001459) + test_exon_type_long: .: (0.001716) + test_first: .: (0.001342) + test_initiation_score: .: (0.001414) + test_last: .: (0.007256) + test_number: .: (0.001473) + test_p_value: .: (0.001926) + test_phase: .: (0.001442) + test_range: .: (0.001416) + test_score: .: (0.001748) + test_strand: .: (0.001383) + test_t_score: .: (0.001781) + test_termination_score: .: (0.001393) Bio::TestGenscanReportGene: - test_aaseq: .: (0.002834) - test_naseq: .: (0.001925) - test_number: .: (0.001865) - test_polyA: .: (0.002263) - test_promoter: .: (0.001928) + test_aaseq: .: (0.002070) + test_naseq: .: (0.001495) + test_number: .: (0.001785) + test_polyA: .: (0.001461) + test_promoter: .: (0.001415) Bio::TestHMMERReportClassMethods: - test_reports_ary: .: (0.002668) - test_reports_ary_contents: .: (0.001840) + test_reports_ary: .: (0.001933) + test_reports_ary_contents: .: (0.001402) Bio::TestHMMERReportConstants: - test_rs: .: (0.000570) + test_rs: .: (0.000516) Bio::TestHMMERReportHit: - test_accession: .: (0.002086) - test_append_hsp: .: (0.002196) - test_bit_score: .: (0.001844) - test_definition: .: (0.001759) - test_description: .: (0.001762) - test_each: .: (0.002258) - test_each_hsp: .: (0.001912) - test_entry_id: .: (0.001766) - test_evalue: .: (0.002183) - test_hit: .: (0.001825) - test_hit_id: .: (0.001737) - test_hsps: .: (0.001743) - test_num: .: (0.002242) - test_score: .: (0.001844) - test_target_def: .: (0.001724) - test_target_id: .: (0.001740) + test_accession: .: (0.001974) + test_append_hsp: .: (0.001526) + test_bit_score: .: (0.001402) + test_definition: .: (0.001346) + test_description: .: (0.001661) + test_each: .: (0.001485) + test_each_hsp: .: (0.001419) + test_entry_id: .: (0.001683) + test_evalue: .: (0.001415) + test_hit: .: (0.001436) + test_hit_id: .: (0.001359) + test_hsps: .: (0.001701) + test_num: .: (0.001472) + test_score: .: (0.001313) + test_target_def: .: (0.001435) + test_target_id: .: (0.001471) Bio::TestHMMERReportHmmpfam: - test_domain_top_hits: .: (0.002665) - test_each: .: (0.001835) - test_each_hit: .: (0.001721) - test_histogram: .: (0.002374) - test_hits: .: (0.001929) - test_hsps: .: (0.001773) - test_parameter: .: (0.001806) - test_program: .: (0.002471) - test_query_info: .: (0.002019) - test_statistical_detail: .: (0.001750) - test_total_seq_searched: .: (0.001732) - test_whole_seq_top_hits: .: (0.002339) + test_domain_top_hits: .: (0.001649) + test_each: .: (0.001376) + test_each_hit: .: (0.001782) + test_histogram: .: (0.001566) + test_hits: .: (0.001340) + test_hsps: .: (0.001409) + test_parameter: .: (0.001927) + test_program: .: (0.001742) + test_query_info: .: (0.001508) + test_statistical_detail: .: (0.001354) + test_total_seq_searched: .: (0.001907) + test_whole_seq_top_hits: .: (0.001394) Bio::TestHMMERReportHmmsearch: - test_domain_top_hits: .: (0.002518) - test_histogram: .: (0.001989) - test_statistical_detail: .: (0.002909) - test_total_seq_searched: .: (0.002062) - test_whole_seq_top_hit: .: (0.002084) + test_domain_top_hits: .: (0.002264) + test_histogram: .: (0.002012) + test_statistical_detail: .: (0.001816) + test_total_seq_searched: .: (0.001562) + test_whole_seq_top_hit: .: (0.002210) Bio::TestHMMERReportHsp: - test_accession: .: (0.002130) - test_bit_score: .: (0.002630) - test_csline: .: (0.001796) - test_domain: .: (0.001748) - test_evalue: .: (0.002477) - test_flatseq: .: (0.002016) - test_hmm_f: .: (0.001724) - test_hmm_t: .: (0.001741) - test_hmmseq: .: (0.002605) - test_hsp: .: (0.002156) - test_midline: .: (0.001800) - test_query_frame: .: (0.001849) - test_query_from: .: (0.002440) - test_query_seq: .: (0.002007) - test_query_to: .: (0.001796) - test_rfline: .: (0.001802) - test_score: .: (0.002500) - test_seq_f: .: (0.001926) - test_seq_ft: .: (0.001852) - test_seq_t: .: (0.001718) - test_set_alignment: .: (0.002460) - test_targat_to: .: (0.001729) - test_target_frame: .: (0.015289) - test_target_from: .: (0.001987) - test_target_seq: .: (0.015480) + test_accession: .: (0.001640) + test_bit_score: .: (0.001404) + test_csline: .: (0.001353) + test_domain: .: (0.002139) + test_evalue: .: (0.001398) + test_flatseq: .: (0.001549) + test_hmm_f: .: (0.001958) + test_hmm_t: .: (0.001748) + test_hmmseq: .: (0.001396) + test_hsp: .: (0.001423) + test_midline: .: (0.001877) + test_query_frame: .: (0.001516) + test_query_from: .: (0.001317) + test_query_seq: .: (0.001227) + test_query_to: .: (0.001864) + test_rfline: .: (0.001495) + test_score: .: (0.001226) + test_seq_f: .: (0.001275) + test_seq_ft: .: (0.001794) + test_seq_t: .: (0.001721) + test_set_alignment: .: (0.001376) + test_targat_to: .: (0.001237) + test_target_frame: .: (0.012103) + test_target_from: .: (0.001632) + test_target_seq: .: (0.012151) Bio::TestHetatmFinder: - test_each_hetatm: .: (0.012576) - test_find_hetatm: .: (0.000789) - test_hetatms: .: (0.013183) + test_each_hetatm: .: (0.009449) + test_find_hetatm: .: (0.000619) + test_hetatms: .: (0.010282) Bio::TestHeterogen: - test_addAtom: .: (0.001166) - test_each: .: (0.014141) - test_each_hetatm: .: (0.000643) - test_get_residue_id_from_atom: .: (0.000606) - test_het_atom: .: (0.011924) - test_iCode: .: (0.000590) - test_inspect: .: (0.000571) - test_resSeq: .: (0.000516) - test_sort: .: (0.012900) - test_square_bracket: .: (0.000713) - test_to_s: .: (0.000805) - test_update_resudue_id: .: (0.007307) + test_addAtom: .: (0.011396) + test_each: .: (0.000566) + test_each_hetatm: .: (0.000447) + test_get_residue_id_from_atom: .: (0.000450) + test_het_atom: .: (0.009696) + test_iCode: .: (0.000425) + test_inspect: .: (0.000403) + test_resSeq: .: (0.000347) + test_sort: .: (0.010105) + test_square_bracket: .: (0.000446) + test_to_s: .: (0.000555) + test_update_resudue_id: .: (0.005337) Bio::TestHeterogenFinder: - test_each_heterogen: .: (0.000825) - test_find_heterogen: .: (0.000435) - test_heterogens: .: (0.000475) + test_each_heterogen: .: (0.000603) + test_find_heterogen: .: (0.000336) + test_heterogens: .: (0.013547) Bio::TestIprscanPTxtReport: - test_match_accession: .: (0.018709) - test_match_description: .: (0.000553) - test_match_evalue: .: (0.000505) - test_match_ipr_description: .: (0.000499) - test_match_ipr_id: .: (0.000490) - test_match_match_end: .: (0.000505) - test_match_match_start: .: (0.000499) - test_match_method: .: (0.000550) - test_matches_size: .: (0.001280) - test_query_id: .: (0.000483) - test_query_length: .: (0.000475) + test_match_accession: .: (0.000724) + test_match_description: .: (0.000380) + test_match_evalue: .: (0.000352) + test_match_ipr_description: .: (0.000364) + test_match_ipr_id: .: (0.000361) + test_match_match_end: .: (0.000352) + test_match_match_start: .: (0.000356) + test_match_method: .: (0.000816) + test_matches_size: .: (0.000397) + test_query_id: .: (0.000349) + test_query_length: .: (0.000362) Bio::TestIprscanRawReport: - test_entry_id: .: (0.006756) - test_match_accession: .: (0.006146) - test_match_crc64: .: (0.006772) - test_match_date: .: (0.006347) - test_match_description: .: (0.006209) - test_match_evalue: .: (0.006366) - test_match_go_terms: .: (0.006298) - test_match_ipr_description: .: (0.006343) - test_match_ipr_id: .: (0.006226) - test_match_match_end: .: (0.006402) - test_match_match_start: .: (0.006202) - test_match_method: .: (0.006412) - test_match_query_id: .: (0.009768) - test_match_query_length: .: (0.006169) - test_match_status: .: (0.005913) - test_obj: .: (0.006494) - test_query_id: .: (0.006141) - test_query_length: .: (0.005837) - test_self_reports_in_raw: .: (0.011976) + test_entry_id: .: (0.004704) + test_match_accession: .: (0.004391) + test_match_crc64: .: (0.004740) + test_match_date: .: (0.004554) + test_match_description: .: (0.004439) + test_match_evalue: .: (0.005008) + test_match_go_terms: .: (0.004665) + test_match_ipr_description: .: (0.004496) + test_match_ipr_id: .: (0.004468) + test_match_match_end: .: (0.004500) + test_match_match_start: .: (0.004573) + test_match_method: .: (0.004696) + test_match_query_id: .: (0.007328) + test_match_query_length: .: (0.004398) + test_match_status: .: (0.004946) + test_obj: .: (0.004389) + test_query_id: .: (0.004418) + test_query_length: .: (0.004125) + test_self_reports_in_raw: .: (0.008745) Bio::TestIprscanReport: - test_output_raw: .: (0.001944) - test_to_raw: .: (0.001349) + test_output_raw: .: (0.001310) + test_to_raw: .: (0.001081) Bio::TestIprscanTxtEntry: test_iprscan_report_class: .: (0.001679) - test_match_accession: .: (0.001325) - test_match_date: .: (0.002001) - test_match_description: .: (0.001294) - test_match_evalue: .: (0.001320) - test_match_go_terms: .: (0.001802) - test_match_ipr_description: .: (0.001396) - test_match_ipr_id: .: (0.001367) - test_match_match_end: .: (0.001300) - test_match_match_start: .: (0.001347) - test_match_method: .: (0.001496) - test_match_status: .: (0.001320) - test_matches_size: .: (0.001380) - test_query_id: .: (0.001320) - test_query_length: .: (0.001743) + test_match_accession: .: (0.000999) + test_match_date: .: (0.001000) + test_match_description: .: (0.000997) + test_match_evalue: .: (0.000942) + test_match_go_terms: .: (0.001362) + test_match_ipr_description: .: (0.001052) + test_match_ipr_id: .: (0.000958) + test_match_match_end: .: (0.000934) + test_match_match_start: .: (0.001324) + test_match_method: .: (0.001078) + test_match_status: .: (0.000974) + test_matches_size: .: (0.000992) + test_query_id: .: (0.001337) + test_query_length: .: (0.001018) Bio::TestIprscanTxtEntryList: - test_to_hash: .: (0.001796) - test_to_hash_match?: .: (0.001812) + test_to_hash: .: (0.001385) + test_to_hash_match?: .: (0.001341) Bio::TestIprscanTxtReport: - test_parse_txt: .: (0.004063) + test_parse_txt: .: (0.002967) Bio::TestKeggCompound: - test_comment: .: (0.001192) - test_dblinks_as_hash: .: (0.001007) - test_dblinks_as_strings: .: (0.001411) - test_entry_id: .: (0.000800) - test_enzymes: .: (0.001587) - test_formula: .: (0.000853) - test_kcf: .: (0.000720) - test_mass: .: (0.000771) - test_name: .: (0.001071) - test_names: .: (0.000929) - test_pathways_as_hash: .: (0.001320) - test_pathways_as_strings: .: (0.005635) - test_reactions: .: (0.001723) - test_remark: .: (0.000825) - test_rpairs: .: (0.000809) + test_comment: .: (0.000937) + test_dblinks_as_hash: .: (0.000734) + test_dblinks_as_strings: .: (0.000787) + test_entry_id: .: (0.000636) + test_enzymes: .: (0.001186) + test_formula: .: (0.000611) + test_kcf: .: (0.000545) + test_mass: .: (0.000685) + test_name: .: (0.000898) + test_names: .: (0.000645) + test_pathways_as_hash: .: (0.004459) + test_pathways_as_strings: .: (0.000914) + test_reactions: .: (0.001436) + test_remark: .: (0.000646) + test_rpairs: .: (0.000597) Bio::TestKeggEnzyme: - test_all_reac: .: (0.002334) - test_classes: .: (0.001204) - test_cofactors: .: (0.001250) - test_comment: .: (0.001253) - test_dblinks_as_hash: .: (0.001367) - test_dblinks_as_strings: .: (0.001217) - test_diseases: .: (0.001989) - test_entry: .: (0.001541) - test_entry_id: .: (0.001477) - test_genes: .: (0.038491) - test_genes_as_hash: .: (0.038354) - test_genes_as_strings: .: (0.010344) - test_inhibitors: .: (0.001530) - test_iubmb_reactions: .: (0.001696) - test_kegg_reactions: .: (0.001551) - test_motifs: .: (0.001434) - test_name: .: (0.001710) - test_names: .: (0.001738) - test_obsolete?: .: (0.001523) - test_orthologs_as_hash: .: (0.001541) - test_orthologs_as_strings: .: (0.001544) - test_pathways_as_hash: .: (0.001771) - test_pathways_as_strings: .: (0.001631) - test_products: .: (0.001505) - test_reaction: .: (0.001686) - test_structures: .: (0.001965) - test_substrates: .: (0.001614) - test_sysname: .: (0.001427) + test_all_reac: .: (0.001847) + test_classes: .: (0.001019) + test_cofactors: .: (0.000935) + test_comment: .: (0.001076) + test_dblinks_as_hash: .: (0.001122) + test_dblinks_as_strings: .: (0.001327) + test_diseases: .: (0.001162) + test_entry: .: (0.001219) + test_entry_id: .: (0.001152) + test_genes: .: (0.027257) + test_genes_as_hash: .: (0.027578) + test_genes_as_strings: .: (0.007463) + test_inhibitors: .: (0.001186) + test_iubmb_reactions: .: (0.001315) + test_kegg_reactions: .: (0.001200) + test_motifs: .: (0.001110) + test_name: .: (0.001312) + test_names: .: (0.001317) + test_obsolete?: .: (0.001095) + test_orthologs_as_hash: .: (0.001132) + test_orthologs_as_strings: .: (0.001228) + test_pathways_as_hash: .: (0.001275) + test_pathways_as_strings: .: (0.001218) + test_products: .: (0.001187) + test_reaction: .: (0.001188) + test_structures: .: (0.001631) + test_substrates: .: (0.001143) + test_sysname: .: (0.001124) Bio::TestKeggGenesDblinks: - test_data: .: (0.000927) - test_dblinks_0: .: (0.000430) - test_dblinks_1: .: (0.000390) - test_dblinks_2: .: (0.000383) + test_data: .: (0.000666) + test_dblinks_0: .: (0.000381) + test_dblinks_1: .: (0.000287) + test_dblinks_2: .: (0.000273) Bio::TestKeggGenesStructure: - test_data: .: (0.000758) - test_ids: .: (0.000505) - test_ids_in_array: .: (0.000492) + test_data: .: (0.000559) + test_ids: .: (0.000360) + test_ids_in_array: .: (0.000312) Bio::TestKeggKGML::TestKGMLEntry1: - test_components: .: (0.022926) - test_graphics__size: .: (0.021523) - test_id: .: (0.021049) - test_link: .: (0.020855) - test_name: .: (0.020797) - test_reaction: .: (0.021183) - test_type: .: (0.021521) + test_components: .: (0.015428) + test_graphics__size: .: (0.014725) + test_id: .: (0.014779) + test_link: .: (0.014779) + test_name: .: (0.014730) + test_reaction: .: (0.014434) + test_type: .: (0.014434) Bio::TestKeggKGML::TestKGMLEntry1234: - test_components: .: (0.031693) - test_graphics__size: .: (0.023614) - test_id: .: (0.024058) - test_link: .: (0.023544) - test_name: .: (0.023403) - test_reaction: .: (0.023632) - test_type: .: (0.021090) + test_components: .: (0.022764) + test_graphics__size: .: (0.016560) + test_id: .: (0.016973) + test_link: .: (0.017044) + test_name: .: (0.016338) + test_reaction: .: (0.016628) + test_type: .: (0.015048) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: - test_bgcolor=: .: (0.021298) - test_category: .: (0.020707) - test_entry_id: .: (0.020736) - test_fgcolor=: .: (0.020803) - test_height=: .: (0.021013) - test_label=: .: (0.020931) - test_shape=: .: (0.023931) - test_width=: .: (0.023107) - test_x=: .: (0.022374) - test_y=: .: (0.022137) + test_bgcolor=: .: (0.014896) + test_category: .: (0.014606) + test_entry_id: .: (0.014551) + test_fgcolor=: .: (0.014712) + test_height=: .: (0.014779) + test_label=: .: (0.014860) + test_shape=: .: (0.017340) + test_width=: .: (0.015946) + test_x=: .: (0.015837) + test_y=: .: (0.015637) Bio::TestKeggKGML::TestKGMLEntry567: - test_components: .: (0.021820) - test_graphics__size: .: (0.021686) - test_id: .: (0.021256) - test_link: .: (0.021174) - test_name: .: (0.020686) - test_reaction: .: (0.020894) - test_type: .: (0.020876) + test_components: .: (0.015313) + test_graphics__size: .: (0.015306) + test_id: .: (0.014749) + test_link: .: (0.015194) + test_name: .: (0.015161) + test_reaction: .: (0.014945) + test_type: .: (0.014740) Bio::TestKeggKGML::TestKGMLEntrySetter: - test_components=: .: (0.000708) - test_graphics=: .: (0.000344) - test_id=: .: (0.000369) - test_link=: .: (0.000344) - test_name=: .: (0.000364) - test_reaction=: .: (0.000336) - test_type=: .: (0.000791) + test_components=: .: (0.000892) + test_graphics=: .: (0.000333) + test_id=: .: (0.000299) + test_link=: .: (0.000276) + test_name=: .: (0.000317) + test_reaction=: .: (0.000288) + test_type=: .: (0.000277) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: - test_bgcolor=: .: (0.000715) - test_category=: .: (0.000445) - test_entry_id=: .: (0.000419) - test_fgcolor=: .: (0.000432) - test_height=: .: (0.000442) - test_label=: .: (0.000467) - test_pathway=: .: (0.000431) - test_shape=: .: (0.000447) - test_width=: .: (0.000403) - test_x=: .: (0.000683) - test_y=: .: (0.000410) + test_bgcolor=: .: (0.000548) + test_category=: .: (0.000343) + test_entry_id=: .: (0.000341) + test_fgcolor=: .: (0.000394) + test_height=: .: (0.000546) + test_label=: .: (0.000440) + test_pathway=: .: (0.000304) + test_shape=: .: (0.000350) + test_width=: .: (0.000332) + test_x=: .: (0.000329) + test_y=: .: (0.000321) Bio::TestKeggKGML::TestKGMLGraphics1234: - test_bgcolor: .: (0.021240) - test_coords: .: (0.020816) - test_fgcolor: .: (0.025171) - test_height: .: (0.022268) - test_name: .: (0.021925) - test_type: .: (0.022048) - test_width: .: (0.021600) - test_x: .: (0.021499) - test_y: .: (0.021367) + test_bgcolor: .: (0.015011) + test_coords: .: (0.014620) + test_fgcolor: .: (0.017354) + test_height: .: (0.015790) + test_name: .: (0.015212) + test_type: .: (0.015298) + test_width: .: (0.015173) + test_x: .: (0.014977) + test_y: .: (0.014820) Bio::TestKeggKGML::TestKGMLGraphics1_0: - test_bgcolor: .: (0.021604) - test_coords: .: (0.021107) - test_fgcolor: .: (0.021183) - test_height: .: (0.021284) - test_name: .: (0.020761) - test_type: .: (0.021163) - test_width: .: (0.024671) - test_x: .: (0.022025) - test_y: .: (0.021924) + test_bgcolor: .: (0.015275) + test_coords: .: (0.014827) + test_fgcolor: .: (0.014771) + test_height: .: (0.015218) + test_name: .: (0.015155) + test_type: .: (0.014697) + test_width: .: (0.017116) + test_x: .: (0.015302) + test_y: .: (0.015297) Bio::TestKeggKGML::TestKGMLGraphicsSetter: - test_bgcolor=: .: (0.000789) - test_coords=: .: (0.000431) - test_fgcolor=: .: (0.000373) - test_height=: .: (0.000310) - test_name=: .: (0.000306) - test_type=: .: (0.000309) - test_width=: .: (0.000339) - test_x=: .: (0.000358) - test_y=: .: (0.000427) + test_bgcolor=: .: (0.000623) + test_coords=: .: (0.000292) + test_fgcolor=: .: (0.000277) + test_height=: .: (0.000272) + test_name=: .: (0.000281) + test_type=: .: (0.000281) + test_width=: .: (0.000299) + test_x=: .: (0.000277) + test_y=: .: (0.000285) Bio::TestKeggKGML::TestKGMLPathway: - test_entries=: .: (0.022291) - test_entries__size: .: (0.021512) - test_image: .: (0.021436) - test_link: .: (0.021426) - test_name: .: (0.020986) - test_number: .: (0.021194) - test_org: .: (0.020986) - test_reactions=: .: (0.021234) - test_reactions__size: .: (0.021029) - test_relations=: .: (0.023790) - test_relations__size: .: (0.022385) - test_title: .: (0.022089) + test_entries=: .: (0.015963) + test_entries__size: .: (0.014920) + test_image: .: (0.015016) + test_link: .: (0.014957) + test_name: .: (0.015176) + test_number: .: (0.014908) + test_org: .: (0.014954) + test_reactions=: .: (0.014914) + test_reactions__size: .: (0.014797) + test_relations=: .: (0.014867) + test_relations__size: .: (0.017446) + test_title: .: (0.015724) Bio::TestKeggKGML::TestKGMLProduct: - test_id: .: (0.043803) - test_name: .: (0.042290) + test_id: .: (0.029967) + test_name: .: (0.029683) Bio::TestKeggKGML::TestKGMLProductSetter: - test_id=: .: (0.000802) - test_initialize_0: .: (0.000389) - test_initialize_1: .: (0.000429) - test_initialize_2: .: (0.000413) - test_name=: .: (0.000514) + test_id=: .: (0.000552) + test_initialize_0: .: (0.000237) + test_initialize_1: .: (0.000269) + test_initialize_2: .: (0.000244) + test_name=: .: (0.000289) Bio::TestKeggKGML::TestKGMLReaction: - test_id: .: (0.021645) - test_name: .: (0.021174) - test_products: .: (0.021172) - test_substrates: .: (0.021240) - test_type: .: (0.021339) + test_id: .: (0.015161) + test_name: .: (0.015024) + test_products: .: (0.014775) + test_substrates: .: (0.014947) + test_type: .: (0.014746) Bio::TestKeggKGML::TestKGMLReactionSetter: - test_id=: .: (0.000791) - test_name=: .: (0.000490) - test_products=: .: (0.000530) - test_substraces=: .: (0.000487) - test_type=: .: (0.000492) + test_id=: .: (0.000548) + test_name=: .: (0.000310) + test_products=: .: (0.000299) + test_substraces=: .: (0.000288) + test_type=: .: (0.000368) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: - test_direction=: .: (0.000853) - test_entry_id=: .: (0.000837) + test_direction=: .: (0.000524) + test_entry_id=: .: (0.000373) Bio::TestKeggKGML::TestKGMLRelation: - test_entry1: .: (0.021238) - test_entry2: .: (0.024460) - test_name: .: (0.022164) - test_type: .: (0.022118) - test_value: .: (0.022421) + test_entry1: .: (0.015004) + test_entry2: .: (0.017275) + test_name: .: (0.015515) + test_type: .: (0.015247) + test_value: .: (0.015430) Bio::TestKeggKGML::TestKGMLRelationDeprecated: - test_edge: .: (0.000697) - test_node1=: .: (0.000556) - test_node2=: .: (0.000546) - test_rel=: .: (0.000590) + test_edge: .: (0.000459) + test_node1=: .: (0.000354) + test_node2=: .: (0.000333) + test_rel=: .: (0.000343) Bio::TestKeggKGML::TestKGMLRelationSetter: - test_entry1=: .: (0.000778) - test_entry2=: .: (0.000367) - test_name=: .: (0.000333) - test_type=: .: (0.000331) - test_value=: .: (0.000327) + test_entry1=: .: (0.000483) + test_entry2=: .: (0.000394) + test_name=: .: (0.000305) + test_type=: .: (0.000561) + test_value=: .: (0.000307) Bio::TestKeggKGML::TestKGMLSubstrate: - test_id: .: (0.043405) - test_name: .: (0.042272) + test_id: .: (0.030243) + test_name: .: (0.029453) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: - test_id=: .: (0.001054) - test_initialize_0: .: (0.000391) - test_initialize_1: .: (0.000426) - test_initialize_2: .: (0.000396) - test_name=: .: (0.000483) + test_id=: .: (0.000739) + test_initialize_0: .: (0.000224) + test_initialize_1: .: (0.000223) + test_initialize_2: .: (0.000222) + test_name=: .: (0.000282) Bio::TestKeggKGML::TestKGMLSubstrateSetter: - test_id=: .: (0.000782) - test_initialize_0: .: (0.000430) - test_initialize_1: .: (0.000391) - test_initialize_2: .: (0.000396) - test_name=: .: (0.000486) + test_id=: .: (0.000506) + test_initialize_0: .: (0.000223) + test_initialize_1: .: (0.000215) + test_initialize_2: .: (0.000227) + test_name=: .: (0.000285) Bio::TestKeggModule: - test_compounds: .: (0.001322) - test_compounds_as_hash: .: (0.001223) - test_compounds_as_strings: .: (0.000822) - test_definition: .: (0.000837) - test_entry_id: .: (0.000689) - test_keggclass: .: (0.000688) - test_name: .: (0.000690) - test_new: .: (0.000663) - test_orthologs: .: (0.000949) - test_orthologs_as_array: .: (0.000893) - test_orthologs_as_hash: .: (0.001186) - test_orthologs_as_strings: .: (0.000842) - test_pathways: .: (0.000620) - test_pathways_as_hash: .: (0.000587) - test_pathways_as_strings: .: (0.000568) - test_reactions: .: (0.000829) - test_reactions_as_hash: .: (0.000850) - test_reactions_as_strings: .: (0.000682) + test_compounds: .: (0.000864) + test_compounds_as_hash: .: (0.000629) + test_compounds_as_strings: .: (0.000589) + test_definition: .: (0.000514) + test_entry_id: .: (0.000456) + test_keggclass: .: (0.000447) + test_name: .: (0.000447) + test_new: .: (0.000480) + test_orthologs: .: (0.000628) + test_orthologs_as_array: .: (0.000674) + test_orthologs_as_hash: .: (0.000884) + test_orthologs_as_strings: .: (0.000654) + test_pathways: .: (0.000474) + test_pathways_as_hash: .: (0.000504) + test_pathways_as_strings: .: (0.000420) + test_reactions: .: (0.000617) + test_reactions_as_hash: .: (0.000561) + test_reactions_as_strings: .: (0.000513) Bio::TestKeggOrthology: - test_dblinks: .: (0.001694) - test_dblinks_as_hash: .: (0.001097) - test_dblinks_as_strings: .: (0.000972) - test_definition: .: (0.001085) - test_entry_id: .: (0.001043) - test_genes_as_hash: .: (0.031355) - test_genes_as_strings: .: (0.010623) - test_keggclass: .: (0.001732) - test_keggclasses: .: (0.001315) - test_modules: .: (0.001007) - test_modules_as_hash: .: (0.001024) - test_modules_as_strings: .: (0.000950) - test_name: .: (0.000995) - test_names: .: (0.001014) - test_pathways_as_strings: .: (0.001313) - test_pathways_in_keggclass: .: (0.001328) - test_references: .: (0.001455) + test_dblinks: .: (0.001392) + test_dblinks_as_hash: .: (0.000915) + test_dblinks_as_strings: .: (0.000778) + test_definition: .: (0.000809) + test_entry_id: .: (0.000830) + test_genes_as_hash: .: (0.021492) + test_genes_as_strings: .: (0.007289) + test_keggclass: .: (0.001050) + test_keggclasses: .: (0.001193) + test_modules: .: (0.000792) + test_modules_as_hash: .: (0.000778) + test_modules_as_strings: .: (0.000739) + test_name: .: (0.000778) + test_names: .: (0.000827) + test_pathways_as_strings: .: (0.000751) + test_pathways_in_keggclass: .: (0.000994) + test_references: .: (0.001323) Bio::TestKeggPathway_map00052: - test_compounds_as_hash: .: (0.000978) - test_compounds_as_strings: .: (0.000642) - test_dblinks_as_hash: .: (0.000636) - test_dblinks_as_strings: .: (0.000694) - test_description: .: (0.000665) - test_diseases_as_hash: .: (0.001075) - test_diseases_as_strings: .: (0.000657) - test_entry_id: .: (0.000745) - test_enzymes_as_strings: .: (0.000621) - test_genes_as_hash: .: (0.000614) - test_genes_as_strings: .: (0.000602) - test_keggclass: .: (0.000717) - test_ko_pathway: .: (0.000738) - test_modules_as_hash: .: (0.000821) - test_modules_as_strings: .: (0.000687) - test_name: .: (0.000670) - test_organism: .: (0.005848) - test_orthologs_as_hash: .: (0.000756) - test_orthologs_as_strings: .: (0.000625) - test_pathways_as_hash: .: (0.000719) - test_pathways_as_strings: .: (0.000788) - test_reactions_as_hash: .: (0.000748) - test_reactions_as_strings: .: (0.000628) - test_references: .: (0.000629) - test_rel_pathways_as_hash: .: (0.000796) - test_rel_pathways_as_strings: .: (0.001221) + test_compounds_as_hash: .: (0.000771) + test_compounds_as_strings: .: (0.000491) + test_dblinks_as_hash: .: (0.000433) + test_dblinks_as_strings: .: (0.000428) + test_description: .: (0.000486) + test_diseases_as_hash: .: (0.000452) + test_diseases_as_strings: .: (0.000505) + test_entry_id: .: (0.000504) + test_enzymes_as_strings: .: (0.000449) + test_genes_as_hash: .: (0.000419) + test_genes_as_strings: .: (0.000421) + test_keggclass: .: (0.000704) + test_ko_pathway: .: (0.000566) + test_modules_as_hash: .: (0.000628) + test_modules_as_strings: .: (0.000490) + test_name: .: (0.000481) + test_organism: .: (0.000446) + test_orthologs_as_hash: .: (0.000450) + test_orthologs_as_strings: .: (0.000435) + test_pathways_as_hash: .: (0.000518) + test_pathways_as_strings: .: (0.000672) + test_reactions_as_hash: .: (0.000453) + test_reactions_as_strings: .: (0.000419) + test_references: .: (0.000432) + test_rel_pathways_as_hash: .: (0.000528) + test_rel_pathways_as_strings: .: (0.000454) Bio::TestKeggReaction: - test_definition: .: (0.001111) - test_entry_id: .: (0.000753) - test_enzymes: .: (0.000747) - test_equation: .: (0.000732) - test_name: .: (0.000741) - test_orthologs_as_hash: .: (0.000851) - test_orthologs_as_strings: .: (0.001233) - test_pathways_as_hash: .: (0.000807) - test_pathways_as_strings: .: (0.000668) - test_rpairs_as_hash: .: (0.000857) - test_rpairs_as_strings: .: (0.000743) - test_rpairs_as_tokens: .: (0.000808) + test_definition: .: (0.000835) + test_entry_id: .: (0.000537) + test_enzymes: .: (0.004349) + test_equation: .: (0.000718) + test_name: .: (0.000552) + test_orthologs_as_hash: .: (0.000629) + test_orthologs_as_strings: .: (0.000499) + test_pathways_as_hash: .: (0.000579) + test_pathways_as_strings: .: (0.000482) + test_rpairs_as_hash: .: (0.000595) + test_rpairs_as_strings: .: (0.000998) + test_rpairs_as_tokens: .: (0.000652) Bio::TestLasergene: - test_methods: .: (0.018809) + test_methods: .: (0.013485) Bio::TestLocations: - test_complement: .: (0.000826) - test_hat: .: (0.000496) - test_normal: .: (0.000443) - test_replace_single_base: .: (0.000435) - test_should_not_modify_argument: .: (0.000394) + test_complement: .: (0.000711) + test_hat: .: (0.000429) + test_normal: .: (0.000309) + test_replace_single_base: .: (0.000258) + test_should_not_modify_argument: .: (0.000629) Bio::TestLocationsRoundTrip: - test_locations_roundtrip: .: (0.011262) - test_locations_to_s: .: (0.004840) + test_locations_roundtrip: .: (0.007216) + test_locations_to_s: .: (0.003223) Bio::TestMEDLINE: - test_authors: .: (0.002159) - test_authors_with_last_name_all_caps: .: (0.000444) - test_authors_with_suffix: .: (0.000774) + test_authors: .: (0.001420) + test_authors_with_last_name_all_caps: .: (0.000231) + test_authors_with_suffix: .: (0.000276) Bio::TestMEDLINE_20146148: - test_ab: .: (0.001544) - test_ad: .: (0.001144) - test_au: .: (0.001071) - test_authors: .: (0.001760) - test_doi: .: (0.001289) - test_dp: .: (0.001151) - test_ip: .: (0.001207) - test_mh: .: (0.001592) - test_pages: .: (0.001203) - test_pg: .: (0.001219) - test_pii: .: (0.001096) - test_pmid: .: (0.001446) - test_pt: .: (0.001153) - test_reference: .: (0.001579) - test_self_new: .: (0.001152) - test_so: .: (0.001324) - test_ta: .: (0.001067) - test_ti: .: (0.001183) - test_ui: .: (0.001023) - test_vi: .: (0.001410) - test_year: .: (0.001128) + test_ab: .: (0.001489) + test_ad: .: (0.000869) + test_au: .: (0.000808) + test_authors: .: (0.000776) + test_doi: .: (0.001153) + test_dp: .: (0.000799) + test_ip: .: (0.000675) + test_mh: .: (0.000774) + test_pages: .: (0.001031) + test_pg: .: (0.000754) + test_pii: .: (0.000672) + test_pmid: .: (0.000639) + test_pt: .: (0.000899) + test_reference: .: (0.001232) + test_self_new: .: (0.000712) + test_so: .: (0.000649) + test_ta: .: (0.000912) + test_ti: .: (0.000784) + test_ui: .: (0.000699) + test_vi: .: (0.000639) + test_year: .: (0.000939) Bio::TestMapSimple: - test_attributes: .: (0.000853) + test_attributes: .: (0.000633) Bio::TestMapping: - test_add_mapping_as_map: .: (0.000890) - test_add_mapping_as_marker: .: (0.000538) - test_contains_marker?: .: (0.000520) - test_mapped_to?: .: (0.000874) - test_mapping_location_comparison: .: (0.000993) - test_mappings_as_map_each: .: (0.000430) - test_mappings_as_marker_each: .: (0.000515) - test_mappings_on: .: (0.000639) - test_multiple_mappings_between_same_marker_and_map: .: (0.000933) - test_positions_on: .: (0.000594) - test_raise_error_kind_of: .: (0.001011) + test_add_mapping_as_map: .: (0.000582) + test_add_mapping_as_marker: .: (0.000346) + test_contains_marker?: .: (0.000239) + test_mapped_to?: .: (0.000224) + test_mapping_location_comparison: .: (0.000555) + test_mappings_as_map_each: .: (0.000250) + test_mappings_as_marker_each: .: (0.000296) + test_mappings_on: .: (0.000375) + test_multiple_mappings_between_same_marker_and_map: .: (0.000588) + test_positions_on: .: (0.000374) + test_raise_error_kind_of: .: (0.000671) Bio::TestMast: - test_check_options_with_empty_opts: .: (0.000998) - test_check_options_with_invalid_opts: .: (0.000596) - test_check_options_with_valid_opts: .: (0.000531) - test_command_to_be_run: .: (0.000594) - test_config_defaults: .: (0.000505) - test_minimal_config: .: (0.000501) - test_more_config: .: (0.000463) - test_run: .: (0.000343) + test_check_options_with_empty_opts: .: (0.000615) + test_check_options_with_invalid_opts: .: (0.000328) + test_check_options_with_valid_opts: .: (0.000463) + test_command_to_be_run: .: (0.000341) + test_config_defaults: .: (0.000256) + test_minimal_config: .: (0.000320) + test_more_config: .: (0.000256) + test_run: .: (0.000185) Bio::TestMastReport: - test_parse_hit_list_with_bad_data: .: (0.001256) - test_report_has_motifs: .: (0.000784) + test_parse_hit_list_with_bad_data: .: (0.000794) + test_report_has_motifs: .: (0.000450) Bio::TestModel: - test_addChain: .: (0.000921) - test_comp: .: (0.000401) - test_each: .: (0.000386) - test_each_chain: .: (0.000371) - test_inspect: .: (0.000346) - test_rehash: .: (0.000344) - test_square_brace: .: (0.000349) - test_to_s: .: (0.000337) + test_addChain: .: (0.000403) + test_comp: .: (0.000434) + test_each: .: (0.000258) + test_each_chain: .: (0.000210) + test_inspect: .: (0.000182) + test_rehash: .: (0.000170) + test_square_brace: .: (0.000183) + test_to_s: .: (0.000188) Bio::TestModelFinder: - test_find_model: .: (0.000662) + test_find_model: .: (0.000410) Bio::TestMotif: - test_creation_and_attributes: .: (0.000744) - test_length: .: (0.000386) + test_creation_and_attributes: .: (0.000498) + test_length: .: (0.000170) Bio::TestMyGraph: - test_cliquishness: .: (0.001782) + test_cliquishness: .: (0.001235) Bio::TestNA: - test_accessor: .: (0.000637) - test_na: .: (0.000302) - test_name: .: (0.000319) - test_names: .: (0.000341) - test_to_re: .: (0.000638) - test_weight: .: (0.000425) - test_weight_rna: .: (0.000345) + test_accessor: .: (0.000406) + test_na: .: (0.000226) + test_name: .: (0.000221) + test_names: .: (0.000206) + test_to_re: .: (0.000496) + test_weight: .: (0.000257) + test_weight_rna: .: (0.000250) Bio::TestNAConstants: - test_NAMES: .: (0.000546) - test_NAMES_1_to_name: .: (0.000379) - test_WEIGHT: .: (0.000386) + test_NAMES: .: (0.000426) + test_NAMES_1_to_name: .: (0.000220) + test_WEIGHT: .: (0.000240) Bio::TestNATranslate: - test_translate: .: (0.000860) - test_translate_1: .: (0.000547) - test_translate_2: .: (0.000844) - test_translate_3: .: (0.000375) - test_translate_4: .: (0.000661) - test_translate_5: .: (0.000450) - test_translate_6: .: (0.000369) + test_translate: .: (0.000745) + test_translate_1: .: (0.000414) + test_translate_2: .: (0.000235) + test_translate_3: .: (0.000224) + test_translate_4: .: (0.000379) + test_translate_5: .: (0.000243) + test_translate_6: .: (0.000254) Bio::TestNCBIDB: - test_fetch: .: (0.000784) - test_p_entry2hash: .: (0.000383) - test_p_subtag2array: .: (0.000285) - test_p_toptag2array: .: (0.000296) + test_fetch: .: (0.000513) + test_p_entry2hash: .: (0.000186) + test_p_subtag2array: .: (0.000224) + test_p_toptag2array: .: (0.000215) Bio::TestNewick: - test_reparse: .: (0.003524) - test_reparse_before_lazy_parsing: .: (0.001445) - test_string_tree: .: (0.002389) + test_reparse: .: (0.002662) + test_reparse_before_lazy_parsing: .: (0.000832) + test_string_tree: .: (0.001622) Bio::TestNewick2: - test_string_tree: .: (0.001999) + test_string_tree: .: (0.001324) Bio::TestNewickPrivate: - test_parse_newick_get_tokens_for_leaf: .: (0.000742) - test_parse_newick_leaf: .: (0.000690) - test_parse_newick_tokenize: .: (0.001030) + test_parse_newick_get_tokens_for_leaf: .: (0.000736) + test_parse_newick_leaf: .: (0.000425) + test_parse_newick_tokenize: .: (0.000711) Bio::TestNexus: - test_nexus: .: (0.033297) + test_nexus: .: (0.021580) Bio::TestOSLine: - test_period_trancation_O63147: .: (0.000777) - test_uncapitalized_letter_Q32725_9POAL: .: (0.000472) + test_period_trancation_O63147: .: (0.000705) + test_uncapitalized_letter_Q32725_9POAL: .: (0.000295) Bio::TestPAMLCodeml::TestCodeml: - test_dump_parameters: .: (0.000693) - test_load_parameters: .: (0.000390) - test_parameters: .: (0.000312) - test_set_default_parameters: .: (0.000368) + test_dump_parameters: .: (0.000490) + test_load_parameters: .: (0.000299) + test_parameters: .: (0.000206) + test_set_default_parameters: .: (0.000266) Bio::TestPAMLCodeml::TestCodemlControlGeneration: - test_control_file_generated: .: (0.004047) - test_expected_parameters_set_in_control_file: .: (0.002355) + test_control_file_generated: .: (0.002008) + test_expected_parameters_set_in_control_file: .: (0.001547) Bio::TestPAMLCodeml::TestCodemlInitialize: - test_new_with_one_argument: .: (0.000756) - test_new_with_parameters: .: (0.000449) - test_new_with_two_argument: .: (0.000468) - test_new_without_argument: .: (0.000464) + test_new_with_one_argument: .: (0.000456) + test_new_with_parameters: .: (0.000280) + test_new_with_two_argument: .: (0.000232) + test_new_without_argument: .: (0.000211) Bio::TestPAMLCodeml::TestCodemlRates: - test_rates_first_position: .: (0.003896) - test_rates_hundred_and_fiftieth_position: .: (0.003678) - test_rates_last_position: .: (0.003756) + test_rates_first_position: .: (0.002886) + test_rates_hundred_and_fiftieth_position: .: (0.002652) + test_rates_last_position: .: (0.002688) Bio::TestPAMLCodeml::TestCodemlReport: - test_alpha: .: (0.026351) - test_tree: .: (0.026047) - test_tree_length: .: (0.026092) - test_tree_log_likelihood: .: (0.025940) + test_alpha: .: (0.020245) + test_tree: .: (0.019958) + test_tree_length: .: (0.019897) + test_tree_log_likelihood: .: (0.019892) Bio::TestPAMLCodeml::TestControlFileUsage: - test_correct_parameters_should_be_loaded: .: (0.001622) - test_parameters_should_be_loaded_from_control: .: (0.000843) + test_correct_parameters_should_be_loaded: .: (0.001308) + test_parameters_should_be_loaded_from_control: .: (0.000640) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: - test_error_thrown_if_seqfile_does_not_specified: .: (0.003750) + test_error_thrown_if_seqfile_does_not_specified: .: (0.002724) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: - test_alpha: .: (0.001402) - test_dN_dS: .: (0.000716) - test_kappa: .: (0.000564) - test_lnL: .: (0.000493) - test_m3_classes: .: (0.000704) - test_m3_lnL: .: (0.000516) - test_m3_to_s: .: (0.000495) - test_m3_tree: .: (0.001900) - test_omega: .: (0.000483) - test_to_s: .: (0.000486) - test_tree: .: (0.001723) - test_tree_length: .: (0.000484) + test_alpha: .: (0.000675) + test_dN_dS: .: (0.000562) + test_kappa: .: (0.000385) + test_lnL: .: (0.000435) + test_m3_classes: .: (0.000548) + test_m3_lnL: .: (0.000387) + test_m3_to_s: .: (0.000380) + test_m3_tree: .: (0.001468) + test_omega: .: (0.000387) + test_to_s: .: (0.000375) + test_tree: .: (0.001326) + test_tree_length: .: (0.000398) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: - test_dN_dS: .: (0.001357) - test_p: .: (0.002052) - test_position: .: (0.001000) - test_probability: .: (0.001049) - test_w: .: (0.002121) + test_dN_dS: .: (0.001699) + test_p: .: (0.000841) + test_position: .: (0.000739) + test_probability: .: (0.001290) + test_w: .: (0.000767) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: - test_graph: .: (0.001649) - test_graph_omega: .: (0.001450) + test_graph: .: (0.001220) + test_graph_omega: .: (0.001368) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: - test_descr: .: (0.001452) - test_footer: .: (0.000506) - test_header: .: (0.000546) - test_initialize: .: (0.000565) - test_models: .: (0.000570) - test_nb_sites: .: (0.001611) - test_num_codons: .: (0.000662) - test_num_sequences: .: (0.000564) - test_significant: .: (0.000589) + test_descr: .: (0.000671) + test_footer: .: (0.000376) + test_header: .: (0.000482) + test_initialize: .: (0.000405) + test_models: .: (0.000459) + test_nb_sites: .: (0.001576) + test_num_codons: .: (0.000437) + test_num_sequences: .: (0.000429) + test_significant: .: (0.000417) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: - test_models: .: (0.001097) - test_nb_sites: .: (0.000751) - test_significant: .: (0.000536) - test_sites: .: (0.003452) + test_models: .: (0.000738) + test_nb_sites: .: (0.000584) + test_significant: .: (0.000416) + test_sites: .: (0.002448) Bio::TestPDB: - test_accession: .: (0.003223) - test_addModel: .: (0.002660) - test_authors: .: (0.002116) - test_bracket: .: (0.002704) - test_classification: .: (0.002134) - test_dbref: .: (0.002938) - test_definition: .: (0.002206) - test_each: .: (0.002184) - test_each_model: .: (0.003056) - test_entry_id: .: (0.002245) - test_helix: .: (0.003024) - test_inspect: .: (0.002201) - test_jrnl: .: (0.003031) - test_keywords: .: (0.002249) - test_record: .: (0.002824) - test_remark: .: (0.002757) - test_seqres: .: (0.003613) - test_sheet: .: (0.003005) - test_ssbond: .: (0.002497) - test_to_s: .: (0.017897) - test_turn: .: (0.002407) - test_version: .: (0.003075) + test_accession: .: (0.002667) + test_addModel: .: (0.001565) + test_authors: .: (0.001882) + test_bracket: .: (0.001505) + test_classification: .: (0.001800) + test_dbref: .: (0.001750) + test_definition: .: (0.001509) + test_each: .: (0.001971) + test_each_model: .: (0.001577) + test_entry_id: .: (0.001976) + test_helix: .: (0.001687) + test_inspect: .: (0.002054) + test_jrnl: .: (0.001568) + test_keywords: .: (0.002058) + test_record: .: (0.001559) + test_remark: .: (0.002358) + test_seqres: .: (0.002051) + test_sheet: .: (0.003440) + test_ssbond: .: (0.001782) + test_to_s: .: (0.002397) + test_turn: .: (0.001673) + test_version: .: (0.001861) Bio::TestPDBRecord::TestANISOU: - test_U11: .: (0.000834) - test_U12: .: (0.000469) - test_U13: .: (0.000445) - test_U22: .: (0.000442) - test_U23: .: (0.000462) - test_U33: .: (0.000480) - test_altLoc: .: (0.000454) - test_chainID: .: (0.000485) - test_charge: .: (0.000449) - test_element: .: (0.000446) - test_iCode: .: (0.000450) - test_name: .: (0.001259) - test_resName: .: (0.000674) - test_resSeq: .: (0.000439) - test_segID: .: (0.000433) - test_serial: .: (0.000429) -Bio::TestPDBRecord::TestATOM: - test_altLoc: .: (0.000676) - test_anisou: .: (0.000357) - test_chainID: .: (0.000375) - test_charge: .: (0.000337) - test_comparable: .: (0.000413) - test_do_parse: .: (0.000356) - test_element: .: (0.000340) - test_iCode: .: (0.001261) - test_name: .: (0.000427) - test_occupancy: .: (0.000500) - test_original_data: .: (0.000362) - test_record_name: .: (0.000336) - test_resName: .: (0.000334) + test_U11: .: (0.000610) + test_U12: .: (0.000523) + test_U13: .: (0.000363) + test_U22: .: (0.000366) + test_U23: .: (0.000351) + test_U33: .: (0.012304) + test_altLoc: .: (0.000418) + test_chainID: .: (0.000374) + test_charge: .: (0.000298) + test_element: .: (0.000346) + test_iCode: .: (0.000319) + test_name: .: (0.000310) + test_resName: .: (0.000353) test_resSeq: .: (0.000330) - test_residue: .: (0.000345) - test_segID: .: (0.000336) - test_serial: .: (0.000357) - test_sigatm: .: (0.000332) - test_tempFactor: .: (0.000426) - test_ter: .: (0.000330) - test_to_a: .: (0.000347) - test_to_s: .: (0.001217) - test_x: .: (0.000451) - test_xyz: .: (0.000442) - test_y: .: (0.000423) - test_z: .: (0.000419) + test_segID: .: (0.000306) + test_serial: .: (0.000307) +Bio::TestPDBRecord::TestATOM: + test_altLoc: .: (0.000548) + test_anisou: .: (0.000872) + test_chainID: .: (0.000283) + test_charge: .: (0.000225) + test_comparable: .: (0.000338) + test_do_parse: .: (0.000232) + test_element: .: (0.000253) + test_iCode: .: (0.000235) + test_name: .: (0.000239) + test_occupancy: .: (0.000355) + test_original_data: .: (0.000245) + test_record_name: .: (0.000270) + test_resName: .: (0.000249) + test_resSeq: .: (0.000237) + test_residue: .: (0.000230) + test_segID: .: (0.000261) + test_serial: .: (0.000268) + test_sigatm: .: (0.000242) + test_tempFactor: .: (0.000309) + test_ter: .: (0.000289) + test_to_a: .: (0.000262) + test_to_s: .: (0.000383) + test_x: .: (0.000354) + test_xyz: .: (0.000325) + test_y: .: (0.000320) + test_z: .: (0.000298) Bio::TestPDBRecord::TestAUTHOR: - test_authorList: .: (0.000696) + test_authorList: .: (0.000562) Bio::TestPDBRecord::TestCAVEAT: - test_comment: .: (0.000691) - test_idcode: .: (0.000345) + test_comment: .: (0.000650) + test_idcode: .: (0.000244) Bio::TestPDBRecord::TestCISPEP: - test_chainID1: .: (0.000734) - test_chainID2: .: (0.000429) - test_icode1: .: (0.001062) - test_icode2: .: (0.000460) - test_measure: .: (0.000493) - test_modNum: .: (0.000414) - test_pep1: .: (0.000413) - test_pep2: .: (0.000468) - test_seqNum1: .: (0.000433) - test_seqNum2: .: (0.000452) - test_serNum: .: (0.000453) + test_chainID1: .: (0.000551) + test_chainID2: .: (0.000316) + test_icode1: .: (0.000299) + test_icode2: .: (0.000300) + test_measure: .: (0.000301) + test_modNum: .: (0.000342) + test_pep1: .: (0.000288) + test_pep2: .: (0.000241) + test_seqNum1: .: (0.000249) + test_seqNum2: .: (0.000284) + test_serNum: .: (0.000256) Bio::TestPDBRecord::TestCOMPND: - test_compound: .: (0.000674) + test_compound: .: (0.000460) Bio::TestPDBRecord::TestCONECT: - test_serial: .: (0.000654) + test_serial: .: (0.000405) Bio::TestPDBRecord::TestCRYST1: - test_a: .: (0.000778) - test_alpha: .: (0.000380) - test_b: .: (0.000423) - test_beta: .: (0.000368) - test_c: .: (0.000362) - test_gamma: .: (0.000407) - test_sGroup: .: (0.000394) - test_z: .: (0.000386) + test_a: .: (0.000433) + test_alpha: .: (0.000209) + test_b: .: (0.000206) + test_beta: .: (0.000213) + test_c: .: (0.000201) + test_gamma: .: (0.000199) + test_sGroup: .: (0.000203) + test_z: .: (0.000203) Bio::TestPDBRecord::TestDBREF: - test_chainID: .: (0.000837) - test_database: .: (0.000484) - test_dbAccession: .: (0.000465) - test_dbIdCode: .: (0.000489) - test_dbseqBegin: .: (0.000538) - test_dbseqEnd: .: (0.000532) - test_idCode: .: (0.000477) - test_idbnsBeg: .: (0.000471) - test_insertBegin: .: (0.000549) - test_insertEnd: .: (0.000540) - test_seqBegin: .: (0.000509) - test_seqEnd: .: (0.000469) + test_chainID: .: (0.000522) + test_database: .: (0.000285) + test_dbAccession: .: (0.000264) + test_dbIdCode: .: (0.000261) + test_dbseqBegin: .: (0.000303) + test_dbseqEnd: .: (0.000269) + test_idCode: .: (0.000276) + test_idbnsBeg: .: (0.000265) + test_insertBegin: .: (0.000270) + test_insertEnd: .: (0.000276) + test_seqBegin: .: (0.000567) + test_seqEnd: .: (0.000291) Bio::TestPDBRecord::TestDefault: - test_text: .: (0.000632) + test_text: .: (0.000453) Bio::TestPDBRecord::TestENDMDL: - test_serial: .: (0.000635) + test_serial: .: (0.000384) Bio::TestPDBRecord::TestEXPDTA: - test_technique: .: (0.000763) + test_technique: .: (0.000397) Bio::TestPDBRecord::TestEnd: - test_serial: .: (0.001335) + test_serial: .: (0.000379) Bio::TestPDBRecord::TestHEADER: - test_classification: .: (0.000686) - test_depDate: .: (0.000377) - test_idCode: .: (0.000457) + test_classification: .: (0.000401) + test_depDate: .: (0.000286) + test_idCode: .: (0.000209) Bio::TestPDBRecord::TestHET: - test_ChainID: .: (0.000693) - test_hetID: .: (0.000464) - test_iCode: .: (0.000393) - test_numHetAtoms: .: (0.000424) - test_seqNum: .: (0.000390) - test_text: .: (0.000474) + test_ChainID: .: (0.001067) + test_hetID: .: (0.000219) + test_iCode: .: (0.000220) + test_numHetAtoms: .: (0.000213) + test_seqNum: .: (0.000215) + test_text: .: (0.000211) Bio::TestPDBRecord::TestHETATM: - test_altLoc: .: (0.000701) - test_anisou: .: (0.000401) - test_chainID: .: (0.001146) - test_charge: .: (0.000395) - test_comparable: .: (0.000458) - test_do_parse: .: (0.000418) - test_element: .: (0.000339) - test_iCode: .: (0.000383) - test_name: .: (0.000336) - test_occupancy: .: (0.000501) - test_original_data: .: (0.000390) - test_record_name: .: (0.000397) - test_resName: .: (0.000350) - test_resSeq: .: (0.000333) - test_residue: .: (0.000337) - test_segID: .: (0.000335) - test_serial: .: (0.001102) - test_sigatm: .: (0.000394) - test_tempFactor: .: (0.000466) - test_ter: .: (0.000336) - test_to_a: .: (0.000344) - test_to_s: .: (0.000420) - test_x: .: (0.000431) - test_xyz: .: (0.000414) - test_y: .: (0.000431) - test_z: .: (0.000535) + test_altLoc: .: (0.000414) + test_anisou: .: (0.000192) + test_chainID: .: (0.000184) + test_charge: .: (0.000185) + test_comparable: .: (0.000237) + test_do_parse: .: (0.000194) + test_element: .: (0.000184) + test_iCode: .: (0.000180) + test_name: .: (0.000679) + test_occupancy: .: (0.000286) + test_original_data: .: (0.000192) + test_record_name: .: (0.000179) + test_resName: .: (0.000183) + test_resSeq: .: (0.000186) + test_residue: .: (0.000178) + test_segID: .: (0.000179) + test_serial: .: (0.000173) + test_sigatm: .: (0.000205) + test_tempFactor: .: (0.000240) + test_ter: .: (0.000181) + test_to_a: .: (0.000187) + test_to_s: .: (0.000242) + test_x: .: (0.000234) + test_xyz: .: (0.000812) + test_y: .: (0.000389) + test_z: .: (0.000243) Bio::TestPDBRecord::TestHYDBND: - test_Chain1: .: (0.000840) - test_ChainH: .: (0.001191) - test_ICode1: .: (0.000558) - test_altLoc1: .: (0.000503) - test_altLoc2: .: (0.000494) - test_altLocH: .: (0.000490) - test_chainID2: .: (0.000557) - test_iCode2: .: (0.000521) - test_iCodeH: .: (0.000491) - test_name1: .: (0.000493) - test_name2: .: (0.000496) - test_nameH: .: (0.001202) - test_resName1: .: (0.000549) - test_resName2: .: (0.000565) - test_resSeq1: .: (0.000515) - test_resSeq2: .: (0.000668) - test_resSeqH: .: (0.000529) - test_sym1: .: (0.000498) - test_sym2: .: (0.000520) + test_Chain1: .: (0.000614) + test_ChainH: .: (0.000300) + test_ICode1: .: (0.000290) + test_altLoc1: .: (0.000299) + test_altLoc2: .: (0.000309) + test_altLocH: .: (0.000298) + test_chainID2: .: (0.000295) + test_iCode2: .: (0.000324) + test_iCodeH: .: (0.000280) + test_name1: .: (0.000311) + test_name2: .: (0.000275) + test_nameH: .: (0.000272) + test_resName1: .: (0.000272) + test_resName2: .: (0.000271) + test_resSeq1: .: (0.000281) + test_resSeq2: .: (0.000411) + test_resSeqH: .: (0.000339) + test_sym1: .: (0.000762) + test_sym2: .: (0.000340) Bio::TestPDBRecord::TestKEYWDS: - test_keywds: .: (0.000733) + test_keywds: .: (0.000467) Bio::TestPDBRecord::TestLINK: - test_altLoc1: .: (0.001252) - test_altLoc2: .: (0.000476) - test_chainID1: .: (0.000551) - test_chainID2: .: (0.000488) - test_iCode1: .: (0.000454) - test_iCode2: .: (0.000449) - test_name1: .: (0.000471) - test_name2: .: (0.000438) - test_resName1: .: (0.000477) - test_resName2: .: (0.000450) - test_resSeq1: .: (0.000487) - test_resSeq2: .: (0.000546) - test_sym1: .: (0.000997) - test_sym2: .: (0.000478) + test_altLoc1: .: (0.000478) + test_altLoc2: .: (0.000265) + test_chainID1: .: (0.000259) + test_chainID2: .: (0.000307) + test_iCode1: .: (0.000258) + test_iCode2: .: (0.000251) + test_name1: .: (0.000255) + test_name2: .: (0.000297) + test_resName1: .: (0.000695) + test_resName2: .: (0.000272) + test_resSeq1: .: (0.000260) + test_resSeq2: .: (0.000306) + test_sym1: .: (0.000266) + test_sym2: .: (0.000299) Bio::TestPDBRecord::TestMASTER: - test_numConect: .: (0.000748) - test_numCoord: .: (0.000365) - test_numHelix: .: (0.000359) - test_numHet: .: (0.000355) - test_numRemark: .: (0.000383) - test_numSeq: .: (0.000359) - test_numSheet: .: (0.000364) - test_numSite: .: (0.000346) - test_numTer: .: (0.000394) - test_numTurn: .: (0.000405) - test_numXform: .: (0.000360) + test_numConect: .: (0.000468) + test_numCoord: .: (0.000204) + test_numHelix: .: (0.000200) + test_numHet: .: (0.000199) + test_numRemark: .: (0.000194) + test_numSeq: .: (0.000199) + test_numSheet: .: (0.000661) + test_numSite: .: (0.000280) + test_numTer: .: (0.000259) + test_numTurn: .: (0.000337) + test_numXform: .: (0.000258) Bio::TestPDBRecord::TestMODEL: - test_serial: .: (0.000612) + test_serial: .: (0.000491) Bio::TestPDBRecord::TestMODRES: - test_chainID: .: (0.001162) - test_comment: .: (0.000462) - test_iCode: .: (0.000396) - test_idCode: .: (0.000416) - test_resName: .: (0.000457) - test_seqNum: .: (0.000425) - test_stdRes: .: (0.000433) + test_chainID: .: (0.000510) + test_comment: .: (0.000274) + test_iCode: .: (0.000234) + test_idCode: .: (0.000231) + test_resName: .: (0.000226) + test_seqNum: .: (0.000273) + test_stdRes: .: (0.000230) Bio::TestPDBRecord::TestMTRIX1: - test_Mn1: .: (0.000702) - test_Mn2: .: (0.000480) - test_Mn3: .: (0.000349) - test_Vn: .: (0.000352) - test_iGiven: .: (0.000352) - test_serial: .: (0.000369) + test_Mn1: .: (0.000462) + test_Mn2: .: (0.000292) + test_Mn3: .: (0.000234) + test_Vn: .: (0.000193) + test_iGiven: .: (0.000189) + test_serial: .: (0.000306) Bio::TestPDBRecord::TestMTRIX2: - test_Mn1: .: (0.000829) - test_Mn2: .: (0.000385) - test_Mn3: .: (0.000356) - test_Vn: .: (0.000866) - test_iGiven: .: (0.000411) - test_serial: .: (0.000379) + test_Mn1: .: (0.000544) + test_Mn2: .: (0.000308) + test_Mn3: .: (0.000196) + test_Vn: .: (0.000189) + test_iGiven: .: (0.000199) + test_serial: .: (0.000188) Bio::TestPDBRecord::TestMTRIX3: - test_Mn1: .: (0.000669) - test_Mn2: .: (0.000383) - test_Mn3: .: (0.000353) - test_Vn: .: (0.000356) - test_iGiven: .: (0.000403) - test_serial: .: (0.000383) + test_Mn1: .: (0.000479) + test_Mn2: .: (0.000295) + test_Mn3: .: (0.000196) + test_Vn: .: (0.000522) + test_iGiven: .: (0.000245) + test_serial: .: (0.000187) Bio::TestPDBRecord::TestOBSLTE: - test_idCode: .: (0.000699) - test_rIdCode: .: (0.000393) - test_repDate: .: (0.000442) + test_idCode: .: (0.000475) + test_rIdCode: .: (0.000276) + test_repDate: .: (0.000257) Bio::TestPDBRecord::TestORIGX1: - test_On1: .: (0.000691) - test_On2: .: (0.000374) - test_On3: .: (0.000402) - test_Tn: .: (0.000868) + test_On1: .: (0.000413) + test_On2: .: (0.000187) + test_On3: .: (0.000184) + test_Tn: .: (0.000186) Bio::TestPDBRecord::TestREVDAT: - test_modDate: .: (0.000680) - test_modId: .: (0.000439) - test_modNum: .: (0.000382) - test_modType: .: (0.000417) - test_record: .: (0.000392) + test_modDate: .: (0.000480) + test_modId: .: (0.000212) + test_modNum: .: (0.000215) + test_modType: .: (0.000680) + test_record: .: (0.000228) Bio::TestPDBRecord::TestRemarkN: - test_remarkNum: .: (0.000626) - test_text: .: (0.000376) + test_remarkNum: .: (0.000462) + test_text: .: (0.000250) Bio::TestPDBRecord::TestSCALE1: - test_Sn1: .: (0.000682) - test_Sn2: .: (0.000379) - test_Sn3: .: (0.000371) - test_Un: .: (0.000350) + test_Sn1: .: (0.000555) + test_Sn2: .: (0.000243) + test_Sn3: .: (0.000176) + test_Un: .: (0.000188) Bio::TestPDBRecord::TestSCALE2: - test_Sn1: .: (0.000638) - test_Sn2: .: (0.000929) - test_Sn3: .: (0.000379) - test_Un: .: (0.000385) + test_Sn1: .: (0.000399) + test_Sn2: .: (0.000195) + test_Sn3: .: (0.000225) + test_Un: .: (0.000202) Bio::TestPDBRecord::TestSCALE3: - test_Sn1: .: (0.000642) - test_Sn2: .: (0.000374) - test_Sn3: .: (0.000365) - test_Un: .: (0.000370) + test_Sn1: .: (0.000455) + test_Sn2: .: (0.000249) + test_Sn3: .: (0.000648) + test_Un: .: (0.000303) Bio::TestPDBRecord::TestSEQADV: - test_chainID: .: (0.000885) - test_conflict: .: (0.000481) - test_database: .: (0.000446) - test_dbIdCode: .: (0.000528) - test_dbRes: .: (0.000449) - test_dbSeq: .: (0.000464) - test_iCode: .: (0.000440) - test_idCode: .: (0.001079) - test_resName: .: (0.000536) - test_seqNum: .: (0.000431) + test_chainID: .: (0.000589) + test_conflict: .: (0.000291) + test_database: .: (0.000240) + test_dbIdCode: .: (0.000240) + test_dbRes: .: (0.000233) + test_dbSeq: .: (0.000234) + test_iCode: .: (0.000296) + test_idCode: .: (0.000244) + test_resName: .: (0.000360) + test_seqNum: .: (0.000304) Bio::TestPDBRecord::TestSEQRES: - test_chainID: .: (0.000920) - test_numRes: .: (0.000523) - test_resName: .: (0.000502) + test_chainID: .: (0.000460) + test_numRes: .: (0.000745) + test_resName: .: (0.000250) Bio::TestPDBRecord::TestSHEET: - test_curAtom: .: (0.000893) - test_curChainId: .: (0.000612) - test_curICode: .: (0.000652) - test_curResName: .: (0.001141) - test_curResSeq: .: (0.000581) - test_endChainID: .: (0.000605) - test_endICode: .: (0.000585) - test_endResName: .: (0.000609) - test_endSeqNum: .: (0.000590) - test_initChainID: .: (0.000582) - test_initICode: .: (0.000609) - test_initResName: .: (0.000533) - test_initSeqNum: .: (0.000614) - test_numStrands: .: (0.001168) - test_prevAtom: .: (0.000622) - test_prevChainId: .: (0.000597) - test_prevICode: .: (0.000643) - test_prevResName: .: (0.000619) - test_prevResSeq: .: (0.000610) - test_sense: .: (0.000591) - test_sheetID: .: (0.000561) - test_strand: .: (0.000593) + test_curAtom: .: (0.000599) + test_curChainId: .: (0.000302) + test_curICode: .: (0.000306) + test_curResName: .: (0.000410) + test_curResSeq: .: (0.000304) + test_endChainID: .: (0.000300) + test_endICode: .: (0.000299) + test_endResName: .: (0.000313) + test_endSeqNum: .: (0.000355) + test_initChainID: .: (0.000793) + test_initICode: .: (0.000293) + test_initResName: .: (0.000317) + test_initSeqNum: .: (0.000284) + test_numStrands: .: (0.000284) + test_prevAtom: .: (0.000285) + test_prevChainId: .: (0.000376) + test_prevICode: .: (0.000342) + test_prevResName: .: (0.000297) + test_prevResSeq: .: (0.000349) + test_sense: .: (0.000317) + test_sheetID: .: (0.000330) + test_strand: .: (0.000294) Bio::TestPDBRecord::TestSIGATM: - test_altLoc: .: (0.000856) - test_chainID: .: (0.000484) - test_charge: .: (0.000526) - test_element: .: (0.001167) - test_iCode: .: (0.000516) - test_name: .: (0.000514) - test_resName: .: (0.000459) - test_resSeq: .: (0.000505) - test_segID: .: (0.000466) - test_serial: .: (0.000502) - test_sigOcc: .: (0.000505) - test_sigTemp: .: (0.000508) - test_sigX: .: (0.000458) - test_sigY: .: (0.000665) - test_sigZ: .: (0.000501) + test_altLoc: .: (0.000633) + test_chainID: .: (0.000252) + test_charge: .: (0.000239) + test_element: .: (0.000280) + test_iCode: .: (0.000247) + test_name: .: (0.000240) + test_resName: .: (0.000241) + test_resSeq: .: (0.000276) + test_segID: .: (0.000260) + test_serial: .: (0.000296) + test_sigOcc: .: (0.000661) + test_sigTemp: .: (0.000259) + test_sigX: .: (0.000233) + test_sigY: .: (0.000415) + test_sigZ: .: (0.000251) Bio::TestPDBRecord::TestSIGUIJ: - test_SigmaU11: .: (0.000840) - test_SigmaU12: .: (0.000539) - test_SigmaU13: .: (0.001127) - test_SigmaU22: .: (0.000521) - test_SigmaU23: .: (0.000471) - test_SigmaU33: .: (0.000458) - test_altLoc: .: (0.000488) - test_chainID: .: (0.000453) - test_charge: .: (0.000496) - test_element: .: (0.000449) - test_iCode: .: (0.000445) - test_name: .: (0.000456) - test_resName: .: (0.000436) - test_resSeq: .: (0.000630) - test_segID: .: (0.000509) - test_serial: .: (0.000459) + test_SigmaU11: .: (0.000513) + test_SigmaU12: .: (0.000269) + test_SigmaU13: .: (0.000332) + test_SigmaU22: .: (0.000287) + test_SigmaU23: .: (0.000246) + test_SigmaU33: .: (0.000243) + test_altLoc: .: (0.000251) + test_chainID: .: (0.000242) + test_charge: .: (0.000288) + test_element: .: (0.000642) + test_iCode: .: (0.000246) + test_name: .: (0.000308) + test_resName: .: (0.000288) + test_resSeq: .: (0.000396) + test_segID: .: (0.000253) + test_serial: .: (0.000241) Bio::TestPDBRecord::TestSITE: - test_chainID1: .: (0.001539) - test_chainID2: .: (0.000513) - test_chainID3: .: (0.000525) - test_chainID4: .: (0.000515) - test_iCode1: .: (0.000469) - test_iCode2: .: (0.000509) - test_iCode3: .: (0.000574) - test_iCode4: .: (0.000528) - test_numRes: .: (0.000487) - test_resName1: .: (0.000522) - test_resName2: .: (0.000538) - test_resName3: .: (0.001128) - test_resName4: .: (0.000568) - test_seq1: .: (0.000570) - test_seq2: .: (0.000507) - test_seq3: .: (0.000548) - test_seq4: .: (0.000549) - test_seqNum: .: (0.000475) - test_siteID: .: (0.000535) + test_chainID1: .: (0.000595) + test_chainID2: .: (0.000336) + test_chainID3: .: (0.000277) + test_chainID4: .: (0.000270) + test_iCode1: .: (0.000279) + test_iCode2: .: (0.000265) + test_iCode3: .: (0.000292) + test_iCode4: .: (0.000259) + test_numRes: .: (0.000263) + test_resName1: .: (0.000256) + test_resName2: .: (0.000328) + test_resName3: .: (0.000370) + test_resName4: .: (0.000269) + test_seq1: .: (0.000288) + test_seq2: .: (0.000269) + test_seq3: .: (0.000313) + test_seq4: .: (0.000264) + test_seqNum: .: (0.000266) + test_siteID: .: (0.000690) Bio::TestPDBRecord::TestSLTBRG: - test_altLoc1: .: (0.000821) - test_altLoc2: .: (0.000492) - test_atom1: .: (0.000462) - test_atom2: .: (0.000462) - test_chainID1: .: (0.000411) - test_chainID2: .: (0.000436) - test_iCode1: .: (0.000870) - test_iCode2: .: (0.000517) - test_resName1: .: (0.000437) - test_resName2: .: (0.000460) - test_resSeq1: .: (0.000399) - test_resSeq2: .: (0.000442) - test_sym1: .: (0.000441) - test_sym2: .: (0.000441) + test_altLoc1: .: (0.000548) + test_altLoc2: .: (0.000228) + test_atom1: .: (0.000217) + test_atom2: .: (0.000261) + test_chainID1: .: (0.000235) + test_chainID2: .: (0.000252) + test_iCode1: .: (0.000233) + test_iCode2: .: (0.000227) + test_resName1: .: (0.000226) + test_resName2: .: (0.000227) + test_resSeq1: .: (0.000223) + test_resSeq2: .: (0.000221) + test_sym1: .: (0.000229) + test_sym2: .: (0.000227) Bio::TestPDBRecord::TestSOURCE: - test_srcName: .: (0.000776) + test_srcName: .: (0.000919) Bio::TestPDBRecord::TestSPRSDE: - test_idCode: .: (0.000704) - test_sIdCode: .: (0.000391) - test_sprsdeDate: .: (0.000369) + test_idCode: .: (0.000514) + test_sIdCode: .: (0.000209) + test_sprsdeDate: .: (0.000202) Bio::TestPDBRecord::TestTER: - test_chainID: .: (0.000754) - test_iCode: .: (0.000930) - test_resName: .: (0.000431) - test_resSeq: .: (0.000383) - test_serial: .: (0.000363) + test_chainID: .: (0.000591) + test_iCode: .: (0.000218) + test_resName: .: (0.000204) + test_resSeq: .: (0.000203) + test_serial: .: (0.000220) Bio::TestPDBRecord::TestTITLE: - test_title: .: (0.000715) + test_title: .: (0.000466) Bio::TestPDBRecord::TestTVECT: - test_serial: .: (0.000754) - test_t1: .: (0.000377) - test_t2: .: (0.000392) - test_t3: .: (0.000366) - test_text: .: (0.000417) + test_serial: .: (0.000479) + test_t1: .: (0.000332) + test_t2: .: (0.000270) + test_t3: .: (0.000666) + test_text: .: (0.000270) Bio::TestPROSITE: - test_ac: .: (0.005291) - test_cc: .: (0.004506) - test_de: .: (0.004445) - test_division: .: (0.004450) - test_dr: .: (0.134987) - test_dt: .: (0.017527) - test_false_neg: .: (0.019588) - test_false_pos: .: (0.004799) - test_false_positive_sequences: .: (0.004318) - test_list_falsenegative: .: (0.041648) - test_list_falsepositive: .: (0.041369) - test_list_potentialhit: .: (0.041913) - test_list_truepositive: .: (0.043149) - test_list_unknown: .: (0.040483) - test_list_xref: .: (0.041296) - test_ma: .: (0.003823) - test_max_repeat: .: (0.004251) - test_name: .: (0.004412) - test_nr: .: (0.005528) - test_pa: .: (0.005541) - test_pa2re: .: (0.005156) - test_partial: .: (0.004420) - test_pdb_xref: .: (0.004329) - test_pdoc_xref: .: (0.004766) - test_positive: .: (0.004289) - test_positive_hits: .: (0.004740) - test_positive_sequences: .: (0.004634) - test_release: .: (0.005631) - test_ru: .: (0.005316) - test_self_pa2re: .: (0.005717) - test_site: .: (0.005307) - test_skip_flag: .: (0.005347) - test_swissprot_release_number: .: (0.005215) - test_swissprot_release_sequences: .: (0.005281) - test_taxon_range: .: (0.005189) - test_total: .: (0.005310) - test_total_hits: .: (0.004395) - test_total_sequences: .: (0.005394) - test_unknown: .: (0.005391) - test_unknown_hits: .: (0.005295) - test_unknown_sequences: .: (0.004870) + test_ac: .: (0.003097) + test_cc: .: (0.003117) + test_de: .: (0.003089) + test_division: .: (0.003104) + test_dr: .: (0.080555) + test_dt: .: (0.010930) + test_false_neg: .: (0.017129) + test_false_pos: .: (0.021011) + test_false_positive_sequences: .: (0.003492) + test_list_falsenegative: .: (0.031716) + test_list_falsepositive: .: (0.031160) + test_list_potentialhit: .: (0.031586) + test_list_truepositive: .: (0.032272) + test_list_unknown: .: (0.030163) + test_list_xref: .: (0.031894) + test_ma: .: (0.003546) + test_max_repeat: .: (0.002670) + test_name: .: (0.003009) + test_nr: .: (0.003833) + test_pa: .: (0.003732) + test_pa2re: .: (0.003707) + test_partial: .: (0.003699) + test_pdb_xref: .: (0.003777) + test_pdoc_xref: .: (0.003052) + test_positive: .: (0.004108) + test_positive_hits: .: (0.007446) + test_positive_sequences: .: (0.003438) + test_release: .: (0.003958) + test_ru: .: (0.003872) + test_self_pa2re: .: (0.003900) + test_site: .: (0.003634) + test_skip_flag: .: (0.003865) + test_swissprot_release_number: .: (0.003584) + test_swissprot_release_sequences: .: (0.004036) + test_taxon_range: .: (0.004177) + test_total: .: (0.003679) + test_total_hits: .: (0.003997) + test_total_sequences: .: (0.003880) + test_unknown: .: (0.003824) + test_unknown_hits: .: (0.003495) + test_unknown_sequences: .: (0.003708) Bio::TestPROSITEConst: - test_delimiter: .: (0.000743) - test_tagsize: .: (0.000435) + test_delimiter: .: (0.000504) + test_tagsize: .: (0.000187) Bio::TestPTS1: - test_function_set: .: (0.000718) - test_function_set_number_1: .: (0.000436) - test_function_set_number_2: .: (0.000436) - test_function_set_number_3: .: (0.000460) - test_function_show: .: (0.000378) + test_function_set: .: (0.000455) + test_function_set_number_1: .: (0.000256) + test_function_set_number_2: .: (0.000237) + test_function_set_number_3: .: (0.000242) + test_function_show: .: (0.000230) Bio::TestPTS1Constant: - test_FUNCTION: .: (0.001430) + test_FUNCTION: .: (0.000470) Bio::TestPTS1New: - test_fungi: .: (0.000710) - test_general: .: (0.000412) - test_metazoa: .: (0.000409) + test_fungi: .: (0.000424) + test_general: .: (0.000939) + test_metazoa: .: (0.000237) Bio::TestQualifier: - test_qualifier: .: (0.000659) - test_value: .: (0.000424) + test_qualifier: .: (0.000440) + test_value: .: (0.000214) Bio::TestREBASE: - test_methods: .: (0.003520) + test_methods: .: (0.001678) Bio::TestRPSBlast::TestRPSBlastHSP: - test_align_len: .: (0.002329) - test_bit_score: .: (0.001593) - test_evalue: .: (0.001533) - test_gaps: .: (0.002642) - test_hit_from: .: (0.002102) - test_hit_to: .: (0.001583) - test_hseq: .: (0.001627) - test_identity: .: (0.001495) - test_midline: .: (0.003084) - test_percent_identity: .: (0.001494) - test_positive: .: (0.001542) - test_qseq: .: (0.001566) - test_query_from: .: (0.002599) - test_query_to: .: (0.001909) - test_score: .: (0.001551) + test_align_len: .: (0.002577) + test_bit_score: .: (0.001249) + test_evalue: .: (0.001161) + test_gaps: .: (0.001319) + test_hit_from: .: (0.001350) + test_hit_to: .: (0.002411) + test_hseq: .: (0.001332) + test_identity: .: (0.001249) + test_midline: .: (0.001340) + test_percent_identity: .: (0.001262) + test_positive: .: (0.002359) + test_qseq: .: (0.001338) + test_query_from: .: (0.001257) + test_query_to: .: (0.001350) + test_score: .: (0.001277) Bio::TestRPSBlast::TestRPSBlastReport: - test_db: .: (0.001655) - test_hits_size: .: (0.004372) - test_iterations_size: .: (0.003134) - test_program: .: (0.001360) - test_query_def: .: (0.003752) - test_query_len: .: (0.003247) - test_version: .: (0.001387) - test_version_date: .: (0.001283) - test_version_number: .: (0.001315) + test_db: .: (0.002416) + test_hits_size: .: (0.002688) + test_iterations_size: .: (0.002491) + test_program: .: (0.001231) + test_query_def: .: (0.002466) + test_query_len: .: (0.002572) + test_version: .: (0.001315) + test_version_date: .: (0.001129) + test_version_number: .: (0.001103) Bio::TestRPSBlast::TestRPSBlastReportHit: - test_bit_score: .: (0.003095) - test_definition: .: (0.001655) - test_evalue: .: (0.001567) - test_hsps_size: .: (0.001479) - test_identity: .: (0.001562) - test_lap_at: .: (0.002595) - test_len: .: (0.001684) - test_midline: .: (0.001742) - test_overlap: .: (0.001560) - test_query_end: .: (0.003014) - test_query_seq: .: (0.002145) - test_query_start: .: (0.001713) - test_target_def: .: (0.001581) - test_target_end: .: (0.001755) - test_target_len: .: (0.001557) - test_target_seq: .: (0.001998) - test_target_start: .: (0.001745) + test_bit_score: .: (0.001641) + test_definition: .: (0.001344) + test_evalue: .: (0.001330) + test_hsps_size: .: (0.001197) + test_identity: .: (0.001274) + test_lap_at: .: (0.001343) + test_len: .: (0.002226) + test_midline: .: (0.001392) + test_overlap: .: (0.001332) + test_query_end: .: (0.001352) + test_query_seq: .: (0.002080) + test_query_start: .: (0.001708) + test_target_def: .: (0.001290) + test_target_end: .: (0.001383) + test_target_len: .: (0.001285) + test_target_seq: .: (0.001994) + test_target_start: .: (0.001758) Bio::TestRPSBlast::TestRPSBlastSplitter: - test_entry_pos: .: (0.001335) - test_get_entry: .: (0.001285) - test_rewind: .: (0.000337) - test_skip_leader: .: (0.000590) + test_entry_pos: .: (0.001065) + test_get_entry: .: (0.000939) + test_rewind: .: (0.000311) + test_skip_leader: .: (0.000450) Bio::TestReference: - test_abstract: .: (0.001472) - test_affiliations: .: (0.000330) - test_authors: .: (0.000290) - test_format_bibitem: .: (0.000476) - test_format_bibtex: .: (0.000627) - test_format_bibtex_with_arguments: .: (0.000604) - test_format_cell: .: (0.000355) - test_format_current: .: (0.000351) - test_format_endnote: .: (0.000444) - test_format_general: .: (0.000402) - test_format_genome_biol: .: (0.001088) - test_format_genome_res: .: (0.000398) - test_format_nar: .: (0.000374) - test_format_nature: .: (0.000414) - test_format_rd: .: (0.000393) - test_format_science: .: (0.000502) - test_format_trends: .: (0.000371) - test_issue: .: (0.000273) - test_journal: .: (0.000935) - test_mesh: .: (0.000292) - test_pages: .: (0.000286) - test_pubmed: .: (0.000260) - test_pubmed_url: .: (0.000299) - test_url: .: (0.000268) - test_volume: .: (0.001008) - test_year: .: (0.000288) + test_abstract: .: (0.001062) + test_affiliations: .: (0.000225) + test_authors: .: (0.000230) + test_format_bibitem: .: (0.000346) + test_format_bibtex: .: (0.000459) + test_format_bibtex_with_arguments: .: (0.000460) + test_format_cell: .: (0.000255) + test_format_current: .: (0.000278) + test_format_endnote: .: (0.000312) + test_format_general: .: (0.000312) + test_format_genome_biol: .: (0.000291) + test_format_genome_res: .: (0.000895) + test_format_nar: .: (0.000306) + test_format_nature: .: (0.000359) + test_format_rd: .: (0.000282) + test_format_science: .: (0.000374) + test_format_trends: .: (0.000251) + test_issue: .: (0.000222) + test_journal: .: (0.000858) + test_mesh: .: (0.000286) + test_pages: .: (0.000234) + test_pubmed: .: (0.000216) + test_pubmed_url: .: (0.000226) + test_url: .: (0.000253) + test_volume: .: (0.000220) + test_year: .: (0.000775) Bio::TestReference_noURL: - test_format_endnote: .: (0.000687) - test_url: .: (0.000300) + test_format_endnote: .: (0.000666) + test_url: .: (0.000248) Bio::TestReferences: - test_append: .: (0.000728) - test_each: .: (0.000362) + test_append: .: (0.000545) + test_each: .: (0.000284) Bio::TestRelation: - test_comparison_operator: .: (0.000677) - test_uniq: .: (0.000396) + test_comparison_operator: .: (0.000502) + test_uniq: .: (0.000305) Bio::TestResidue: - test_addAtom: .: (0.001955) - test_each: .: (0.000605) - test_each_atom: .: (0.000568) - test_get_residue_id_from_atom: .: (0.000527) - test_het_atom: .: (0.000437) - test_iCode: .: (0.000495) - test_inspect: .: (0.000496) - test_resSeq: .: (0.000438) - test_sort: .: (0.001505) - test_square_bracket: .: (0.000509) - test_to_s: .: (0.000978) - test_update_resudue_id: .: (0.000470) + test_addAtom: .: (0.000729) + test_each: .: (0.000918) + test_each_atom: .: (0.000427) + test_get_residue_id_from_atom: .: (0.000364) + test_het_atom: .: (0.000312) + test_iCode: .: (0.000331) + test_inspect: .: (0.000493) + test_resSeq: .: (0.000355) + test_sort: .: (0.001118) + test_square_bracket: .: (0.000384) + test_to_s: .: (0.000854) + test_update_resudue_id: .: (0.000434) Bio::TestResidueFinder: - test_each_residue: .: (0.000684) - test_find_residue: .: (0.000407) - test_residues: .: (0.000427) + test_each_residue: .: (0.000558) + test_find_residue: .: (0.000291) + test_residues: .: (0.000330) Bio::TestRestrictionEnzyme::TestAnalysis: - test_cut: .: (0.356041) - test_cut_from_bio_sequence_na: .: (0.092178) - test_cut_without_permutations: .: (0.063537) - test_view_ranges: .: (0.063330) + test_cut: .: (0.246775) + test_cut_from_bio_sequence_na: .: (0.069926) + test_cut_without_permutations: .: (0.042945) + test_view_ranges: .: (0.042384) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: - test_cuts: .: (0.003540) - test_cuts_after_remove_incomplete_cuts: .: (0.002541) - test_strands_for_display: .: (0.009304) - test_strands_for_display_current: .: (0.002456) + test_cuts: .: (0.002999) + test_cuts_after_remove_incomplete_cuts: .: (0.001451) + test_strands_for_display: .: (0.006125) + test_strands_for_display_current: .: (0.001751) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: - test_fragments: .: (0.001580) - test_fragments_for_display_1: .: (0.002305) - test_fragments_for_display_10: .: (0.003538) - test_fragments_for_display_2: .: (0.002384) - test_fragments_for_display_3: .: (0.004747) - test_fragments_for_display_4: .: (0.002813) - test_fragments_for_display_5: .: (0.002690) - test_fragments_for_display_6: .: (0.001828) - test_fragments_for_display_7: .: (0.002294) - test_fragments_for_display_8: .: (0.001677) - test_fragments_for_display_9: .: (0.002913) + test_fragments: .: (0.001180) + test_fragments_for_display_1: .: (0.002079) + test_fragments_for_display_10: .: (0.001988) + test_fragments_for_display_2: .: (0.001653) + test_fragments_for_display_3: .: (0.003387) + test_fragments_for_display_4: .: (0.002636) + test_fragments_for_display_5: .: (0.001288) + test_fragments_for_display_6: .: (0.001275) + test_fragments_for_display_7: .: (0.001712) + test_fragments_for_display_8: .: (0.001783) + test_fragments_for_display_9: .: (0.001603) Bio::TestRestrictionEnzyme::TestCutRanges: - test_obj_2: .: (0.001025) - test_obj_3: .: (0.000785) - test_obj_7: .: (0.000709) - test_obj_z: .: (0.000703) + test_obj_2: .: (0.000799) + test_obj_3: .: (0.001041) + test_obj_7: .: (0.000552) + test_obj_z: .: (0.000771) Bio::TestRestrictionEnzyme::TestCutSymbol: - test_methods: .: (0.001531) + test_methods: .: (0.000737) Bio::TestRestrictionEnzyme::TestDenseIntArray: - test_bracket: .: (0.001020) - test_bracket_eq: .: (0.000454) - test_concat: .: (0.000389) - test_delete: .: (0.000385) - test_dup: .: (0.000508) - test_each: .: (0.000492) - test_eqeq: .: (0.000390) - test_eqeq_false: .: (0.000310) - test_eqeq_other: .: (0.000280) - test_eqeq_self: .: (0.000272) - test_include?: .: (0.000318) - test_internal_data: .: (0.000304) - test_internal_data_eq: .: (0.000351) - test_length: .: (0.000308) - test_ltlt: .: (0.000375) - test_ltlt_larger: .: (0.000340) - test_ltlt_middle: .: (0.000357) - test_plus: .: (0.000386) - test_plus_error: .: (0.000425) - test_push: .: (0.000360) - test_reverse_each: .: (0.000512) - test_self_bracket: .: (0.000301) - test_self_new: .: (0.000383) - test_size: .: (0.000296) - test_sort!: .: (0.000278) - test_to_a: .: (0.000304) - test_uniq!: .: (0.000283) - test_unshift: .: (0.000373) + test_bracket: .: (0.000665) + test_bracket_eq: .: (0.000336) + test_concat: .: (0.000329) + test_delete: .: (0.000295) + test_dup: .: (0.000419) + test_each: .: (0.000563) + test_eqeq: .: (0.000287) + test_eqeq_false: .: (0.000249) + test_eqeq_other: .: (0.000225) + test_eqeq_self: .: (0.000267) + test_include?: .: (0.000264) + test_internal_data: .: (0.000250) + test_internal_data_eq: .: (0.000294) + test_length: .: (0.000223) + test_ltlt: .: (0.000264) + test_ltlt_larger: .: (0.000268) + test_ltlt_middle: .: (0.000264) + test_plus: .: (0.000301) + test_plus_error: .: (0.000340) + test_push: .: (0.000316) + test_reverse_each: .: (0.000644) + test_self_bracket: .: (0.000238) + test_self_new: .: (0.000299) + test_size: .: (0.000238) + test_sort!: .: (0.000212) + test_to_a: .: (0.000316) + test_uniq!: .: (0.000236) + test_unshift: .: (0.000331) Bio::TestRestrictionEnzyme::TestDoubleStranded: - test_argument_error: .: (0.012877) - test_complement: .: (0.016712) - test_complement_with_cut_symbols: .: (0.013066) - test_cut_locations: .: (0.012228) - test_cut_locations_in_enzyme_notation: .: (0.012170) - test_primary: .: (0.012090) - test_primary_with_cut_symbols: .: (0.012425) - test_to_re: .: (0.011840) + test_argument_error: .: (0.008753) + test_complement: .: (0.007749) + test_complement_with_cut_symbols: .: (0.012903) + test_cut_locations: .: (0.007978) + test_cut_locations_in_enzyme_notation: .: (0.008154) + test_primary: .: (0.007955) + test_primary_with_cut_symbols: .: (0.008147) + test_to_re: .: (0.007967) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: - test_align: .: (0.002787) - test_align_with_cuts: .: (0.002604) - test_argument_error: .: (0.003398) - test_ds: .: (0.002358) + test_align: .: (0.002040) + test_align_with_cuts: .: (0.001792) + test_argument_error: .: (0.002369) + test_ds: .: (0.001794) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: - test_argument_error: .: (0.001227) - test_complement: .: (0.000868) - test_contents: .: (0.000596) - test_primary: .: (0.000590) + test_argument_error: .: (0.001153) + test_complement: .: (0.000379) + test_contents: .: (0.000355) + test_primary: .: (0.000386) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: - test_argument_error: .: (0.001051) - test_complement: .: (0.000579) - test_contents: .: (0.000564) - test_primary: .: (0.000595) + test_argument_error: .: (0.000847) + test_complement: .: (0.000423) + test_contents: .: (0.000425) + test_primary: .: (0.000675) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: - test_complement: .: (0.000831) - test_contents: .: (0.000465) - test_primary: .: (0.000422) + test_complement: .: (0.000568) + test_contents: .: (0.000363) + test_primary: .: (0.000329) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: - test_complement: .: (0.000800) - test_complement_to_array_index: .: (0.000703) - test_complement_to_array_index_class: .: (0.000652) - test_contents: .: (0.000518) - test_primary: .: (0.000478) - test_primary_to_array_index: .: (0.000683) - test_primary_to_array_index_class: .: (0.000969) - test_to_array_index: .: (0.001302) - test_to_array_index_class: .: (0.001177) + test_complement: .: (0.000579) + test_complement_to_array_index: .: (0.000522) + test_complement_to_array_index_class: .: (0.000526) + test_contents: .: (0.000389) + test_primary: .: (0.000354) + test_primary_to_array_index: .: (0.000767) + test_primary_to_array_index_class: .: (0.000461) + test_to_array_index: .: (0.000901) + test_to_array_index_class: .: (0.000878) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: - test_enzyme_name: .: (0.001394) - test_rebase: .: (0.000452) + test_enzyme_name: .: (0.001013) + test_rebase: .: (0.000337) Bio::TestRestrictionEnzyme::TestSingleStrand: - test_argument_error: .: (0.002834) - test_creation_with_no_cuts: .: (0.001343) - test_cut_locations: .: (0.001374) - test_cut_locations_in_enzyme_notation: .: (0.001751) - test_orientation: .: (0.001248) - test_pattern: .: (0.001433) - test_pattern_palindromic?: .: (0.001874) - test_stripped: .: (0.001304) - test_to_re: .: (0.001183) - test_with_cut_symbols: .: (0.001351) - test_with_spaces: .: (0.001903) + test_argument_error: .: (0.002108) + test_creation_with_no_cuts: .: (0.001031) + test_cut_locations: .: (0.000971) + test_cut_locations_in_enzyme_notation: .: (0.001242) + test_orientation: .: (0.000944) + test_pattern: .: (0.000987) + test_pattern_palindromic?: .: (0.001409) + test_stripped: .: (0.000903) + test_to_re: .: (0.000831) + test_with_cut_symbols: .: (0.001220) + test_with_spaces: .: (0.001157) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: - test_argument_error: .: (0.002346) - test_creation_with_no_cuts: .: (0.001700) - test_cut_locations: .: (0.001337) - test_cut_locations_in_enzyme_notation: .: (0.001413) - test_orientation: .: (0.001600) - test_pattern: .: (0.001411) - test_pattern_palindromic?: .: (0.001668) - test_stripped: .: (0.001600) - test_to_re: .: (0.001178) - test_with_cut_symbols: .: (0.001361) - test_with_spaces: .: (0.001846) + test_argument_error: .: (0.001746) + test_creation_with_no_cuts: .: (0.001227) + test_cut_locations: .: (0.000981) + test_cut_locations_in_enzyme_notation: .: (0.000981) + test_orientation: .: (0.001144) + test_pattern: .: (0.001036) + test_pattern_palindromic?: .: (0.001162) + test_stripped: .: (0.001135) + test_to_re: .: (0.000811) + test_with_cut_symbols: .: (0.001008) + test_with_spaces: .: (0.001097) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: - test_argument_error: .: (0.001312) - test_initialize_with_pattern: .: (0.000975) - test_max: .: (0.000441) - test_min: .: (0.000466) - test_to_array_index: .: (0.000516) + test_argument_error: .: (0.001296) + test_initialize_with_pattern: .: (0.000721) + test_max: .: (0.000413) + test_min: .: (0.000367) + test_to_array_index: .: (0.000389) Bio::TestRestrictionEnzyme::TestSortedNumArray: - test_bracket: .: (0.000701) - test_bracket_eq: .: (0.000395) - test_concat: .: (0.000342) - test_delete: .: (0.000320) - test_dup: .: (0.000459) - test_each: .: (0.000503) - test_eqeq: .: (0.000310) - test_eqeq_false: .: (0.000270) - test_eqeq_other: .: (0.000257) - test_eqeq_self: .: (0.000256) - test_include?: .: (0.000295) - test_internal_data_hash: .: (0.000279) - test_internal_data_hash_eq: .: (0.000321) - test_length: .: (0.000306) - test_ltlt: .: (0.000307) - test_ltlt_noeffect: .: (0.000302) - test_plus: .: (0.000290) - test_plus_error: .: (0.000671) - test_private_push_element: .: (0.000323) - test_private_push_element_intermediate: .: (0.000359) - test_private_push_element_last: .: (0.000322) - test_private_push_element_noeffect: .: (0.000355) - test_private_sorted_keys: .: (0.000281) - test_private_unshift_element: .: (0.000331) - test_private_unshift_element_first: .: (0.000323) - test_private_unshift_element_intermediate: .: (0.000306) - test_private_unshift_element_noeffect: .: (0.000296) - test_push: .: (0.000314) - test_reverse_each: .: (0.000511) - test_self_bracket: .: (0.000277) - test_self_new: .: (0.000318) - test_size: .: (0.000533) - test_sort!: .: (0.000262) - test_to_a: .: (0.000267) - test_uniq!: .: (0.000254) - test_unshift: .: (0.000307) + test_bracket: .: (0.000535) + test_bracket_eq: .: (0.000320) + test_concat: .: (0.000265) + test_delete: .: (0.000252) + test_dup: .: (0.000321) + test_each: .: (0.000644) + test_eqeq: .: (0.000256) + test_eqeq_false: .: (0.000217) + test_eqeq_other: .: (0.000207) + test_eqeq_self: .: (0.000210) + test_include?: .: (0.000228) + test_internal_data_hash: .: (0.000228) + test_internal_data_hash_eq: .: (0.000251) + test_length: .: (0.000212) + test_ltlt: .: (0.000266) + test_ltlt_noeffect: .: (0.000230) + test_plus: .: (0.000246) + test_plus_error: .: (0.000346) + test_private_push_element: .: (0.000249) + test_private_push_element_intermediate: .: (0.000257) + test_private_push_element_last: .: (0.000442) + test_private_push_element_noeffect: .: (0.000248) + test_private_sorted_keys: .: (0.000180) + test_private_unshift_element: .: (0.000196) + test_private_unshift_element_first: .: (0.000198) + test_private_unshift_element_intermediate: .: (0.000245) + test_private_unshift_element_noeffect: .: (0.000200) + test_push: .: (0.000204) + test_reverse_each: .: (0.000314) + test_self_bracket: .: (0.000206) + test_self_new: .: (0.000253) + test_size: .: (0.000173) + test_sort!: .: (0.000166) + test_to_a: .: (0.000174) + test_uniq!: .: (0.000352) + test_unshift: .: (0.000196) Bio::TestRestrictionEnzyme::TestStringFormatting: - test_add_spacing: .: (0.000638) - test_left_padding: .: (0.000457) - test_right_padding: .: (0.000383) - test_strip_padding: .: (0.000404) + test_add_spacing: .: (0.000550) + test_left_padding: .: (0.000246) + test_right_padding: .: (0.000235) + test_strip_padding: .: (0.000246) Bio::TestSOFT: - test_dataset: .: (0.020282) - test_series: .: (0.020203) + test_dataset: .: (0.014175) + test_series: .: (0.014128) Bio::TestSOSUIReport: - test_entry_id: .: (0.000797) - test_prediction: .: (0.000496) - test_tmh: .: (0.000440) - test_tmhs: .: (0.008572) + test_entry_id: .: (0.000619) + test_prediction: .: (0.000348) + test_tmh: .: (0.000380) + test_tmhs: .: (0.000432) Bio::TestSOSUIReportConst: - test_delimiter: .: (0.000533) - test_rs: .: (0.000257) + test_delimiter: .: (0.000464) + test_rs: .: (0.000220) Bio::TestSOSUITMH: - test_grade: .: (0.000734) - test_range: .: (0.000464) - test_sequence: .: (0.000474) + test_grade: .: (0.000503) + test_range: .: (0.000329) + test_sequence: .: (0.000323) Bio::TestSampleGraph: - test_bellman_ford: .: (0.001311) - test_bfs_shortest_path: .: (0.000583) - test_breadth_first_search: .: (0.001167) - test_depth_first_search: .: (0.000909) - test_dijkstra: .: (0.000713) - test_dump_list: .: (0.000710) - test_dump_matrix: .: (0.000998) - test_extract_subgraph_by_label: .: (0.000629) - test_extract_subgraph_by_list: .: (0.001041) - test_extract_subgraph_retains_disconnected_nodes: .: (0.000532) - test_small_world_aka_node_degree_histogram: .: (0.000505) - test_to_matrix: .: (0.001061) - test_to_matrix_fixed_index: .: (0.000768) - test_undirected_cliquishness: .: (0.000998) + test_bellman_ford: .: (0.000954) + test_bfs_shortest_path: .: (0.000416) + test_breadth_first_search: .: (0.000420) + test_depth_first_search: .: (0.007616) + test_dijkstra: .: (0.000574) + test_dump_list: .: (0.000519) + test_dump_matrix: .: (0.000703) + test_extract_subgraph_by_label: .: (0.000488) + test_extract_subgraph_by_list: .: (0.000518) + test_extract_subgraph_retains_disconnected_nodes: .: (0.000401) + test_small_world_aka_node_degree_histogram: .: (0.000779) + test_to_matrix: .: (0.000729) + test_to_matrix_fixed_index: .: (0.000536) + test_undirected_cliquishness: .: (0.000715) Bio::TestScf_version_2: - test_complement: .: (0.031223) - test_seq: .: (0.029457) - test_to_biosequence: .: (0.029486) + test_complement: .: (0.020105) + test_seq: .: (0.018761) + test_to_biosequence: .: (0.018873) Bio::TestScf_version_3: - test_complement: .: (0.092602) - test_seq: .: (0.092010) - test_to_biosequence: .: (0.091817) + test_complement: .: (0.063065) + test_seq: .: (0.062064) + test_to_biosequence: .: (0.061834) Bio::TestSequence: - test_AA_new_blank_sequence: .: (0.001185) - test_AA_new_sequence_all_legal_symbols: .: (0.000309) - test_AA_new_sequence_removes_whitespace: .: (0.000293) - test_AA_new_sequence_upcases_symbols: .: (0.000291) - test_DNA_new_blank_sequence: .: (0.000300) - test_DNA_new_sequence_downcases_symbols: .: (0.000280) - test_DNA_new_sequence_removes_whitespace: .: (0.000273) - test_NA_randomize_with_counts: .: (0.002619) - test_NA_randomize_with_counts_and_block: .: (0.002730) - test_RNA_new_sequence: .: (0.000315) - test_ambiguous_dna_sequence_complement: .: (0.000310) - test_ambiguous_rna_sequence_complement: .: (0.000308) - test_amino_acid_codes: .: (0.000358) - test_amino_acid_molecular_weight: .: (0.000607) - test_amino_acid_names: .: (0.000383) - test_amino_acid_randomize_can_be_chained: .: (0.003602) - test_amino_acid_randomize_has_same_composition: .: (0.002170) - test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.001831) - test_dna_composition: .: (0.000385) - test_dna_gc_percent: .: (0.000816) - test_dna_molecular_weight: .: (0.000555) - test_dna_pikachu: .: (0.000319) - test_dna_sequence_complement: .: (0.000335) - test_dna_sequence_translate: .: (0.001077) - test_dna_to_re: .: (0.000480) - test_element_reference_operator_with_one_argument: .: (0.000301) - test_element_reference_operator_with_two_arguments: .: (0.000293) - test_invalid_nucleic_acid_illegal_bases: .: (0.000390) - test_invalid_nucleic_acid_illegal_bases_more: .: (0.000439) - test_nucleic_acid_names: .: (0.000332) - test_randomize_dna_can_be_chained: .: (0.001410) - test_randomize_dna_retains_composition: .: (0.000784) - test_randomize_dna_with_block: .: (0.000904) - test_rna_composition: .: (0.000378) - test_rna_gc_percent: .: (0.000441) - test_rna_molecular_weight: .: (0.000508) - test_rna_pikachu: .: (0.000792) - test_rna_sequence_complement: .: (0.000466) - test_rna_sequence_translate: .: (0.000849) - test_rna_to_re: .: (0.000496) - test_total: .: (0.000323) - test_two_consecutive_dna_randomizations_not_equal: .: (0.000782) - test_valid_dna_sequence_illegal_bases: .: (0.000301) + test_AA_new_blank_sequence: .: (0.000503) + test_AA_new_sequence_all_legal_symbols: .: (0.000245) + test_AA_new_sequence_removes_whitespace: .: (0.000274) + test_AA_new_sequence_upcases_symbols: .: (0.000554) + test_DNA_new_blank_sequence: .: (0.000235) + test_DNA_new_sequence_downcases_symbols: .: (0.000248) + test_DNA_new_sequence_removes_whitespace: .: (0.000227) + test_NA_randomize_with_counts: .: (0.001411) + test_NA_randomize_with_counts_and_block: .: (0.002061) + test_RNA_new_sequence: .: (0.000208) + test_ambiguous_dna_sequence_complement: .: (0.000250) + test_ambiguous_rna_sequence_complement: .: (0.000592) + test_amino_acid_codes: .: (0.000330) + test_amino_acid_molecular_weight: .: (0.000440) + test_amino_acid_names: .: (0.000301) + test_amino_acid_randomize_can_be_chained: .: (0.002414) + test_amino_acid_randomize_has_same_composition: .: (0.001174) + test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.001553) + test_dna_composition: .: (0.000296) + test_dna_gc_percent: .: (0.000289) + test_dna_molecular_weight: .: (0.000324) + test_dna_pikachu: .: (0.000500) + test_dna_sequence_complement: .: (0.000161) + test_dna_sequence_translate: .: (0.000812) + test_dna_to_re: .: (0.000279) + test_element_reference_operator_with_one_argument: .: (0.000156) + test_element_reference_operator_with_two_arguments: .: (0.000152) + test_invalid_nucleic_acid_illegal_bases: .: (0.000259) + test_invalid_nucleic_acid_illegal_bases_more: .: (0.000251) + test_nucleic_acid_names: .: (0.000196) + test_randomize_dna_can_be_chained: .: (0.000638) + test_randomize_dna_retains_composition: .: (0.000822) + test_randomize_dna_with_block: .: (0.000634) + test_rna_composition: .: (0.000327) + test_rna_gc_percent: .: (0.000318) + test_rna_molecular_weight: .: (0.000393) + test_rna_pikachu: .: (0.000253) + test_rna_sequence_complement: .: (0.000285) + test_rna_sequence_translate: .: (0.000638) + test_rna_to_re: .: (0.000389) + test_total: .: (0.000305) + test_two_consecutive_dna_randomizations_not_equal: .: (0.000937) + test_valid_dna_sequence_illegal_bases: .: (0.000292) Bio::TestSequenceAA: - test_codes: .: (0.000608) - test_molecular_weight: .: (0.000526) - test_names: .: (0.000361) - test_to_re: .: (0.000851) - test_to_s: .: (0.000299) + test_codes: .: (0.000502) + test_molecular_weight: .: (0.000381) + test_names: .: (0.000279) + test_to_re: .: (0.000335) + test_to_s: .: (0.000248) Bio::TestSequenceAACompat: - test_aa_self_randomize: .: (0.000769) + test_aa_self_randomize: .: (0.000550) Bio::TestSequenceAANew: - test_new: .: (0.000532) - test_new_n: .: (0.000275) - test_new_r: .: (0.000255) - test_new_t: .: (0.000252) + test_new: .: (0.000407) + test_new_n: .: (0.000227) + test_new_r: .: (0.000222) + test_new_t: .: (0.000563) Bio::TestSequenceCommon::TestSequenceCommon: - test_composition: .: (0.000655) - test_concat: .: (0.000319) - test_push: .: (0.000274) - test_seq: .: (0.000291) - test_splicing: .: (0.000928) - test_sum: .: (0.000281) - test_to_s: .: (0.000254) - test_to_str: .: (0.000254) - test_total: .: (0.000298) - test_window_search: .: (0.000812) + test_composition: .: (0.000524) + test_concat: .: (0.000268) + test_push: .: (0.000211) + test_seq: .: (0.000206) + test_splicing: .: (0.000428) + test_sum: .: (0.000200) + test_to_s: .: (0.000213) + test_to_str: .: (0.000215) + test_total: .: (0.000237) + test_window_search: .: (0.000595) Bio::TestSequenceCommon::TestSequenceCommonNormalize: - test_no_normalize: .: (0.000510) - test_normalize_A: .: (0.000286) - test_normalize_a: .: (0.000269) + test_no_normalize: .: (0.000409) + test_normalize_A: .: (0.000537) + test_normalize_a: .: (0.000237) Bio::TestSequenceCommon::TestSequenceCommonRandomize: - test_randomize: .: (0.003397) - test_randomize_with_block: .: (0.011846) - test_randomize_with_hash: .: (0.004467) - test_randomize_with_hash_block: .: (0.028383) + test_randomize: .: (0.002309) + test_randomize_with_block: .: (0.008347) + test_randomize_with_hash: .: (0.002608) + test_randomize_with_hash_block: .: (0.010174) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== -: (0.016584) +: (0.011607) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== -: (0.015313) +: (0.014517) Bio::TestSequenceCommon::TestSequenceCommonSubseq: - test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000876) - test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000428) - test_subseq_returns_subsequence: .: (0.000360) - test_to_s_returns_self_as_string: .: (0.000453) + test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.008673) + test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000368) + test_subseq_returns_subsequence: .: (0.000236) + test_to_s_returns_self_as_string: .: (0.000280) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: - test_window_search_with_width_3_default_step_no_residual: .: (0.000698) - test_window_search_with_width_3_step_two_with_residual: .: (0.000413) + test_window_search_with_width_3_default_step_no_residual: .: (0.000543) + test_window_search_with_width_3_step_two_with_residual: .: (0.011173) Bio::TestSequenceCompat::TestSequenceCommonCompat: - test_to_fasta: .: (0.000978) + test_to_fasta: .: (0.000622) Bio::TestSequenceCompat::TestSequenceCompat: - test_to_s: .: (0.000786) + test_to_s: .: (0.000396) Bio::TestSequenceCompat::TestSequenceNACompat: - test_aa_self_randomize: .: (0.001042) - test_na_self_randomize: .: (0.013491) + test_aa_self_randomize: .: (0.011822) + test_na_self_randomize: .: (0.000411) Bio::TestSequenceDBLink: - test_database: .: (0.000700) - test_id: .: (0.000330) - test_secondary_ids: .: (0.000317) + test_database: .: (0.000443) + test_id: .: (0.000274) + test_secondary_ids: .: (0.000233) Bio::TestSequenceDBLinkClassMethods: - test_parse_embl_DR_line: .: (0.000775) - test_parse_uniprot_DR_line: .: (0.000449) + test_parse_embl_DR_line: .: (0.008018) + test_parse_uniprot_DR_line: .: (0.000409) Bio::TestSequenceFormatFormatterFasta_numeric: - test_output: .: (0.029908) - test_output_width_35: .: (0.022772) - test_output_width_nil: .: (0.001070) + test_output: .: (0.013162) + test_output_width_35: .: (0.010824) + test_output_width_nil: .: (0.000774) Bio::TestSequenceFormatFormatterQual: - test_output: .: (0.001665) - test_output_after_adding_sequence: .: (0.001075) - test_output_after_truncating_sequence: .: (0.001432) - test_output_from_error_probabilities: .: (0.011672) - test_output_width45: .: (0.000863) - test_output_with_converting_score_phred2solexa: .: (0.002588) - test_output_with_converting_score_solexa2phred: .: (0.001243) - test_output_with_default_score: .: (0.000835) + test_output: .: (0.008863) + test_output_after_adding_sequence: .: (0.008251) + test_output_after_truncating_sequence: .: (0.000517) + test_output_from_error_probabilities: .: (0.007797) + test_output_width45: .: (0.000567) + test_output_with_converting_score_phred2solexa: .: (0.001718) + test_output_with_converting_score_solexa2phred: .: (0.000762) + test_output_with_default_score: .: (0.000508) Bio::TestSequenceMasker: - test_mask: .: (0.001256) - test_mask_with_enumerator: .: (0.000630) - test_mask_with_enumerator_empty_mask_char: .: (0.000598) - test_mask_with_enumerator_excess: .: (0.001825) - test_mask_with_enumerator_longer_mask_char: .: (0.000592) - test_mask_with_enumerator_shorter: .: (0.000743) - test_mask_with_error_probability: .: (0.000597) - test_mask_with_quality_score: .: (0.000558) + test_mask: .: (0.000904) + test_mask_with_enumerator: .: (0.000415) + test_mask_with_enumerator_empty_mask_char: .: (0.000358) + test_mask_with_enumerator_excess: .: (0.001139) + test_mask_with_enumerator_longer_mask_char: .: (0.000352) + test_mask_with_enumerator_shorter: .: (0.000500) + test_mask_with_error_probability: .: (0.000340) + test_mask_with_quality_score: .: (0.000326) Bio::TestSequenceNA: - test_at_content: .: (0.001329) - test_at_skew: .: (0.000947) - test_codon_usage: .: (0.000505) - test_complement: .: (0.000432) - test_dna: .: (0.000421) - test_dna!: .: (0.000392) - test_forward_complement: .: (0.000577) - test_gc_content: .: (0.000988) - test_gc_percent: .: (0.001224) - test_gc_skew: .: (0.001258) - test_iliegal_bases: .: (0.000450) - test_molecular_weight: .: (0.000592) - test_names: .: (0.000527) - test_reverse_complement: .: (0.000552) - test_rna: .: (0.000396) - test_rna!: .: (0.000412) - test_splicing: .: (0.000580) - test_to_re: .: (0.000566) - test_to_s: .: (0.000346) + test_at_content: .: (0.000890) + test_at_skew: .: (0.000620) + test_codon_usage: .: (0.000305) + test_complement: .: (0.000307) + test_dna: .: (0.000249) + test_dna!: .: (0.000235) + test_forward_complement: .: (0.000362) + test_gc_content: .: (0.001022) + test_gc_percent: .: (0.000440) + test_gc_skew: .: (0.000768) + test_iliegal_bases: .: (0.000290) + test_molecular_weight: .: (0.000349) + test_names: .: (0.000318) + test_reverse_complement: .: (0.000379) + test_rna: .: (0.000297) + test_rna!: .: (0.000232) + test_splicing: .: (0.000344) + test_to_re: .: (0.000354) + test_to_s: .: (0.000217) Bio::TestSequenceNACommon: - test_composition: .: (0.000929) - test_concat: .: (0.000383) - test_push: .: (0.000362) - test_seq: .: (0.000361) - test_splicing: .: (0.000599) - test_sum: .: (0.000378) - test_to_s: .: (0.000380) - test_to_str: .: (0.000346) - test_total: .: (0.000384) - test_window_search: .: (0.000912) + test_composition: .: (0.000934) + test_concat: .: (0.000246) + test_push: .: (0.000250) + test_seq: .: (0.000272) + test_splicing: .: (0.000341) + test_sum: .: (0.000255) + test_to_s: .: (0.000211) + test_to_str: .: (0.000211) + test_total: .: (0.000238) + test_window_search: .: (0.000632) Bio::TestSequenceNANew: - test_new: .: (0.000675) - test_new_n: .: (0.000367) - test_new_r: .: (0.000357) - test_new_t: .: (0.001720) + test_new: .: (0.000409) + test_new_n: .: (0.000235) + test_new_r: .: (0.000171) + test_new_t: .: (0.000258) Bio::TestSequenceNATranslation: - test_translate: .: (0.001298) - test_translate_0: .: (0.002386) - test_translate_1: .: (0.000816) - test_translate_2: .: (0.000747) - test_translate_3: .: (0.000771) - test_translate_4: .: (0.000883) - test_translate_5: .: (0.000755) - test_translate_6: .: (0.001271) - test_translate_7: .: (0.001680) - test_translate_given_codon_table: .: (0.128100) - test_translate_n1: .: (0.001709) - test_translate_n2: .: (0.001533) - test_translate_n3: .: (0.001454) - test_translate_unknown_o: .: (0.000852) - test_translate_unknown_x: .: (0.000836) + test_translate: .: (0.001128) + test_translate_0: .: (0.001575) + test_translate_1: .: (0.000553) + test_translate_2: .: (0.000466) + test_translate_3: .: (0.000448) + test_translate_4: .: (0.000520) + test_translate_5: .: (0.000516) + test_translate_6: .: (0.000765) + test_translate_7: .: (0.001085) + test_translate_given_codon_table: .: (0.086352) + test_translate_n1: .: (0.001182) + test_translate_n2: .: (0.000916) + test_translate_n3: .: (0.000903) + test_translate_unknown_o: .: (0.000754) + test_translate_unknown_x: .: (0.000574) Bio::TestSequenceQualityScore::TestConverter: - test_convert_nothing: .: (0.000971) - test_convert_scores_from_phred_to_solexa: .: (0.001580) - test_convert_scores_from_solexa_to_phred: .: (0.000702) + test_convert_nothing: .: (0.000478) + test_convert_scores_from_phred_to_solexa: .: (0.000931) + test_convert_scores_from_solexa_to_phred: .: (0.000730) Bio::TestSequenceQualityScore::TestPhred: - test_convert_nothing: .: (0.000646) - test_convert_scores_from_phred: .: (0.000997) - test_convert_scores_from_phred_to_solexa: .: (0.001433) - test_convert_scores_from_solexa: .: (0.000707) - test_convert_scores_from_solexa_to_phred: .: (0.000995) - test_convert_scores_to_phred: .: (0.000359) - test_convert_scores_to_solexa: .: (0.001413) - test_p2q: .: (0.000855) - test_phred_p2q: .: (0.001114) - test_phred_q2p: .: (0.015796) - test_q2p: .: (0.016422) - test_quality_score_type: .: (0.000387) - test_self_convert_scores_to_solexa: .: (0.001487) - test_self_p2q: .: (0.000629) - test_self_q2p: .: (0.016712) + test_convert_nothing: .: (0.000406) + test_convert_scores_from_phred: .: (0.000231) + test_convert_scores_from_phred_to_solexa: .: (0.000895) + test_convert_scores_from_solexa: .: (0.000655) + test_convert_scores_from_solexa_to_phred: .: (0.000401) + test_convert_scores_to_phred: .: (0.000206) + test_convert_scores_to_solexa: .: (0.001307) + test_p2q: .: (0.000553) + test_phred_p2q: .: (0.000351) + test_phred_q2p: .: (0.010410) + test_q2p: .: (0.010412) + test_quality_score_type: .: (0.000527) + test_self_convert_scores_to_solexa: .: (0.001000) + test_self_p2q: .: (0.000388) + test_self_q2p: .: (0.011244) Bio::TestSequenceQualityScore::TestSolexa: - test_convert_nothing: .: (0.000697) - test_convert_scores_from_phred: .: (0.002638) - test_convert_scores_from_phred_to_solexa: .: (0.001441) - test_convert_scores_from_solexa: .: (0.000428) - test_convert_scores_from_solexa_to_phred: .: (0.000888) - test_convert_scores_to_phred: .: (0.004895) - test_convert_scores_to_solexa: .: (0.000401) - test_p2q: .: (0.000940) - test_q2p: .: (0.017793) - test_quality_score_type: .: (0.000422) - test_self_convert_scores_to_phred: .: (0.000792) - test_self_p2q: .: (0.001105) - test_self_q2p: .: (0.017002) - test_solexa_p2q: .: (0.000835) - test_solexa_q2p: .: (0.016204) + test_convert_nothing: .: (0.000546) + test_convert_scores_from_phred: .: (0.001487) + test_convert_scores_from_phred_to_solexa: .: (0.000958) + test_convert_scores_from_solexa: .: (0.000220) + test_convert_scores_from_solexa_to_phred: .: (0.000468) + test_convert_scores_to_phred: .: (0.000415) + test_convert_scores_to_solexa: .: (0.000179) + test_p2q: .: (0.001075) + test_q2p: .: (0.015167) + test_quality_score_type: .: (0.000279) + test_self_convert_scores_to_phred: .: (0.000747) + test_self_p2q: .: (0.000627) + test_self_q2p: .: (0.013507) + test_solexa_p2q: .: (0.000555) + test_solexa_q2p: .: (0.010930) Bio::TestSequenceRuby3::TestSequenceCommon: - test_capitalize: .: (0.000808) - test_center: .: (0.000440) - test_chomp: .: (0.000523) - test_chop: .: (0.000531) - test_delete: .: (0.000419) - test_delete_prefix: .: (0.000560) - test_delete_suffix: .: (0.001255) - test_downcase: .: (0.000425) - test_each_char: .: (0.000634) - test_each_char_enum: .: (0.000550) - test_each_grapheme_cluster: .: (0.001103) - test_each_grapheme_cluster_enum: .: (0.000578) - test_each_line: .: (0.000632) - test_each_line_enum: .: (0.000512) - test_gsub: .: (0.000478) - test_gsub_with_block: .: (0.001430) - test_ljust: .: (0.000438) - test_lstrip: .: (0.000419) - test_multiply: .: (0.000412) - test_next: .: (0.000417) - test_reverse: .: (0.000436) - test_rjust: .: (0.000404) - test_rstrip: .: (0.000406) - test_slice: .: (0.000403) - test_slice2: .: (0.000391) - test_split: .: (0.000514) - test_squeeze: .: (0.000428) - test_strip: .: (0.000404) - test_sub: .: (0.000664) - test_sub_with_block: .: (0.000799) - test_succ: .: (0.000399) - test_swapcase: .: (0.000399) - test_tr: .: (0.000404) - test_tr_s: .: (0.000465) - test_upcase: .: (0.000407) + test_capitalize: .: (0.000552) + test_center: .: (0.000345) + test_chomp: .: (0.000305) + test_chop: .: (0.000295) + test_delete: .: (0.000275) + test_delete_prefix: .: (0.000259) + test_delete_suffix: .: (0.000288) + test_downcase: .: (0.000417) + test_each_char: .: (0.000427) + test_each_char_enum: .: (0.000389) + test_each_grapheme_cluster: .: (0.000960) + test_each_grapheme_cluster_enum: .: (0.000377) + test_each_line: .: (0.000400) + test_each_line_enum: .: (0.000324) + test_gsub: .: (0.000307) + test_gsub_with_block: .: (0.001070) + test_ljust: .: (0.000349) + test_lstrip: .: (0.000253) + test_multiply: .: (0.000262) + test_next: .: (0.000253) + test_reverse: .: (0.000261) + test_rjust: .: (0.000260) + test_rstrip: .: (0.000255) + test_slice: .: (0.000253) + test_slice2: .: (0.000249) + test_split: .: (0.000322) + test_squeeze: .: (0.000258) + test_strip: .: (0.000296) + test_sub: .: (0.000335) + test_sub_with_block: .: (0.000535) + test_succ: .: (0.000289) + test_swapcase: .: (0.000258) + test_tr: .: (0.000304) + test_tr_s: .: (0.000251) + test_upcase: .: (0.000256) Bio::TestSequenceRuby3::TestSequenceCommonPartition: - test_partition: .: (0.000835) - test_partition_nomatch: .: (0.000538) - test_partition_sep_TSeq: .: (0.000501) - test_partition_sep_regexp: .: (0.000698) + test_partition: .: (0.000609) + test_partition_nomatch: .: (0.000330) + test_partition_sep_TSeq: .: (0.000312) + test_partition_sep_regexp: .: (0.000351) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: - test_rpartition: .: (0.000803) - test_rpartition_nomatch: .: (0.000527) - test_rpartition_sep_TSeq: .: (0.000505) - test_rpartition_sep_regexp: .: (0.000596) + test_rpartition: .: (0.000534) + test_rpartition_nomatch: .: (0.000333) + test_rpartition_sep_TSeq: .: (0.000479) + test_rpartition_sep_regexp: .: (0.000343) Bio::TestShRNA: - test_blocK_it: .: (0.072562) - test_blocK_it_: .: (0.077596) - test_blocK_it_BLOCK_IT: .: (0.073956) - test_blocK_it_BLOCK_iT: .: (0.073308) - test_blocK_it_piGene: .: (0.075142) - test_bottom_strand: .: (0.072758) - test_bottom_strand_class: .: (0.073554) - test_bottom_strand_nil: .: (0.074946) - test_design: .: (0.074567) - test_design_BLOCK_IT: .: (0.074191) - test_report: .: (0.074982) - test_report_before_design: .: (0.073512) - test_top_strand: .: (0.073520) - test_top_strand_class: .: (0.074746) - test_top_strand_nil: .: (0.072944) + test_blocK_it: .: (0.051693) + test_blocK_it_: .: (0.056007) + test_blocK_it_BLOCK_IT: .: (0.054416) + test_blocK_it_BLOCK_iT: .: (0.050399) + test_blocK_it_piGene: .: (0.052772) + test_bottom_strand: .: (0.050199) + test_bottom_strand_class: .: (0.050625) + test_bottom_strand_nil: .: (0.052494) + test_design: .: (0.050858) + test_design_BLOCK_IT: .: (0.053806) + test_report: .: (0.051064) + test_report_before_design: .: (0.051648) + test_top_strand: .: (0.052346) + test_top_strand_class: .: (0.050776) + test_top_strand_nil: .: (0.053409) Bio::TestShRNANew: - test_new: .: (0.001230) + test_new: .: (0.000850) Bio::TestSiRNA: - test_antisense_size: .: (0.000648) - test_design: .: (0.073518) - test_design_reynolds: .: (0.093390) - test_design_uitei: .: (0.073249) - test_max_gc_percent: .: (0.000397) - test_min_gc_percent: .: (0.000376) - test_reynolds: .: (0.090079) - test_reynolds?: .: (0.000412) - test_uitei: .: (0.075432) - test_uitei?: .: (0.000473) + test_antisense_size: .: (0.000461) + test_design: .: (0.051783) + test_design_reynolds: .: (0.063537) + test_design_uitei: .: (0.051640) + test_max_gc_percent: .: (0.000232) + test_min_gc_percent: .: (0.000258) + test_reynolds: .: (0.061392) + test_reynolds?: .: (0.000413) + test_uitei: .: (0.052098) + test_uitei?: .: (0.000320) Bio::TestSiRNANew: - test_new: .: (0.001149) + test_new: .: (0.000773) Bio::TestSiRNAPair: - test_antisense: .: (0.073294) - test_gc_percent: .: (0.072601) - test_report: .: (0.075184) - test_rule: .: (0.073129) - test_sense: .: (0.072179) - test_start: .: (0.074319) - test_stop: .: (0.073254) - test_target: .: (0.072033) + test_antisense: .: (0.053642) + test_gc_percent: .: (0.051010) + test_report: .: (0.053803) + test_rule: .: (0.050768) + test_sense: .: (0.051138) + test_start: .: (0.053362) + test_stop: .: (0.052522) + test_target: .: (0.049893) Bio::TestSiRNAPairNew: - test_new: .: (0.001215) + test_new: .: (0.000954) Bio::TestSim4Report: - test_all_hits: .: (0.001285) - test_each: .: (0.000692) - test_each_hit: .: (0.000645) - test_hits: .: (0.000688) - test_num_hits: .: (0.000575) - test_query_def: .: (0.000580) - test_query_id: .: (0.000597) - test_query_len: .: (0.000618) - test_seq1: .: (0.001228) + test_all_hits: .: (0.000855) + test_each: .: (0.000572) + test_each_hit: .: (0.000449) + test_hits: .: (0.000933) + test_num_hits: .: (0.000386) + test_query_def: .: (0.000407) + test_query_id: .: (0.000390) + test_query_len: .: (0.000380) + test_seq1: .: (0.000564) Bio::TestSim4Report2: - test_all_hits: .: (0.001121) - test_each: .: (0.000694) - test_each_hit: .: (0.000637) - test_hits: .: (0.000656) - test_num_hits: .: (0.000560) - test_query_def: .: (0.000567) - test_query_id: .: (0.000608) - test_query_len: .: (0.000564) - test_seq1: .: (0.000699) + test_all_hits: .: (0.000757) + test_each: .: (0.000445) + test_each_hit: .: (0.000432) + test_hits: .: (0.000889) + test_num_hits: .: (0.000412) + test_query_def: .: (0.000380) + test_query_id: .: (0.000356) + test_query_len: .: (0.000408) + test_seq1: .: (0.000490) Bio::TestSim4Report4: - test_all_hits: .: (0.001658) - test_each: .: (0.000684) - test_each_hit: .: (0.000661) - test_hits: .: (0.000701) - test_num_hits: .: (0.000625) - test_query_def: .: (0.000590) - test_query_id: .: (0.000585) - test_query_len: .: (0.000582) - test_seq1: .: (0.000766) + test_all_hits: .: (0.000733) + test_each: .: (0.000472) + test_each_hit: .: (0.000499) + test_hits: .: (0.000778) + test_num_hits: .: (0.000503) + test_query_def: .: (0.000399) + test_query_id: .: (0.000379) + test_query_len: .: (0.000402) + test_seq1: .: (0.000556) Bio::TestSim4ReportHit: - test_align: .: (0.001061) - test_complement?: .: (0.000652) - test_definition: .: (0.000553) - test_each: .: (0.001047) - test_exons: .: (0.000898) - test_hit_id: .: (0.000517) - test_hsps: .: (0.000889) - test_introns: .: (0.001530) - test_len: .: (0.000807) - test_query_def: .: (0.000522) - test_query_id: .: (0.000539) - test_query_len: .: (0.000544) - test_segmentpairs: .: (0.000931) - test_seq1: .: (0.000664) - test_seq2: .: (0.000657) - test_target_def: .: (0.000523) - test_target_id: .: (0.000567) - test_target_len: .: (0.000512) + test_align: .: (0.000782) + test_complement?: .: (0.000415) + test_definition: .: (0.000381) + test_each: .: (0.001351) + test_exons: .: (0.001018) + test_hit_id: .: (0.000483) + test_hsps: .: (0.000717) + test_introns: .: (0.000641) + test_len: .: (0.000513) + test_query_def: .: (0.000429) + test_query_id: .: (0.000427) + test_query_len: .: (0.000409) + test_segmentpairs: .: (0.001192) + test_seq1: .: (0.000686) + test_seq2: .: (0.000522) + test_target_def: .: (0.000446) + test_target_id: .: (0.000370) + test_target_len: .: (0.000472) Bio::TestSim4ReportHit2: - test_align: .: (0.001796) - test_complement?: .: (0.000527) - test_definition: .: (0.000518) - test_each: .: (0.000878) - test_exons: .: (0.000887) - test_hit_id: .: (0.000542) - test_hsps: .: (0.000951) - test_introns: .: (0.000836) - test_len: .: (0.000665) - test_query_def: .: (0.000576) - test_query_id: .: (0.000524) - test_query_len: .: (0.000554) - test_segmentpairs: .: (0.001128) - test_seq1: .: (0.000675) - test_seq2: .: (0.000663) - test_target_def: .: (0.000551) - test_target_id: .: (0.000574) - test_target_len: .: (0.000514) + test_align: .: (0.000888) + test_complement?: .: (0.000438) + test_definition: .: (0.000906) + test_each: .: (0.000899) + test_exons: .: (0.000739) + test_hit_id: .: (0.000415) + test_hsps: .: (0.000691) + test_introns: .: (0.000711) + test_len: .: (0.000457) + test_query_def: .: (0.000418) + test_query_id: .: (0.000750) + test_query_len: .: (0.000509) + test_segmentpairs: .: (0.000696) + test_seq1: .: (0.000549) + test_seq2: .: (0.000498) + test_target_def: .: (0.000386) + test_target_id: .: (0.000397) + test_target_len: .: (0.000382) Bio::TestSim4ReportHit4: - test_align: .: (0.001205) - test_complement?: .: (0.000674) - test_definition: .: (0.000552) - test_each: .: (0.001179) - test_exons: .: (0.001203) - test_hit_id: .: (0.000626) - test_hsps: .: (0.001618) - test_introns: .: (0.001243) - test_len: .: (0.000595) - test_query_def: .: (0.000546) - test_query_id: .: (0.000538) - test_query_len: .: (0.000529) - test_segmentpairs: .: (0.001739) - test_seq1: .: (0.000798) - test_seq2: .: (0.000699) - test_target_def: .: (0.000539) - test_target_id: .: (0.000558) - test_target_len: .: (0.000573) + test_align: .: (0.003823) + test_complement?: .: (0.000590) + test_definition: .: (0.000415) + test_each: .: (0.000952) + test_exons: .: (0.000904) + test_hit_id: .: (0.000430) + test_hsps: .: (0.001330) + test_introns: .: (0.001024) + test_len: .: (0.000552) + test_query_def: .: (0.000443) + test_query_id: .: (0.000381) + test_query_len: .: (0.000411) + test_segmentpairs: .: (0.000919) + test_seq1: .: (0.001032) + test_seq2: .: (0.000544) + test_target_def: .: (0.000412) + test_target_id: .: (0.000407) + test_target_len: .: (0.000407) Bio::TestSim4ReportSegment: - test_from: .: (0.000561) - test_self_new: .: (0.000378) - test_seq: .: (0.000288) - test_to: .: (0.000272) + test_from: .: (0.000513) + test_self_new: .: (0.000299) + test_seq: .: (0.000222) + test_to: .: (0.000209) Bio::TestSim4ReportSegmentPair2_exon: - test_align_len: .: (0.001974) - test_direction: .: (0.000779) - test_hit_from: .: (0.000747) - test_hit_to: .: (0.000754) - test_hseq: .: (0.000757) - test_midline: .: (0.000751) - test_percent_identity: .: (0.000739) - test_qseq: .: (0.001008) - test_query_from: .: (0.000804) - test_query_to: .: (0.000760) - test_seq1: .: (0.000917) - test_seq2: .: (0.000935) + test_align_len: .: (0.001287) + test_direction: .: (0.000791) + test_hit_from: .: (0.000634) + test_hit_to: .: (0.000566) + test_hseq: .: (0.000587) + test_midline: .: (0.000549) + test_percent_identity: .: (0.000546) + test_qseq: .: (0.001140) + test_query_from: .: (0.000808) + test_query_to: .: (0.000612) + test_seq1: .: (0.000647) + test_seq2: .: (0.000623) Bio::TestSim4ReportSegmentPair2_intron: - test_align_len: .: (0.001659) - test_direction: .: (0.000780) - test_hit_from: .: (0.000793) - test_hit_to: .: (0.000754) - test_hseq: .: (0.000752) - test_midline: .: (0.000782) - test_percent_identity: .: (0.000804) - test_qseq: .: (0.001349) - test_query_from: .: (0.000753) - test_query_to: .: (0.000748) - test_seq1: .: (0.000894) - test_seq2: .: (0.000850) + test_align_len: .: (0.001364) + test_direction: .: (0.000645) + test_hit_from: .: (0.000558) + test_hit_to: .: (0.000539) + test_hseq: .: (0.000557) + test_midline: .: (0.000639) + test_percent_identity: .: (0.000566) + test_qseq: .: (0.000961) + test_query_from: .: (0.000646) + test_query_to: .: (0.000562) + test_seq1: .: (0.000735) + test_seq2: .: (0.000639) Bio::TestSim4ReportSegmentPair4_exon: - test_align_len: .: (0.001923) - test_direction: .: (0.000959) - test_hit_from: .: (0.000936) - test_hit_to: .: (0.000955) - test_hseq: .: (0.000973) - test_midline: .: (0.001389) - test_percent_identity: .: (0.001080) - test_qseq: .: (0.000991) - test_query_from: .: (0.000925) - test_query_to: .: (0.000919) - test_seq1: .: (0.001669) - test_seq2: .: (0.001054) + test_align_len: .: (0.001451) + test_direction: .: (0.000725) + test_hit_from: .: (0.000758) + test_hit_to: .: (0.000728) + test_hseq: .: (0.000689) + test_midline: .: (0.001086) + test_percent_identity: .: (0.000884) + test_qseq: .: (0.000705) + test_query_from: .: (0.000697) + test_query_to: .: (0.000676) + test_seq1: .: (0.001181) + test_seq2: .: (0.000901) Bio::TestSim4ReportSegmentPair4_intron: - test_align_len: .: (0.001240) - test_direction: .: (0.000973) - test_hit_from: .: (0.001556) - test_hit_to: .: (0.001199) - test_hseq: .: (0.000933) - test_midline: .: (0.000951) - test_percent_identity: .: (0.000982) - test_qseq: .: (0.001537) - test_query_from: .: (0.001047) - test_query_to: .: (0.000964) - test_seq1: .: (0.001074) - test_seq2: .: (0.001037) + test_align_len: .: (0.000924) + test_direction: .: (0.000617) + test_hit_from: .: (0.001149) + test_hit_to: .: (0.000877) + test_hseq: .: (0.000645) + test_midline: .: (0.000605) + test_percent_identity: .: (0.000655) + test_qseq: .: (0.001019) + test_query_from: .: (0.000782) + test_query_to: .: (0.000634) + test_seq1: .: (0.000691) + test_seq2: .: (0.001079) Bio::TestSim4ReportSegmentPair4_intron1: - test_align_len: .: (0.001850) - test_direction: .: (0.000945) - test_hit_from: .: (0.000923) - test_hit_to: .: (0.000942) - test_hseq: .: (0.000964) - test_midline: .: (0.000921) - test_percent_identity: .: (0.001434) - test_qseq: .: (0.001089) - test_query_from: .: (0.000932) - test_query_to: .: (0.000916) - test_seq1: .: (0.001065) - test_seq2: .: (0.001572) + test_align_len: .: (0.000931) + test_direction: .: (0.000626) + test_hit_from: .: (0.000634) + test_hit_to: .: (0.000609) + test_hseq: .: (0.000976) + test_midline: .: (0.000837) + test_percent_identity: .: (0.000661) + test_qseq: .: (0.000666) + test_query_from: .: (0.001035) + test_query_to: .: (0.000820) + test_seq1: .: (0.000861) + test_seq2: .: (0.000758) Bio::TestSim4ReportSegmentPair_exon: - test_align_len: .: (0.001054) - test_direction: .: (0.000824) - test_hit_from: .: (0.000742) - test_hit_to: .: (0.000726) - test_hseq: .: (0.001349) - test_midline: .: (0.000926) - test_percent_identity: .: (0.000739) - test_qseq: .: (0.000748) - test_query_from: .: (0.000780) - test_query_to: .: (0.000784) - test_seq1: .: (0.000851) - test_seq2: .: (0.001431) + test_align_len: .: (0.000772) + test_direction: .: (0.000658) + test_hit_from: .: (0.000501) + test_hit_to: .: (0.000469) + test_hseq: .: (0.000466) + test_midline: .: (0.000457) + test_percent_identity: .: (0.000509) + test_qseq: .: (0.000470) + test_query_from: .: (0.000936) + test_query_to: .: (0.000694) + test_seq1: .: (0.000580) + test_seq2: .: (0.000538) Bio::TestSim4ReportSegmentPair_intron: - test_align_len: .: (0.001066) - test_direction: .: (0.000746) - test_hit_from: .: (0.000743) - test_hit_to: .: (0.000764) - test_hseq: .: (0.000809) - test_midline: .: (0.001288) - test_percent_identity: .: (0.000936) - test_qseq: .: (0.000775) - test_query_from: .: (0.000737) - test_query_to: .: (0.000745) - test_seq1: .: (0.000862) - test_seq2: .: (0.000839) + test_align_len: .: (0.000750) + test_direction: .: (0.000565) + test_hit_from: .: (0.000958) + test_hit_to: .: (0.000715) + test_hseq: .: (0.000516) + test_midline: .: (0.000469) + test_percent_identity: .: (0.000454) + test_qseq: .: (0.000470) + test_query_from: .: (0.000457) + test_query_to: .: (0.001003) + test_seq1: .: (0.000861) + test_seq2: .: (0.000559) Bio::TestSim4ReportSeqDesc: - test_definition: .: (0.001114) - test_entry_id: .: (0.000349) - test_filename: .: (0.000336) - test_len: .: (0.000347) - test_self_new: .: (0.000368) - test_self_parse: .: (0.000490) + test_definition: .: (0.000430) + test_entry_id: .: (0.000182) + test_filename: .: (0.000182) + test_len: .: (0.000183) + test_self_new: .: (0.000206) + test_self_parse: .: (0.000256) Bio::TestTMHMMReport: - test_entry_id: .: (0.001216) - test_exp_aas_in_tmhs: .: (0.000922) - test_exp_first_60aa: .: (0.001559) - test_helix: .: (0.000989) - test_predicted_tmhs: .: (0.000909) - test_query_len: .: (0.000921) - test_tmhs: .: (0.000926) - test_to_s: .: (0.002116) - test_total_prob_of_N_in: .: (0.000924) + test_entry_id: .: (0.001299) + test_exp_aas_in_tmhs: .: (0.000596) + test_exp_first_60aa: .: (0.000534) + test_helix: .: (0.000623) + test_predicted_tmhs: .: (0.001046) + test_query_len: .: (0.000547) + test_tmhs: .: (0.000592) + test_to_s: .: (0.000840) + test_total_prob_of_N_in: .: (0.001146) Bio::TestTMHMMReport_reports: - test_reports: .: (0.000607) + test_reports: .: (0.000482) Bio::TestTMHMMTMH: - test_entry_id: .: (0.001161) - test_pos: .: (0.000937) - test_range: .: (0.001469) - test_status: .: (0.000926) - test_version: .: (0.000932) + test_entry_id: .: (0.000841) + test_pos: .: (0.000621) + test_range: .: (0.000567) + test_status: .: (0.000606) + test_version: .: (0.001204) Bio::TestTargetPReport: - test_cleavage_site_prediction: .: (0.000953) - test_cutoff: .: (0.000646) - test_entry_id: .: (0.001381) - test_length: .: (0.000636) - test_loc: .: (0.000634) - test_name: .: (0.000628) - test_networks: .: (0.000654) - test_prediction: .: (0.000723) - test_query_len: .: (0.000639) - test_query_sequences: .: (0.000626) - test_rc: .: (0.000622) - test_version: .: (0.000642) + test_cleavage_site_prediction: .: (0.000656) + test_cutoff: .: (0.000400) + test_entry_id: .: (0.000389) + test_length: .: (0.000407) + test_loc: .: (0.000437) + test_name: .: (0.000389) + test_networks: .: (0.000381) + test_prediction: .: (0.000932) + test_query_len: .: (0.000393) + test_query_sequences: .: (0.000367) + test_rc: .: (0.000398) + test_version: .: (0.000366) Bio::TestTargetPReportConst: - test_delimiter: .: (0.000547) - test_rs: .: (0.000289) + test_delimiter: .: (0.000403) + test_rs: .: (0.000164) Bio::TestTogoWSAccessWait: - test_reset_togows_access_wait: .: (0.000703) - test_togows_access_wait: .: (2.005856) + test_reset_togows_access_wait: .: (0.000413) + test_togows_access_wait: .: (2.004612) Bio::TestTogoWSREST: - test_debug: .: (0.001314) - test_debug_default: .: (0.000535) - test_internal_http: .: (0.000642) + test_debug: .: (0.001040) + test_debug_default: .: (0.000811) + test_internal_http: .: (0.000422) Bio::TestTogoWSRESTclassMethod: - test_convert: .: (0.000572) - test_entry: .: (0.000302) - test_entry_database_list: .: (0.000300) - test_new: .: (0.000589) - test_new_with_uri_object: .: (0.000666) - test_new_with_uri_string: .: (0.001129) - test_retrieve: .: (0.000312) - test_search: .: (0.000307) - test_search_database_list: .: (0.000294) + test_convert: .: (0.000405) + test_entry: .: (0.000174) + test_entry_database_list: .: (0.000165) + test_new: .: (0.000394) + test_new_with_uri_object: .: (0.000413) + test_new_with_uri_string: .: (0.000444) + test_retrieve: .: (0.000167) + test_search: .: (0.000164) + test_search_database_list: .: (0.000161) Bio::TestTogoWSRESTprivate: - test_make_path: .: (0.001028) - test_prepare_return_value: .: (0.000644) + test_make_path: .: (0.000634) + test_prepare_return_value: .: (0.000797) Bio::TestTopologicalSort: - test_dfs_topological_sort: .: (0.001134) + test_dfs_topological_sort: .: (0.001672) Bio::TestTree: - test_get_edge_distance: .: (0.000713) - test_get_edge_distance_string: .: (0.000468) - test_get_node_name: .: (0.000883) - test_initialize: .: (0.000375) - test_options: .: (0.000348) - test_root: .: (0.000313) - test_root=: .: (0.000342) + test_get_edge_distance: .: (0.000520) + test_get_edge_distance_string: .: (0.000274) + test_get_node_name: .: (0.000200) + test_initialize: .: (0.000207) + test_options: .: (0.000187) + test_root: .: (0.000156) + test_root=: .: (0.000186) Bio::TestTree2: - test_add_edge: .: (0.000933) - test_add_node: .: (0.000668) - test_adjacency_matrix: .: (0.000666) - test_adjacency_matrix_with_block: .: (0.000679) - test_adjacent_nodes: .: (0.000741) - test_adjacent_nodes_nonexistent: .: (0.000487) - test_ancestors: .: (0.000584) - test_children: .: (0.001104) - test_clear: .: (0.000606) - test_clear_node: .: (0.000664) - test_clear_node_nonexistent: .: (0.000763) - test_collect_edge!: .: (0.000833) - test_collect_node!: .: (0.000862) - test_concat: .: (0.000815) - test_descendents: .: (0.000595) - test_distance_matrix: .: (0.002048) - test_each_edge: .: (0.000692) - test_each_node: .: (0.000645) - test_each_out_edge: .: (0.000595) - test_each_out_edge_chimpanzee: .: (0.000609) - test_each_out_edge_human: .: (0.000589) - test_each_out_edge_mammals: .: (0.000675) - test_each_out_edge_nonexistent: .: (0.000513) - test_each_out_edge_primates: .: (0.000905) - test_each_out_edge_rat: .: (0.001192) - test_each_out_edge_rodents: .: (0.000748) - test_edges: .: (0.000535) - test_get_edge: .: (0.001121) - test_get_edge_indirect: .: (0.000498) - test_get_edge_merged: .: (0.000574) - test_get_edge_nonexistent: .: (0.000465) - test_get_node_bootstrap: .: (0.000485) - test_get_node_bootstrap_string=: .: (0.000486) - test_get_node_by_name: .: (0.000726) - test_get_node_by_name_noexistent: .: (0.000512) - test_include?: .: (0.000646) - test_include_nonexistent: .: (0.000482) - test_insert_node: .: (0.001019) - test_leaves: .: (0.000624) - test_leaves_noargs: .: (0.000549) - test_lowest_common_ancestor: .: (0.000559) - test_nodes: .: (0.000492) - test_number_of_edges: .: (0.000464) - test_number_of_nodes: .: (0.000500) - test_out_degree: .: (0.001185) - test_out_degree_nonexistent: .: (0.000488) - test_out_edges: .: (0.000600) - test_out_edges_mammals: .: (0.000681) - test_out_edges_nonexistent: .: (0.000512) - test_out_edges_primates: .: (0.000798) - test_out_edges_rodents: .: (0.000756) - test_parent: .: (0.000577) - test_path: .: (0.000560) - test_remove_edge: .: (0.000585) - test_remove_edge_if: .: (0.001123) - test_remove_edge_if_nothing_removed: .: (0.000636) - test_remove_edge_nonexistent: .: (0.000826) - test_remove_node: .: (0.000687) - test_remove_node_if: .: (0.000584) - test_remove_node_if_false: .: (0.000586) - test_remove_node_nonexistent: .: (0.000560) - test_remove_nonsense_nodes: .: (0.000582) - test_subtree: .: (0.000732) - test_subtree_with_all_paths: .: (0.001046) - test_total_distance: .: (0.001060) + test_add_edge: .: (0.001213) + test_add_node: .: (0.000899) + test_adjacency_matrix: .: (0.000424) + test_adjacency_matrix_with_block: .: (0.000400) + test_adjacent_nodes: .: (0.000442) + test_adjacent_nodes_nonexistent: .: (0.000270) + test_ancestors: .: (0.000360) + test_children: .: (0.000292) + test_clear: .: (0.000371) + test_clear_node: .: (0.000413) + test_clear_node_nonexistent: .: (0.000436) + test_collect_edge!: .: (0.001139) + test_collect_node!: .: (0.000769) + test_concat: .: (0.000850) + test_descendents: .: (0.000463) + test_distance_matrix: .: (0.001033) + test_each_edge: .: (0.000458) + test_each_node: .: (0.000519) + test_each_out_edge: .: (0.000786) + test_each_out_edge_chimpanzee: .: (0.000398) + test_each_out_edge_human: .: (0.000346) + test_each_out_edge_mammals: .: (0.000449) + test_each_out_edge_nonexistent: .: (0.000339) + test_each_out_edge_primates: .: (0.000638) + test_each_out_edge_rat: .: (0.000435) + test_each_out_edge_rodents: .: (0.000476) + test_edges: .: (0.000424) + test_get_edge: .: (0.001265) + test_get_edge_indirect: .: (0.000345) + test_get_edge_merged: .: (0.000333) + test_get_edge_nonexistent: .: (0.000270) + test_get_node_bootstrap: .: (0.000372) + test_get_node_bootstrap_string=: .: (0.000333) + test_get_node_by_name: .: (0.000477) + test_get_node_by_name_noexistent: .: (0.000337) + test_include?: .: (0.000402) + test_include_nonexistent: .: (0.000292) + test_insert_node: .: (0.001099) + test_leaves: .: (0.000505) + test_leaves_noargs: .: (0.000296) + test_lowest_common_ancestor: .: (0.000326) + test_nodes: .: (0.000327) + test_number_of_edges: .: (0.000263) + test_number_of_nodes: .: (0.000262) + test_out_degree: .: (0.000387) + test_out_degree_nonexistent: .: (0.000273) + test_out_edges: .: (0.000352) + test_out_edges_mammals: .: (0.000886) + test_out_edges_nonexistent: .: (0.000286) + test_out_edges_primates: .: (0.000443) + test_out_edges_rodents: .: (0.000455) + test_parent: .: (0.000350) + test_path: .: (0.000322) + test_remove_edge: .: (0.000329) + test_remove_edge_if: .: (0.000361) + test_remove_edge_if_nothing_removed: .: (0.000373) + test_remove_edge_nonexistent: .: (0.000547) + test_remove_node: .: (0.000417) + test_remove_node_if: .: (0.000725) + test_remove_node_if_false: .: (0.000343) + test_remove_node_nonexistent: .: (0.000438) + test_remove_nonsense_nodes: .: (0.000368) + test_subtree: .: (0.000429) + test_subtree_with_all_paths: .: (0.000684) + test_total_distance: .: (0.000299) Bio::TestTreeEdge: - test_distance: .: (0.000573) - test_distance=: .: (0.000425) - test_distance_string: .: (0.000322) - test_distance_string=: .: (0.000412) - test_initialize: .: (0.000379) - test_inspect: .: (0.000295) - test_to_s: .: (0.000283) + test_distance: .: (0.000431) + test_distance=: .: (0.000246) + test_distance_string: .: (0.000165) + test_distance_string=: .: (0.000233) + test_initialize: .: (0.000535) + test_inspect: .: (0.000192) + test_to_s: .: (0.000160) Bio::TestTreeNode: - test_bootstrap: .: (0.000518) - test_bootstrap=: .: (0.000386) - test_bootstrap_string: .: (0.000260) - test_bootstrap_string=: .: (0.000444) - test_initialize: .: (0.000342) - test_inspect: .: (0.000352) - test_name: .: (0.000949) - test_to_s: .: (0.000322) + test_bootstrap: .: (0.000406) + test_bootstrap=: .: (0.000231) + test_bootstrap_string: .: (0.000145) + test_bootstrap_string=: .: (0.000282) + test_initialize: .: (0.000237) + test_inspect: .: (0.000206) + test_name: .: (0.000169) + test_to_s: .: (0.000150) Bio::TestUniProt: - test_gene_name: .: (0.012981) + test_gene_name: .: (0.010167) Bio::TestUniProtKB: - test_ac: .: (0.013413) - test_accession: .: (0.012196) - test_cc: .: (0.026587) - test_cc_alternative_products: .: (0.017328) - test_cc_database: .: (0.017064) - test_cc_mass_spectrometry: .: (0.016939) - test_de: .: (0.013282) - test_dr: .: (0.018321) - test_dr_with_key: .: (0.017547) - test_dr_with_key_empty: .: (0.017314) - test_dt: .: (0.012901) - test_dt_annotation: .: (0.012828) - test_dt_created: .: (0.063521) - test_dt_sequence: .: (0.083465) - test_entry: .: (0.013358) - test_ft: .: (0.033168) - test_gene_name: .: (0.013079) - test_gene_names: .: (0.011981) - test_gn: .: (0.012968) - test_gn_old_parser: .: (0.012692) - test_gn_uniprot_parser: .: (0.013047) - test_id_line: .: (0.012367) - test_id_line_data_class: .: (0.012336) - test_id_line_entry_name: .: (0.013146) - test_id_line_molecule_type: .: (0.012125) - test_id_line_sequence_length: .: (0.012008) - test_kw: .: (0.015702) - test_molecule: .: (0.012817) - test_oc: .: (0.012566) - test_og_1: .: (0.012452) - test_og_2: .: (0.012108) - test_og_3: .: (0.012698) - test_og_4: .: (0.012073) - test_og_5: .: (0.012678) - test_og_6: .: (0.012138) - test_os: .: (0.012406) - test_os_access: .: (0.012720) - test_os_access2: .: (0.012681) - test_ox: .: (0.012414) - test_protein_name: .: (0.014219) - test_ref: .: (0.030767) - test_seq: .: (0.012267) - test_sequence_length: .: (0.012784) - test_sq: .: (0.012495) - test_sq_crc64: .: (0.012963) - test_sq_len: .: (0.012456) - test_sq_mw: .: (0.012478) - test_synonyms: .: (0.013164) + test_ac: .: (0.009537) + test_accession: .: (0.009145) + test_cc: .: (0.012800) + test_cc_alternative_products: .: (0.020294) + test_cc_database: .: (0.012753) + test_cc_mass_spectrometry: .: (0.012945) + test_de: .: (0.010130) + test_dr: .: (0.014522) + test_dr_with_key: .: (0.012769) + test_dr_with_key_empty: .: (0.013316) + test_dt: .: (0.009262) + test_dt_annotation: .: (0.010062) + test_dt_created: .: (0.042342) + test_dt_sequence: .: (0.056651) + test_entry: .: (0.029338) + test_ft: .: (0.023864) + test_gene_name: .: (0.009384) + test_gene_names: .: (0.010479) + test_gn: .: (0.009036) + test_gn_old_parser: .: (0.010300) + test_gn_uniprot_parser: .: (0.008929) + test_id_line: .: (0.009797) + test_id_line_data_class: .: (0.009071) + test_id_line_entry_name: .: (0.009897) + test_id_line_molecule_type: .: (0.009240) + test_id_line_sequence_length: .: (0.008937) + test_kw: .: (0.011184) + test_molecule: .: (0.008994) + test_oc: .: (0.009808) + test_og_1: .: (0.010493) + test_og_2: .: (0.009222) + test_og_3: .: (0.009313) + test_og_4: .: (0.009300) + test_og_5: .: (0.009861) + test_og_6: .: (0.009162) + test_os: .: (0.009742) + test_os_access: .: (0.009996) + test_os_access2: .: (0.009224) + test_ox: .: (0.009073) + test_protein_name: .: (0.010254) + test_ref: .: (0.023079) + test_seq: .: (0.009594) + test_sequence_length: .: (0.009233) + test_sq: .: (0.009046) + test_sq_crc64: .: (0.009820) + test_sq_len: .: (0.009260) + test_sq_mw: .: (0.009845) + test_synonyms: .: (0.009711) Bio::TestUniProtKB_CC: - test_allergen: .: (0.000880) - test_alternative_products_access_as_hash: .: (0.000659) - test_alternative_products_ai: .: (0.000885) - test_alternative_products_apu: .: (0.001881) - test_alternative_products_as: .: (0.001005) - test_alternative_products_rf: .: (0.000333) - test_biophysicochemical_properties: .: (0.001308) - test_biotechnology: .: (0.000700) - test_catalytic_activity: .: (0.000593) - test_caution: .: (0.000654) - test_cofactor: .: (0.001133) - test_developmental_stage: .: (0.000665) - test_disease: .: (0.000958) - test_domain: .: (0.001015) - test_enzyme_regulation: .: (0.000655) - test_function: .: (0.000681) - test_induction: .: (0.000554) - test_interaction: .: (0.000740) - test_mass_spectrometry: .: (0.001583) - test_miscellaneous: .: (0.000600) - test_pathway: .: (0.000672) - test_pharmaceutical: .: (0.000627) - test_polymorphism: .: (0.000874) - test_ptm: .: (0.000615) - test_rna_editing: .: (0.000749) - test_similarity: .: (0.000575) - test_subcellular_location: .: (0.000705) - test_subunit: .: (0.000513) - test_tissue_specificity: .: (0.001378) - test_toxic_dose: .: (0.000541) - test_web_resource: .: (0.000884) + test_allergen: .: (0.000723) + test_alternative_products_access_as_hash: .: (0.000514) + test_alternative_products_ai: .: (0.000643) + test_alternative_products_apu: .: (0.001422) + test_alternative_products_as: .: (0.000754) + test_alternative_products_rf: .: (0.000216) + test_biophysicochemical_properties: .: (0.000940) + test_biotechnology: .: (0.000521) + test_catalytic_activity: .: (0.000437) + test_caution: .: (0.000481) + test_cofactor: .: (0.000440) + test_developmental_stage: .: (0.000802) + test_disease: .: (0.000732) + test_domain: .: (0.000714) + test_enzyme_regulation: .: (0.000425) + test_function: .: (0.000469) + test_induction: .: (0.000368) + test_interaction: .: (0.000529) + test_mass_spectrometry: .: (0.000603) + test_miscellaneous: .: (0.000882) + test_pathway: .: (0.000561) + test_pharmaceutical: .: (0.000393) + test_polymorphism: .: (0.000546) + test_ptm: .: (0.000340) + test_rna_editing: .: (0.000465) + test_similarity: .: (0.000385) + test_subcellular_location: .: (0.000411) + test_subunit: .: (0.000295) + test_tissue_specificity: .: (0.000915) + test_toxic_dose: .: (0.000441) + test_web_resource: .: (0.000601) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: - test_cc_web_resource: .: (0.001179) + test_cc_web_resource: .: (0.000821) Bio::TestUniProtKB_DE_since_rel14_0: - test_private_parse_DE_line_rel14: .: (0.001376) - test_protein_name: .: (0.001036) - test_synonyms: .: (0.001286) + test_private_parse_DE_line_rel14: .: (0.001102) + test_protein_name: .: (0.000678) + test_synonyms: .: (0.001295) Bio::TestUniProtKB_ID_since_rel9_0: - test_aalen: .: (0.000644) - test_entry: .: (0.000392) - test_entry_id: .: (0.000425) - test_entry_name: .: (0.000377) - test_id_line: .: (0.000377) - test_molecule: .: (0.000352) - test_sequence_length: .: (0.000350) + test_aalen: .: (0.000459) + test_entry: .: (0.000279) + test_entry_id: .: (0.000211) + test_entry_name: .: (0.000202) + test_id_line: .: (0.000243) + test_molecule: .: (0.000230) + test_sequence_length: .: (0.000237) Bio::TestUniProtKB_P03589: - test_ac: .: (0.002339) - test_accession: .: (0.001425) - test_cc: .: (0.002006) - test_cc_alternative_products: .: (0.002565) - test_cc_database: .: (0.001923) - test_cc_mass_spectrometry: .: (0.001895) - test_de: .: (0.002110) - test_dr: .: (0.002188) - test_dr_with_key: .: (0.002553) - test_dr_with_key_empty: .: (0.002168) - test_dt: .: (0.001299) - test_dt_annotation: .: (0.002018) - test_dt_created: .: (0.001290) - test_dt_sequence: .: (0.001330) - test_entry: .: (0.001359) - test_ft: .: (0.002403) - test_gene_name: .: (0.005374) - test_gene_names: .: (0.001564) - test_gn: .: (0.001570) - test_gn_old_parser: .: (0.002276) - test_gn_uniprot_parser: .: (0.001504) - test_id_line: .: (0.001426) - test_id_line_data_class: .: (0.001980) - test_id_line_entry_name: .: (0.001515) - test_id_line_sequence_length: .: (0.001407) - test_kw: .: (0.002053) - test_oc: .: (0.001589) - test_oh: .: (0.002857) - test_os: .: (0.001498) - test_os_access: .: (0.001511) - test_os_access2: .: (0.001447) - test_ox: .: (0.002353) - test_protein_name: .: (0.001522) - test_protein_name_after_calling_de: .: (0.001597) - test_ref: .: (0.002254) - test_seq: .: (0.002299) - test_sequence_length: .: (0.002259) - test_sq: .: (0.001430) - test_sq_crc64: .: (0.001479) - test_sq_len: .: (0.002199) - test_sq_mw: .: (0.001615) - test_synonyms: .: (0.001549) + test_ac: .: (0.001895) + test_accession: .: (0.001169) + test_cc: .: (0.001496) + test_cc_alternative_products: .: (0.002143) + test_cc_database: .: (0.001608) + test_cc_mass_spectrometry: .: (0.001554) + test_de: .: (0.001662) + test_dr: .: (0.001689) + test_dr_with_key: .: (0.001478) + test_dr_with_key_empty: .: (0.001851) + test_dt: .: (0.000934) + test_dt_annotation: .: (0.000867) + test_dt_created: .: (0.001570) + test_dt_sequence: .: (0.000989) + test_entry: .: (0.000942) + test_ft: .: (0.001903) + test_gene_name: .: (0.001043) + test_gene_names: .: (0.000921) + test_gn: .: (0.004472) + test_gn_old_parser: .: (0.001314) + test_gn_uniprot_parser: .: (0.001169) + test_id_line: .: (0.001539) + test_id_line_data_class: .: (0.001120) + test_id_line_entry_name: .: (0.000966) + test_id_line_sequence_length: .: (0.001354) + test_kw: .: (0.001260) + test_oc: .: (0.001040) + test_oh: .: (0.002068) + test_os: .: (0.001028) + test_os_access: .: (0.000999) + test_os_access2: .: (0.001446) + test_ox: .: (0.000991) + test_protein_name: .: (0.001022) + test_protein_name_after_calling_de: .: (0.001570) + test_ref: .: (0.001109) + test_seq: .: (0.002263) + test_sequence_length: .: (0.001127) + test_sq: .: (0.001114) + test_sq_crc64: .: (0.001610) + test_sq_len: .: (0.001271) + test_sq_mw: .: (0.001095) + test_synonyms: .: (0.001733) Bio::TestUniProtKB_P28907: - test_ac: .: (0.005794) - test_accession: .: (0.004742) - test_cc: .: (0.005939) - test_cc_alternative_products: .: (0.006845) - test_cc_database: .: (0.006321) - test_cc_mass_spectrometry: .: (0.005962) - test_de: .: (0.004904) - test_dr: .: (0.012396) - test_dr_with_key: .: (0.012380) - test_dr_with_key_empty: .: (0.011971) - test_dt: .: (0.004878) - test_dt_annotation: .: (0.004839) - test_dt_created: .: (0.004760) - test_dt_sequence: .: (0.004796) - test_entry: .: (0.004921) - test_ft: .: (0.009214) - test_gene_name: .: (0.004991) - test_gene_names: .: (0.005676) - test_gn: .: (0.004826) - test_gn_old_parser: .: (0.004847) - test_gn_uniprot_parser: .: (0.004991) - test_id_line: .: (0.004894) - test_id_line_data_class: .: (0.004717) - test_id_line_entry_name: .: (0.005111) - test_id_line_sequence_length: .: (0.008482) - test_kw: .: (0.005088) - test_oc: .: (0.005519) - test_os: .: (0.004893) - test_os_access: .: (0.004784) - test_os_access2: .: (0.005111) - test_ox: .: (0.005322) - test_protein_name: .: (0.005020) - test_protein_name_after_calling_de: .: (0.005014) - test_ref: .: (0.007936) - test_seq: .: (0.005501) - test_sequence_length: .: (0.005108) - test_sq: .: (0.004836) - test_sq_crc64: .: (0.004707) - test_sq_len: .: (0.004778) - test_sq_mw: .: (0.005845) - test_synonyms: .: (0.005566) - test_synonyms_after_calling_de: .: (0.005614) + test_ac: .: (0.004217) + test_accession: .: (0.003615) + test_cc: .: (0.004890) + test_cc_alternative_products: .: (0.005270) + test_cc_database: .: (0.004865) + test_cc_mass_spectrometry: .: (0.005066) + test_de: .: (0.003750) + test_dr: .: (0.009081) + test_dr_with_key: .: (0.008627) + test_dr_with_key_empty: .: (0.008747) + test_dt: .: (0.003330) + test_dt_annotation: .: (0.003778) + test_dt_created: .: (0.003431) + test_dt_sequence: .: (0.003471) + test_entry: .: (0.003515) + test_ft: .: (0.006662) + test_gene_name: .: (0.004004) + test_gene_names: .: (0.003638) + test_gn: .: (0.003985) + test_gn_old_parser: .: (0.004266) + test_gn_uniprot_parser: .: (0.003672) + test_id_line: .: (0.003417) + test_id_line_data_class: .: (0.003593) + test_id_line_entry_name: .: (0.003279) + test_id_line_sequence_length: .: (0.003501) + test_kw: .: (0.006681) + test_oc: .: (0.004052) + test_os: .: (0.003722) + test_os_access: .: (0.003556) + test_os_access2: .: (0.003869) + test_ox: .: (0.003667) + test_protein_name: .: (0.003727) + test_protein_name_after_calling_de: .: (0.003497) + test_ref: .: (0.005646) + test_seq: .: (0.004128) + test_sequence_length: .: (0.003519) + test_sq: .: (0.003506) + test_sq_crc64: .: (0.003627) + test_sq_len: .: (0.004003) + test_sq_mw: .: (0.003976) + test_synonyms: .: (0.004272) + test_synonyms_after_calling_de: .: (0.004921) Bio::TestUniProtKB_P49144: - test_ac: .: (0.003293) - test_accession: .: (0.002143) - test_cc: .: (0.004379) - test_cc_alternative_products: .: (0.003924) - test_cc_database: .: (0.003228) - test_cc_mass_spectrometry: .: (0.003728) - test_de: .: (0.002166) - test_dr: .: (0.004174) - test_dr_with_key: .: (0.004228) - test_dr_with_key_empty: .: (0.004184) - test_dt: .: (0.002536) - test_dt_annotation: .: (0.002109) - test_dt_created: .: (0.002635) - test_dt_sequence: .: (0.002076) - test_entry: .: (0.002667) - test_ft: .: (0.005671) - test_gene_name: .: (0.002735) - test_gene_names: .: (0.002354) - test_gn: .: (0.002835) - test_gn_old_parser: .: (0.002336) - test_gn_uniprot_parser: .: (0.002771) - test_id_line: .: (0.002142) - test_id_line_data_class: .: (0.002645) - test_id_line_entry_name: .: (0.002104) - test_id_line_sequence_length: .: (0.002675) - test_kw: .: (0.002798) - test_oc: .: (0.002167) - test_os: .: (0.002801) - test_os_access: .: (0.002197) - test_os_access2: .: (0.002716) - test_ox: .: (0.002177) - test_protein_name: .: (0.002875) - test_protein_name_after_calling_de: .: (0.002280) - test_ref: .: (0.003250) - test_seq: .: (0.006262) - test_sequence_length: .: (0.002187) - test_sq: .: (0.003021) - test_sq_crc64: .: (0.002224) - test_sq_len: .: (0.002945) - test_sq_mw: .: (0.002085) - test_synonyms: .: (0.002501) - test_synonyms_after_calling_de: .: (0.003258) + test_ac: .: (0.001958) + test_accession: .: (0.002023) + test_cc: .: (0.002575) + test_cc_alternative_products: .: (0.003245) + test_cc_database: .: (0.002317) + test_cc_mass_spectrometry: .: (0.003005) + test_de: .: (0.001623) + test_dr: .: (0.003048) + test_dr_with_key: .: (0.003189) + test_dr_with_key_empty: .: (0.002713) + test_dt: .: (0.002045) + test_dt_annotation: .: (0.001524) + test_dt_created: .: (0.001906) + test_dt_sequence: .: (0.001507) + test_entry: .: (0.001983) + test_ft: .: (0.003977) + test_gene_name: .: (0.002166) + test_gene_names: .: (0.001500) + test_gn: .: (0.002053) + test_gn_old_parser: .: (0.001556) + test_gn_uniprot_parser: .: (0.002066) + test_id_line: .: (0.001521) + test_id_line_data_class: .: (0.001918) + test_id_line_entry_name: .: (0.001563) + test_id_line_sequence_length: .: (0.002011) + test_kw: .: (0.001691) + test_oc: .: (0.002096) + test_os: .: (0.001594) + test_os_access: .: (0.002031) + test_os_access2: .: (0.001533) + test_ox: .: (0.002033) + test_protein_name: .: (0.001581) + test_protein_name_after_calling_de: .: (0.002058) + test_ref: .: (0.002217) + test_seq: .: (0.001882) + test_sequence_length: .: (0.001663) + test_sq: .: (0.004566) + test_sq_crc64: .: (0.002301) + test_sq_len: .: (0.001743) + test_sq_mw: .: (0.002098) + test_synonyms: .: (0.001673) + test_synonyms_after_calling_de: .: (0.002228) Bio::TestUniProtKB_Ref: - test_RA: .: (0.001613) - test_RC: .: (0.000934) - test_RG: .: (0.000988) - test_RL: .: (0.001569) - test_RN: .: (0.000982) - test_RP: .: (0.000920) - test_RT: .: (0.001033) - test_RX: .: (0.000897) - test_ref: .: (0.001065) + test_RA: .: (0.000851) + test_RC: .: (0.000647) + test_RG: .: (0.001004) + test_RL: .: (0.000641) + test_RN: .: (0.000550) + test_RP: .: (0.000548) + test_RT: .: (0.001017) + test_RX: .: (0.000665) + test_ref: .: (0.000613) Bio::TestUniProtKB_SwissProtRel41_0: - test_multiple_RP_lines: .: (0.000853) + test_multiple_RP_lines: .: (0.000661) Bio::TestUniProtKB_SwissProtRel41_1: - test_alternative_products: .: (0.001433) - test_alternative_products_with_ft: .: (0.002698) + test_alternative_products: .: (0.001523) + test_alternative_products_with_ft: .: (0.001730) Bio::TestUniProtKB_SwissProtRel41_10: - test_RC_lines: .: (0.001373) + test_RC_lines: .: (0.000728) Bio::TestUniProtKB_SwissProtRel41_20: - test_CC_allergen: .: (0.000952) - test_RL_lines: .: (0.000526) + test_CC_allergen: .: (0.000700) + test_RL_lines: .: (0.000343) Bio::TestUniProtKB_SwissProtRel42_6: - test_CC_rna_editing: .: (0.002384) + test_CC_rna_editing: .: (0.001079) Bio::TestUniProtKB_UniProtRel1_12: - test_DOI_in_RX_line: .: (0.000851) - test_RG_line: .: (0.000573) + test_DOI_in_RX_line: .: (0.000535) + test_RG_line: .: (0.000335) Bio::TestUniProtKB_UniProtRel2_0: - test_GN_line: .: (0.001732) + test_GN_line: .: (0.001468) Bio::TestUniProtKB_UniProtRel2_1: - test_CC_mass_spectrometry: .: (0.000952) + test_CC_mass_spectrometry: .: (0.000657) Bio::TestUniProtKB_UniProtRel2_3: - test_DR_PDB: .: (0.001628) - test_RL_line: .: (0.000531) + test_DR_PDB: .: (0.000463) + test_RL_line: .: (0.000330) Bio::TestUniProtKB_UniProtRel3_4: - test_CC_biophysiochemical_properties: .: (0.002147) - test_RP_line: .: (0.000809) + test_CC_biophysiochemical_properties: .: (0.001398) + test_RP_line: .: (0.000881) Bio::TestUniProtKB_UniProtRel3_5: - test_entry_name_format: .: (0.000548) + test_entry_name_format: .: (0.000370) Bio::TestUniProtKB_UniProtRel4_0: - test_CC_interaction: .: (0.001435) - test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000803) - test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000706) - test_CC_interaction_isoform: .: (0.000712) - test_CC_interaction_no_gene_name: .: (0.000662) - test_CC_interaction_self_association: .: (0.000823) + test_CC_interaction: .: (0.000674) + test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000491) + test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000412) + test_CC_interaction_isoform: .: (0.000406) + test_CC_interaction_no_gene_name: .: (0.000408) + test_CC_interaction_self_association: .: (0.000460) Bio::TestUniProtKB_UniProtRel5_0: - test_DR_line: .: (0.000893) + test_DR_line: .: (0.001038) Bio::TestUniProtKB_UniProtRel5_4: - test_multiple_cofactors: .: (0.000967) + test_multiple_cofactors: .: (0.000637) Bio::TestUniProtKB_UniProtRel6_0: - test_OG_line: .: (0.001479) + test_OG_line: .: (0.000743) Bio::TestUniProtKB_UniProtRel6_1: - test_FT_metal: .: (0.001009) + test_FT_metal: .: (0.000580) Bio::TestUniProtKB_UniProtRel6_5: - test_HI_line: .: (0.000981) + test_HI_line: .: (0.000963) Bio::TestUniProtKB_UniProtRel7_0: - test_CC_copyright_statement: .: (0.000810) - test_DT_line: .: (0.000650) + test_CC_copyright_statement: .: (0.000561) + test_DT_line: .: (0.000319) Bio::TestUniProtKB_UniProtRel7_6: - test_10000aa: .: (0.011211) + test_10000aa: .: (0.007896) Bio::TestUniProtKB_UniProtRel8_0: - test_CC_alternative_products: .: (0.002421) - test_CC_web_resource: .: (0.000389) - test_FT_VER_SEQ: .: (0.000756) - test_OH_line_exception: .: (0.000932) - test_OH_lines: .: (0.001121) + test_CC_alternative_products: .: (0.001858) + test_CC_web_resource: .: (0.000193) + test_FT_VER_SEQ: .: (0.000416) + test_OH_line_exception: .: (0.000480) + test_OH_lines: .: (0.000720) Bio::TestUtils: - test_centreOfGravity: .: (0.001499) - test_dihedral_angle: .: (0.001864) - test_distance: .: (0.001200) - test_geometricCentre: .: (0.001014) - test_rad2deg: .: (0.001262) + test_centreOfGravity: .: (0.001484) + test_dihedral_angle: .: (0.000890) + test_distance: .: (0.000723) + test_geometricCentre: .: (0.001034) + test_rad2deg: .: (0.000422) Bio::TestWeightedGraph: - test_bellman_ford_on_negative_weighted_graph: .: (0.000883) - test_dijkstra_on_weighted_graph: .: (0.000624) + test_bellman_ford_on_negative_weighted_graph: .: (0.000596) + test_dijkstra_on_weighted_graph: .: (0.000302) -Finished in 41.773821904 seconds. +Finished in 32.00292479 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- -94.34 tests/s, 517.09 assertions/s +123.14 tests/s, 674.97 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ @@ -5533,12 +5569,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/19956/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/13000 and its subdirectories -I: Current time: Mon Dec 23 09:59:48 -12 2024 -I: pbuilder-time-stamp: 1734991188 +I: removing directory /srv/workspace/pbuilder/19956 and its subdirectories +I: Current time: Tue Dec 24 12:02:13 +14 2024 +I: pbuilder-time-stamp: 1734991333