Diff of the two buildlogs: -- --- b1/build.log 2025-09-29 12:43:57.659033474 +0000 +++ b2/build.log 2025-09-29 12:44:58.747106875 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 29 00:42:59 -12 2025 -I: pbuilder-time-stamp: 1759149779 +I: Current time: Mon Nov 2 09:06:59 +14 2026 +I: pbuilder-time-stamp: 1793560019 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ 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/515837/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/526850/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Nov 1 19:07 /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/526850/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/526850/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='0a9a5394c8d64090938d536e1b5faa11' - 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='515837' - PS1='# ' - PS2='> ' + INVOCATION_ID=4648992dea71475b8798b55d1326d79f + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=526850 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.P5Ot3IT8/pbuilderrc_LSNI --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/b1 --logfile b1/build.log ruby-bio_2.0.6-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.P5Ot3IT8/pbuilderrc_KKTl --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P5Ot3IT8/b2 --logfile b2/build.log ruby-bio_2.0.6-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/515837/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/526850/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -84,7 +116,7 @@ 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 ... 20022 files and directories currently installed.) +(Reading database ... 20001 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: @@ -246,10 +278,10 @@ Get: 127 http://deb.debian.org/debian forky/main arm64 ruby-rd all 0.6.38-5 [62.0 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 rdtool all 0.6.38-5 [42.5 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 ruby-libxml arm64 5.0.5-1 [75.8 kB] -Fetched 37.0 MB in 0s (119 MB/s) +Fetched 37.0 MB in 0s (101 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. -(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 ... 20022 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 .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. @@ -262,7 +294,7 @@ Setting up libexpat1:arm64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20356 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 ... 20335 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_arm64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. @@ -298,7 +330,7 @@ Unpacking libpython3-stdlib:arm64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... 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 ... 21371 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 ... 21350 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_arm64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. @@ -678,8 +710,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Sep 29 12:43:23 UTC 2025. -Universal Time is now: Mon Sep 29 12:43:23 UTC 2025. +Local time is now: Sun Nov 1 19:07:29 UTC 2026. +Universal Time is now: Sun Nov 1 19:07:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ruby-minitest (5.25.4-3) ... @@ -800,7 +832,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ruby-bio-2.0.6/ && 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_2.0.6-1_source.changes +I: user script /srv/workspace/pbuilder/526850/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/526850/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ruby-bio-2.0.6/ && 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_2.0.6-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.6-1 dpkg-buildpackage: info: source distribution unstable @@ -1057,4392 +1093,4392 @@ Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: - test_db_ids: .: (0.000414) - test_dbs: .: (0.000130) - test_go_ids: .: (0.000113) - test_go_terms: .: (0.000108) - test_parser: .: (0.000259) - test_set_date: .: (0.000120) - test_set_desc: .: (0.000108) - test_to_str: .: (0.000117) + test_db_ids: .: (0.000438) + test_dbs: .: (0.000158) + test_go_ids: .: (0.000134) + test_go_terms: .: (0.000154) + test_parser: .: (0.000275) + test_set_date: .: (0.000128) + test_set_desc: .: (0.000115) + test_to_str: .: (0.000118) Bio::FuncTestCommandBackports: - test_mktmpdir_with_block: .: (0.000494) - test_mktmpdir_without_block: .: (0.000325) - test_remove_entry_secure: .: (0.000259) + test_mktmpdir_with_block: .: (0.000475) + test_mktmpdir_without_block: .: (0.000331) + test_remove_entry_secure: .: (0.000266) Bio::FuncTestCommandCallMisc1: - test_call_command: .: (0.003102) - test_call_command_fork: .: (0.000110) - test_call_command_open3: .: (0.002681) - test_call_command_popen: .: (0.002177) + test_call_command: .: (0.004689) + test_call_command_fork: .: (0.000112) + test_call_command_open3: .: (0.004659) + test_call_command_popen: .: (0.003869) Bio::FuncTestCommandCallSimple: - test_call_command: .: (0.002414) - test_call_command_fork: .: (0.000091) - test_call_command_open3: .: (0.002204) - test_call_command_popen: .: (0.001653) + test_call_command: .: (0.003786) + test_call_command_fork: .: (0.000100) + test_call_command_open3: .: (0.004761) + test_call_command_popen: .: (0.004595) Bio::FuncTestCommandCallWithSpace: - test_call_command: .: (0.001577) - test_call_command_fork: .: (0.000090) - test_call_command_open3: .: (0.002219) - test_call_command_popen: .: (0.002214) + test_call_command: .: (0.002885) + test_call_command_fork: .: (0.000195) + test_call_command_open3: .: (0.002649) + test_call_command_popen: .: (0.002813) Bio::FuncTestCommandChdir: - test_call_command_chdir: .: (0.002508) - test_call_command_fork_chdir: .: (0.000218) - test_call_command_popen_chdir: .: (0.001370) - test_query_command_chdir: .: (0.002306) - test_query_command_fork_chdir: .: (0.000217) - test_query_command_popen_chdir: .: (0.002362) + test_call_command_chdir: .: (0.002664) + test_call_command_fork_chdir: .: (0.000242) + test_call_command_popen_chdir: .: (0.002265) + test_query_command_chdir: .: (0.002549) + test_query_command_fork_chdir: .: (0.000232) + test_query_command_popen_chdir: .: (0.002405) Bio::FuncTestCommandQuery: - test_query_command: .: (0.004473) - test_query_command_fork: .: (0.001772) - test_query_command_open3: .: (0.003512) - test_query_command_popen: .: (0.004932) + test_query_command: .: (0.003556) + test_query_command_fork: .: (0.001603) + test_query_command_open3: .: (0.006325) + test_query_command_popen: .: (0.005473) Bio::FuncTestCommandTmpdir: - test_close!: .: (0.000584) - test_initialize: .: (0.000208) - test_path: .: (0.000131) - test_path_after_close: .: (0.000243) + test_close!: .: (0.000709) + test_initialize: .: (0.000244) + test_path: .: (0.000167) + test_path_after_close: .: (0.000271) Bio::FuncTestSequenceOutputEMBL: - test_output_embl: .: (0.014581) - test_output_fasta: .: (0.004422) + test_output_embl: .: (0.014967) + test_output_fasta: .: (0.004409) Bio::NCBIDB::TestCommon: - test_acc_version: .: (0.000452) - test_accession: .: (0.000143) - test_accessions: .: (0.000093) - test_comment: .: (0.000072) - test_common_name: .: (0.000107) - test_definition: .: (0.000094) - test_features: .: (0.000213) - test_gi: .: (0.000083) - test_keywords: .: (0.000074) - test_locus: .: (0.000050) - test_nid: .: (0.000074) - test_organism: .: (0.000092) - test_origin: .: (0.000096) - test_references: .: (0.000376) - test_segment: .: (0.000096) - test_source: .: (0.000171) - test_taxonomy: .: (0.000100) - test_version: .: (0.000088) - test_versions: .: (0.000072) + test_acc_version: .: (0.000290) + test_accession: .: (0.000098) + test_accessions: .: (0.000662) + test_comment: .: (0.000092) + test_common_name: .: (0.000115) + test_definition: .: (0.000093) + test_features: .: (0.000226) + test_gi: .: (0.000089) + test_keywords: .: (0.000077) + test_locus: .: (0.000051) + test_nid: .: (0.000077) + test_organism: .: (0.000094) + test_origin: .: (0.000072) + test_references: .: (0.000404) + test_segment: .: (0.000111) + test_source: .: (0.000166) + test_taxonomy: .: (0.000093) + test_version: .: (0.000089) + test_versions: .: (0.000076) Bio::TestAA: - test_13: .: (0.000148) - test_1n: .: (0.000050) + test_13: .: (0.000156) + test_1n: .: (0.000047) test_name2one: .: (0.000085) - test_name2three: .: (0.000051) - test_one2name: .: (0.000042) - test_one2three: .: (0.000038) - test_three2name: .: (0.000036) - test_three2one: .: (0.000048) - test_to_1_1: .: (0.000039) - test_to_1_3: .: (0.000049) - test_to_1_name: .: (0.000047) - test_to_3_1: .: (0.000038) - test_to_3_3: .: (0.000036) - test_to_3_name: .: (0.000047) - test_to_re: .: (0.000071) + test_name2three: .: (0.000050) + test_one2name: .: (0.000060) + test_one2three: .: (0.000043) + test_three2name: .: (0.000039) + test_three2one: .: (0.000054) + test_to_1_1: .: (0.000041) + test_to_1_3: .: (0.000050) + test_to_1_name: .: (0.000050) + test_to_3_1: .: (0.000041) + test_to_3_3: .: (0.000038) + test_to_3_name: .: (0.000050) + test_to_re: .: (0.000073) Bio::TestAAConstants: - test_bio_aminoacid: .: (0.000117) + test_bio_aminoacid: .: (0.000123) Bio::TestAAindex: - test_api: .: (0.000078) - test_auto_aax1: .: (0.000180) - test_auto_aax2: .: (0.000119) + test_api: .: (0.000086) + test_auto_aax1: .: (0.000196) + test_auto_aax2: .: (0.000136) Bio::TestAAindex1: - test_author: .: (0.000193) - test_comment: .: (0.000120) - test_correlation_coefficient: .: (0.000235) - test_dblinks: .: (0.000113) - test_definition: .: (0.000107) - test_entry_id: .: (0.000121) - test_index: .: (0.000172) - test_journal: .: (0.000129) - test_title: .: (0.000114) + test_author: .: (0.000219) + test_comment: .: (0.000137) + test_correlation_coefficient: .: (0.000248) + test_dblinks: .: (0.000123) + test_definition: .: (0.000117) + test_entry_id: .: (0.000104) + test_index: .: (0.000183) + test_journal: .: (0.000148) + test_title: .: (0.000120) Bio::TestAAindex2: - test_access_A_R: .: (0.000531) - test_access_R_A: .: (0.000401) - test_author: .: (0.000133) - test_cols: .: (0.000114) - test_comment: .: (0.000113) - test_dblinks: .: (0.000112) - test_definition: .: (0.000115) - test_entry_id: .: (0.000106) - test_journal: .: (0.000123) + test_access_A_R: .: (0.000540) + test_access_R_A: .: (0.000430) + test_author: .: (0.000155) + test_cols: .: (0.000127) + test_comment: .: (0.000122) + test_dblinks: .: (0.000110) + test_definition: .: (0.000112) + test_entry_id: .: (0.000120) + test_journal: .: (0.000133) test_matrix: .: (0.000407) - test_matrix_1_2: .: (0.000404) - test_matrix_2_2: .: (0.008501) - test_matrix_A_R: .: (0.000502) - test_matrix_R_A: .: (0.000424) - test_matrix_determinant: .: (0.001701) - test_matrix_rank: .: (0.001333) - test_matrix_transpose: .: (0.000495) - test_rows: .: (0.000151) - test_title: .: (0.000150) + test_matrix_1_2: .: (0.000418) + test_matrix_2_2: .: (0.008117) + test_matrix_A_R: .: (0.001155) + test_matrix_R_A: .: (0.000489) + test_matrix_determinant: .: (0.001337) + test_matrix_rank: .: (0.001632) + test_matrix_transpose: .: (0.000526) + test_rows: .: (0.000146) + test_title: .: (0.000165) Bio::TestAAindexConstant: - test_delimiter: .: (0.000154) - test_tagsize: .: (0.000043) + test_delimiter: .: (0.000175) + test_tagsize: .: (0.000046) Bio::TestAbif: - test_complement: .: (0.005621) - test_seq: .: (0.005566) - test_to_biosequence: .: (0.005955) + test_complement: .: (0.005680) + test_seq: .: (0.005624) + test_to_biosequence: .: (0.006081) Bio::TestActsLikeMap: - test_mixin: .: (0.000236) + test_mixin: .: (0.000243) Bio::TestActsLikeMapAndMarker: - test_mixin: .: (0.000191) + test_mixin: .: (0.000215) Bio::TestActsLikeMarker: - test_mixin: .: (0.000116) + test_mixin: .: (0.000161) Bio::TestAlignment: - test_add_seq_no_key: .: (0.000203) - test_add_seq_using_seq_with_aaseq_method: .: (0.000082) - test_add_seq_using_seq_with_definition_method: .: (0.000054) - test_add_seq_using_seq_with_entry_id_method: .: (0.000057) - test_add_seq_using_seq_with_naseq_method: .: (0.000065) + test_add_seq_no_key: .: (0.000243) + test_add_seq_using_seq_with_aaseq_method: .: (0.000104) + test_add_seq_using_seq_with_definition_method: .: (0.000069) + test_add_seq_using_seq_with_entry_id_method: .: (0.000074) + test_add_seq_using_seq_with_naseq_method: .: (0.000080) test_add_seq_using_seq_with_seq_method: .: (0.000064) - test_consensus_iupac_gap_modes: .: (0.000274) - test_consensus_iupac_missing_char: .: (0.000097) - test_consensus_iupac_missing_char_option: .: (0.000106) - test_consensus_iupac_no_gaps: .: (0.000150) - test_consensus_iupac_of_ambiguous_bases: .: (0.000201) - test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002585) - test_consensus_opt_gap_mode: .: (0.000323) - test_consensus_opt_missing_char: .: (0.000195) - test_consensus_string_no_gaps: .: (0.000128) - test_consensus_threshold_four_sequences: .: (0.000165) - test_consensus_threshold_two_sequences: .: (0.000191) - test_convert_match: .: (0.000186) - test_convert_unmatch: .: (0.000086) - test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000076) - test_convert_unmatch_different_match_char: .: (0.000067) + test_consensus_iupac_gap_modes: .: (0.000313) + test_consensus_iupac_missing_char: .: (0.000118) + test_consensus_iupac_missing_char_option: .: (0.000107) + test_consensus_iupac_no_gaps: .: (0.000142) + test_consensus_iupac_of_ambiguous_bases: .: (0.000195) + test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.002661) + test_consensus_opt_gap_mode: .: (0.000354) + test_consensus_opt_missing_char: .: (0.000173) + test_consensus_string_no_gaps: .: (0.000215) + test_consensus_threshold_four_sequences: .: (0.000189) + test_consensus_threshold_two_sequences: .: (0.000189) + test_convert_match: .: (0.000193) + test_convert_unmatch: .: (0.000092) + test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000078) + test_convert_unmatch_different_match_char: .: (0.000065) test_convert_unmatch_multiple_sequences: .: (0.000102) test_default_gap_char: .: (0.000041) - test_default_gap_regexp_matches_default_gap_char: .: (0.000050) - test_default_missing_char: .: (0.000051) - test_each_site_equal_length: .: (0.000093) - test_each_site_unequal_length: .: (0.000081) - test_equals: .: (0.000115) - test_match_line_protein: .: (0.000277) - test_normalizebang_extends_sequences_with_gaps: .: (0.000083) - test_seq_length_is_max_seq_length: .: (0.000053) - test_seq_length_when_one_sequence: .: (0.000102) - test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000059) - test_seqclass_when_seqclass_set: .: (0.000063) - test_seqclass_when_sequence_used: .: (0.000047) - test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000046) - test_set_and_get_gap_char: .: (0.000042) - test_store_cannot_override_key: .: (0.000048) - test_store_with_default_keys_and_user_defined_keys: .: (0.000052) - test_store_with_nil_key_uses_next_number_for_key: .: (0.000045) + test_default_gap_regexp_matches_default_gap_char: .: (0.000051) + test_default_missing_char: .: (0.000040) + test_each_site_equal_length: .: (0.000151) + test_each_site_unequal_length: .: (0.000088) + test_equals: .: (0.000130) + test_match_line_protein: .: (0.000288) + test_normalizebang_extends_sequences_with_gaps: .: (0.000089) + test_seq_length_is_max_seq_length: .: (0.000052) + test_seq_length_when_one_sequence: .: (0.000045) + test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000052) + test_seqclass_when_seqclass_set: .: (0.000165) + test_seqclass_when_sequence_used: .: (0.000063) + test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000051) + test_set_and_get_gap_char: .: (0.000045) + test_store_cannot_override_key: .: (0.000049) + test_store_with_default_keys_and_user_defined_keys: .: (0.000055) + test_store_with_nil_key_uses_next_number_for_key: .: (0.000048) Bio::TestAlignmentEnumerableExtension: - test_alignment_collect: .: (0.000168) - test_alignment_concat: .: (0.000086) - test_alignment_length: .: (0.000041) - test_alignment_lstrip!: .: (0.000097) - test_alignment_lstrip_nil: .: (0.000131) - test_alignment_normalize!: .: (0.000053) - test_alignment_rstrip!: .: (0.000126) - test_alignment_rstrip_nil: .: (0.000054) - test_alignment_site: .: (0.000054) - test_alignment_slice: .: (0.007794) - test_alignment_strip!: .: (0.000162) - test_alignment_strip_nil: .: (0.000074) - test_alignment_subseq: .: (0.000191) - test_alignment_window: .: (0.000058) - test_collect_each_site: .: (0.000097) - test_consensus_each_site_default: .: (0.000098) - test_consensus_each_site_gap_mode_1: .: (0.000091) - test_consensus_each_site_gap_mode_minus1: .: (0.000091) + test_alignment_collect: .: (0.000171) + test_alignment_concat: .: (0.000089) + test_alignment_length: .: (0.000044) + test_alignment_lstrip!: .: (0.000096) + test_alignment_lstrip_nil: .: (0.000059) + test_alignment_normalize!: .: (0.000145) + test_alignment_rstrip!: .: (0.000115) + test_alignment_rstrip_nil: .: (0.000057) + test_alignment_site: .: (0.000055) + test_alignment_slice: .: (0.000051) + test_alignment_strip!: .: (0.000100) + test_alignment_strip_nil: .: (0.000057) + test_alignment_subseq: .: (0.000075) + test_alignment_window: .: (0.000048) + test_collect_each_site: .: (0.000068) + test_consensus_each_site_default: .: (0.000080) + test_consensus_each_site_gap_mode_1: .: (0.008127) + test_consensus_each_site_gap_mode_minus1: .: (0.000187) test_consensus_iupac: .: (0.000238) - test_consensus_string_default: .: (0.000097) - test_consensus_string_half: .: (0.000075) - test_convert_match: .: (0.000084) - test_convert_unmatch: .: (0.000091) - test_each_seq: .: (0.000060) - test_each_site: .: (0.000103) - test_each_site_step: .: (0.000066) - test_each_window: .: (0.000099) - test_match_line: .: (0.000596) - test_match_line_amino: .: (0.000981) - test_match_line_nuc: .: (0.000107) - test_private_alignment_site: .: (0.000066) - test_remove_all_gaps!: .: (0.000077) - test_seqclass: .: (0.000057) - test_seqclass=: .: (0.000073) - test_seqclass_default: .: (0.000185) + test_consensus_string_default: .: (0.000113) + test_consensus_string_half: .: (0.000089) + test_convert_match: .: (0.000226) + test_convert_unmatch: .: (0.000080) + test_each_seq: .: (0.000072) + test_each_site: .: (0.000119) + test_each_site_step: .: (0.000078) + test_each_window: .: (0.000126) + test_match_line: .: (0.000903) + test_match_line_amino: .: (0.001110) + test_match_line_nuc: .: (0.000165) + test_private_alignment_site: .: (0.000077) + test_remove_all_gaps!: .: (0.000087) + test_seqclass: .: (0.000067) + test_seqclass=: .: (0.000070) + test_seqclass_default: .: (0.000040) Bio::TestAlignmentMultiFastaFormat: - test_alignment: .: (0.002267) - test_determine_seq_method: .: (0.012404) - test_entries: .: (0.002963) + test_alignment: .: (0.002453) + test_determine_seq_method: .: (0.007397) + test_entries: .: (0.000696) Bio::TestAlignmentOutput: - test_avoid_same_name: .: (0.001581) - test_avoid_same_name_numbering: .: (0.000176) - test_clustal_have_same_name_true: .: (0.002910) - test_have_same_name_false: .: (0.000113) + test_avoid_same_name: .: (0.002762) + test_avoid_same_name_numbering: .: (0.000133) + test_clustal_have_same_name_true: .: (0.000063) + test_have_same_name_false: .: (0.001310) Bio::TestAlignmentPropertyMethods: - test_gap_char=: .: (0.000947) - test_gap_char_default: .: (0.000074) - test_gap_char_never_nil: .: (0.000043) - test_gap_regexp: .: (0.000045) - test_gap_regexp=: .: (0.001352) - test_gap_regexp_never_nil: .: (0.001169) - test_get_all_property_default: .: (0.001607) - test_get_all_property_nodefault: .: (0.001200) - test_is_gap_default_false: .: (0.001257) - test_is_gap_default_true: .: (0.001093) - test_is_gap_nodefault_false: .: (0.001427) - test_is_gap_nodefault_true: .: (0.001999) - test_missing_char=: .: (0.000685) - test_missing_char_default: .: (0.001429) + test_gap_char=: .: (0.000169) + test_gap_char_default: .: (0.000051) + test_gap_char_never_nil: .: (0.001296) + test_gap_regexp: .: (0.000052) + test_gap_regexp=: .: (0.000059) + test_gap_regexp_never_nil: .: (0.000043) + test_get_all_property_default: .: (0.001370) + test_get_all_property_nodefault: .: (0.002537) + test_is_gap_default_false: .: (0.002532) + test_is_gap_default_true: .: (0.000112) + test_is_gap_nodefault_false: .: (0.000822) + test_is_gap_nodefault_true: .: (0.000057) + test_missing_char=: .: (0.000050) + test_missing_char_default: .: (0.000664) test_missing_char_never_nil: .: (0.000052) - test_seqclass=: .: (0.000061) + test_seqclass=: .: (0.000055) test_seqclass_default: .: (0.000045) - test_seqclass_never_nil: .: (0.000041) - test_set_all_property: .: (0.000062) + test_seqclass_never_nil: .: (0.002291) + test_set_all_property: .: (0.000872) Bio::TestAlignmentSite: - test_consensus_iupac: .: (0.000524) - test_consensus_string_50percent: .: (0.000075) - test_consensus_string_50percent_nil: .: (0.000057) - test_consensus_string_default: .: (0.000045) - test_consensus_string_default_nil: .: (0.000046) - test_has_gap_false: .: (0.000062) - test_has_gap_true: .: (0.000044) - test_match_line_amino_100percent: .: (0.000072) - test_match_line_amino_missing: .: (0.000100) - test_match_line_amino_strong: .: (0.000066) - test_match_line_amino_weak: .: (0.000502) - test_match_line_nuc_100percent: .: (0.000092) - test_match_line_nuc_missing: .: (0.000075) - test_remove_gaps!: .: (0.000057) - test_remove_gaps_bang_not_removed: .: (0.000045) + test_consensus_iupac: .: (0.004539) + test_consensus_string_50percent: .: (0.003925) + test_consensus_string_50percent_nil: .: (0.001931) + test_consensus_string_default: .: (0.000059) + test_consensus_string_default_nil: .: (0.000051) + test_has_gap_false: .: (0.000061) + test_has_gap_true: .: (0.000048) + test_match_line_amino_100percent: .: (0.000083) + test_match_line_amino_missing: .: (0.000108) + test_match_line_amino_strong: .: (0.000068) + test_match_line_amino_weak: .: (0.000081) + test_match_line_nuc_100percent: .: (0.000063) + test_match_line_nuc_missing: .: (0.000178) + test_remove_gaps!: .: (0.000061) + test_remove_gaps_bang_not_removed: .: (0.000046) Bio::TestAtomFinder: - test_atoms: .: (0.012661) - test_each_atom: .: (0.000139) - test_find_atom: .: (0.000221) + test_atoms: .: (0.013417) + test_each_atom: .: (0.000152) + test_find_atom: .: (0.000282) Bio::TestBioFastaDefline: - test_acc_version: .: (0.000352) - test_accession: .: (0.000276) - test_accessions: .: (0.000206) - test_description: .: (0.000165) - test_descriptions: .: (0.000160) - test_entry_id: .: (0.000152) - test_get: .: (0.000184) - test_get_all_by_type: .: (0.000163) - test_get_by_type: .: (0.000155) - test_gi: .: (0.000133) - test_id_strings: .: (0.000377) - test_locus: .: (0.000136) - test_method_missing: .: (0.000191) - test_to_s: .: (0.000189) - test_words: .: (0.000408) + test_acc_version: .: (0.000364) + test_accession: .: (0.000329) + test_accessions: .: (0.000229) + test_description: .: (0.000180) + test_descriptions: .: (0.000181) + test_entry_id: .: (0.000159) + test_get: .: (0.000196) + test_get_all_by_type: .: (0.000143) + test_get_by_type: .: (0.000158) + test_gi: .: (0.000139) + test_id_strings: .: (0.000367) + test_locus: .: (0.000145) + test_method_missing: .: (0.000189) + test_to_s: .: (0.000177) + test_words: .: (0.000424) Bio::TestBioGOOntology: - test_dag_edit_format_parser: .: (0.000651) - test_goid2term: .: (0.000227) - test_parse_goids: .: (0.000210) + test_dag_edit_format_parser: .: (0.000646) + test_goid2term: .: (0.000290) + test_parse_goids: .: (0.000245) Bio::TestBioGenBank: - test_basecount: .: (0.000289) - test_circular: .: (0.000164) - test_classification: .: (0.000199) - test_date: .: (0.000168) - test_date_modified: .: (0.000484) - test_division: .: (0.000174) - test_each_cds_feature: .: (0.000477) - test_each_cds_qualifiers: .: (0.005326) - test_each_gene: .: (0.000586) - test_entry_id: .: (0.000179) - test_length: .: (0.000153) - test_locus_circular: .: (0.000199) - test_locus_class: .: (0.000233) - test_locus_date: .: (0.000179) - test_locus_division: .: (0.000166) - test_locus_entry_id: .: (0.000171) - test_locus_length: .: (0.000257) - test_locus_natype: .: (0.000161) - test_locus_strand: .: (0.000158) - test_natype: .: (0.000136) - test_seq: .: (0.000188) - test_seq_len: .: (0.000168) - test_strand: .: (0.000139) - test_strandedness: .: (0.000147) - test_to_biosequence: .: (0.001656) + test_basecount: .: (0.000309) + test_circular: .: (0.000183) + test_classification: .: (0.000219) + test_date: .: (0.000158) + test_date_modified: .: (0.000492) + test_division: .: (0.000177) + test_each_cds_feature: .: (0.000513) + test_each_cds_qualifiers: .: (0.000490) + test_each_gene: .: (0.000469) + test_entry_id: .: (0.005157) + test_length: .: (0.000275) + test_locus_circular: .: (0.000233) + test_locus_class: .: (0.000190) + test_locus_date: .: (0.000198) + test_locus_division: .: (0.000186) + test_locus_entry_id: .: (0.000206) + test_locus_length: .: (0.000195) + test_locus_natype: .: (0.000182) + test_locus_strand: .: (0.000168) + test_natype: .: (0.000181) + test_seq: .: (0.000216) + test_seq_len: .: (0.000182) + test_strand: .: (0.000559) + test_strandedness: .: (0.000233) + test_to_biosequence: .: (0.001468) Bio::TestBioGenPept: - test_circular: .: (0.000297) - test_date: .: (0.000142) - test_dbsource: .: (0.000112) - test_division: .: (0.000109) - test_entry_id: .: (0.000104) - test_length: .: (0.000102) - test_locus: .: (0.000107) - test_seq: .: (0.000131) - test_seq_len: .: (0.000116) + test_circular: .: (0.000333) + test_date: .: (0.000165) + test_dbsource: .: (0.000128) + test_division: .: (0.000124) + test_entry_id: .: (0.000112) + test_length: .: (0.000519) + test_locus: .: (0.000268) + test_seq: .: (0.000178) + test_seq_len: .: (0.000142) Bio::TestBioKEGGGENES_b0529: - test_aalen: .: (0.000874) - test_aaseq: .: (0.000210) - test_chromosome: .: (0.000143) - test_codon_usage: .: (0.000219) - test_cu_list: .: (0.000117) - test_dblinks_as_hash: .: (0.000156) - test_dblinks_as_strings: .: (0.000124) - test_definition: .: (0.000138) - test_division: .: (0.000161) - test_eclinks: .: (0.000163) - test_entry: .: (0.000126) - test_entry_id: .: (0.000115) - test_gbposition: .: (0.000149) - test_gene: .: (0.000146) - test_genes: .: (0.000125) - test_keggclass: .: (0.000143) - test_keggclasses: .: (0.000153) - test_locations: .: (0.000262) - test_motifs_as_hash: .: (0.000189) - test_motifs_as_strings: .: (0.000122) - test_name: .: (0.000128) - test_names_as_array: .: (0.000374) - test_new: .: (0.000136) - test_ntlen: .: (0.000183) - test_ntseq: .: (0.000215) - test_organism: .: (0.000122) - test_orthologs_as_hash: .: (0.000150) - test_orthologs_as_strings: .: (0.000112) - test_pathway: .: (0.000138) - test_pathway_after_pathways_as_strings: .: (0.000186) - test_pathway_before_pathways_as_strings: .: (0.000174) - test_pathways_as_hash: .: (0.000142) - test_pathways_as_strings: .: (0.000115) - test_position: .: (0.000139) - test_structure: .: (0.000155) + test_aalen: .: (0.000641) + test_aaseq: .: (0.000227) + test_chromosome: .: (0.000161) + test_codon_usage: .: (0.000240) + test_cu_list: .: (0.000141) + test_dblinks_as_hash: .: (0.000179) + test_dblinks_as_strings: .: (0.000390) + test_definition: .: (0.000208) + test_division: .: (0.000144) + test_eclinks: .: (0.000161) + test_entry: .: (0.000135) + test_entry_id: .: (0.000129) + test_gbposition: .: (0.000148) + test_gene: .: (0.000172) + test_genes: .: (0.000147) + test_keggclass: .: (0.000165) + test_keggclasses: .: (0.000168) + test_locations: .: (0.000260) + test_motifs_as_hash: .: (0.000186) + test_motifs_as_strings: .: (0.000124) + test_name: .: (0.000132) + test_names_as_array: .: (0.000135) + test_new: .: (0.000139) + test_ntlen: .: (0.000188) + test_ntseq: .: (0.000412) + test_organism: .: (0.000147) + test_orthologs_as_hash: .: (0.000156) + test_orthologs_as_strings: .: (0.000157) + test_pathway: .: (0.000170) + test_pathway_after_pathways_as_strings: .: (0.000190) + test_pathway_before_pathways_as_strings: .: (0.000179) + test_pathways_as_hash: .: (0.000146) + test_pathways_as_strings: .: (0.000119) + test_position: .: (0.000131) + test_structure: .: (0.000160) Bio::TestBioKEGGGENOME_T00005: - test_chromosomes: .: (0.000841) - test_comment: .: (0.000248) - test_data_source: .: (0.000226) - test_definition: .: (0.000212) - test_disease: .: (0.000206) - test_entry_id: .: (0.000199) - test_lineage: .: (0.000222) - test_nalen: .: (0.000211) - test_name: .: (0.000200) - test_new: .: (0.000226) - test_num_gene: .: (0.000207) - test_num_rna: .: (0.000201) - test_original_databases: .: (0.000247) - test_original_db: .: (0.000212) - test_plasmids: .: (0.000197) - test_references: .: (0.001736) - test_statistics: .: (0.000250) - test_taxid: .: (0.000228) - test_taxonomy: .: (0.000232) + test_chromosomes: .: (0.000881) + test_comment: .: (0.000265) + test_data_source: .: (0.000224) + test_definition: .: (0.000228) + test_disease: .: (0.000218) + test_entry_id: .: (0.000213) + test_lineage: .: (0.000233) + test_nalen: .: (0.000261) + test_name: .: (0.000225) + test_new: .: (0.000218) + test_num_gene: .: (0.000203) + test_num_rna: .: (0.000223) + test_original_databases: .: (0.000232) + test_original_db: .: (0.000216) + test_plasmids: .: (0.000229) + test_references: .: (0.001541) + test_statistics: .: (0.000260) + test_taxid: .: (0.000294) + test_taxonomy: .: (0.000258) Bio::TestBioKEGGGENOME_T00070: - test_chromosomes: .: (0.000355) - test_comment: .: (0.000275) - test_data_source: .: (0.000147) - test_definition: .: (0.000135) - test_disease: .: (0.000119) - test_entry_id: .: (0.005620) - test_lineage: .: (0.000436) - test_nalen: .: (0.000155) - test_name: .: (0.000144) - test_new: .: (0.000140) - test_num_gene: .: (0.000132) - test_num_rna: .: (0.000129) - test_original_databases: .: (0.000157) - test_original_db: .: (0.000151) - test_plasmids: .: (0.000227) - test_references: .: (0.000292) - test_statistics: .: (0.000159) - test_taxid: .: (0.000646) - test_taxonomy: .: (0.000312) + test_chromosomes: .: (0.000369) + test_comment: .: (0.000188) + test_data_source: .: (0.000176) + test_definition: .: (0.000163) + test_disease: .: (0.000144) + test_entry_id: .: (0.000148) + test_lineage: .: (0.000261) + test_nalen: .: (0.000162) + test_name: .: (0.000136) + test_new: .: (0.000133) + test_num_gene: .: (0.000125) + test_num_rna: .: (0.000114) + test_original_databases: .: (0.000120) + test_original_db: .: (0.000129) + test_plasmids: .: (0.000190) + test_references: .: (0.006052) + test_statistics: .: (0.000408) + test_taxid: .: (0.000209) + test_taxonomy: .: (0.000181) Bio::TestBioKEGGPATHWAY_ec00072: - test_compounds_as_hash: .: (0.000314) - test_compounds_as_strings: .: (0.000133) - test_dblinks_as_hash: .: (0.000108) - test_dblinks_as_strings: .: (0.000096) - test_description: .: (0.000128) - test_diseases_as_hash: .: (0.000107) - test_diseases_as_strings: .: (0.000095) - test_entry_id: .: (0.000117) - test_enzymes_as_strings: .: (0.000115) - test_genes_as_hash: .: (0.000102) - test_genes_as_strings: .: (0.000331) - test_keggclass: .: (0.000163) - test_ko_pathway: .: (0.000112) - test_modules_as_hash: .: (0.000118) - test_modules_as_strings: .: (0.000100) - test_name: .: (0.000129) - test_new: .: (0.000129) - test_organism: .: (0.000115) - test_orthologs_as_hash: .: (0.000100) - test_orthologs_as_strings: .: (0.000090) - test_pathways_as_hash: .: (0.000105) - test_pathways_as_strings: .: (0.000095) - test_reactions_as_hash: .: (0.000093) - test_reactions_as_strings: .: (0.000090) - test_references: .: (0.000094) - test_rel_pathways_as_hash: .: (0.000122) - test_rel_pathways_as_strings: .: (0.000329) + test_compounds_as_hash: .: (0.000331) + test_compounds_as_strings: .: (0.000154) + test_dblinks_as_hash: .: (0.000125) + test_dblinks_as_strings: .: (0.000104) + test_description: .: (0.000145) + test_diseases_as_hash: .: (0.000119) + test_diseases_as_strings: .: (0.000117) + test_entry_id: .: (0.000141) + test_enzymes_as_strings: .: (0.000159) + test_genes_as_hash: .: (0.000667) + test_genes_as_strings: .: (0.000289) + test_keggclass: .: (0.000178) + test_ko_pathway: .: (0.000136) + test_modules_as_hash: .: (0.000138) + test_modules_as_strings: .: (0.000115) + test_name: .: (0.000137) + test_new: .: (0.000142) + test_organism: .: (0.000141) + test_orthologs_as_hash: .: (0.000154) + test_orthologs_as_strings: .: (0.000113) + test_pathways_as_hash: .: (0.000125) + test_pathways_as_strings: .: (0.000114) + test_reactions_as_hash: .: (0.000109) + test_reactions_as_strings: .: (0.000104) + test_references: .: (0.000112) + test_rel_pathways_as_hash: .: (0.000423) + test_rel_pathways_as_strings: .: (0.000177) Bio::TestBioKEGGPATHWAY_hsa00790: - test_compounds_as_hash: .: (0.000385) - test_compounds_as_strings: .: (0.000181) - test_dblinks_as_hash: .: (0.000129) - test_dblinks_as_strings: .: (0.000114) - test_description: .: (0.000129) - test_diseases_as_hash: .: (0.000127) - test_diseases_as_strings: .: (0.000115) - test_entry_id: .: (0.000128) - test_enzymes_as_strings: .: (0.000137) - test_genes_as_hash: .: (0.000178) - test_genes_as_strings: .: (0.000144) - test_keggclass: .: (0.000133) - test_ko_pathway: .: (0.000353) - test_modules_as_hash: .: (0.000132) - test_modules_as_strings: .: (0.000113) - test_name: .: (0.000125) - test_new: .: (0.000129) - test_organism: .: (0.000125) - test_orthologs_as_hash: .: (0.000416) - test_orthologs_as_strings: .: (0.000116) - test_pathways_as_hash: .: (0.000118) - test_pathways_as_strings: .: (0.000108) - test_reactions_as_hash: .: (0.000105) - test_reactions_as_strings: .: (0.000099) - test_references: .: (0.000105) + test_compounds_as_hash: .: (0.000414) + test_compounds_as_strings: .: (0.000206) + test_dblinks_as_hash: .: (0.000146) + test_dblinks_as_strings: .: (0.000121) + test_description: .: (0.000161) + test_diseases_as_hash: .: (0.000147) + test_diseases_as_strings: .: (0.000168) + test_entry_id: .: (0.000138) + test_enzymes_as_strings: .: (0.000117) + test_genes_as_hash: .: (0.000174) + test_genes_as_strings: .: (0.000149) + test_keggclass: .: (0.000139) + test_ko_pathway: .: (0.000130) + test_modules_as_hash: .: (0.000389) + test_modules_as_strings: .: (0.000134) + test_name: .: (0.000136) + test_new: .: (0.000141) + test_organism: .: (0.000134) + test_orthologs_as_hash: .: (0.000114) + test_orthologs_as_strings: .: (0.000169) + test_pathways_as_hash: .: (0.000141) + test_pathways_as_strings: .: (0.000116) + test_reactions_as_hash: .: (0.000110) + test_reactions_as_strings: .: (0.000107) + test_references: .: (0.000113) test_rel_pathways_as_hash: .: (0.000134) - test_rel_pathways_as_strings: .: (0.000118) + test_rel_pathways_as_strings: .: (0.015264) Bio::TestBioKEGGPATHWAY_ko00312: - test_compounds_as_hash: .: (0.000246) - test_compounds_as_strings: .: (0.000110) - test_dblinks_as_hash: .: (0.000096) - test_dblinks_as_strings: .: (0.000087) - test_description: .: (0.000136) - test_diseases_as_hash: .: (0.000102) - test_diseases_as_strings: .: (0.000211) - test_entry_id: .: (0.000128) - test_enzymes_as_strings: .: (0.000111) - test_genes_as_hash: .: (0.000101) - test_genes_as_strings: .: (0.000091) - test_keggclass: .: (0.000111) - test_ko_pathway: .: (0.000100) - test_modules_as_hash: .: (0.000091) - test_modules_as_strings: .: (0.000085) - test_name: .: (0.000101) - test_new: .: (0.000105) - test_organism: .: (0.000099) - test_orthologs_as_hash: .: (0.000136) - test_orthologs_as_strings: .: (0.000110) - test_pathways_as_hash: .: (0.000099) - test_pathways_as_strings: .: (0.000091) - test_reactions_as_hash: .: (0.000091) - test_reactions_as_strings: .: (0.000088) - test_references: .: (0.000087) - test_rel_pathways_as_hash: .: (0.000101) - test_rel_pathways_as_strings: .: (0.000097) + test_compounds_as_hash: .: (0.000341) + test_compounds_as_strings: .: (0.000132) + test_dblinks_as_hash: .: (0.000112) + test_dblinks_as_strings: .: (0.000101) + test_description: .: (0.000129) + test_diseases_as_hash: .: (0.000131) + test_diseases_as_strings: .: (0.000112) + test_entry_id: .: (0.000122) + test_enzymes_as_strings: .: (0.000098) + test_genes_as_hash: .: (0.000095) + test_genes_as_strings: .: (0.000095) + test_keggclass: .: (0.000123) + test_ko_pathway: .: (0.000117) + test_modules_as_hash: .: (0.000112) + test_modules_as_strings: .: (0.000109) + test_name: .: (0.000436) + test_new: .: (0.000148) + test_organism: .: (0.000133) + test_orthologs_as_hash: .: (0.000162) + test_orthologs_as_strings: .: (0.000123) + test_pathways_as_hash: .: (0.000134) + test_pathways_as_strings: .: (0.000130) + test_reactions_as_hash: .: (0.000109) + test_reactions_as_strings: .: (0.000094) + test_references: .: (0.000091) + test_rel_pathways_as_hash: .: (0.000108) + test_rel_pathways_as_strings: .: (0.000100) Bio::TestBioKEGGPATHWAY_map00030: - test_compounds_as_hash: .: (0.000251) - test_compounds_as_strings: .: (0.000116) - test_dblinks_as_hash: .: (0.000124) - test_dblinks_as_strings: .: (0.000110) - test_description: .: (0.000203) - test_diseases_as_hash: .: (0.000143) - test_diseases_as_strings: .: (0.000121) - test_entry_id: .: (0.000129) - test_enzymes_as_strings: .: (0.000107) - test_genes_as_hash: .: (0.000107) + test_compounds_as_hash: .: (0.000267) + test_compounds_as_strings: .: (0.000150) + test_dblinks_as_hash: .: (0.000168) + test_dblinks_as_strings: .: (0.000125) + test_description: .: (0.000225) + test_diseases_as_hash: .: (0.000132) + test_diseases_as_strings: .: (0.000116) + test_entry_id: .: (0.000135) + test_enzymes_as_strings: .: (0.000117) + test_genes_as_hash: .: (0.000105) test_genes_as_strings: .: (0.000103) - test_keggclass: .: (0.000129) - test_ko_pathway: .: (0.000121) - test_modules_as_hash: .: (0.000168) - test_modules_as_strings: .: (0.000125) - test_name: .: (0.000121) - test_new: .: (0.000127) - test_organism: .: (0.000127) - test_orthologs_as_hash: .: (0.000109) - test_orthologs_as_strings: .: (0.000105) - test_pathways_as_hash: .: (0.000122) - test_pathways_as_strings: .: (0.000109) - test_reactions_as_hash: .: (0.000108) - test_reactions_as_strings: .: (0.000103) - test_references: .: (0.000482) - test_rel_pathways_as_hash: .: (0.000175) - test_rel_pathways_as_strings: .: (0.000125) + test_keggclass: .: (0.000123) + test_ko_pathway: .: (0.000122) + test_modules_as_hash: .: (0.000171) + test_modules_as_strings: .: (0.000128) + test_name: .: (0.000143) + test_new: .: (0.000128) + test_organism: .: (0.000159) + test_orthologs_as_hash: .: (0.000156) + test_orthologs_as_strings: .: (0.000150) + test_pathways_as_hash: .: (0.000139) + test_pathways_as_strings: .: (0.000128) + test_reactions_as_hash: .: (0.000117) + test_reactions_as_strings: .: (0.000106) + test_references: .: (0.000475) + test_rel_pathways_as_hash: .: (0.000232) + test_rel_pathways_as_strings: .: (0.000138) Bio::TestBioKeggDRUG: - test_activity: .: (0.000294) - test_comment: .: (0.000144) - test_dblinks_as_hash: .: (0.005874) - test_dblinks_as_strings: .: (0.000452) - test_entry_id: .: (0.000179) - test_formula: .: (0.000143) - test_kcf: .: (0.000124) - test_mass: .: (0.000140) - test_name: .: (0.000158) - test_names: .: (0.000160) - test_pathways_as_hash: .: (0.000165) - test_pathways_as_strings: .: (0.000138) - test_products: .: (0.000151) - test_remark: .: (0.000169) -Bio::TestBioKeggGLYCAN: - test_comment: .: (0.000702) - test_composition: .: (0.000296) - test_compounds: .: (0.000155) - test_dblinks_as_hash: .: (0.000625) - test_dblinks_as_strings: .: (0.000205) - test_entry_id: .: (0.000150) - test_enzymes: .: (0.000152) + test_activity: .: (0.000303) + test_comment: .: (0.000149) + test_dblinks_as_hash: .: (0.000191) + test_dblinks_as_strings: .: (0.000142) + test_entry_id: .: (0.000143) + test_formula: .: (0.000131) test_kcf: .: (0.000117) - test_keggclass: .: (0.000464) - test_mass: .: (0.000160) - test_name: .: (0.000125) - test_orthologs_as_hash: .: (0.000187) - test_orthologs_as_strings: .: (0.000174) - test_pathways_as_hash: .: (0.000151) - test_pathways_as_strings: .: (0.000121) - test_reactions: .: (0.000137) - test_references: .: (0.000192) - test_remark: .: (0.000143) + test_mass: .: (0.000133) + test_name: .: (0.000152) + test_names: .: (0.000151) + test_pathways_as_hash: .: (0.000146) + test_pathways_as_strings: .: (0.006421) + test_products: .: (0.000238) + test_remark: .: (0.000199) +Bio::TestBioKeggGLYCAN: + test_comment: .: (0.000327) + test_composition: .: (0.000197) + test_compounds: .: (0.000161) + test_dblinks_as_hash: .: (0.000879) + test_dblinks_as_strings: .: (0.000208) + test_entry_id: .: (0.000155) + test_enzymes: .: (0.000157) + test_kcf: .: (0.000121) + test_keggclass: .: (0.000512) + test_mass: .: (0.000199) + test_name: .: (0.000145) + test_orthologs_as_hash: .: (0.000202) + test_orthologs_as_strings: .: (0.000153) + test_pathways_as_hash: .: (0.000152) + test_pathways_as_strings: .: (0.000126) + test_reactions: .: (0.000143) + test_references: .: (0.000176) + test_remark: .: (0.000141) Bio::TestBioKeggGLYCAN_G01366: - test_comment: .: (0.000243) - test_composition: .: (0.000427) - test_compounds: .: (0.000139) - test_dblinks_as_hash: .: (0.000143) - test_dblinks_as_strings: .: (0.000108) - test_entry_id: .: (0.000110) - test_enzymes: .: (0.000104) - test_kcf: .: (0.000092) - test_keggclass: .: (0.000109) - test_mass: .: (0.000109) - test_name: .: (0.000426) - test_orthologs_as_hash: .: (0.000122) - test_orthologs_as_strings: .: (0.000091) - test_pathways_as_hash: .: (0.000095) - test_pathways_as_strings: .: (0.000088) - test_reactions: .: (0.000102) - test_references: .: (0.000122) - test_remark: .: (0.000112) + test_comment: .: (0.000268) + test_composition: .: (0.000511) + test_compounds: .: (0.000166) + test_dblinks_as_hash: .: (0.000159) + test_dblinks_as_strings: .: (0.000121) + test_entry_id: .: (0.000132) + test_enzymes: .: (0.000121) + test_kcf: .: (0.000105) + test_keggclass: .: (0.000129) + test_mass: .: (0.000128) + test_name: .: (0.000403) + test_orthologs_as_hash: .: (0.000139) + test_orthologs_as_strings: .: (0.000104) + test_pathways_as_hash: .: (0.000099) + test_pathways_as_strings: .: (0.000091) + test_reactions: .: (0.000110) + test_references: .: (0.000101) + test_remark: .: (0.000111) Bio::TestBioKeggPathway_rn00250: - test_compounds_as_hash: .: (0.000389) - test_compounds_as_strings: .: (0.000196) - test_dblinks_as_hash: .: (0.000148) - test_dblinks_as_strings: .: (0.000131) - test_description: .: (0.000138) - test_diseases_as_hash: .: (0.000151) - test_diseases_as_strings: .: (0.000135) - test_entry_id: .: (0.000142) - test_enzymes_as_strings: .: (0.000124) - test_genes_as_hash: .: (0.000127) - test_genes_as_strings: .: (0.000124) - test_keggclass: .: (0.000139) - test_ko_pathway: .: (0.000142) - test_modules_as_hash: .: (0.000191) - test_modules_as_strings: .: (0.000154) - test_name: .: (0.000146) - test_new: .: (0.000143) - test_organism: .: (0.000136) - test_orthologs_as_hash: .: (0.000130) - test_orthologs_as_strings: .: (0.000115) - test_pathways_as_hash: .: (0.000169) - test_pathways_as_strings: .: (0.000141) - test_reactions_as_hash: .: (0.000333) - test_reactions_as_strings: .: (0.000244) - test_references: .: (0.000366) - test_rel_pathways_as_hash: .: (0.000244) - test_rel_pathways_as_strings: .: (0.000179) + test_compounds_as_hash: .: (0.000412) + test_compounds_as_strings: .: (0.000207) + test_dblinks_as_hash: .: (0.000159) + test_dblinks_as_strings: .: (0.000159) + test_description: .: (0.000173) + test_diseases_as_hash: .: (0.000171) + test_diseases_as_strings: .: (0.000537) + test_entry_id: .: (0.000196) + test_enzymes_as_strings: .: (0.000172) + test_genes_as_hash: .: (0.000155) + test_genes_as_strings: .: (0.000138) + test_keggclass: .: (0.000167) + test_ko_pathway: .: (0.000151) + test_modules_as_hash: .: (0.000197) + test_modules_as_strings: .: (0.000169) + test_name: .: (0.000161) + test_new: .: (0.000154) + test_organism: .: (0.000159) + test_orthologs_as_hash: .: (0.000133) + test_orthologs_as_strings: .: (0.000124) + test_pathways_as_hash: .: (0.000137) + test_pathways_as_strings: .: (0.000131) + test_reactions_as_hash: .: (0.000328) + test_reactions_as_strings: .: (0.000239) + test_references: .: (0.000363) + test_rel_pathways_as_hash: .: (0.000254) + test_rel_pathways_as_strings: .: (0.000210) Bio::TestBioLITDB: - test_author: .: (0.000285) - test_entry_id: .: (0.000112) - test_field: .: (0.000106) - test_journal: .: (0.000100) - test_keyword: .: (0.000123) - test_reference: .: (0.000235) - test_title: .: (0.000135) - test_volume: .: (0.000108) + test_author: .: (0.000322) + test_entry_id: .: (0.000130) + test_field: .: (0.000115) + test_journal: .: (0.000109) + test_keyword: .: (0.000134) + test_reference: .: (0.000243) + test_title: .: (0.000138) + test_volume: .: (0.000116) Bio::TestBioNBRF: - test_aalen: .: (0.000232) - test_aaseq: .: (0.000092) - test_entry: .: (0.000077) - test_length: .: (0.005528) - test_nalen: .: (0.000487) - test_naseq: .: (0.000133) - test_seq: .: (0.000107) - test_seq_class: .: (0.000093) - test_to_nbrf: .: (0.000116) + test_aalen: .: (0.000240) + test_aaseq: .: (0.000104) + test_entry: .: (0.000085) + test_length: .: (0.000085) + test_nalen: .: (0.000149) + test_naseq: .: (0.000114) + test_seq: .: (0.000097) + test_seq_class: .: (0.000110) + test_to_nbrf: .: (0.000113) Bio::TestBioTreeOutputPrivate: - test_to_newick_format_label: .: (0.000257) - test_to_newick_format_leaf: .: (0.000180) - test_to_newick_format_leaf_NHX: .: (0.000149) + test_to_newick_format_label: .: (0.000227) + test_to_newick_format_leaf: .: (0.000158) + test_to_newick_format_leaf_NHX: .: (0.000138) Bio::TestBl2seqReport: - test_db_len: .: (0.000553) - test_db_num: .: (0.000783) - test_new: .: (0.000247) - test_undefed_methods: .: (0.000704) - test_undefed_methods_for_iteration: .: (0.000650) + test_db_len: .: (0.000566) + test_db_num: .: (0.006125) + test_new: .: (0.000560) + test_undefed_methods: .: (0.000713) + test_undefed_methods_for_iteration: .: (0.000695) Bio::TestBl2seqReportConstants: - test_rs: .: (0.000173) + test_rs: .: (0.000187) Bio::TestBl2seqReportHit: - test_empty_hits: .: (0.000284) - test_hits: .: (0.000203) + test_empty_hits: .: (0.000330) + test_hits: .: (0.000223) Bio::TestBlast: - test_blast_reports_format0: .: (0.004744) - test_blast_reports_format0_with_block: .: (0.000893) - test_blast_reports_format7: .: (0.043943) - test_blast_reports_format7_with_block: .: (0.007277) - test_blast_reports_format7_with_parser: .: (0.006789) - test_blast_reports_format7_with_parser_with_block: .: (0.009845) - test_blast_reports_format8: .: (0.000737) - test_blast_reports_format8_with_block: .: (0.000395) - test_blast_reports_format8_with_parser: .: (0.000200) - test_blast_reports_format8_with_parser_with_block: .: (0.000162) - test_blast_reports_xml: .: (0.007367) - test_blast_reports_xml_with_block: .: (0.006511) - test_blastll: .: (0.000173) - test_db: .: (0.000084) - test_exec_genomenet: .: (0.000066) - test_exec_local: .: (0.000061) - test_exec_ncbi: .: (0.000063) - test_filter: .: (0.000074) - test_format: .: (0.000081) - test_make_command_line: .: (0.000274) - test_make_command_line_2: .: (0.000205) - test_matrix: .: (0.000074) - test_new: .: (0.000174) + test_blast_reports_format0: .: (0.005075) + test_blast_reports_format0_with_block: .: (0.000680) + test_blast_reports_format7: .: (0.045152) + test_blast_reports_format7_with_block: .: (0.008333) + test_blast_reports_format7_with_parser: .: (0.006355) + test_blast_reports_format7_with_parser_with_block: .: (0.006827) + test_blast_reports_format8: .: (0.000674) + test_blast_reports_format8_with_block: .: (0.000391) + test_blast_reports_format8_with_parser: .: (0.000205) + test_blast_reports_format8_with_parser_with_block: .: (0.000260) + test_blast_reports_xml: .: (0.010513) + test_blast_reports_xml_with_block: .: (0.006892) + test_blastll: .: (0.000170) + test_db: .: (0.000085) + test_exec_genomenet: .: (0.000072) + test_exec_local: .: (0.000064) + test_exec_ncbi: .: (0.000065) + test_filter: .: (0.000186) + test_format: .: (0.000086) + test_make_command_line: .: (0.000286) + test_make_command_line_2: .: (0.000234) + test_matrix: .: (0.000080) + test_new: .: (0.000131) test_new_opt_string: .: (0.000136) - test_option: .: (0.000092) - test_option_set: .: (0.000132) - test_option_set_m0: .: (0.000109) - test_options: .: (0.000071) - test_output: .: (0.000070) - test_parse_result: .: (0.006057) - test_parser: .: (0.000160) - test_program: .: (0.000089) - test_query: .: (0.000077) - test_self_local: .: (0.000136) - test_self_remote: .: (0.001427) - test_server: .: (0.000139) + test_option: .: (0.000099) + test_option_set: .: (0.000140) + test_option_set_m0: .: (0.000113) + test_options: .: (0.000072) + test_output: .: (0.000072) + test_parse_result: .: (0.006330) + test_parser: .: (0.000175) + test_program: .: (0.000083) + test_query: .: (0.000066) + test_self_local: .: (0.000143) + test_self_remote: .: (0.001367) + test_server: .: (0.000145) Bio::TestBlastNCBIOptions: - test_add_options: .: (0.000276) - test_delete: .: (0.000186) - test_equal_equal: .: (0.000199) - test_get: .: (0.000287) - test_make_command_line_options: .: (0.000175) - test_normalize!: .: (0.000111) - test_parse: .: (0.000126) - test_set: .: (0.000324) + test_add_options: .: (0.000303) + test_delete: .: (0.000215) + test_equal_equal: .: (0.000214) + test_get: .: (0.000182) + test_make_command_line_options: .: (0.000188) + test_normalize!: .: (0.000126) + test_parse: .: (0.000135) + test_set: .: (0.000243) Bio::TestBlastReport: - test_db: .: (0.011096) - test_db_len: .: (0.006492) - test_db_num: .: (0.006635) - test_each_hit: .: (0.009592) - test_each_iteration: .: (0.006641) - test_eff_space: .: (0.006227) - test_entrez_query: .: (0.005943) - test_entropy: .: (0.009294) - test_expect: .: (0.006473) - test_filter: .: (0.006336) - test_gap_extend: .: (0.008645) - test_gap_open: .: (0.006577) - test_hits: .: (0.006347) - test_hsp_len: .: (0.005945) - test_inclusion: .: (0.008634) - test_iterations: .: (0.006421) - test_kappa: .: (0.006240) - test_lambda: .: (0.008223) - test_matrix: .: (0.006424) - test_message: .: (0.006276) - test_parameters: .: (0.007483) - test_pattern: .: (0.007365) - test_program: .: (0.006194) - test_query_def: .: (0.006278) - test_query_id: .: (0.008509) - test_query_len: .: (0.006705) - test_reference: .: (0.006626) - test_sc_match: .: (0.007664) - test_sc_mismatch: .: (0.007624) - test_statistics: .: (0.006544) - test_version: .: (0.006301) + test_db: .: (0.011157) + test_db_len: .: (0.006790) + test_db_num: .: (0.006443) + test_each_hit: .: (0.008928) + test_each_iteration: .: (0.007670) + test_eff_space: .: (0.006498) + test_entrez_query: .: (0.006254) + test_entropy: .: (0.009250) + test_expect: .: (0.006713) + test_filter: .: (0.006306) + test_gap_extend: .: (0.008142) + test_gap_open: .: (0.007548) + test_hits: .: (0.006352) + test_hsp_len: .: (0.006220) + test_inclusion: .: (0.008700) + test_iterations: .: (0.006655) + test_kappa: .: (0.006383) + test_lambda: .: (0.007830) + test_matrix: .: (0.007489) + test_message: .: (0.006493) + test_parameters: .: (0.006118) + test_pattern: .: (0.008586) + test_program: .: (0.006682) + test_query_def: .: (0.006393) + test_query_id: .: (0.008566) + test_query_len: .: (0.006572) + test_reference: .: (0.006271) + test_sc_match: .: (0.006225) + test_sc_mismatch: .: (0.009115) + test_statistics: .: (0.006481) + test_version: .: (0.006347) Bio::TestBlastReportDefault: - test_db: .: (0.000641) - test_db_len: .: (0.000448) - test_db_num: .: (0.000400) - test_each_hit: .: (0.000395) - test_each_iteration: .: (0.000343) - test_eff_space: .: (0.000445) - test_entropy: .: (0.000437) - test_expect: .: (0.000417) - test_gap_extend: .: (0.000398) - test_gap_open: .: (0.000394) - test_gapped_entropy: .: (0.000370) - test_gapped_kappa: .: (0.000360) - test_gapped_lambda: .: (0.000361) - test_hits: .: (0.000415) - test_iterations: .: (0.000385) - test_kappa: .: (0.000375) - test_lambda: .: (0.000355) - test_matrix: .: (0.000425) - test_message: .: (0.000333) - test_pattern: .: (0.000327) - test_program: .: (0.000362) - test_query_def: .: (0.000414) - test_query_len: .: (0.000361) - test_reference: .: (0.000402) - test_sc_match: .: (0.000413) - test_sc_mismatch: .: (0.000399) - test_version: .: (0.000343) + test_db: .: (0.000531) + test_db_len: .: (0.000335) + test_db_num: .: (0.000321) + test_each_hit: .: (0.000360) + test_each_iteration: .: (0.000278) + test_eff_space: .: (0.000377) + test_entropy: .: (0.000349) + test_expect: .: (0.000343) + test_gap_extend: .: (0.000324) + test_gap_open: .: (0.000316) + test_gapped_entropy: .: (0.000290) + test_gapped_kappa: .: (0.000278) + test_gapped_lambda: .: (0.000267) + test_hits: .: (0.000288) + test_iterations: .: (0.000252) + test_kappa: .: (0.000298) + test_lambda: .: (0.000284) + test_matrix: .: (0.000335) + test_message: .: (0.000263) + test_pattern: .: (0.000311) + test_program: .: (0.000299) + test_query_def: .: (0.000290) + test_query_len: .: (0.000268) + test_reference: .: (0.000289) + test_sc_match: .: (0.000316) + test_sc_mismatch: .: (0.000307) + test_version: .: (0.000273) Bio::TestBlastReportHit: - test_Hit_accession: .: (0.009684) - test_Hit_bit_score: .: (0.006658) - test_Hit_definition: .: (0.006436) - test_Hit_evalue: .: (0.009021) - test_Hit_hit_id: .: (0.006751) - test_Hit_hsps: .: (0.006514) - test_Hit_identity: .: (0.009038) - test_Hit_lap_at: .: (0.006822) - test_Hit_len: .: (0.006462) - test_Hit_midline: .: (0.007988) - test_Hit_num: .: (0.007687) - test_Hit_overlap: .: (0.006569) - test_Hit_query_def: .: (0.006516) - test_Hit_query_end: .: (0.008461) - test_Hit_query_id: .: (0.006796) - test_Hit_query_len: .: (0.006573) - test_Hit_query_seq: .: (0.008708) - test_Hit_query_start: .: (0.006965) - test_Hit_taeget_def: .: (0.006525) - test_Hit_target_end: .: (0.007665) - test_Hit_target_id: .: (0.007742) - test_Hit_target_len: .: (0.006572) - test_Hit_target_seq: .: (0.006379) - test_Hit_target_start: .: (0.008530) + test_Hit_accession: .: (0.009515) + test_Hit_bit_score: .: (0.006792) + test_Hit_definition: .: (0.006322) + test_Hit_evalue: .: (0.009180) + test_Hit_hit_id: .: (0.006670) + test_Hit_hsps: .: (0.006324) + test_Hit_identity: .: (0.008406) + test_Hit_lap_at: .: (0.007768) + test_Hit_len: .: (0.006650) + test_Hit_midline: .: (0.006104) + test_Hit_num: .: (0.008832) + test_Hit_overlap: .: (0.006769) + test_Hit_query_def: .: (0.006279) + test_Hit_query_end: .: (0.008577) + test_Hit_query_id: .: (0.006671) + test_Hit_query_len: .: (0.006351) + test_Hit_query_seq: .: (0.008769) + test_Hit_query_start: .: (0.006751) + test_Hit_taeget_def: .: (0.006336) + test_Hit_target_end: .: (0.007911) + test_Hit_target_id: .: (0.007830) + test_Hit_target_len: .: (0.006454) + test_Hit_target_seq: .: (0.006210) + test_Hit_target_start: .: (0.008563) Bio::TestBlastReportHitDefault: - test_Hit_bit_score: .: (0.001046) - test_Hit_definition: .: (0.000537) - test_Hit_evalue: .: (0.000496) - test_Hit_hsps: .: (0.000413) - test_Hit_identity: .: (0.000413) - test_Hit_lap_at: .: (0.000674) - test_Hit_len: .: (0.000432) - test_Hit_midline: .: (0.000517) - test_Hit_overlap: .: (0.000401) - test_Hit_query_end: .: (0.000461) - test_Hit_query_seq: .: (0.000475) - test_Hit_query_start: .: (0.000607) - test_Hit_taeget_def: .: (0.000373) - test_Hit_target_end: .: (0.000494) - test_Hit_target_id: .: (0.000412) - test_Hit_target_len: .: (0.000367) - test_Hit_target_seq: .: (0.000648) - test_Hit_target_start: .: (0.000454) + test_Hit_bit_score: .: (0.000808) + test_Hit_definition: .: (0.000380) + test_Hit_evalue: .: (0.000563) + test_Hit_hsps: .: (0.000299) + test_Hit_identity: .: (0.000285) + test_Hit_lap_at: .: (0.000431) + test_Hit_len: .: (0.000336) + test_Hit_midline: .: (0.000416) + test_Hit_overlap: .: (0.000561) + test_Hit_query_end: .: (0.000412) + test_Hit_query_seq: .: (0.000399) + test_Hit_query_start: .: (0.000379) + test_Hit_taeget_def: .: (0.000314) + test_Hit_target_end: .: (0.000637) + test_Hit_target_id: .: (0.000357) + test_Hit_target_len: .: (0.000307) + test_Hit_target_seq: .: (0.000379) + test_Hit_target_start: .: (0.000367) Bio::TestBlastReportHitMulti: - test_Hit_accession: .: (0.020172) - test_Hit_bit_score: .: (0.019922) - test_Hit_definition: .: (0.020452) - test_Hit_evalue: .: (0.020340) - test_Hit_hit_id: .: (0.019690) - test_Hit_hsps: .: (0.019599) - test_Hit_identity: .: (0.019682) - test_Hit_lap_at: .: (0.019602) - test_Hit_len: .: (0.019881) - test_Hit_midline: .: (0.019872) - test_Hit_num: .: (0.019761) - test_Hit_overlap: .: (0.019788) - test_Hit_query_def: .: (0.019821) - test_Hit_query_end: .: (0.019678) - test_Hit_query_id: .: (0.019829) - test_Hit_query_len: .: (0.019915) - test_Hit_query_seq: .: (0.019787) - test_Hit_query_start: .: (0.032428) - test_Hit_taeget_def: .: (0.029249) - test_Hit_target_end: .: (0.020234) - test_Hit_target_id: .: (0.020009) - test_Hit_target_len: .: (0.019818) - test_Hit_target_seq: .: (0.020033) - test_Hit_target_start: .: (0.019825) + test_Hit_accession: .: (0.020423) + test_Hit_bit_score: .: (0.020202) + test_Hit_definition: .: (0.020375) + test_Hit_evalue: .: (0.020257) + test_Hit_hit_id: .: (0.019775) + test_Hit_hsps: .: (0.019609) + test_Hit_identity: .: (0.019840) + test_Hit_lap_at: .: (0.019470) + test_Hit_len: .: (0.019498) + test_Hit_midline: .: (0.019428) + test_Hit_num: .: (0.019516) + test_Hit_overlap: .: (0.019469) + test_Hit_query_def: .: (0.019335) + test_Hit_query_end: .: (0.019450) + test_Hit_query_id: .: (0.019343) + test_Hit_query_len: .: (0.019376) + test_Hit_query_seq: .: (0.019320) + test_Hit_query_start: .: (0.019558) + test_Hit_taeget_def: .: (0.019747) + test_Hit_target_end: .: (0.019327) + test_Hit_target_id: .: (0.019442) + test_Hit_target_len: .: (0.019507) + test_Hit_target_seq: .: (0.019434) + test_Hit_target_start: .: (0.019803) Bio::TestBlastReportHitMultiREXML: - test_Hit_accession: .: (0.020018) - test_Hit_bit_score: .: (0.019791) - test_Hit_definition: .: (0.019789) - test_Hit_evalue: .: (0.019803) - test_Hit_hit_id: .: (0.019801) - test_Hit_hsps: .: (0.019801) - test_Hit_identity: .: (0.019859) - test_Hit_lap_at: .: (0.019746) - test_Hit_len: .: (0.019719) - test_Hit_midline: .: (0.019652) - test_Hit_num: .: (0.019636) - test_Hit_overlap: .: (0.019936) - test_Hit_query_def: .: (0.019767) - test_Hit_query_end: .: (0.019759) - test_Hit_query_id: .: (0.019605) - test_Hit_query_len: .: (0.019898) - test_Hit_query_seq: .: (0.019847) - test_Hit_query_start: .: (0.019717) - test_Hit_taeget_def: .: (0.019561) - test_Hit_target_end: .: (0.019642) - test_Hit_target_id: .: (0.037882) - test_Hit_target_len: .: (0.037754) - test_Hit_target_seq: .: (0.040306) - test_Hit_target_start: .: (0.040236) + test_Hit_accession: .: (0.019654) + test_Hit_bit_score: .: (0.019467) + test_Hit_definition: .: (0.019633) + test_Hit_evalue: .: (0.019658) + test_Hit_hit_id: .: (0.019307) + test_Hit_hsps: .: (0.019364) + test_Hit_identity: .: (0.019389) + test_Hit_lap_at: .: (0.019532) + test_Hit_len: .: (0.019387) + test_Hit_midline: .: (0.019117) + test_Hit_num: .: (0.019391) + test_Hit_overlap: .: (0.019259) + test_Hit_query_def: .: (0.019318) + test_Hit_query_end: .: (0.019334) + test_Hit_query_id: .: (0.019357) + test_Hit_query_len: .: (0.019362) + test_Hit_query_seq: .: (0.019261) + test_Hit_query_start: .: (0.019184) + test_Hit_taeget_def: .: (0.019290) + test_Hit_target_end: .: (0.019248) + test_Hit_target_id: .: (0.019411) + test_Hit_target_len: .: (0.019176) + test_Hit_target_seq: .: (0.019277) + test_Hit_target_start: .: (0.019309) Bio::TestBlastReportHitREXML: - test_Hit_accession: .: (0.017106) - test_Hit_bit_score: .: (0.013216) - test_Hit_definition: .: (0.012319) - test_Hit_evalue: .: (0.018160) - test_Hit_hit_id: .: (0.017647) - test_Hit_hsps: .: (0.011804) - test_Hit_identity: .: (0.017158) - test_Hit_lap_at: .: (0.014944) - test_Hit_len: .: (0.010596) - test_Hit_midline: .: (0.019128) - test_Hit_num: .: (0.013331) - test_Hit_overlap: .: (0.011433) - test_Hit_query_def: .: (0.019055) - test_Hit_query_end: .: (0.015056) - test_Hit_query_id: .: (0.018468) - test_Hit_query_len: .: (0.019800) - test_Hit_query_seq: .: (0.013098) - test_Hit_query_start: .: (0.010637) - test_Hit_taeget_def: .: (0.018110) - test_Hit_target_end: .: (0.013354) - test_Hit_target_id: .: (0.011366) - test_Hit_target_len: .: (0.016015) - test_Hit_target_seq: .: (0.011582) - test_Hit_target_start: .: (0.013427) + test_Hit_accession: .: (0.008321) + test_Hit_bit_score: .: (0.006436) + test_Hit_definition: .: (0.006202) + test_Hit_evalue: .: (0.008260) + test_Hit_hit_id: .: (0.006507) + test_Hit_hsps: .: (0.006179) + test_Hit_identity: .: (0.008222) + test_Hit_lap_at: .: (0.006527) + test_Hit_len: .: (0.006227) + test_Hit_midline: .: (0.008429) + test_Hit_num: .: (0.006464) + test_Hit_overlap: .: (0.006185) + test_Hit_query_def: .: (0.008291) + test_Hit_query_end: .: (0.006455) + test_Hit_query_id: .: (0.006231) + test_Hit_query_len: .: (0.008195) + test_Hit_query_seq: .: (0.006436) + test_Hit_query_start: .: (0.006179) + test_Hit_taeget_def: .: (0.008155) + test_Hit_target_end: .: (0.006459) + test_Hit_target_id: .: (0.006170) + test_Hit_target_len: .: (0.008231) + test_Hit_target_seq: .: (0.006457) + test_Hit_target_start: .: (0.006124) Bio::TestBlastReportHitTabular: - test_Hit_accession: .: (0.000366) - test_Hit_bit_score: .: (0.006048) - test_Hit_definition: .: (0.000298) - test_Hit_evalue: .: (0.000179) - test_Hit_hit_id: .: (0.000166) - test_Hit_hsps: .: (0.000145) - test_Hit_identity: .: (0.000144) - test_Hit_lap_at: .: (0.000158) - test_Hit_len: .: (0.000136) - test_Hit_midline: .: (0.000137) - test_Hit_num: .: (0.000148) - test_Hit_overlap: .: (0.000147) - test_Hit_query_def: .: (0.000150) - test_Hit_query_end: .: (0.000135) - test_Hit_query_id: .: (0.000136) - test_Hit_query_len: .: (0.000135) - test_Hit_query_seq: .: (0.000127) - test_Hit_query_start: .: (0.000138) - test_Hit_taeget_def: .: (0.000143) - test_Hit_target_end: .: (0.000194) - test_Hit_target_id: .: (0.000151) - test_Hit_target_len: .: (0.000135) - test_Hit_target_seq: .: (0.000136) - test_Hit_target_start: .: (0.000140) + test_Hit_accession: .: (0.000352) + test_Hit_bit_score: .: (0.000125) + test_Hit_definition: .: (0.000096) + test_Hit_evalue: .: (0.000085) + test_Hit_hit_id: .: (0.000098) + test_Hit_hsps: .: (0.000082) + test_Hit_identity: .: (0.000077) + test_Hit_lap_at: .: (0.000088) + test_Hit_len: .: (0.000073) + test_Hit_midline: .: (0.000075) + test_Hit_num: .: (0.000077) + test_Hit_overlap: .: (0.000073) + test_Hit_query_def: .: (0.000088) + test_Hit_query_end: .: (0.000077) + test_Hit_query_id: .: (0.000081) + test_Hit_query_len: .: (0.000077) + test_Hit_query_seq: .: (0.000076) + test_Hit_query_start: .: (0.000077) + test_Hit_taeget_def: .: (0.000078) + test_Hit_target_end: .: (0.000074) + test_Hit_target_id: .: (0.000074) + test_Hit_target_len: .: (0.000073) + test_Hit_target_seq: .: (0.000072) + test_Hit_target_start: .: (0.000071) Bio::TestBlastReportHsp: - test_Hsp_align_len: .: (0.017900) - test_Hsp_bit_score: .: (0.012900) - test_Hsp_density: .: (0.015960) - test_Hsp_evalue: .: (0.017442) - test_Hsp_gaps: .: (0.014086) - test_Hsp_hit_frame: .: (0.015705) - test_Hsp_hit_from: .: (0.016593) - test_Hsp_hit_to: .: (0.010952) - test_Hsp_hseq: .: (0.015699) - test_Hsp_identity: .: (0.017339) - test_Hsp_midline: .: (0.015223) - test_Hsp_mismatch_count: .: (0.010844) - test_Hsp_num: .: (0.016913) - test_Hsp_pattern_from: .: (0.014971) - test_Hsp_pattern_to: .: (0.010731) - test_Hsp_percent_identity: .: (0.019103) - test_Hsp_positive: .: (0.013364) - test_Hsp_qseq: .: (0.015931) - test_Hsp_query_frame: .: (0.017344) - test_Hsp_query_from: .: (0.012644) - test_Hsp_query_to: .: (0.012749) - test_Hsp_score: .: (0.018025) + test_Hsp_align_len: .: (0.008746) + test_Hsp_bit_score: .: (0.006621) + test_Hsp_density: .: (0.006260) + test_Hsp_evalue: .: (0.008489) + test_Hsp_gaps: .: (0.006459) + test_Hsp_hit_frame: .: (0.006161) + test_Hsp_hit_from: .: (0.008427) + test_Hsp_hit_to: .: (0.006524) + test_Hsp_hseq: .: (0.006221) + test_Hsp_identity: .: (0.008447) + test_Hsp_midline: .: (0.006490) + test_Hsp_mismatch_count: .: (0.006167) + test_Hsp_num: .: (0.008277) + test_Hsp_pattern_from: .: (0.006439) + test_Hsp_pattern_to: .: (0.006269) + test_Hsp_percent_identity: .: (0.008578) + test_Hsp_positive: .: (0.006624) + test_Hsp_qseq: .: (0.006272) + test_Hsp_query_frame: .: (0.008549) + test_Hsp_query_from: .: (0.006364) + test_Hsp_query_to: .: (0.006233) + test_Hsp_score: .: (0.008325) Bio::TestBlastReportHspDefault: - test_Hsp_align_len: .: (0.000967) - test_Hsp_bit_score: .: (0.000473) - test_Hsp_evalue: .: (0.000433) - test_Hsp_gaps: .: (0.003885) - test_Hsp_hit_frame: .: (0.000616) - test_Hsp_hit_from: .: (0.000528) - test_Hsp_hit_to: .: (0.000486) - test_Hsp_hseq: .: (0.000486) - test_Hsp_identity: .: (0.000392) - test_Hsp_midline: .: (0.000483) - test_Hsp_percent_identity: .: (0.004146) - test_Hsp_positive: .: (0.000588) - test_Hsp_qseq: .: (0.000546) - test_Hsp_query_frame: .: (0.000406) - test_Hsp_query_from: .: (0.000467) - test_Hsp_query_to: .: (0.000445) - test_Hsp_score: .: (0.000528) + test_Hsp_align_len: .: (0.000701) + test_Hsp_bit_score: .: (0.000332) + test_Hsp_evalue: .: (0.000421) + test_Hsp_gaps: .: (0.000319) + test_Hsp_hit_frame: .: (0.000341) + test_Hsp_hit_from: .: (0.000390) + test_Hsp_hit_to: .: (0.000373) + test_Hsp_hseq: .: (0.000593) + test_Hsp_identity: .: (0.000325) + test_Hsp_midline: .: (0.000385) + test_Hsp_percent_identity: .: (0.000293) + test_Hsp_positive: .: (0.000286) + test_Hsp_qseq: .: (0.000373) + test_Hsp_query_frame: .: (0.000516) + test_Hsp_query_from: .: (0.000404) + test_Hsp_query_to: .: (0.000363) + test_Hsp_score: .: (0.000288) Bio::TestBlastReportHspMulti: - test_Hsp_align_len: .: (0.038618) - test_Hsp_bit_score: .: (0.043414) - test_Hsp_density: .: (0.041761) - test_Hsp_evalue: .: (0.040850) - test_Hsp_gaps: .: (0.038092) - test_Hsp_hit_frame: .: (0.040009) - test_Hsp_hit_from: .: (0.040690) - test_Hsp_hit_to: .: (0.040706) - test_Hsp_hseq: .: (0.042060) - test_Hsp_identity: .: (0.028424) - test_Hsp_midline: .: (0.019901) - test_Hsp_mismatch_count: .: (0.020075) - test_Hsp_num: .: (0.020056) - test_Hsp_pattern_from: .: (0.020216) - test_Hsp_pattern_to: .: (0.020027) - test_Hsp_percent_identity: .: (0.019794) - test_Hsp_positive: .: (0.019846) - test_Hsp_qseq: .: (0.019876) - test_Hsp_query_frame: .: (0.019933) - test_Hsp_query_from: .: (0.019951) - test_Hsp_query_to: .: (0.019967) - test_Hsp_score: .: (0.019981) + test_Hsp_align_len: .: (0.020242) + test_Hsp_bit_score: .: (0.020611) + test_Hsp_density: .: (0.020508) + test_Hsp_evalue: .: (0.020102) + test_Hsp_gaps: .: (0.019721) + test_Hsp_hit_frame: .: (0.020276) + test_Hsp_hit_from: .: (0.019802) + test_Hsp_hit_to: .: (0.019791) + test_Hsp_hseq: .: (0.019767) + test_Hsp_identity: .: (0.019480) + test_Hsp_midline: .: (0.019560) + test_Hsp_mismatch_count: .: (0.019528) + test_Hsp_num: .: (0.019531) + test_Hsp_pattern_from: .: (0.019757) + test_Hsp_pattern_to: .: (0.019690) + test_Hsp_percent_identity: .: (0.019476) + test_Hsp_positive: .: (0.019509) + test_Hsp_qseq: .: (0.019365) + test_Hsp_query_frame: .: (0.019449) + test_Hsp_query_from: .: (0.019605) + test_Hsp_query_to: .: (0.019426) + test_Hsp_score: .: (0.019534) Bio::TestBlastReportHspMultiREXML: - test_Hsp_align_len: .: (0.020145) - test_Hsp_bit_score: .: (0.019809) - test_Hsp_density: .: (0.019846) - test_Hsp_evalue: .: (0.019689) - test_Hsp_gaps: .: (0.019622) - test_Hsp_hit_frame: .: (0.019652) - test_Hsp_hit_from: .: (0.019800) - test_Hsp_hit_to: .: (0.019723) - test_Hsp_hseq: .: (0.019651) - test_Hsp_identity: .: (0.019751) - test_Hsp_midline: .: (0.019851) - test_Hsp_mismatch_count: .: (0.019595) - test_Hsp_num: .: (0.019878) - test_Hsp_pattern_from: .: (0.019971) - test_Hsp_pattern_to: .: (0.020294) - test_Hsp_percent_identity: .: (0.041779) - test_Hsp_positive: .: (0.030470) - test_Hsp_qseq: .: (0.020309) - test_Hsp_query_frame: .: (0.020348) - test_Hsp_query_from: .: (0.020172) - test_Hsp_query_to: .: (0.020153) - test_Hsp_score: .: (0.021848) + test_Hsp_align_len: .: (0.019334) + test_Hsp_bit_score: .: (0.019347) + test_Hsp_density: .: (0.019346) + test_Hsp_evalue: .: (0.018997) + test_Hsp_gaps: .: (0.019189) + test_Hsp_hit_frame: .: (0.019018) + test_Hsp_hit_from: .: (0.019034) + test_Hsp_hit_to: .: (0.019192) + test_Hsp_hseq: .: (0.019169) + test_Hsp_identity: .: (0.019223) + test_Hsp_midline: .: (0.018956) + test_Hsp_mismatch_count: .: (0.019177) + test_Hsp_num: .: (0.019247) + test_Hsp_pattern_from: .: (0.019452) + test_Hsp_pattern_to: .: (0.019283) + test_Hsp_percent_identity: .: (0.019289) + test_Hsp_positive: .: (0.019398) + test_Hsp_qseq: .: (0.019275) + test_Hsp_query_frame: .: (0.019007) + test_Hsp_query_from: .: (0.019105) + test_Hsp_query_to: .: (0.019065) + test_Hsp_score: .: (0.019015) Bio::TestBlastReportHspREXML: - test_Hsp_align_len: .: (0.009240) - test_Hsp_bit_score: .: (0.006981) - test_Hsp_density: .: (0.006399) - test_Hsp_evalue: .: (0.009113) - test_Hsp_gaps: .: (0.007113) - test_Hsp_hit_frame: .: (0.006468) - test_Hsp_hit_from: .: (0.010019) - test_Hsp_hit_to: .: (0.007081) - test_Hsp_hseq: .: (0.006387) - test_Hsp_identity: .: (0.009021) - test_Hsp_midline: .: (0.007162) - test_Hsp_mismatch_count: .: (0.006566) - test_Hsp_num: .: (0.009118) - test_Hsp_pattern_from: .: (0.007034) - test_Hsp_pattern_to: .: (0.006424) - test_Hsp_percent_identity: .: (0.008929) - test_Hsp_positive: .: (0.007124) - test_Hsp_qseq: .: (0.006513) - test_Hsp_query_frame: .: (0.009049) - test_Hsp_query_from: .: (0.007154) - test_Hsp_query_to: .: (0.006485) - test_Hsp_score: .: (0.008937) + test_Hsp_align_len: .: (0.008470) + test_Hsp_bit_score: .: (0.006478) + test_Hsp_density: .: (0.006010) + test_Hsp_evalue: .: (0.008320) + test_Hsp_gaps: .: (0.006451) + test_Hsp_hit_frame: .: (0.005945) + test_Hsp_hit_from: .: (0.008356) + test_Hsp_hit_to: .: (0.006420) + test_Hsp_hseq: .: (0.006092) + test_Hsp_identity: .: (0.008191) + test_Hsp_midline: .: (0.006442) + test_Hsp_mismatch_count: .: (0.006063) + test_Hsp_num: .: (0.008335) + test_Hsp_pattern_from: .: (0.006473) + test_Hsp_pattern_to: .: (0.006258) + test_Hsp_percent_identity: .: (0.008219) + test_Hsp_positive: .: (0.006488) + test_Hsp_qseq: .: (0.006063) + test_Hsp_query_frame: .: (0.008199) + test_Hsp_query_from: .: (0.006586) + test_Hsp_query_to: .: (0.006037) + test_Hsp_score: .: (0.008253) Bio::TestBlastReportHspTabular: - test_Hsp_align_len: .: (0.000594) - test_Hsp_bit_score: .: (0.000223) - test_Hsp_density: .: (0.000195) - test_Hsp_evalue: .: (0.000188) - test_Hsp_gaps: .: (0.000187) - test_Hsp_hit_frame: .: (0.000231) - test_Hsp_hit_from: .: (0.000188) - test_Hsp_hit_to: .: (0.000203) - test_Hsp_hseq: .: (0.000185) - test_Hsp_identity: .: (0.000177) - test_Hsp_midline: .: (0.000179) - test_Hsp_mismatch_count: .: (0.000198) - test_Hsp_num: .: (0.000184) - test_Hsp_pattern_from: .: (0.000173) - test_Hsp_pattern_to: .: (0.000173) - test_Hsp_percent_identity: .: (0.000199) - test_Hsp_positive: .: (0.000192) - test_Hsp_qseq: .: (0.000169) - test_Hsp_query_frame: .: (0.000169) - test_Hsp_query_from: .: (0.000198) - test_Hsp_query_to: .: (0.000177) - test_Hsp_score: .: (0.000202) + test_Hsp_align_len: .: (0.000415) + test_Hsp_bit_score: .: (0.000116) + test_Hsp_density: .: (0.000103) + test_Hsp_evalue: .: (0.000096) + test_Hsp_gaps: .: (0.000094) + test_Hsp_hit_frame: .: (0.000082) + test_Hsp_hit_from: .: (0.000113) + test_Hsp_hit_to: .: (0.000093) + test_Hsp_hseq: .: (0.000083) + test_Hsp_identity: .: (0.000174) + test_Hsp_midline: .: (0.000101) + test_Hsp_mismatch_count: .: (0.000089) + test_Hsp_num: .: (0.000081) + test_Hsp_pattern_from: .: (0.000077) + test_Hsp_pattern_to: .: (0.000078) + test_Hsp_percent_identity: .: (0.000074) + test_Hsp_positive: .: (0.000075) + test_Hsp_qseq: .: (0.000074) + test_Hsp_query_frame: .: (0.000071) + test_Hsp_query_from: .: (0.000076) + test_Hsp_query_to: .: (0.000074) + test_Hsp_score: .: (0.000071) Bio::TestBlastReportIteration: - test_hits: .: (0.006984) - test_message: .: (0.008317) - test_num: .: (0.007892) - test_statistics: .: (0.006997) + test_hits: .: (0.006503) + test_message: .: (0.007651) + test_num: .: (0.007261) + test_statistics: .: (0.006349) Bio::TestBlastReportIterationDefault: - test_hits: .: (0.000680) - test_message: .: (0.000405) - test_num: .: (0.000372) + test_hits: .: (0.000504) + test_message: .: (0.000278) + test_num: .: (0.000290) Bio::TestBlastReportIterationMulti: - test_each: .: (0.020530) - test_hits: .: (0.020688) - test_message: .: (0.020989) - test_num: .: (0.020503) - test_query_def: .: (0.021532) - test_query_id: .: (0.020609) - test_query_len: .: (0.020899) - test_statistics: .: (0.020917) + test_each: .: (0.019842) + test_hits: .: (0.019513) + test_message: .: (0.020004) + test_num: .: (0.019423) + test_query_def: .: (0.020858) + test_query_id: .: (0.020600) + test_query_len: .: (0.019841) + test_statistics: .: (0.019855) Bio::TestBlastReportIterationMultiREXML: - test_each: .: (0.020815) - test_hits: .: (0.023890) - test_message: .: (0.021494) - test_num: .: (0.021693) - test_query_def: .: (0.021133) - test_query_id: .: (0.020260) - test_query_len: .: (0.020130) - test_statistics: .: (0.020053) + test_each: .: (0.019712) + test_hits: .: (0.019681) + test_message: .: (0.019635) + test_num: .: (0.020666) + test_query_def: .: (0.020292) + test_query_id: .: (0.019758) + test_query_len: .: (0.019511) + test_statistics: .: (0.019403) Bio::TestBlastReportIterationREXML: - test_hits: .: (0.008959) - test_message: .: (0.006884) - test_num: .: (0.006852) - test_statistics: .: (0.008778) + test_hits: .: (0.008781) + test_message: .: (0.006538) + test_num: .: (0.006375) + test_statistics: .: (0.008445) Bio::TestBlastReportIterationTabular: - test_hits: .: (0.000706) - test_message: .: (0.000221) - test_num: .: (0.000180) - test_statistics: .: (0.000215) + test_hits: .: (0.000613) + test_message: .: (0.000161) + test_num: .: (0.000097) + test_statistics: .: (0.000078) Bio::TestBlastReportMulti: - test_db: .: (0.020800) - test_db_len: .: (0.020332) - test_db_num: .: (0.020062) - test_each_hit: .: (0.021766) - test_each_iteration: .: (0.021277) - test_eff_space: .: (0.020511) - test_entropy: .: (0.020043) - test_expect: .: (0.021883) - test_filter: .: (0.020906) - test_gap_extend: .: (0.020368) - test_gap_open: .: (0.020170) - test_hits: .: (0.022129) - test_hsp_len: .: (0.021051) - test_iterations: .: (0.044986) - test_kappa: .: (0.034967) - test_lambda: .: (0.050168) - test_matrix: .: (0.041502) - test_message: .: (0.040831) - test_parameters: .: (0.050328) - test_pattern: .: (0.042364) - test_program: .: (0.022861) - test_query_def: .: (0.026372) - test_query_id: .: (0.024197) - test_query_len: .: (0.025383) - test_reference: .: (0.025083) - test_reports: .: (0.066448) - test_statistics: .: (0.023453) - test_version: .: (0.024077) + test_db: .: (0.019478) + test_db_len: .: (0.019496) + test_db_num: .: (0.019647) + test_each_hit: .: (0.020871) + test_each_iteration: .: (0.020149) + test_eff_space: .: (0.019345) + test_entropy: .: (0.019424) + test_expect: .: (0.020684) + test_filter: .: (0.019941) + test_gap_extend: .: (0.019313) + test_gap_open: .: (0.019468) + test_hits: .: (0.021159) + test_hsp_len: .: (0.020046) + test_iterations: .: (0.019506) + test_kappa: .: (0.019722) + test_lambda: .: (0.021223) + test_matrix: .: (0.019291) + test_message: .: (0.019555) + test_parameters: .: (0.021490) + test_pattern: .: (0.019507) + test_program: .: (0.019742) + test_query_def: .: (0.021055) + test_query_id: .: (0.019490) + test_query_len: .: (0.020925) + test_reference: .: (0.020050) + test_reports: .: (0.056841) + test_statistics: .: (0.019267) + test_version: .: (0.019391) Bio::TestBlastReportMultiREXML: - test_db: .: (0.024068) - test_db_len: .: (0.024339) - test_db_num: .: (0.025247) - test_each_hit: .: (0.025155) - test_each_iteration: .: (0.023660) - test_eff_space: .: (0.024141) - test_entropy: .: (0.025228) - test_expect: .: (0.023859) - test_filter: .: (0.024426) - test_gap_extend: .: (0.023707) - test_gap_open: .: (0.024039) - test_hits: .: (0.024119) - test_hsp_len: .: (0.025325) - test_iterations: .: (0.024861) - test_kappa: .: (0.024102) - test_lambda: .: (0.024026) - test_matrix: .: (0.023658) - test_message: .: (0.025837) - test_parameters: .: (0.024965) - test_pattern: .: (0.024255) - test_program: .: (0.023665) - test_query_def: .: (0.026538) - test_query_id: .: (0.025035) - test_query_len: .: (0.024176) - test_reference: .: (0.023137) - test_reports: .: (0.026464) - test_statistics: .: (0.024146) - test_version: .: (0.023817) + test_db: .: (0.019553) + test_db_len: .: (0.019373) + test_db_num: .: (0.019276) + test_each_hit: .: (0.019086) + test_each_iteration: .: (0.020539) + test_eff_space: .: (0.019407) + test_entropy: .: (0.019213) + test_expect: .: (0.020066) + test_filter: .: (0.019549) + test_gap_extend: .: (0.019163) + test_gap_open: .: (0.019520) + test_hits: .: (0.019463) + test_hsp_len: .: (0.020457) + test_iterations: .: (0.019897) + test_kappa: .: (0.019262) + test_lambda: .: (0.019165) + test_matrix: .: (0.019063) + test_message: .: (0.020417) + test_parameters: .: (0.020330) + test_pattern: .: (0.019333) + test_program: .: (0.019338) + test_query_def: .: (0.020849) + test_query_id: .: (0.020539) + test_query_len: .: (0.019315) + test_reference: .: (0.019262) + test_reports: .: (0.021253) + test_statistics: .: (0.019430) + test_version: .: (0.019223) Bio::TestBlastReportREXML: - test_db: .: (0.010734) - test_db_len: .: (0.008301) - test_db_num: .: (0.009943) - test_each_hit: .: (0.007966) - test_each_iteration: .: (0.007884) - test_eff_space: .: (0.010634) - test_entrez_query: .: (0.008336) - test_entropy: .: (0.010121) - test_expect: .: (0.008595) - test_filter: .: (0.009198) - test_gap_extend: .: (0.009092) - test_gap_open: .: (0.007981) - test_hits: .: (0.009750) - test_hsp_len: .: (0.008266) - test_inclusion: .: (0.009984) - test_iterations: .: (0.008373) - test_kappa: .: (0.006700) - test_lambda: .: (0.010384) - test_matrix: .: (0.008254) - test_message: .: (0.009924) - test_parameters: .: (0.008311) - test_pattern: .: (0.009096) - test_program: .: (0.009105) - test_query_def: .: (0.008208) - test_query_id: .: (0.010049) - test_query_len: .: (0.008440) - test_reference: .: (0.010089) - test_sc_match: .: (0.008419) - test_sc_mismatch: .: (0.007526) - test_statistics: .: (0.010721) - test_version: .: (0.007931) + test_db: .: (0.008631) + test_db_len: .: (0.006572) + test_db_num: .: (0.008062) + test_each_hit: .: (0.006545) + test_each_iteration: .: (0.005926) + test_eff_space: .: (0.008514) + test_entrez_query: .: (0.006468) + test_entropy: .: (0.008087) + test_expect: .: (0.006662) + test_filter: .: (0.007564) + test_gap_extend: .: (0.007407) + test_gap_open: .: (0.006493) + test_hits: .: (0.008293) + test_hsp_len: .: (0.006737) + test_inclusion: .: (0.008119) + test_iterations: .: (0.006359) + test_kappa: .: (0.006211) + test_lambda: .: (0.008340) + test_matrix: .: (0.006636) + test_message: .: (0.008212) + test_parameters: .: (0.006750) + test_pattern: .: (0.007371) + test_program: .: (0.007541) + test_query_def: .: (0.006647) + test_query_id: .: (0.008370) + test_query_len: .: (0.006800) + test_reference: .: (0.008495) + test_sc_match: .: (0.006689) + test_sc_mismatch: .: (0.006116) + test_statistics: .: (0.008615) + test_version: .: (0.006762) Bio::TestBlastReportTabular: - test_db: .: (0.000432) - test_db_len: .: (0.000207) - test_db_num: .: (0.000220) - test_each_hit: .: (0.000192) - test_each_iteration: .: (0.000121) - test_eff_space: .: (0.000099) - test_entrez_query: .: (0.000101) - test_entropy: .: (0.000073) - test_expect: .: (0.000065) - test_filter: .: (0.000063) - test_gap_extend: .: (0.000063) - test_gap_open: .: (0.000069) - test_hits: .: (0.000071) - test_hsp_len: .: (0.000067) - test_inclusion: .: (0.000082) - test_iterations: .: (0.000073) - test_kappa: .: (0.000063) - test_lambda: .: (0.000060) - test_matrix: .: (0.000069) - test_message: .: (0.000069) - test_parameters: .: (0.000069) - test_pattern: .: (0.000065) - test_program: .: (0.000062) - test_query_def: .: (0.000073) - test_query_id: .: (0.000064) - test_query_len: .: (0.000067) - test_reference: .: (0.000061) - test_sc_match: .: (0.000063) - test_sc_mismatch: .: (0.000061) - test_statistics: .: (0.000064) - test_version: .: (0.000060) + test_db: .: (0.000297) + test_db_len: .: (0.000099) + test_db_num: .: (0.000085) + test_each_hit: .: (0.000090) + test_each_iteration: .: (0.000079) + test_eff_space: .: (0.000076) + test_entrez_query: .: (0.000100) + test_entropy: .: (0.000087) + test_expect: .: (0.000080) + test_filter: .: (0.000077) + test_gap_extend: .: (0.000076) + test_gap_open: .: (0.000078) + test_hits: .: (0.000082) + test_hsp_len: .: (0.000076) + test_inclusion: .: (0.000074) + test_iterations: .: (0.000067) + test_kappa: .: (0.000070) + test_lambda: .: (0.000069) + test_matrix: .: (0.000073) + test_message: .: (0.000078) + test_parameters: .: (0.000107) + test_pattern: .: (0.000084) + test_program: .: (0.000080) + test_query_def: .: (0.000088) + test_query_id: .: (0.000079) + test_query_len: .: (0.000072) + test_reference: .: (0.000070) + test_sc_match: .: (0.000074) + test_sc_mismatch: .: (0.000075) + test_statistics: .: (0.000080) + test_version: .: (0.000073) Bio::TestChain: - test_aaseq: .: (0.000281) - test_addLigand: .: (0.000053) - test_addResidue: .: (0.000045) - test_atom_seq: .: (0.000051) - test_comp: .: (0.000075) - test_each: .: (0.000050) - test_each_heterogen: .: (0.000051) - test_each_residue: .: (0.000049) - test_get_heterogen_by_id: .: (0.000048) - test_get_residue_by_id: .: (0.000048) - test_inspect: .: (0.000068) - test_rehash: .: (0.000051) - test_rehash_heterogens: .: (0.000280) - test_rehash_residues: .: (0.000131) - test_square_brace: .: (0.000155) - test_to_s: .: (0.000159) + test_aaseq: .: (0.000300) + test_addLigand: .: (0.000061) + test_addResidue: .: (0.000052) + test_atom_seq: .: (0.000061) + test_comp: .: (0.000086) + test_each: .: (0.000059) + test_each_heterogen: .: (0.000060) + test_each_residue: .: (0.000057) + test_get_heterogen_by_id: .: (0.000056) + test_get_residue_by_id: .: (0.000053) + test_inspect: .: (0.000078) + test_rehash: .: (0.000057) + test_rehash_heterogens: .: (0.000047) + test_rehash_residues: .: (0.000047) + test_square_brace: .: (0.000060) + test_to_s: .: (0.000069) Bio::TestChainFinder: - test_chains: .: (0.002255) - test_each_chain: .: (0.000179) - test_find_chain: .: (0.000176) + test_chains: .: (0.001886) + test_each_chain: .: (0.000085) + test_find_chain: .: (0.000067) Bio::TestClustalWReport::TestClustalWReport: - test_alignment: .: (0.006812) - test_header: .: (0.000667) - test_match_line: .: (0.000789) - test_sequence0: .: (0.000596) - test_sequence1: .: (0.000740) + test_alignment: .: (0.005578) + test_header: .: (0.000509) + test_match_line: .: (0.000388) + test_sequence0: .: (0.000522) + test_sequence1: .: (0.000640) Bio::TestClustalWReport::TestClustalWReportSeqnos: - test_alignment: .: (0.005895) - test_header: .: (0.000990) - test_match_line: .: (0.000810) - test_sequence0: .: (0.000787) - test_sequence1: .: (0.000736) + test_alignment: .: (0.004915) + test_header: .: (0.000604) + test_match_line: .: (0.000542) + test_sequence0: .: (0.000529) + test_sequence1: .: (0.000539) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: - test_alignment: .: (0.006395) - test_header: .: (0.000658) - test_match_line: .: (0.000593) - test_sequence0: .: (0.002894) - test_sequence1: .: (0.000821) + test_alignment: .: (0.005693) + test_header: .: (0.000461) + test_match_line: .: (0.000392) + test_sequence0: .: (0.002506) + test_sequence1: .: (0.000536) Bio::TestCodonTable: - test_Tables: .: (0.000316) - test_accessor: .: (0.000164) - test_definition: .: (0.000108) - test_each: .: (0.000142) - test_revtrans: .: (0.000190) - test_self_accessor: .: (0.000132) - test_self_copy: .: (0.000670) - test_set_accessor: .: (0.049544) - test_start: .: (0.000195) - test_start_codon?: .: (0.000174) - test_stop: .: (0.000146) - test_stop_codon?: .: (0.000148) - test_table: .: (0.000115) + test_Tables: .: (0.000211) + test_accessor: .: (0.000089) + test_definition: .: (0.000061) + test_each: .: (0.000096) + test_revtrans: .: (0.000121) + test_self_accessor: .: (0.000062) + test_self_copy: .: (0.000539) + test_set_accessor: .: (0.045294) + test_start: .: (0.000109) + test_start_codon?: .: (0.000069) + test_stop: .: (0.000090) + test_stop_codon?: .: (0.000106) + test_table: .: (0.000075) Bio::TestCodonTableConstants: - test_Definitions: .: (0.000267) - test_Starts: .: (0.000169) - test_Tables: .: (0.000099) - test_stops: .: (0.000160) + test_Definitions: .: (0.000222) + test_Starts: .: (0.000122) + test_Tables: .: (0.000084) + test_stops: .: (0.000068) Bio::TestColorScheme: - test_buried: .: (0.001004) + test_buried: .: (0.000760) Bio::TestCommand: - test_command_constants: .: (0.000269) - test_escape_shell: .: (0.000183) - test_escape_shell_unix: .: (0.000122) - test_escape_shell_windows: .: (0.002986) - test_make_cgi_params_by_array_of_array: .: (0.000557) - test_make_cgi_params_by_array_of_hash: .: (0.000348) - test_make_cgi_params_by_array_of_string: .: (0.000196) - test_make_cgi_params_by_hash_in_string: .: (0.000427) - test_make_cgi_params_by_hash_in_symbol: .: (0.000450) - test_make_cgi_params_by_string: .: (0.000198) - test_make_command_line: .: (0.001477) - test_make_command_line_unix: .: (0.000158) - test_make_command_line_windows: .: (0.000137) - test_safe_command_line_array: .: (0.000175) - test_safe_command_line_array_passthrough: .: (0.000137) + test_command_constants: .: (0.000155) + test_escape_shell: .: (0.000108) + test_escape_shell_unix: .: (0.000071) + test_escape_shell_windows: .: (0.002535) + test_make_cgi_params_by_array_of_array: .: (0.000333) + test_make_cgi_params_by_array_of_hash: .: (0.000232) + test_make_cgi_params_by_array_of_string: .: (0.000103) + test_make_cgi_params_by_hash_in_string: .: (0.000288) + test_make_cgi_params_by_hash_in_symbol: .: (0.000272) + test_make_cgi_params_by_string: .: (0.000118) + test_make_command_line: .: (0.000090) + test_make_command_line_unix: .: (0.001204) + test_make_command_line_windows: .: (0.000080) + test_safe_command_line_array: .: (0.000082) + test_safe_command_line_array_passthrough: .: (0.000061) Bio::TestContingencyTable: - test_lite_example: .: (0.080078) + test_lite_example: .: (0.073205) Bio::TestDB: - test_entry_id: .: (0.000411) - test_exists: .: (0.000172) - test_fetch: .: (0.000224) - test_get: .: (0.000141) - test_open: .: (0.000326) - test_tags: .: (0.000132) + test_entry_id: .: (0.000268) + test_exists: .: (0.000061) + test_fetch: .: (0.000108) + test_get: .: (0.000081) + test_open: .: (0.000052) + test_tags: .: (0.000046) Bio::TestDataType: - test_const_like_method: .: (0.000563) - test_pdb_achar: .: (0.000283) - test_pdb_atom: .: (0.000242) - test_pdb_character: .: (0.000279) - test_pdb_date: .: (0.000253) - test_pdb_idcode: .: (0.000254) - test_pdb_integer: .: (0.000151) - test_pdb_list: .: (0.000125) - test_pdb_lstring: .: (0.000219) - test_pdb_real: .: (0.000200) - test_pdb_resudue_name: .: (0.000246) - test_pdb_slist: .: (0.000134) - test_pdb_string: .: (0.000243) - test_pdb_stringrj: .: (0.000125) - test_pdb_symop: .: (0.000466) - test_specification_list: .: (0.000175) + test_const_like_method: .: (0.000387) + test_pdb_achar: .: (0.000157) + test_pdb_atom: .: (0.000121) + test_pdb_character: .: (0.000110) + test_pdb_date: .: (0.000112) + test_pdb_idcode: .: (0.000111) + test_pdb_integer: .: (0.000058) + test_pdb_list: .: (0.000064) + test_pdb_lstring: .: (0.000115) + test_pdb_real: .: (0.000095) + test_pdb_resudue_name: .: (0.000124) + test_pdb_slist: .: (0.000055) + test_pdb_string: .: (0.000117) + test_pdb_stringrj: .: (0.000064) + test_pdb_symop: .: (0.000347) + test_specification_list: .: (0.000103) Bio::TestEMBL: - test_ac: .: (0.000562) - test_accession: .: (0.000347) - test_cc: .: (0.000308) - test_de: .: (0.000350) - test_division: .: (0.000356) - test_dr: .: (0.000308) - test_dt: .: (0.000310) - test_dt_created: .: (0.000485) - test_dt_iterator: .: (0.000306) - test_dt_updated: .: (0.000308) - test_each_cds: .: (0.000481) - test_each_gene: .: (0.000424) - test_entry: .: (0.000364) - test_fh: .: (0.000463) - test_ft: .: (0.000459) - test_ft_accessor: .: (0.000449) - test_ft_iterator: .: (0.000467) - test_id_line: .: (0.000345) - test_id_line_data_class: .: (0.000329) - test_id_line_division: .: (0.000475) - test_id_line_entry_name: .: (0.000353) - test_id_line_iterator: .: (0.000317) - test_id_line_molecule_type: .: (0.000312) - test_id_line_sequence_length: .: (0.000334) - test_kw: .: (0.000335) - test_molecule: .: (0.000372) - test_oc: .: (0.000399) - test_og: .: (0.000330) - test_os: .: (0.000551) - test_ref: .: (0.000408) - test_references: .: (0.000519) - test_seq: .: (0.000560) - test_sequence_length: .: (0.000363) - test_sq: .: (0.000333) - test_sq_get: .: (0.000317) - test_sv: .: (0.000330) - test_version: .: (0.000520) + test_ac: .: (0.000405) + test_accession: .: (0.000211) + test_cc: .: (0.000170) + test_de: .: (0.000189) + test_division: .: (0.000237) + test_dr: .: (0.000178) + test_dt: .: (0.000200) + test_dt_created: .: (0.000323) + test_dt_iterator: .: (0.000213) + test_dt_updated: .: (0.000180) + test_each_cds: .: (0.000327) + test_each_gene: .: (0.000267) + test_entry: .: (0.000227) + test_fh: .: (0.000180) + test_ft: .: (0.000464) + test_ft_accessor: .: (0.000321) + test_ft_iterator: .: (0.000291) + test_id_line: .: (0.000232) + test_id_line_data_class: .: (0.000214) + test_id_line_division: .: (0.000188) + test_id_line_entry_name: .: (0.000182) + test_id_line_iterator: .: (0.000348) + test_id_line_molecule_type: .: (0.000192) + test_id_line_sequence_length: .: (0.000183) + test_kw: .: (0.000194) + test_molecule: .: (0.000199) + test_oc: .: (0.000233) + test_og: .: (0.000171) + test_os: .: (0.000206) + test_ref: .: (0.000427) + test_references: .: (0.000396) + test_seq: .: (0.000366) + test_sequence_length: .: (0.000232) + test_sq: .: (0.000201) + test_sq_get: .: (0.000180) + test_sv: .: (0.000168) + test_version: .: (0.000170) Bio::TestEMBL89: - test_ac: .: (0.000519) - test_accession: .: (0.000357) - test_cc: .: (0.000281) - test_de: .: (0.002848) - test_division: .: (0.000806) - test_dr: .: (0.000343) - test_dt: .: (0.000313) - test_dt_created: .: (0.000309) - test_dt_iterator: .: (0.000259) - test_dt_updated: .: (0.000300) - test_each_cds: .: (0.000434) - test_each_gene: .: (0.000408) - test_entry: .: (0.000379) - test_fh: .: (0.000318) - test_ft: .: (0.000431) - test_ft_accessor: .: (0.000415) - test_ft_iterator: .: (0.000420) - test_id_line: .: (0.000344) - test_id_line_data_class: .: (0.000346) - test_id_line_division: .: (0.000321) - test_id_line_entry_name: .: (0.000292) - test_id_line_iterator: .: (0.000361) - test_id_line_molecule_type: .: (0.000315) - test_id_line_sequence_length: .: (0.000344) - test_id_line_sequence_version: .: (0.000341) - test_kw: .: (0.000316) - test_molecule: .: (0.000329) - test_oc: .: (0.000413) - test_og: .: (0.000301) - test_os: .: (0.004329) - test_ref: .: (0.000882) - test_references: .: (0.000604) - test_seq: .: (0.000575) - test_sequence_length: .: (0.000380) - test_sq: .: (0.000363) - test_sq_get: .: (0.001107) - test_sv: .: (0.000716) - test_version: .: (0.000434) + test_ac: .: (0.000499) + test_accession: .: (0.000184) + test_cc: .: (0.000153) + test_de: .: (0.001606) + test_division: .: (0.000249) + test_dr: .: (0.000191) + test_dt: .: (0.000177) + test_dt_created: .: (0.000160) + test_dt_iterator: .: (0.000155) + test_dt_updated: .: (0.000153) + test_each_cds: .: (0.000290) + test_each_gene: .: (0.000246) + test_entry: .: (0.000215) + test_fh: .: (0.000169) + test_ft: .: (0.000261) + test_ft_accessor: .: (0.000256) + test_ft_iterator: .: (0.000257) + test_id_line: .: (0.000224) + test_id_line_data_class: .: (0.000197) + test_id_line_division: .: (0.000183) + test_id_line_entry_name: .: (0.000180) + test_id_line_iterator: .: (0.000180) + test_id_line_molecule_type: .: (0.000178) + test_id_line_sequence_length: .: (0.000218) + test_id_line_sequence_version: .: (0.000187) + test_kw: .: (0.000186) + test_molecule: .: (0.000203) + test_oc: .: (0.000240) + test_og: .: (0.000153) + test_os: .: (0.003704) + test_ref: .: (0.000505) + test_references: .: (0.000375) + test_seq: .: (0.000390) + test_sequence_length: .: (0.000249) + test_sq: .: (0.000248) + test_sq_get: .: (0.000214) + test_sv: .: (0.001104) + test_version: .: (0.000252) Bio::TestEMBLAPI: - test_ac: .: (0.000368) - test_accessions: .: (0.000192) + test_ac: .: (0.000231) + test_accessions: .: (0.000089) Bio::TestEMBLCommon: - test_ac: .: (0.000314) - test_accession: .: (0.000133) - test_accessions: .: (0.000135) - test_de: .: (0.000080) - test_definition: .: (0.000062) - test_description: .: (0.000143) - test_dr: .: (0.000112) - test_keywords: .: (0.000121) - test_kw: .: (0.000116) - test_oc: .: (0.000063) - test_og: .: (0.000055) - test_os: .: (0.000041) + test_ac: .: (0.000143) + test_accession: .: (0.000050) + test_accessions: .: (0.000044) + test_de: .: (0.000041) + test_definition: .: (0.000042) + test_description: .: (0.000043) + test_dr: .: (0.000044) + test_keywords: .: (0.000047) + test_kw: .: (0.000043) + test_oc: .: (0.000044) + test_og: .: (0.000276) + test_os: .: (0.000054) test_ref: .: (0.000042) - test_references: .: (0.000037) + test_references: .: (0.000039) Bio::TestEMBLDB: - test_fetch: .: (0.000274) - test_p_entry2hash: .: (0.000040) + test_fetch: .: (0.000190) + test_p_entry2hash: .: (0.000043) Bio::TestEMBLToBioSequence: - test_classification: .: (0.002958) - test_date_created: .: (0.000617) - test_date_modified: .: (0.000488) - test_definition: .: (0.000408) - test_division: .: (0.000399) - test_entry_id: .: (0.000450) - test_entry_version: .: (0.000571) - test_features: .: (0.000540) - test_keywords: .: (0.000411) - test_molecule_type: .: (0.000408) - test_primary_accession: .: (0.000357) - test_references: .: (0.000558) - test_release_created: .: (0.000383) - test_release_modified: .: (0.000397) - test_secondary_accessions: .: (0.000376) - test_sequence_version: .: (0.000531) - test_species: .: (0.000367) - test_topology: .: (0.000384) + test_classification: .: (0.002380) + test_date_created: .: (0.000434) + test_date_modified: .: (0.000299) + test_definition: .: (0.000254) + test_division: .: (0.000252) + test_entry_id: .: (0.000263) + test_entry_version: .: (0.000248) + test_features: .: (0.000444) + test_keywords: .: (0.000237) + test_molecule_type: .: (0.000269) + test_primary_accession: .: (0.000241) + test_references: .: (0.000398) + test_release_created: .: (0.000338) + test_release_modified: .: (0.000222) + test_secondary_accessions: .: (0.000219) + test_sequence_version: .: (0.000241) + test_species: .: (0.000212) + test_topology: .: (0.000234) Bio::TestEMBLToBioSequenceRoundTrip: - test_classification: .: (0.002855) - test_date_created: .: (0.003173) - test_date_modified: .: (0.002408) - test_definition: .: (0.002361) - test_division: .: (0.007327) - test_entry_id: .: (0.003453) - test_entry_version: .: (0.002825) - test_features: .: (0.002862) - test_keywords: .: (0.002669) - test_molecule_type: .: (0.002605) - test_primary_accession: .: (0.002921) - test_references: .: (0.002442) - test_release_created: .: (0.002418) - test_release_modified: .: (0.007781) - test_secondary_accessions: .: (0.003680) - test_sequence_version: .: (0.002777) - test_species: .: (0.002320) - test_topology: .: (0.002301) + test_classification: .: (0.002207) + test_date_created: .: (0.002348) + test_date_modified: .: (0.001729) + test_definition: .: (0.001658) + test_division: .: (0.005940) + test_entry_id: .: (0.002640) + test_entry_version: .: (0.002143) + test_features: .: (0.001990) + test_keywords: .: (0.001893) + test_molecule_type: .: (0.001815) + test_primary_accession: .: (0.002115) + test_references: .: (0.001748) + test_release_created: .: (0.001653) + test_release_modified: .: (0.006177) + test_secondary_accessions: .: (0.002572) + test_sequence_version: .: (0.001988) + test_species: .: (0.001853) + test_topology: .: (0.001839) Bio::TestFasta: - test_db: .: (0.000241) - test_format: .: (0.000080) - test_format_arg_integer: .: (0.000099) - test_format_arg_str: .: (0.000090) - test_ktup: .: (0.000094) - test_matrix: .: (0.000088) - test_option: .: (0.000143) - test_options: .: (0.000090) - test_output: .: (0.000074) - test_program: .: (0.000085) - test_server: .: (0.000085) + test_db: .: (0.000190) + test_format: .: (0.000052) + test_format_arg_integer: .: (0.000087) + test_format_arg_str: .: (0.000053) + test_ktup: .: (0.000052) + test_matrix: .: (0.000051) + test_option: .: (0.000176) + test_options: .: (0.000064) + test_output: .: (0.000040) + test_program: .: (0.000045) + test_server: .: (0.000045) Bio::TestFastaDeflineEmb: - test_acc_version: .: (0.000262) - test_accession: .: (0.000119) - test_accessions: .: (0.000168) - test_description: .: (0.000099) - test_descriptions: .: (0.000115) - test_entry_id: .: (0.000091) - test_get_all_by_type: .: (0.000102) - test_gi: .: (0.001764) - test_id_strings: .: (0.000187) - test_list_ids: .: (0.000110) - test_locus: .: (0.000979) - test_words: .: (0.000154) + test_acc_version: .: (0.000169) + test_accession: .: (0.000061) + test_accessions: .: (0.000065) + test_description: .: (0.000053) + test_descriptions: .: (0.000053) + test_entry_id: .: (0.000144) + test_get_all_by_type: .: (0.000067) + test_gi: .: (0.000060) + test_id_strings: .: (0.000903) + test_list_ids: .: (0.000069) + test_locus: .: (0.000061) + test_words: .: (0.000113) Bio::TestFastaDeflineGI1: - test_acc_version: .: (0.000260) - test_accession: .: (0.000725) - test_accessions: .: (0.000159) - test_description: .: (0.000104) - test_descriptions: .: (0.000927) - test_emb: .: (0.000289) - test_entry_id: .: (0.001079) - test_get_all_by_type: .: (0.000122) - test_get_emb: .: (0.000111) - test_gi: .: (0.001662) - test_id_strings: .: (0.000162) - test_list_ids: .: (0.000827) - test_locus: .: (0.000167) - test_words: .: (0.000157) + test_acc_version: .: (0.001687) + test_accession: .: (0.000119) + test_accessions: .: (0.000077) + test_description: .: (0.000831) + test_descriptions: .: (0.000860) + test_emb: .: (0.000086) + test_entry_id: .: (0.000061) + test_get_all_by_type: .: (0.000116) + test_get_emb: .: (0.000637) + test_gi: .: (0.000114) + test_id_strings: .: (0.000111) + test_list_ids: .: (0.000611) + test_locus: .: (0.000081) + test_words: .: (0.000093) Bio::TestFastaDeflineGI2: - test_acc_version: .: (0.000780) - test_accession: .: (0.000116) - test_accessions: .: (0.000157) - test_description: .: (0.000996) - test_descriptions: .: (0.001037) - test_entry_id: .: (0.000104) - test_get_all_by_type: .: (0.000096) - test_gi: .: (0.000400) - test_id_strings: .: (0.000148) - test_list_ids: .: (0.000102) - test_locus: .: (0.000551) - test_sp: .: (0.000120) - test_words: .: (0.000138) + test_acc_version: .: (0.000212) + test_accession: .: (0.000614) + test_accessions: .: (0.000084) + test_description: .: (0.000060) + test_descriptions: .: (0.000264) + test_entry_id: .: (0.000955) + test_get_all_by_type: .: (0.000091) + test_gi: .: (0.000061) + test_id_strings: .: (0.000857) + test_list_ids: .: (0.000072) + test_locus: .: (0.000057) + test_sp: .: (0.001006) + test_words: .: (0.000127) Bio::TestFastaDeflineGIMultiple: - test_acc_version: .: (0.000320) - test_accession: .: (0.001151) - test_accessions: .: (0.000148) - test_description: .: (0.001902) - test_descriptions: .: (0.000162) - test_entry_id: .: (0.000122) - test_get_all_by_type: .: (0.000182) - test_gi: .: (0.000132) - test_id_strings: .: (0.001798) - test_list_ids: .: (0.000933) - test_locus: .: (0.000190) - test_words: .: (0.001048) -Bio::TestFastaDeflineSce: - test_acc_version: .: (0.001133) + test_acc_version: .: (0.000999) test_accession: .: (0.001026) - test_accessions: .: (0.000123) - test_description: .: (0.000943) - test_descriptions: .: (0.000189) - test_entry_id: .: (0.000115) - test_get_all_by_type: .: (0.001044) - test_gi: .: (0.000125) - test_id_strings: .: (0.001178) - test_list_ids: .: (0.000129) - test_locus: .: (0.001047) - test_words: .: (0.001102) + test_accessions: .: (0.000902) + test_description: .: (0.000082) + test_descriptions: .: (0.000978) + test_entry_id: .: (0.000083) + test_get_all_by_type: .: (0.000646) + test_gi: .: (0.000097) + test_id_strings: .: (0.001897) + test_list_ids: .: (0.000103) + test_locus: .: (0.000992) + test_words: .: (0.001049) +Bio::TestFastaDeflineSce: + test_acc_version: .: (0.001058) + test_accession: .: (0.000091) + test_accessions: .: (0.001764) + test_description: .: (0.000107) + test_descriptions: .: (0.000070) + test_entry_id: .: (0.001058) + test_get_all_by_type: .: (0.000917) + test_gi: .: (0.000104) + test_id_strings: .: (0.000953) + test_list_ids: .: (0.000094) + test_locus: .: (0.000713) + test_words: .: (0.000649) Bio::TestFastaDeflineSimple: - test_acc_version: .: (0.000974) - test_accession: .: (0.000103) - test_accessions: .: (0.000095) - test_description: .: (0.001097) - test_descriptions: .: (0.000110) - test_entry_id: .: (0.000551) - test_get_all_by_type: .: (0.000107) - test_gi: .: (0.000503) - test_id_strings: .: (0.000142) - test_list_ids: .: (0.001065) - test_locus: .: (0.000115) - test_words: .: (0.000117) + test_acc_version: .: (0.000639) + test_accession: .: (0.000062) + test_accessions: .: (0.000051) + test_description: .: (0.000071) + test_descriptions: .: (0.000047) + test_entry_id: .: (0.000044) + test_get_all_by_type: .: (0.000969) + test_gi: .: (0.000916) + test_id_strings: .: (0.000086) + test_list_ids: .: (0.000041) + test_locus: .: (0.000582) + test_words: .: (0.000085) Bio::TestFastaDeflineSwissProt: - test_acc_version: .: (0.001534) - test_accession: .: (0.000167) - test_accessions: .: (0.000131) - test_description: .: (0.000691) - test_descriptions: .: (0.000141) - test_entry_id: .: (0.000116) - test_get: .: (0.000630) - test_get_all_by_type: .: (0.000146) - test_id_strings: .: (0.000177) - test_list_ids: .: (0.000871) - test_locus: .: (0.000860) - test_sp: .: (0.000155) - test_words: .: (0.001980) + test_acc_version: .: (0.000725) + test_accession: .: (0.000110) + test_accessions: .: (0.000116) + test_description: .: (0.000060) + test_descriptions: .: (0.000799) + test_entry_id: .: (0.000063) + test_get: .: (0.000065) + test_get_all_by_type: .: (0.000743) + test_id_strings: .: (0.000162) + test_list_ids: .: (0.000713) + test_locus: .: (0.000074) + test_sp: .: (0.000943) + test_words: .: (0.001711) Bio::TestFastaDeflineTrembl: - test_acc_version: .: (0.001259) - test_accession: .: (0.000192) - test_accessions: .: (0.000918) - test_description: .: (0.000947) - test_descriptions: .: (0.000948) - test_entry_id: .: (0.000165) - test_get: .: (0.000186) - test_get_all_by_type: .: (0.000124) - test_id_strings: .: (0.000227) - test_list_ids: .: (0.000144) - test_locus: .: (0.000529) - test_tr: .: (0.000287) - test_words: .: (0.000250) + test_acc_version: .: (0.000680) + test_accession: .: (0.000082) + test_accessions: .: (0.000108) + test_description: .: (0.000410) + test_descriptions: .: (0.001679) + test_entry_id: .: (0.000107) + test_get: .: (0.000073) + test_get_all_by_type: .: (0.000059) + test_id_strings: .: (0.000132) + test_list_ids: .: (0.000058) + test_locus: .: (0.000056) + test_tr: .: (0.000067) + test_words: .: (0.000127) Bio::TestFastaFirstName: - test_first_name1: .: (0.000267) - test_first_name_multi_identifier: .: (0.000121) - test_first_name_single_worded_defintion: .: (0.000117) - test_no_definition: .: (0.000113) - test_space_before_first_name: .: (0.000115) - test_tabbed_defintion: .: (0.000176) + test_first_name1: .: (0.000195) + test_first_name_multi_identifier: .: (0.000061) + test_first_name_single_worded_defintion: .: (0.000051) + test_no_definition: .: (0.000051) + test_space_before_first_name: .: (0.000055) + test_tabbed_defintion: .: (0.000051) Bio::TestFastaFormat: - test_aalen: .: (0.000590) - test_aaseq: .: (0.000144) - test_acc_version: .: (0.000189) - test_accession: .: (0.000163) - test_accessions: .: (0.000174) - test_data: .: (0.000128) - test_definition: .: (0.000121) - test_entry: .: (0.000154) - test_entry_id: .: (0.001648) - test_entry_overrun: .: (0.000378) - test_first_name: .: (0.000141) - test_gi: .: (0.000176) - test_identifiers: .: (0.000169) - test_length: .: (0.000142) - test_query: .: (0.000148) - test_seq: .: (0.000131) + test_aalen: .: (0.000398) + test_aaseq: .: (0.000097) + test_acc_version: .: (0.001760) + test_accession: .: (0.000110) + test_accessions: .: (0.000098) + test_data: .: (0.000059) + test_definition: .: (0.000057) + test_entry: .: (0.000058) + test_entry_id: .: (0.000077) + test_entry_overrun: .: (0.000059) + test_first_name: .: (0.000059) + test_gi: .: (0.000080) + test_identifiers: .: (0.000087) + test_length: .: (0.000069) + test_query: .: (0.000079) + test_seq: .: (0.000061) Bio::TestFastaFormatConst: - test_delimiter: .: (0.000228) + test_delimiter: .: (0.000157) Bio::TestFastaFormatKeggGenesAA: - test_acc_version: .: (0.000275) - test_data: .: (0.000133) - test_definition: .: (0.000124) - test_entry: .: (0.000139) - test_entry_id: .: (0.000141) - test_first_name: .: (0.000062) + test_acc_version: .: (0.000574) + test_data: .: (0.000182) + test_definition: .: (0.000077) + test_entry: .: (0.000066) + test_entry_id: .: (0.000104) + test_first_name: .: (0.000073) Bio::TestFastaFormatKeggGenesNT: - test_nalen: .: (0.000193) - test_naseq: .: (0.000183) - test_naseq_class: .: (0.000118) + test_nalen: .: (0.000155) + test_naseq: .: (0.000056) + test_naseq_class: .: (0.000057) Bio::TestFastaFormatSwissProt: - test_locus: .: (0.000250) + test_locus: .: (0.000168) Bio::TestFastaInitialize: - test_new_1: .: (0.000588) - test_option: .: (0.000121) - test_option_backward_compatibility: .: (0.000149) + test_new_1: .: (0.000370) + test_option: .: (0.000067) + test_option_backward_compatibility: .: (0.000330) Bio::TestFastaNumericFormat: - test_arg: .: (0.000275) - test_data: .: (0.000174) - test_definition: .: (0.000108) - test_each: .: (0.000150) - test_entry: .: (0.000127) - test_entry_id: .: (0.000136) - test_length: .: (0.000149) - test_to_biosequence: .: (0.000775) + test_arg: .: (0.000195) + test_data: .: (0.000080) + test_definition: .: (0.000047) + test_each: .: (0.000073) + test_entry: .: (0.000048) + test_entry_id: .: (0.000059) + test_length: .: (0.000072) + test_to_biosequence: .: (0.000657) Bio::TestFastaQuery: - test_query: .: (0.000195) - test_self_local: .: (0.000104) - test_self_parser: .: (0.000078) - test_self_remote: .: (0.000130) + test_query: .: (0.000119) + test_self_local: .: (0.000039) + test_self_parser: .: (0.000039) + test_self_remote: .: (0.000034) Bio::TestFastacmd: - test_database: .: (0.000298) - test_fastacmd: .: (0.000098) - test_methods: .: (0.000122) + test_database: .: (0.000130) + test_fastacmd: .: (0.000049) + test_methods: .: (0.000067) Bio::TestFastq::TestFastq_error_diff_ids: - test_validate_format: .: (0.000629) + test_validate_format: .: (0.000777) Bio::TestFastq::TestFastq_error_double_qual: - test_validate_format: .: (0.000472) + test_validate_format: .: (0.000427) Bio::TestFastq::TestFastq_error_double_seq: - test_validate_format: .: (0.000411) + test_validate_format: .: (0.000304) Bio::TestFastq::TestFastq_error_long_qual: - test_validate_format: .: (0.000593) + test_validate_format: .: (0.000297) Bio::TestFastq::TestFastq_error_no_qual: - test_validate_format: .: (0.000469) + test_validate_format: .: (0.000351) Bio::TestFastq::TestFastq_error_qual_del: - test_validate_format: .: (0.000417) + test_validate_format: .: (0.000516) Bio::TestFastq::TestFastq_error_qual_escape: - test_validate_format: .: (0.000388) + test_validate_format: .: (0.000382) Bio::TestFastq::TestFastq_error_qual_null: - test_validate_format: .: (0.000395) + test_validate_format: .: (0.000314) Bio::TestFastq::TestFastq_error_qual_space: - test_validate_format: .: (0.000552) + test_validate_format: .: (0.000326) Bio::TestFastq::TestFastq_error_qual_tab: - test_validate_format: .: (0.000453) + test_validate_format: .: (0.000334) Bio::TestFastq::TestFastq_error_qual_unit_sep: - test_validate_format: .: (0.000436) + test_validate_format: .: (0.000306) Bio::TestFastq::TestFastq_error_qual_vtab: - test_validate_format: .: (0.000399) + test_validate_format: .: (0.000353) Bio::TestFastq::TestFastq_error_short_qual: - test_validate_format: .: (0.000382) + test_validate_format: .: (0.000303) Bio::TestFastq::TestFastq_error_spaces: - test_validate_format: .: (0.000935) + test_validate_format: .: (0.000636) Bio::TestFastq::TestFastq_error_tabs: - test_validate_format: .: (0.000767) + test_validate_format: .: (0.000823) Bio::TestFastq::TestFastq_error_trunc_at_plus: - test_validate_format: .: (0.000435) + test_validate_format: .: (0.000339) Bio::TestFastq::TestFastq_error_trunc_at_qual: - test_validate_format: .: (0.000377) + test_validate_format: .: (0.000277) Bio::TestFastq::TestFastq_error_trunc_at_seq: - test_validate_format: .: (0.000407) + test_validate_format: .: (0.000282) Bio::TestFastq::TestFastq_illumina_full_range: - test_error_probabilities_as_illumina: .: (0.002796) - test_error_probabilities_as_sanger: .: (0.001681) - test_error_probabilities_as_solexa: .: (0.001898) - test_quality_scores_as_illumina: .: (0.000376) - test_quality_scores_as_sanger: .: (0.000282) - test_quality_scores_as_solexa: .: (0.000299) - test_validate_format: .: (0.000442) + test_error_probabilities_as_illumina: .: (0.001599) + test_error_probabilities_as_sanger: .: (0.002183) + test_error_probabilities_as_solexa: .: (0.001769) + test_quality_scores_as_illumina: .: (0.000258) + test_quality_scores_as_sanger: .: (0.000206) + test_quality_scores_as_solexa: .: (0.000237) + test_validate_format: .: (0.000390) Bio::TestFastq::TestFastq_longreads_original_sanger: - test_definition: .: (0.000754) - test_entry_id: .: (0.000692) - test_error_probabilities: .: (0.053391) - test_nalen: .: (0.000857) - test_naseq: .: (0.000747) - test_quality_scores: .: (0.001140) - test_quality_string: .: (0.001076) - test_roundtrip: .: (0.053653) - test_seq: .: (0.000740) - test_sequence_string: .: (0.000445) - test_to_biosequence: .: (0.047234) - test_to_biosequence_and_output: .: (0.002937) - test_to_s: .: (0.000756) - test_validate_format: .: (0.000805) - test_validate_format_with_array: .: (0.000718) + test_definition: .: (0.000606) + test_entry_id: .: (0.000577) + test_error_probabilities: .: (0.051489) + test_nalen: .: (0.000684) + test_naseq: .: (0.000545) + test_quality_scores: .: (0.000961) + test_quality_string: .: (0.000494) + test_roundtrip: .: (0.050039) + test_seq: .: (0.000719) + test_sequence_string: .: (0.000497) + test_to_biosequence: .: (0.044729) + test_to_biosequence_and_output: .: (0.002716) + test_to_s: .: (0.000562) + test_validate_format: .: (0.000638) + test_validate_format_with_array: .: (0.000534) Bio::TestFastq::TestFastq_mask: - test_mask_20: .: (0.000632) - test_mask_20_with_empty_string: .: (0.000533) - test_mask_20_with_longer_string: .: (0.000385) - test_mask_20_with_x: .: (0.000331) - test_mask_60: .: (0.000373) + test_mask_20: .: (0.000478) + test_mask_20_with_empty_string: .: (0.000358) + test_mask_20_with_longer_string: .: (0.000250) + test_mask_20_with_x: .: (0.000227) + test_mask_60: .: (0.000264) Bio::TestFastq::TestFastq_sanger_full_range: - test_error_probabilities_as_illumina: .: (0.002944) - test_error_probabilities_as_sanger: .: (0.002231) - test_error_probabilities_as_solexa: .: (0.003789) - test_quality_scores_as_illumina: .: (0.000482) - test_quality_scores_as_sanger: .: (0.000317) - test_quality_scores_as_solexa: .: (0.000366) - test_validate_format: .: (0.000513) + test_error_probabilities_as_illumina: .: (0.002623) + test_error_probabilities_as_sanger: .: (0.001932) + test_error_probabilities_as_solexa: .: (0.003438) + test_quality_scores_as_illumina: .: (0.000299) + test_quality_scores_as_sanger: .: (0.000193) + test_quality_scores_as_solexa: .: (0.000235) + test_validate_format: .: (0.000412) Bio::TestFastq::TestFastq_solexa_full_range: - test_error_probabilities_as_illumina: .: (0.002565) - test_error_probabilities_as_sanger: .: (0.002135) - test_error_probabilities_as_solexa: .: (0.001972) - test_quality_scores_as_illumina: .: (0.000458) - test_quality_scores_as_sanger: .: (0.000370) - test_quality_scores_as_solexa: .: (0.000322) - test_validate_format: .: (0.000506) + test_error_probabilities_as_illumina: .: (0.002402) + test_error_probabilities_as_sanger: .: (0.001816) + test_error_probabilities_as_solexa: .: (0.001641) + test_quality_scores_as_illumina: .: (0.000274) + test_quality_scores_as_sanger: .: (0.000215) + test_quality_scores_as_solexa: .: (0.000170) + test_validate_format: .: (0.000356) Bio::TestFeature: - test_append: .: (0.000415) - test_append_nil: .: (0.000123) - test_assoc: .: (0.000137) - test_each: .: (0.000134) - test_feature: .: (0.000102) - test_locations: .: (0.000177) - test_new: .: (0.000106) - test_position: .: (0.000102) - test_qualifiers: .: (0.000113) + test_append: .: (0.000199) + test_append_nil: .: (0.000182) + test_assoc: .: (0.000078) + test_each: .: (0.000063) + test_feature: .: (0.000043) + test_locations: .: (0.000119) + test_new: .: (0.000054) + test_position: .: (0.000048) + test_qualifiers: .: (0.000040) Bio::TestFeatures: - test_append: .: (0.000286) - test_arg: .: (0.000117) - test_each: .: (0.000108) - test_features: .: (0.000117) + test_append: .: (0.000193) + test_arg: .: (0.000054) + test_each: .: (0.000046) + test_features: .: (0.000054) Bio::TestFlatFile::TestDefaultAutoDetect: - test_aaindex1: .: (0.001011) - test_aaindex2: .: (0.000272) - test_blast: .: (0.000242) - test_blastxml: .: (0.000691) - test_embl: .: (0.000294) - test_embl_oldrelease: .: (0.000249) - test_fastaformat: .: (0.000384) - test_fastanumericformat: .: (0.000158) - test_fastq: .: (0.000213) - test_genbank: .: (0.000216) - test_genpept: .: (0.000242) - test_hmmer: .: (0.000242) - test_maxml_cluster: .: (0.002274) - test_maxml_sequence: .: (0.000153) - test_medline: .: (0.000169) - test_prosite: .: (0.003445) + test_aaindex1: .: (0.000759) + test_aaindex2: .: (0.000191) + test_blast: .: (0.000157) + test_blastxml: .: (0.000558) + test_embl: .: (0.000291) + test_embl_oldrelease: .: (0.000170) + test_fastaformat: .: (0.000294) + test_fastanumericformat: .: (0.000086) + test_fastq: .: (0.000117) + test_genbank: .: (0.000158) + test_genpept: .: (0.000155) + test_hmmer: .: (0.000151) + test_maxml_cluster: .: (0.002470) + test_maxml_sequence: .: (0.000105) + test_medline: .: (0.000103) + test_prosite: .: (0.003311) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. -.: (0.002892) - test_transfac: .: (0.001379) +.: (0.002638) + test_transfac: .: (0.001188) Bio::TestFlatFile::TestFlatFileClassMethod: - test_auto_0arg: .: (0.000366) - test_auto_1arg_filename: .: (0.000487) - test_auto_1arg_io: .: (0.000374) - test_auto_1arg_io_with_block: .: (0.001048) - test_auto_1arg_with_block: .: (0.000538) - test_auto_2arg_filename_mode: .: (0.000341) - test_auto_2arg_filename_mode_with_block: .: (0.000524) - test_auto_3arg: .: (0.000350) - test_auto_3arg_with_block: .: (0.000486) - test_foreach: .: (0.000417) - test_new_2arg_class: .: (0.000202) - test_new_2arg_nil: .: (0.000283) - test_open_0arg: .: (0.000151) - test_open_1arg_class: .: (0.000127) - test_open_1arg_filename: .: (0.000306) - test_open_1arg_io: .: (0.000299) - test_open_1arg_io_with_block: .: (0.000547) - test_open_1arg_nil: .: (0.000149) - test_open_1arg_with_block: .: (0.000492) - test_open_2arg_autodetect: .: (0.000291) - test_open_2arg_autodetect_io: .: (0.000281) - test_open_2arg_autodetect_io_with_block: .: (0.000466) - test_open_2arg_autodetect_with_block: .: (0.000458) - test_open_2arg_class: .: (0.000186) - test_open_2arg_class_io: .: (0.000184) - test_open_2arg_class_io_with_block: .: (0.000416) - test_open_2arg_class_with_block: .: (0.000376) - test_open_2arg_filename_mode: .: (0.000336) - test_open_2arg_filename_mode_with_block: .: (0.000465) - test_open_3arg: .: (0.000502) - test_open_3arg_with_block: .: (0.000998) - test_open_4arg: .: (0.000955) - test_to_a: .: (0.000515) + test_auto_0arg: .: (0.000237) + test_auto_1arg_filename: .: (0.000320) + test_auto_1arg_io: .: (0.000223) + test_auto_1arg_io_with_block: .: (0.000425) + test_auto_1arg_with_block: .: (0.000404) + test_auto_2arg_filename_mode: .: (0.000243) + test_auto_2arg_filename_mode_with_block: .: (0.000371) + test_auto_3arg: .: (0.000225) + test_auto_3arg_with_block: .: (0.000394) + test_foreach: .: (0.000329) + test_new_2arg_class: .: (0.000120) + test_new_2arg_nil: .: (0.000186) + test_open_0arg: .: (0.000089) + test_open_1arg_class: .: (0.000063) + test_open_1arg_filename: .: (0.000203) + test_open_1arg_io: .: (0.000194) + test_open_1arg_io_with_block: .: (0.000366) + test_open_1arg_nil: .: (0.000079) + test_open_1arg_with_block: .: (0.000376) + test_open_2arg_autodetect: .: (0.000222) + test_open_2arg_autodetect_io: .: (0.000208) + test_open_2arg_autodetect_io_with_block: .: (0.000358) + test_open_2arg_autodetect_with_block: .: (0.000359) + test_open_2arg_class: .: (0.000113) + test_open_2arg_class_io: .: (0.000126) + test_open_2arg_class_io_with_block: .: (0.000284) + test_open_2arg_class_with_block: .: (0.000270) + test_open_2arg_filename_mode: .: (0.000225) + test_open_2arg_filename_mode_with_block: .: (0.000367) + test_open_3arg: .: (0.000397) + test_open_3arg_with_block: .: (0.000871) + test_open_4arg: .: (0.000787) + test_to_a: .: (0.000367) Bio::TestFlatFile::TestFlatFileFastaFormat: - test_autodetect: .: (0.000438) - test_close: .: (0.000181) - test_dbclass: .: (0.000159) - test_dbclass_eq: .: (0.000187) - test_dbclass_nil: .: (0.000232) - test_each: .: (0.000328) - test_each_entry: .: (0.000363) - test_ended_pos: .: (0.000276) - test_entry_pos_flag: .: (0.000203) - test_entry_raw: .: (0.000347) - test_eof?: .: (0.002880) - test_next_entry: .: (0.000592) - test_path: .: (0.000235) - test_pos: .: (0.000273) - test_raw: .: (0.000310) - test_rewind: .: (0.000253) - test_start_pos: .: (0.000259) - test_start_pos_ended_pos_not_recorded: .: (0.000261) - test_to_io: .: (0.000195) + test_autodetect: .: (0.000382) + test_close: .: (0.000103) + test_dbclass: .: (0.000078) + test_dbclass_eq: .: (0.000099) + test_dbclass_nil: .: (0.000140) + test_each: .: (0.000179) + test_each_entry: .: (0.000245) + test_ended_pos: .: (0.000161) + test_entry_pos_flag: .: (0.000096) + test_entry_raw: .: (0.002726) + test_eof?: .: (0.000239) + test_next_entry: .: (0.000247) + test_path: .: (0.000103) + test_pos: .: (0.000149) + test_raw: .: (0.000200) + test_rewind: .: (0.000156) + test_start_pos: .: (0.000157) + test_start_pos_ended_pos_not_recorded: .: (0.000164) + test_to_io: .: (0.000109) Bio::TestFlatFile::TestFlatFileWithCustomClass: - test_simpleformat: .: (0.000330) - test_simpleformat2: .: (0.000224) + test_simpleformat: .: (0.000745) + test_simpleformat2: .: (0.000199) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: - test_close: .: (0.000287) - test_eof_false_after_prefetch: .: (0.000698) - test_eof_false_first: .: (0.000135) - test_eof_true: .: (0.000167) - test_getc: .: (0.000136) - test_getc_after_prefetch: .: (0.000140) - test_gets: .: (0.000141) - test_gets_equal_prefetch_gets: .: (0.000144) - test_gets_paragraph_mode: .: (0.000192) - test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000278) - test_gets_paragraph_mode_within_buffer: .: (0.000352) - test_gets_rs: .: (0.000169) - test_gets_rs_equal_prefetch_gets: .: (0.000160) - test_gets_rs_within_buffer: .: (0.000264) - test_pos: .: (0.000143) - test_pos=: .: (0.000141) - test_prefetch_buffer: .: (0.000127) - test_prefetch_gets: .: (0.000152) - test_prefetch_gets_with_arg: .: (0.000359) - test_rewind: .: (0.000093) - test_skip_spaces: .: (0.000077) - test_to_io: .: (0.000077) - test_ungetc: .: (0.000062) + test_close: .: (0.000182) + test_eof_false_after_prefetch: .: (0.000122) + test_eof_false_first: .: (0.000062) + test_eof_true: .: (0.000088) + test_getc: .: (0.000065) + test_getc_after_prefetch: .: (0.000059) + test_gets: .: (0.000084) + test_gets_equal_prefetch_gets: .: (0.000070) + test_gets_paragraph_mode: .: (0.000090) + test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000185) + test_gets_paragraph_mode_within_buffer: .: (0.000206) + test_gets_rs: .: (0.000081) + test_gets_rs_equal_prefetch_gets: .: (0.000078) + test_gets_rs_within_buffer: .: (0.000159) + test_pos: .: (0.000264) + test_pos=: .: (0.000087) + test_prefetch_buffer: .: (0.000064) + test_prefetch_gets: .: (0.000063) + test_prefetch_gets_with_arg: .: (0.000080) + test_rewind: .: (0.000056) + test_skip_spaces: .: (0.000071) + test_to_io: .: (0.000086) + test_ungetc: .: (0.000067) test_ungetc_after_prefetch: .: (0.000064) - test_ungets: .: (0.000076) + test_ungets: .: (0.000070) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: - test_self_for_io: .: (0.000182) + test_self_for_io: .: (0.000175) test_self_open_file: .: (0.000085) - test_self_open_file_with_block: .: (0.052591) + test_self_open_file_with_block: .: (0.021648) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: - test_parse_file_open_arg_int_opt: .: (0.000364) - test_parse_file_open_arg_int_perm: .: (0.000138) - test_parse_file_open_arg_int_perm_opt: .: (0.000133) - test_parse_file_open_arg_integer: .: (0.000123) - test_parse_file_open_arg_nil: .: (0.000115) - test_parse_file_open_arg_opt: .: (0.000172) - test_parse_file_open_arg_opt_with_integer_mode: .: (0.000265) - test_parse_file_open_arg_str: .: (0.000148) - test_parse_file_open_arg_str_opt: .: (0.000130) - test_parse_file_open_arg_str_perm: .: (0.000116) - test_parse_file_open_arg_str_perm_opt: .: (0.000134) - test_parse_file_open_arg_str_with_enc: .: (0.000120) - test_parse_file_open_arg_str_with_ext_enc: .: (0.000108) - test_parse_file_open_mode_integer: .: (0.000117) - test_parse_file_open_mode_nil: .: (0.000119) - test_parse_file_open_mode_str: .: (0.000123) - test_parse_file_open_mode_str_with_enc: .: (0.000146) - test_parse_file_open_mode_str_with_ext_enc: .: (0.000113) + test_parse_file_open_arg_int_opt: .: (0.000210) + test_parse_file_open_arg_int_perm: .: (0.000053) + test_parse_file_open_arg_int_perm_opt: .: (0.000046) + test_parse_file_open_arg_integer: .: (0.000043) + test_parse_file_open_arg_nil: .: (0.000041) + test_parse_file_open_arg_opt: .: (0.000070) + test_parse_file_open_arg_opt_with_integer_mode: .: (0.000055) + test_parse_file_open_arg_str: .: (0.000051) + test_parse_file_open_arg_str_opt: .: (0.000053) + test_parse_file_open_arg_str_perm: .: (0.000169) + test_parse_file_open_arg_str_perm_opt: .: (0.000050) + test_parse_file_open_arg_str_with_enc: .: (0.000053) + test_parse_file_open_arg_str_with_ext_enc: .: (0.000048) + test_parse_file_open_mode_integer: .: (0.000042) + test_parse_file_open_mode_nil: .: (0.000047) + test_parse_file_open_mode_str: .: (0.000047) + test_parse_file_open_mode_str_with_enc: .: (0.000047) + test_parse_file_open_mode_str_with_ext_enc: .: (0.000045) Bio::TestFlatFileSplitter::TestTemplate: - test_dbclass: .: (0.000326) - test_entry: .: (0.000132) - test_entry_ended_pos: .: (0.000070) - test_entry_pos_flag: .: (0.000067) + test_dbclass: .: (0.000153) + test_entry: .: (0.000058) + test_entry_ended_pos: .: (0.000050) + test_entry_pos_flag: .: (0.000059) test_entry_start_pos: .: (0.000046) - test_get_entry: .: (0.000099) - test_rewind: .: (0.000071) - test_skip_leader: .: (0.000065) - test_stream: .: (0.000046) - test_stream_pos: .: (0.000057) + test_get_entry: .: (0.000094) + test_rewind: .: (0.000065) + test_skip_leader: .: (0.000059) + test_stream: .: (0.000219) + test_stream_pos: .: (0.000083) Bio::TestFlatFileSplitter::TestDefault: - test_delimiter: .: (0.000319) - test_delimiter_overrun: .: (0.000047) - test_entry: .: (0.000079) - test_entry_ended_pos: .: (0.000053) - test_entry_ended_pos_default_nil: .: (0.000048) - test_entry_start_pos: .: (0.000048) - test_entry_start_pos_default_nil: .: (0.000047) - test_get_entry: .: (0.000105) - test_get_parsed_entry: .: (0.000117) - test_header: .: (0.000041) - test_skip_leader: .: (0.000063) - test_skip_leader_without_header: .: (0.000065) + test_delimiter: .: (0.000145) + test_delimiter_overrun: .: (0.000046) + test_entry: .: (0.000085) + test_entry_ended_pos: .: (0.000060) + test_entry_ended_pos_default_nil: .: (0.000054) + test_entry_start_pos: .: (0.000054) + test_entry_start_pos_default_nil: .: (0.000050) + test_get_entry: .: (0.000108) + test_get_parsed_entry: .: (0.000146) + test_header: .: (0.000050) + test_skip_leader: .: (0.000073) + test_skip_leader_without_header: .: (0.000071) Bio::TestFlatFileSplitter::TestLineOriented: - test_dbclass: .: (0.000207) - test_entry_ended_pos: .: (0.000116) - test_entry_start_pos: .: (0.000389) - test_flag_to_fetch_header: .: (0.000230) - test_get_entry: .: (0.000284) - test_get_parsed_entry: .: (0.000248) - test_rewind: .: (0.000201) - test_skip_leader: .: (0.000129) + test_dbclass: .: (0.000200) + test_entry_ended_pos: .: (0.000140) + test_entry_start_pos: .: (0.000122) + test_flag_to_fetch_header: .: (0.000297) + test_get_entry: .: (0.000174) + test_get_parsed_entry: .: (0.000150) + test_rewind: .: (0.000112) + test_skip_leader: .: (0.000067) Bio::TestGCGMsf: - test_alignment: .: (0.000893) - test_checksum: .: (0.000444) - test_compcheck: .: (0.000229) - test_date: .: (0.000265) - test_description: .: (0.000208) - test_entry_id: .: (0.000234) - test_gap_length_weight: .: (0.006400) - test_gap_weight: .: (0.000371) - test_heading: .: (0.000253) - test_length: .: (0.000234) - test_seq_type: .: (0.000212) - test_symbol_comparison_table: .: (0.000222) - test_validate_checksum: .: (0.000994) + test_alignment: .: (0.000714) + test_checksum: .: (0.000165) + test_compcheck: .: (0.000161) + test_date: .: (0.000135) + test_description: .: (0.000121) + test_entry_id: .: (0.000112) + test_gap_length_weight: .: (0.000119) + test_gap_weight: .: (0.000114) + test_heading: .: (0.000107) + test_length: .: (0.000131) + test_seq_type: .: (0.000110) + test_symbol_comparison_table: .: (0.000147) + test_validate_checksum: .: (0.000728) Bio::TestGFF: - test_record_class: .: (0.000554) - test_records: .: (0.000287) + test_record_class: .: (0.000353) + test_records: .: (0.000190) Bio::TestGFF2: - test_const_version: .: (0.000484) - test_gff_version: .: (0.000395) - test_metadata: .: (0.000319) - test_metadata_size: .: (0.000305) - test_records_size: .: (0.000325) - test_to_s: .: (0.000528) + test_const_version: .: (0.000351) + test_gff_version: .: (0.000279) + test_metadata: .: (0.000264) + test_metadata_size: .: (0.000227) + test_records_size: .: (0.000216) + test_to_s: .: (0.000436) Bio::TestGFF2ComplexAttributes: - test_attributes_case1: .: (0.004162) - test_attributes_case2: .: (0.000285) - test_attributes_incompatible_backslash_semicolon: .: (0.000261) + test_attributes_case1: .: (0.000188) + test_attributes_case2: .: (0.000099) + test_attributes_incompatible_backslash_semicolon: .: (0.000124) Bio::TestGFF2MetaData: - test_data: .: (0.000216) - test_directive: .: (0.000101) - test_parse: .: (0.000123) + test_data: .: (0.000102) + test_directive: .: (0.000039) + test_parse: .: (0.000050) Bio::TestGFF2Record: - test_attribute: .: (0.000358) - test_attribute_nonexistent: .: (0.000185) - test_attributes: .: (0.000167) - test_attributes_to_hash: .: (0.000167) - test_comment_only?: .: (0.000136) + test_attribute: .: (0.000282) + test_attribute_nonexistent: .: (0.000149) + test_attributes: .: (0.000200) + test_attributes_to_hash: .: (0.000171) + test_comment_only?: .: (0.000145) test_delete_attribute: .: (0.000157) - test_delete_attribute_multiple: .: (0.000158) - test_delete_attribute_multiple2: .: (0.000201) - test_delete_attribute_multiple_nil: .: (0.000153) - test_delete_attribute_nil: .: (0.000382) - test_delete_attribute_nonexistent: .: (0.003676) - test_delete_attributes: .: (0.000465) - test_delete_attributes_multiple: .: (0.000281) - test_delete_attributes_nonexistent: .: (0.000414) - test_end: .: (0.000259) - test_eqeq: .: (0.000546) - test_eqeq_false: .: (0.000475) - test_feature: .: (0.000431) - test_frame: .: (0.000258) - test_get_attribute: .: (0.000435) - test_get_attribute_nonexistent: .: (0.000248) - test_get_attributes: .: (0.000331) - test_get_attributes_nonexistent: .: (0.000236) - test_replace_attributes: .: (0.000468) - test_replace_attributes_multiple_multiple_over: .: (0.000272) - test_replace_attributes_multiple_multiple_same: .: (0.000257) - test_replace_attributes_multiple_multiple_two: .: (0.000279) - test_replace_attributes_multiple_single: .: (0.000299) - test_replace_attributes_nonexistent: .: (0.000322) - test_replace_attributes_nonexistent_multiple: .: (0.003661) - test_replace_attributes_single_multiple: .: (0.000418) - test_score: .: (0.000241) - test_self_parse: .: (0.000665) - test_seqname: .: (0.000255) - test_set_attribute: .: (0.000430) - test_set_attribute_multiple: .: (0.000253) - test_set_attribute_nonexistent: .: (0.000243) - test_sort_attributes_by_tag!: .: (0.000303) - test_sort_attributes_by_tag_bang_test2: .: (0.000293) - test_sort_attributes_by_tag_bang_with_block: .: (0.000202) - test_source: .: (0.000157) - test_start: .: (0.000165) - test_strand: .: (0.000149) + test_delete_attribute_multiple: .: (0.000168) + test_delete_attribute_multiple2: .: (0.000176) + test_delete_attribute_multiple_nil: .: (0.000234) + test_delete_attribute_nil: .: (0.000174) + test_delete_attribute_nonexistent: .: (0.000158) + test_delete_attributes: .: (0.000163) + test_delete_attributes_multiple: .: (0.000157) + test_delete_attributes_nonexistent: .: (0.000152) + test_end: .: (0.000305) + test_eqeq: .: (0.000448) + test_eqeq_false: .: (0.000335) + test_feature: .: (0.000146) + test_frame: .: (0.000301) + test_get_attribute: .: (0.000205) + test_get_attribute_nonexistent: .: (0.000150) + test_get_attributes: .: (0.000202) + test_get_attributes_nonexistent: .: (0.000145) + test_replace_attributes: .: (0.000326) + test_replace_attributes_multiple_multiple_over: .: (0.000185) + test_replace_attributes_multiple_multiple_same: .: (0.000162) + test_replace_attributes_multiple_multiple_two: .: (0.000179) + test_replace_attributes_multiple_single: .: (0.000516) + test_replace_attributes_nonexistent: .: (0.000185) + test_replace_attributes_nonexistent_multiple: .: (0.000158) + test_replace_attributes_single_multiple: .: (0.000173) + test_score: .: (0.000168) + test_self_parse: .: (0.000406) + test_seqname: .: (0.000158) + test_set_attribute: .: (0.000170) + test_set_attribute_multiple: .: (0.000165) + test_set_attribute_nonexistent: .: (0.000183) + test_sort_attributes_by_tag!: .: (0.000211) + test_sort_attributes_by_tag_bang_test2: .: (0.000238) + test_sort_attributes_by_tag_bang_with_block: .: (0.000182) + test_source: .: (0.000142) + test_start: .: (0.000139) + test_strand: .: (0.000138) test_to_s: .: (0.000257) Bio::TestGFF2RecordEmpty: - test_comment: .: (0.000183) - test_comment_eq: .: (0.000042) - test_comment_only?: .: (0.000043) - test_comment_only_false: .: (0.000041) - test_to_s: .: (0.000046) - test_to_s_not_empty: .: (0.000083) + test_comment: .: (0.000182) + test_comment_eq: .: (0.000058) + test_comment_only?: .: (0.000051) + test_comment_only_false: .: (0.000049) + test_to_s: .: (0.000053) + test_to_s_not_empty: .: (0.000087) Bio::TestGFF3: - test_const_version: .: (0.000459) - test_gff_version: .: (0.000251) - test_records: .: (0.000376) - test_sequence_regions: .: (0.000261) - test_sequences: .: (0.000310) - test_to_s: .: (0.008954) + test_const_version: .: (0.000503) + test_gff_version: .: (0.000290) + test_records: .: (0.000393) + test_sequence_regions: .: (0.000295) + test_sequences: .: (0.000346) + test_to_s: .: (0.000572) Bio::TestGFF3MetaData: - test_data: .: (0.000292) - test_directive: .: (0.000127) - test_parse: .: (0.000144) + test_data: .: (0.000137) + test_directive: .: (0.000044) + test_parse: .: (0.000056) Bio::TestGFF3Record: - test_attributes: .: (0.000369) - test_end: .: (0.000189) - test_feature: .: (0.000187) - test_frame: .: (0.000183) - test_id: .: (0.000181) - test_score: .: (0.000178) - test_seqname: .: (0.000220) - test_source: .: (0.000189) - test_start: .: (0.000215) - test_strand: .: (0.000191) - test_to_s: .: (0.006889) - test_to_s_attr_order_changed: .: (0.000544) + test_attributes: .: (0.000234) + test_end: .: (0.000134) + test_feature: .: (0.000115) + test_frame: .: (0.000109) + test_id: .: (0.000108) + test_score: .: (0.000105) + test_seqname: .: (0.000121) + test_source: .: (0.000110) + test_start: .: (0.000108) + test_strand: .: (0.000107) + test_to_s: .: (0.000222) + test_to_s_attr_order_changed: .: (0.000244) Bio::TestGFF3RecordEscape: - test_escape: .: (0.000288) - test_escape_attribute: .: (0.000139) - test_escape_seqid: .: (0.000136) - test_unescape: .: (0.000135) + test_escape: .: (0.000161) + test_escape_attribute: .: (0.000072) + test_escape_seqid: .: (0.000068) + test_unescape: .: (0.000067) Bio::TestGFF3RecordGap: - test___scan_gap: .: (0.000343) - test_eqeq: .: (0.000203) - test_new_from_sequences_na: .: (0.000203) - test_new_from_sequences_na_aa: .: (0.000254) - test_new_from_sequences_na_aa_boundary_gap: .: (0.000368) - test_new_from_sequences_na_aa_example: .: (0.000274) - test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000263) - test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000228) - test_process_sequences_na: .: (0.000220) - test_process_sequences_na_aa: .: (0.000196) - test_process_sequences_na_aa_reverse_frameshift: .: (0.000187) - test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000198) - test_process_sequences_na_aa_tooshort: .: (0.000292) - test_process_sequences_na_tooshort: .: (0.000233) - test_to_s: .: (0.000185) + test___scan_gap: .: (0.000220) + test_eqeq: .: (0.000113) + test_new_from_sequences_na: .: (0.000123) + test_new_from_sequences_na_aa: .: (0.000183) + test_new_from_sequences_na_aa_boundary_gap: .: (0.000232) + test_new_from_sequences_na_aa_example: .: (0.000177) + test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000146) + test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000135) + test_process_sequences_na: .: (0.000153) + test_process_sequences_na_aa: .: (0.000119) + test_process_sequences_na_aa_reverse_frameshift: .: (0.000101) + test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000111) + test_process_sequences_na_aa_tooshort: .: (0.000197) + test_process_sequences_na_tooshort: .: (0.000147) + test_to_s: .: (0.000110) Bio::TestGFF3RecordMisc: - test_attributes_none: .: (0.000305) - test_attributes_one: .: (0.000153) - test_attributes_with_escaping: .: (0.000149) - test_id_multiple: .: (0.000259) - test_id_multiple2: .: (0.000541) - test_id_replace: .: (0.000223) - test_id_set: .: (0.000195) - test_initialize_9: .: (0.000130) - test_phase: .: (0.000187) - test_score: .: (0.000178) - test_to_s_void: .: (0.000168) + test_attributes_none: .: (0.000181) + test_attributes_one: .: (0.000098) + test_attributes_with_escaping: .: (0.000093) + test_id_multiple: .: (0.000160) + test_id_multiple2: .: (0.000134) + test_id_replace: .: (0.000082) + test_id_set: .: (0.000095) + test_initialize_9: .: (0.000055) + test_phase: .: (0.000084) + test_score: .: (0.000074) + test_to_s_void: .: (0.000065) Bio::TestGFF3RecordTarget: - test_end: .: (0.000244) - test_parse: .: (0.000216) - test_start: .: (0.000119) - test_strand: .: (0.000111) - test_target_id: .: (0.000109) - test_to_s: .: (0.016071) + test_end: .: (0.000135) + test_parse: .: (0.004736) + test_start: .: (0.000072) + test_strand: .: (0.000053) + test_target_id: .: (0.000051) + test_to_s: .: (0.000107) Bio::TestGFF3SequenceRegion: - test_end: .: (0.000364) - test_parse: .: (0.000220) - test_seqid: .: (0.000132) - test_start: .: (0.000112) - test_to_s: .: (0.000187) + test_end: .: (0.000160) + test_parse: .: (0.000117) + test_seqid: .: (0.000061) + test_start: .: (0.000049) + test_to_s: .: (0.000096) Bio::TestGFFRecord: - test_attributes: .: (0.000323) - test_comment: .: (0.000189) - test_end: .: (0.000135) - test_feature: .: (0.000090) - test_frame: .: (0.000073) - test_score: .: (0.000064) - test_seqname: .: (0.000063) - test_source: .: (0.000983) - test_start: .: (0.000222) - test_strand: .: (0.000203) + test_attributes: .: (0.000181) + test_comment: .: (0.000093) + test_end: .: (0.000073) + test_feature: .: (0.000067) + test_frame: .: (0.000067) + test_score: .: (0.000729) + test_seqname: .: (0.000081) + test_source: .: (0.000064) + test_start: .: (0.000062) + test_strand: .: (0.000059) Bio::TestGFFRecordConstruct: - test_add_seqname: .: (0.000244) + test_add_seqname: .: (0.000143) Bio::TestGeneAssociation: - test_aspect: .: (0.000541) - test_assigned_by: .: (0.000121) - test_date: .: (0.000080) - test_db: .: (0.000061) - test_db_object_id: .: (0.000059) - test_db_object_name: .: (0.000057) - test_db_object_symbol: .: (0.000073) - test_db_object_synonym: .: (0.000071) - test_db_object_type: .: (0.000067) - test_db_reference: .: (0.000075) - test_evidence: .: (0.000062) - test_goid: .: (0.000073) - test_parser: .: (0.004963) - test_qualifier: .: (0.000152) - test_taxon: .: (0.000126) - test_to_str: .: (0.000142) - test_with: .: (0.000132) + test_aspect: .: (0.000302) + test_assigned_by: .: (0.000069) + test_date: .: (0.000058) + test_db: .: (0.000059) + test_db_object_id: .: (0.000055) + test_db_object_name: .: (0.000058) + test_db_object_symbol: .: (0.000055) + test_db_object_synonym: .: (0.000061) + test_db_object_type: .: (0.000353) + test_db_reference: .: (0.000069) + test_evidence: .: (0.000053) + test_goid: .: (0.000079) + test_parser: .: (0.000374) + test_qualifier: .: (0.000069) + test_taxon: .: (0.000058) + test_to_str: .: (0.000071) + test_with: .: (0.000062) Bio::TestGenscanReport: - test_date_run: .: (0.000956) - test_gccontent: .: (0.000614) - test_genscan_version: .: (0.004112) - test_isochore: .: (0.000812) - test_length: .: (0.000637) - test_matrix: .: (0.000631) - test_predictions_size: .: (0.000799) - test_query_name: .: (0.004392) - test_time: .: (0.000796) + test_date_run: .: (0.000744) + test_gccontent: .: (0.000483) + test_genscan_version: .: (0.000625) + test_isochore: .: (0.000466) + test_length: .: (0.000434) + test_matrix: .: (0.000477) + test_predictions_size: .: (0.000656) + test_query_name: .: (0.000494) + test_time: .: (0.000454) Bio::TestGenscanReportExon: - test_acceptor_score: .: (0.000819) - test_donor_score: .: (0.000770) - test_exon_type: .: (0.000623) - test_exon_type_long: .: (0.000506) - test_first: .: (0.000455) - test_initiation_score: .: (0.007696) - test_last: .: (0.000712) - test_number: .: (0.000593) - test_p_value: .: (0.000573) - test_phase: .: (0.004941) - test_range: .: (0.000803) - test_score: .: (0.000634) - test_strand: .: (0.000629) - test_t_score: .: (0.000600) - test_termination_score: .: (0.000625) + test_acceptor_score: .: (0.000570) + test_donor_score: .: (0.000441) + test_exon_type: .: (0.000606) + test_exon_type_long: .: (0.001678) + test_first: .: (0.000487) + test_initiation_score: .: (0.000447) + test_last: .: (0.000428) + test_number: .: (0.000422) + test_p_value: .: (0.000434) + test_phase: .: (0.000462) + test_range: .: (0.000471) + test_score: .: (0.000449) + test_strand: .: (0.000451) + test_t_score: .: (0.000447) + test_termination_score: .: (0.005676) Bio::TestGenscanReportGene: - test_aaseq: .: (0.015554) - test_naseq: .: (0.000911) - test_number: .: (0.000722) - test_polyA: .: (0.005969) - test_promoter: .: (0.001240) + test_aaseq: .: (0.000858) + test_naseq: .: (0.000552) + test_number: .: (0.000488) + test_polyA: .: (0.001340) + test_promoter: .: (0.000534) Bio::TestHMMERReportClassMethods: - test_reports_ary: .: (0.000968) - test_reports_ary_contents: .: (0.000701) + test_reports_ary: .: (0.000747) + test_reports_ary_contents: .: (0.000540) Bio::TestHMMERReportConstants: - test_rs: .: (0.000271) + test_rs: .: (0.000151) Bio::TestHMMERReportHit: - test_accession: .: (0.007262) - test_append_hsp: .: (0.000814) - test_bit_score: .: (0.000625) - test_definition: .: (0.000627) - test_description: .: (0.000619) - test_each: .: (0.000652) - test_each_hsp: .: (0.000629) - test_entry_id: .: (0.000723) - test_evalue: .: (0.000543) - test_hit: .: (0.005660) - test_hit_id: .: (0.000803) - test_hsps: .: (0.000650) - test_num: .: (0.000525) - test_score: .: (0.000475) - test_target_def: .: (0.000458) - test_target_id: .: (0.000842) + test_accession: .: (0.000875) + test_append_hsp: .: (0.000521) + test_bit_score: .: (0.000491) + test_definition: .: (0.000501) + test_description: .: (0.000491) + test_each: .: (0.000537) + test_each_hsp: .: (0.000633) + test_entry_id: .: (0.000481) + test_evalue: .: (0.000456) + test_hit: .: (0.000460) + test_hit_id: .: (0.000469) + test_hsps: .: (0.000488) + test_num: .: (0.000626) + test_score: .: (0.000505) + test_target_def: .: (0.000467) + test_target_id: .: (0.000455) Bio::TestHMMERReportHmmpfam: - test_domain_top_hits: .: (0.000751) - test_each: .: (0.006400) - test_each_hit: .: (0.000839) - test_histogram: .: (0.000695) - test_hits: .: (0.000644) - test_hsps: .: (0.000600) - test_parameter: .: (0.000774) - test_program: .: (0.000628) - test_query_info: .: (0.001122) - test_statistical_detail: .: (0.005542) - test_total_seq_searched: .: (0.000827) - test_whole_seq_top_hits: .: (0.000696) + test_domain_top_hits: .: (0.000585) + test_each: .: (0.000478) + test_each_hit: .: (0.000496) + test_histogram: .: (0.000492) + test_hits: .: (0.000596) + test_hsps: .: (0.000945) + test_parameter: .: (0.000505) + test_program: .: (0.000494) + test_query_info: .: (0.000503) + test_statistical_detail: .: (0.000464) + test_total_seq_searched: .: (0.000445) + test_whole_seq_top_hits: .: (0.000483) Bio::TestHMMERReportHmmsearch: - test_domain_top_hits: .: (0.000946) - test_histogram: .: (0.000765) - test_statistical_detail: .: (0.000727) - test_total_seq_searched: .: (0.006853) - test_whole_seq_top_hit: .: (0.000978) + test_domain_top_hits: .: (0.000744) + test_histogram: .: (0.000547) + test_statistical_detail: .: (0.000563) + test_total_seq_searched: .: (0.000553) + test_whole_seq_top_hit: .: (0.000564) Bio::TestHMMERReportHsp: - test_accession: .: (0.000738) - test_bit_score: .: (0.000465) - test_csline: .: (0.000445) - test_domain: .: (0.000437) - test_evalue: .: (0.000724) - test_flatseq: .: (0.000574) - test_hmm_f: .: (0.000548) - test_hmm_t: .: (0.015653) - test_hmmseq: .: (0.001037) - test_hsp: .: (0.000723) - test_midline: .: (0.002723) - test_query_frame: .: (0.000710) - test_query_from: .: (0.000714) - test_query_seq: .: (0.000692) - test_query_to: .: (0.000639) - test_rfline: .: (0.001453) - test_score: .: (0.000666) - test_seq_f: .: (0.000611) - test_seq_ft: .: (0.000588) - test_seq_t: .: (0.000595) - test_set_alignment: .: (0.000570) - test_targat_to: .: (0.000881) - test_target_frame: .: (0.000614) - test_target_from: .: (0.000567) - test_target_seq: .: (0.000565) + test_accession: .: (0.000610) + test_bit_score: .: (0.000468) + test_csline: .: (0.000448) + test_domain: .: (0.000459) + test_evalue: .: (0.000447) + test_flatseq: .: (0.000447) + test_hmm_f: .: (0.006179) + test_hmm_t: .: (0.000765) + test_hmmseq: .: (0.000495) + test_hsp: .: (0.000491) + test_midline: .: (0.000492) + test_query_frame: .: (0.000491) + test_query_from: .: (0.000522) + test_query_seq: .: (0.001264) + test_query_to: .: (0.000549) + test_rfline: .: (0.000464) + test_score: .: (0.000496) + test_seq_f: .: (0.000477) + test_seq_ft: .: (0.000497) + test_seq_t: .: (0.000703) + test_set_alignment: .: (0.000468) + test_targat_to: .: (0.000464) + test_target_frame: .: (0.000457) + test_target_from: .: (0.000484) + test_target_seq: .: (0.000479) Bio::TestHetatmFinder: - test_each_hetatm: .: (0.000440) - test_find_hetatm: .: (0.000239) - test_hetatms: .: (0.000566) + test_each_hetatm: .: (0.000586) + test_find_hetatm: .: (0.000140) + test_hetatms: .: (0.000170) Bio::TestHeterogen: - test_addAtom: .: (0.000336) - test_each: .: (0.000205) - test_each_hetatm: .: (0.000185) - test_get_residue_id_from_atom: .: (0.000199) - test_het_atom: .: (0.000147) - test_iCode: .: (0.000147) - test_inspect: .: (0.000164) - test_resSeq: .: (0.000384) - test_sort: .: (0.000199) - test_square_bracket: .: (0.000110) - test_to_s: .: (0.000158) - test_update_resudue_id: .: (0.000086) + test_addAtom: .: (0.000220) + test_each: .: (0.000119) + test_each_hetatm: .: (0.000101) + test_get_residue_id_from_atom: .: (0.000092) + test_het_atom: .: (0.000074) + test_iCode: .: (0.000098) + test_inspect: .: (0.000117) + test_resSeq: .: (0.000078) + test_sort: .: (0.000109) + test_square_bracket: .: (0.000094) + test_to_s: .: (0.000145) + test_update_resudue_id: .: (0.000081) Bio::TestHeterogenFinder: - test_each_heterogen: .: (0.000190) - test_find_heterogen: .: (0.000061) - test_heterogens: .: (0.000078) + test_each_heterogen: .: (0.000167) + test_find_heterogen: .: (0.000089) + test_heterogens: .: (0.000084) Bio::TestIprscanPTxtReport: - test_match_accession: .: (0.000220) - test_match_description: .: (0.000078) - test_match_evalue: .: (0.000071) - test_match_ipr_description: .: (0.000074) - test_match_ipr_id: .: (0.000072) - test_match_match_end: .: (0.000071) - test_match_match_start: .: (0.000089) - test_match_method: .: (0.000194) - test_matches_size: .: (0.000072) - test_query_id: .: (0.000066) - test_query_length: .: (0.000065) + test_match_accession: .: (0.000197) + test_match_description: .: (0.000076) + test_match_evalue: .: (0.000193) + test_match_ipr_description: .: (0.000085) + test_match_ipr_id: .: (0.000073) + test_match_match_end: .: (0.000072) + test_match_match_start: .: (0.000071) + test_match_method: .: (0.000072) + test_matches_size: .: (0.000095) + test_query_id: .: (0.000074) + test_query_length: .: (0.000070) Bio::TestIprscanRawReport: - test_entry_id: .: (0.001365) - test_match_accession: .: (0.001958) - test_match_crc64: .: (0.001350) - test_match_date: .: (0.001338) - test_match_description: .: (0.007442) - test_match_evalue: .: (0.002495) - test_match_go_terms: .: (0.001652) - test_match_ipr_description: .: (0.001579) - test_match_ipr_id: .: (0.002039) - test_match_match_end: .: (0.001376) - test_match_match_start: .: (0.001334) - test_match_method: .: (0.005729) - test_match_query_id: .: (0.002174) - test_match_query_length: .: (0.001586) - test_match_status: .: (0.001724) - test_obj: .: (0.001922) - test_query_id: .: (0.001376) - test_query_length: .: (0.005557) - test_self_reports_in_raw: .: (0.003652) + test_entry_id: .: (0.001334) + test_match_accession: .: (0.001650) + test_match_crc64: .: (0.001152) + test_match_date: .: (0.001124) + test_match_description: .: (0.007166) + test_match_evalue: .: (0.001517) + test_match_go_terms: .: (0.001398) + test_match_ipr_description: .: (0.001309) + test_match_ipr_id: .: (0.001715) + test_match_match_end: .: (0.001158) + test_match_match_start: .: (0.001132) + test_match_method: .: (0.005036) + test_match_query_id: .: (0.001903) + test_match_query_length: .: (0.001329) + test_match_status: .: (0.001867) + test_obj: .: (0.001151) + test_query_id: .: (0.001110) + test_query_length: .: (0.004935) + test_self_reports_in_raw: .: (0.003103) Bio::TestIprscanReport: - test_output_raw: .: (0.000741) - test_to_raw: .: (0.002648) + test_output_raw: .: (0.000550) + test_to_raw: .: (0.000355) Bio::TestIprscanTxtEntry: - test_iprscan_report_class: .: (0.003150) - test_match_accession: .: (0.003641) - test_match_date: .: (0.001201) - test_match_description: .: (0.003210) - test_match_evalue: .: (0.001022) - test_match_go_terms: .: (0.002503) - test_match_ipr_description: .: (0.003622) - test_match_ipr_id: .: (0.003404) - test_match_match_end: .: (0.002565) - test_match_match_start: .: (0.004318) - test_match_method: .: (0.004296) - test_match_status: .: (0.004698) - test_matches_size: .: (0.009482) - test_query_id: .: (0.000731) - test_query_length: .: (0.000482) + test_iprscan_report_class: .: (0.002374) + test_match_accession: .: (0.001151) + test_match_date: .: (0.003376) + test_match_description: .: (0.001355) + test_match_evalue: .: (0.002010) + test_match_go_terms: .: (0.003656) + test_match_ipr_description: .: (0.001267) + test_match_ipr_id: .: (0.002363) + test_match_match_end: .: (0.002395) + test_match_match_start: .: (0.003045) + test_match_method: .: (0.006357) + test_match_status: .: (0.007798) + test_matches_size: .: (0.007638) + test_query_id: .: (0.000502) + test_query_length: .: (0.000322) Bio::TestIprscanTxtEntryList: - test_to_hash: .: (0.000662) - test_to_hash_match?: .: (0.000558) + test_to_hash: .: (0.000536) + test_to_hash_match?: .: (0.000438) Bio::TestIprscanTxtReport: - test_parse_txt: .: (0.002148) + test_parse_txt: .: (0.001826) Bio::TestKeggCompound: - test_comment: .: (0.000776) - test_dblinks_as_hash: .: (0.000382) - test_dblinks_as_strings: .: (0.000313) - test_entry_id: .: (0.000332) - test_enzymes: .: (0.000520) - test_formula: .: (0.000295) - test_kcf: .: (0.000255) - test_mass: .: (0.000276) - test_name: .: (0.000769) - test_names: .: (0.000332) - test_pathways_as_hash: .: (0.000460) - test_pathways_as_strings: .: (0.000364) - test_reactions: .: (0.000526) - test_remark: .: (0.000303) - test_rpairs: .: (0.000289) + test_comment: .: (0.000536) + test_dblinks_as_hash: .: (0.000274) + test_dblinks_as_strings: .: (0.000189) + test_entry_id: .: (0.000188) + test_enzymes: .: (0.000408) + test_formula: .: (0.000218) + test_kcf: .: (0.000181) + test_mass: .: (0.000193) + test_name: .: (0.000659) + test_names: .: (0.000214) + test_pathways_as_hash: .: (0.000306) + test_pathways_as_strings: .: (0.000217) + test_reactions: .: (0.000390) + test_remark: .: (0.000184) + test_rpairs: .: (0.000168) Bio::TestKeggEnzyme: - test_all_reac: .: (0.000634) - test_classes: .: (0.000427) - test_cofactors: .: (0.000638) - test_comment: .: (0.000454) - test_dblinks_as_hash: .: (0.000487) - test_dblinks_as_strings: .: (0.000428) - test_diseases: .: (0.000466) - test_entry: .: (0.000493) - test_entry_id: .: (0.000715) - test_genes: .: (0.012935) - test_genes_as_hash: .: (0.012261) - test_genes_as_strings: .: (0.006210) - test_inhibitors: .: (0.000593) - test_iubmb_reactions: .: (0.000520) - test_kegg_reactions: .: (0.000500) - test_motifs: .: (0.000430) - test_name: .: (0.000520) - test_names: .: (0.000504) - test_obsolete?: .: (0.000467) - test_orthologs_as_hash: .: (0.000559) - test_orthologs_as_strings: .: (0.001407) - test_pathways_as_hash: .: (0.000619) - test_pathways_as_strings: .: (0.000548) - test_products: .: (0.000557) - test_reaction: .: (0.000549) - test_structures: .: (0.000707) - test_substrates: .: (0.000511) - test_sysname: .: (0.000482) + test_all_reac: .: (0.000495) + test_classes: .: (0.000560) + test_cofactors: .: (0.000343) + test_comment: .: (0.000327) + test_dblinks_as_hash: .: (0.000363) + test_dblinks_as_strings: .: (0.000345) + test_diseases: .: (0.000321) + test_entry: .: (0.000385) + test_entry_id: .: (0.000378) + test_genes: .: (0.011828) + test_genes_as_hash: .: (0.011544) + test_genes_as_strings: .: (0.005106) + test_inhibitors: .: (0.000447) + test_iubmb_reactions: .: (0.000376) + test_kegg_reactions: .: (0.000367) + test_motifs: .: (0.000345) + test_name: .: (0.000403) + test_names: .: (0.000395) + test_obsolete?: .: (0.000342) + test_orthologs_as_hash: .: (0.001259) + test_orthologs_as_strings: .: (0.000434) + test_pathways_as_hash: .: (0.000482) + test_pathways_as_strings: .: (0.000465) + test_products: .: (0.000440) + test_reaction: .: (0.000412) + test_structures: .: (0.000606) + test_substrates: .: (0.000433) + test_sysname: .: (0.000544) Bio::TestKeggGenesDblinks: - test_data: .: (0.000514) - test_dblinks_0: .: (0.000161) - test_dblinks_1: .: (0.000168) - test_dblinks_2: .: (0.000131) + test_data: .: (0.000247) + test_dblinks_0: .: (0.000088) + test_dblinks_1: .: (0.000065) + test_dblinks_2: .: (0.000061) Bio::TestKeggGenesStructure: - test_data: .: (0.000279) - test_ids: .: (0.000188) - test_ids_in_array: .: (0.000159) + test_data: .: (0.000155) + test_ids: .: (0.000108) + test_ids_in_array: .: (0.000086) Bio::TestKeggKGML::TestKGMLEntry1: - test_components: .: (0.004613) - test_graphics__size: .: (0.003971) - test_id: .: (0.004100) - test_link: .: (0.003939) - test_name: .: (0.003994) - test_reaction: .: (0.003948) - test_type: .: (0.003989) + test_components: .: (0.004338) + test_graphics__size: .: (0.003817) + test_id: .: (0.003787) + test_link: .: (0.003693) + test_name: .: (0.003630) + test_reaction: .: (0.003631) + test_type: .: (0.003638) Bio::TestKeggKGML::TestKGMLEntry1234: - test_components: .: (0.009613) - test_graphics__size: .: (0.004609) - test_id: .: (0.004347) - test_link: .: (0.004407) - test_name: .: (0.004517) - test_reaction: .: (0.004057) - test_type: .: (0.004022) + test_components: .: (0.008647) + test_graphics__size: .: (0.004202) + test_id: .: (0.003824) + test_link: .: (0.003925) + test_name: .: (0.004013) + test_reaction: .: (0.003657) + test_type: .: (0.003549) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: - test_bgcolor=: .: (0.004116) - test_category: .: (0.008507) - test_entry_id: .: (0.004687) - test_fgcolor=: .: (0.004298) - test_height=: .: (0.004224) - test_label=: .: (0.004754) - test_shape=: .: (0.004164) - test_width=: .: (0.005856) - test_x=: .: (0.004151) - test_y=: .: (0.007735) + test_bgcolor=: .: (0.003875) + test_category: .: (0.007413) + test_entry_id: .: (0.004414) + test_fgcolor=: .: (0.004096) + test_height=: .: (0.003915) + test_label=: .: (0.004147) + test_shape=: .: (0.003749) + test_width=: .: (0.003731) + test_x=: .: (0.003669) + test_y=: .: (0.006957) Bio::TestKeggKGML::TestKGMLEntry567: - test_components: .: (0.005076) - test_graphics__size: .: (0.004404) - test_id: .: (0.004309) - test_link: .: (0.004543) - test_name: .: (0.004164) - test_reaction: .: (0.004023) - test_type: .: (0.003964) + test_components: .: (0.004599) + test_graphics__size: .: (0.004036) + test_id: .: (0.003858) + test_link: .: (0.004061) + test_name: .: (0.003588) + test_reaction: .: (0.003597) + test_type: .: (0.003614) Bio::TestKeggKGML::TestKGMLEntrySetter: - test_components=: .: (0.000289) - test_graphics=: .: (0.000135) - test_id=: .: (0.000145) - test_link=: .: (0.000159) - test_name=: .: (0.000143) - test_reaction=: .: (0.000128) - test_type=: .: (0.000119) + test_components=: .: (0.000195) + test_graphics=: .: (0.000064) + test_id=: .: (0.000067) + test_link=: .: (0.000064) + test_name=: .: (0.000064) + test_reaction=: .: (0.000059) + test_type=: .: (0.000058) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: - test_bgcolor=: .: (0.000277) - test_category=: .: (0.000133) - test_entry_id=: .: (0.000131) - test_fgcolor=: .: (0.000139) - test_height=: .: (0.000129) - test_label=: .: (0.000165) - test_pathway=: .: (0.000115) - test_shape=: .: (0.000134) - test_width=: .: (0.000136) - test_x=: .: (0.000131) - test_y=: .: (0.000129) + test_bgcolor=: .: (0.000191) + test_category=: .: (0.000080) + test_entry_id=: .: (0.000095) + test_fgcolor=: .: (0.000080) + test_height=: .: (0.000073) + test_label=: .: (0.000078) + test_pathway=: .: (0.000066) + test_shape=: .: (0.000083) + test_width=: .: (0.000072) + test_x=: .: (0.000072) + test_y=: .: (0.000074) Bio::TestKeggKGML::TestKGMLGraphics1234: - test_bgcolor: .: (0.009002) - test_coords: .: (0.009520) - test_fgcolor: .: (0.006261) - test_height: .: (0.008053) - test_name: .: (0.004500) - test_type: .: (0.004172) - test_width: .: (0.003926) - test_x: .: (0.005191) - test_y: .: (0.007235) + test_bgcolor: .: (0.007031) + test_coords: .: (0.004410) + test_fgcolor: .: (0.003994) + test_height: .: (0.003833) + test_name: .: (0.004077) + test_type: .: (0.003663) + test_width: .: (0.003601) + test_x: .: (0.003794) + test_y: .: (0.006642) Bio::TestKeggKGML::TestKGMLGraphics1_0: - test_bgcolor: .: (0.005004) - test_coords: .: (0.004255) - test_fgcolor: .: (0.004325) - test_height: .: (0.004331) - test_name: .: (0.004016) - test_type: .: (0.004067) - test_width: .: (0.004135) - test_x: .: (0.007163) - test_y: .: (0.004789) + test_bgcolor: .: (0.004574) + test_coords: .: (0.003851) + test_fgcolor: .: (0.003981) + test_height: .: (0.004023) + test_name: .: (0.003703) + test_type: .: (0.003627) + test_width: .: (0.003637) + test_x: .: (0.006407) + test_y: .: (0.004432) Bio::TestKeggKGML::TestKGMLGraphicsSetter: - test_bgcolor=: .: (0.000294) - test_coords=: .: (0.000145) - test_fgcolor=: .: (0.000139) - test_height=: .: (0.000149) - test_name=: .: (0.000139) - test_type=: .: (0.000069) - test_width=: .: (0.000079) - test_x=: .: (0.000059) - test_y=: .: (0.000051) + test_bgcolor=: .: (0.000252) + test_coords=: .: (0.000067) + test_fgcolor=: .: (0.000058) + test_height=: .: (0.000057) + test_name=: .: (0.000057) + test_type=: .: (0.000054) + test_width=: .: (0.000052) + test_x=: .: (0.000053) + test_y=: .: (0.000054) Bio::TestKeggKGML::TestKGMLPathway: - test_entries=: .: (0.004678) - test_entries__size: .: (0.004566) - test_image: .: (0.003987) - test_link: .: (0.003985) - test_name: .: (0.003930) - test_number: .: (0.006081) - test_org: .: (0.005346) - test_reactions=: .: (0.004413) - test_reactions__size: .: (0.004159) - test_relations=: .: (0.004520) - test_relations__size: .: (0.003944) - test_title: .: (0.003961) + test_entries=: .: (0.004221) + test_entries__size: .: (0.003858) + test_image: .: (0.004088) + test_link: .: (0.003806) + test_name: .: (0.003663) + test_number: .: (0.005659) + test_org: .: (0.004899) + test_reactions=: .: (0.004152) + test_reactions__size: .: (0.003864) + test_relations=: .: (0.003963) + test_relations__size: .: (0.003933) + test_title: .: (0.003657) Bio::TestKeggKGML::TestKGMLProduct: - test_id: .: (0.009837) - test_name: .: (0.009225) + test_id: .: (0.009668) + test_name: .: (0.008462) Bio::TestKeggKGML::TestKGMLProductSetter: - test_id=: .: (0.000322) - test_initialize_0: .: (0.000127) - test_initialize_1: .: (0.000136) - test_initialize_2: .: (0.000128) - test_name=: .: (0.000141) + test_id=: .: (0.000207) + test_initialize_0: .: (0.000046) + test_initialize_1: .: (0.000050) + test_initialize_2: .: (0.000051) + test_name=: .: (0.000060) Bio::TestKeggKGML::TestKGMLReaction: - test_id: .: (0.004308) - test_name: .: (0.004569) - test_products: .: (0.004063) - test_substrates: .: (0.004052) - test_type: .: (0.004083) + test_id: .: (0.004016) + test_name: .: (0.004123) + test_products: .: (0.003641) + test_substrates: .: (0.003690) + test_type: .: (0.003661) Bio::TestKeggKGML::TestKGMLReactionSetter: - test_id=: .: (0.000323) - test_name=: .: (0.000177) - test_products=: .: (0.000141) - test_substraces=: .: (0.000136) - test_type=: .: (0.000132) + test_id=: .: (0.000210) + test_name=: .: (0.000073) + test_products=: .: (0.000066) + test_substraces=: .: (0.000061) + test_type=: .: (0.000063) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: - test_direction=: .: (0.000261) - test_entry_id=: .: (0.000143) + test_direction=: .: (0.000147) + test_entry_id=: .: (0.000076) Bio::TestKeggKGML::TestKGMLRelation: - test_entry1: .: (0.007442) - test_entry2: .: (0.004997) - test_name: .: (0.005411) - test_type: .: (0.004588) - test_value: .: (0.004149) + test_entry1: .: (0.006759) + test_entry2: .: (0.004476) + test_name: .: (0.003980) + test_type: .: (0.003892) + test_value: .: (0.004033) Bio::TestKeggKGML::TestKGMLRelationDeprecated: - test_edge: .: (0.000306) - test_node1=: .: (0.000164) - test_node2=: .: (0.000159) - test_rel=: .: (0.000159) + test_edge: .: (0.000179) + test_node1=: .: (0.000079) + test_node2=: .: (0.000071) + test_rel=: .: (0.000072) Bio::TestKeggKGML::TestKGMLRelationSetter: - test_entry1=: .: (0.000261) - test_entry2=: .: (0.000156) - test_name=: .: (0.000128) - test_type=: .: (0.000114) - test_value=: .: (0.000122) + test_entry1=: .: (0.000149) + test_entry2=: .: (0.000068) + test_name=: .: (0.000070) + test_type=: .: (0.000057) + test_value=: .: (0.000056) Bio::TestKeggKGML::TestKGMLSubstrate: - test_id: .: (0.014823) - test_name: .: (0.014367) + test_id: .: (0.007216) + test_name: .: (0.010881) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: - test_id=: .: (0.000196) - test_initialize_0: .: (0.000043) - test_initialize_1: .: (0.000041) - test_initialize_2: .: (0.000042) - test_name=: .: (0.000056) + test_id=: .: (0.000207) + test_initialize_0: .: (0.000048) + test_initialize_1: .: (0.000046) + test_initialize_2: .: (0.000049) + test_name=: .: (0.000062) Bio::TestKeggKGML::TestKGMLSubstrateSetter: - test_id=: .: (0.000124) - test_initialize_0: .: (0.000036) - test_initialize_1: .: (0.000037) - test_initialize_2: .: (0.000148) - test_name=: .: (0.000055) + test_id=: .: (0.000138) + test_initialize_0: .: (0.000045) + test_initialize_1: .: (0.000043) + test_initialize_2: .: (0.000042) + test_name=: .: (0.000059) Bio::TestKeggModule: - test_compounds: .: (0.000543) - test_compounds_as_hash: .: (0.000290) - test_compounds_as_strings: .: (0.000246) - test_definition: .: (0.000232) - test_entry_id: .: (0.000202) - test_keggclass: .: (0.000199) - test_name: .: (0.000202) - test_new: .: (0.000199) - test_orthologs: .: (0.000265) - test_orthologs_as_array: .: (0.000292) - test_orthologs_as_hash: .: (0.000267) - test_orthologs_as_strings: .: (0.000220) - test_pathways: .: (0.000695) - test_pathways_as_hash: .: (0.000233) - test_pathways_as_strings: .: (0.000179) - test_reactions: .: (0.000252) - test_reactions_as_hash: .: (0.000231) - test_reactions_as_strings: .: (0.000197) + test_compounds: .: (0.000380) + test_compounds_as_hash: .: (0.000326) + test_compounds_as_strings: .: (0.000164) + test_definition: .: (0.000158) + test_entry_id: .: (0.000132) + test_keggclass: .: (0.000125) + test_name: .: (0.000138) + test_new: .: (0.000137) + test_orthologs: .: (0.000187) + test_orthologs_as_array: .: (0.000191) + test_orthologs_as_hash: .: (0.000170) + test_orthologs_as_strings: .: (0.000144) + test_pathways: .: (0.000122) + test_pathways_as_hash: .: (0.000117) + test_pathways_as_strings: .: (0.000106) + test_reactions: .: (0.000168) + test_reactions_as_hash: .: (0.000165) + test_reactions_as_strings: .: (0.000140) Bio::TestKeggOrthology: - test_dblinks: .: (0.000524) - test_dblinks_as_hash: .: (0.000353) - test_dblinks_as_strings: .: (0.000322) - test_definition: .: (0.000343) - test_entry_id: .: (0.000345) - test_genes_as_hash: .: (0.051157) - test_genes_as_strings: .: (0.002927) - test_keggclass: .: (0.000564) - test_keggclasses: .: (0.000432) - test_modules: .: (0.000386) - test_modules_as_hash: .: (0.000340) - test_modules_as_strings: .: (0.000355) - test_name: .: (0.000356) - test_names: .: (0.000707) - test_pathways_as_strings: .: (0.001107) - test_pathways_in_keggclass: .: (0.000486) - test_references: .: (0.000478) + test_dblinks: .: (0.000484) + test_dblinks_as_hash: .: (0.000320) + test_dblinks_as_strings: .: (0.000273) + test_definition: .: (0.000295) + test_entry_id: .: (0.000328) + test_genes_as_hash: .: (0.051724) + test_genes_as_strings: .: (0.002907) + test_keggclass: .: (0.000465) + test_keggclasses: .: (0.000373) + test_modules: .: (0.000330) + test_modules_as_hash: .: (0.000276) + test_modules_as_strings: .: (0.000260) + test_name: .: (0.000282) + test_names: .: (0.000274) + test_pathways_as_strings: .: (0.000386) + test_pathways_in_keggclass: .: (0.000392) + test_references: .: (0.000433) Bio::TestKeggPathway_map00052: - test_compounds_as_hash: .: (0.000367) - test_compounds_as_strings: .: (0.000180) - test_dblinks_as_hash: .: (0.000174) - test_dblinks_as_strings: .: (0.000171) - test_description: .: (0.000204) - test_diseases_as_hash: .: (0.000176) - test_diseases_as_strings: .: (0.000179) - test_entry_id: .: (0.000202) - test_enzymes_as_strings: .: (0.000174) - test_genes_as_hash: .: (0.000175) - test_genes_as_strings: .: (0.000172) - test_keggclass: .: (0.000190) - test_ko_pathway: .: (0.000213) - test_modules_as_hash: .: (0.000239) - test_modules_as_strings: .: (0.000196) - test_name: .: (0.000212) - test_organism: .: (0.000190) - test_orthologs_as_hash: .: (0.000175) - test_orthologs_as_strings: .: (0.000173) - test_pathways_as_hash: .: (0.000196) - test_pathways_as_strings: .: (0.000188) - test_reactions_as_hash: .: (0.000195) - test_reactions_as_strings: .: (0.000175) - test_references: .: (0.000176) - test_rel_pathways_as_hash: .: (0.000211) - test_rel_pathways_as_strings: .: (0.000187) + test_compounds_as_hash: .: (0.000314) + test_compounds_as_strings: .: (0.000179) + test_dblinks_as_hash: .: (0.000128) + test_dblinks_as_strings: .: (0.000113) + test_description: .: (0.000139) + test_diseases_as_hash: .: (0.000120) + test_diseases_as_strings: .: (0.000111) + test_entry_id: .: (0.000132) + test_enzymes_as_strings: .: (0.000111) + test_genes_as_hash: .: (0.000112) + test_genes_as_strings: .: (0.000115) + test_keggclass: .: (0.000127) + test_ko_pathway: .: (0.000126) + test_modules_as_hash: .: (0.000176) + test_modules_as_strings: .: (0.000130) + test_name: .: (0.000132) + test_organism: .: (0.000128) + test_orthologs_as_hash: .: (0.000115) + test_orthologs_as_strings: .: (0.000107) + test_pathways_as_hash: .: (0.000149) + test_pathways_as_strings: .: (0.000125) + test_reactions_as_hash: .: (0.000112) + test_reactions_as_strings: .: (0.000110) + test_references: .: (0.000111) + test_rel_pathways_as_hash: .: (0.000141) + test_rel_pathways_as_strings: .: (0.000120) Bio::TestKeggReaction: - test_definition: .: (0.000392) - test_entry_id: .: (0.000227) - test_enzymes: .: (0.000224) - test_equation: .: (0.000229) - test_name: .: (0.000213) - test_orthologs_as_hash: .: (0.000235) - test_orthologs_as_strings: .: (0.000196) - test_pathways_as_hash: .: (0.000209) - test_pathways_as_strings: .: (0.000189) - test_rpairs_as_hash: .: (0.000220) - test_rpairs_as_strings: .: (0.000190) - test_rpairs_as_tokens: .: (0.000235) + test_definition: .: (0.000352) + test_entry_id: .: (0.000189) + test_enzymes: .: (0.000154) + test_equation: .: (0.000146) + test_name: .: (0.000148) + test_orthologs_as_hash: .: (0.000176) + test_orthologs_as_strings: .: (0.000135) + test_pathways_as_hash: .: (0.000155) + test_pathways_as_strings: .: (0.000127) + test_rpairs_as_hash: .: (0.000159) + test_rpairs_as_strings: .: (0.000132) + test_rpairs_as_tokens: .: (0.000164) Bio::TestLasergene: - test_methods: .: (0.007505) + test_methods: .: (0.007509) Bio::TestLocations: - test_complement: .: (0.000318) - test_hat: .: (0.000141) - test_normal: .: (0.000129) - test_replace_single_base: .: (0.000103) - test_should_not_modify_argument: .: (0.000112) + test_complement: .: (0.000251) + test_hat: .: (0.000092) + test_normal: .: (0.000077) + test_replace_single_base: .: (0.000068) + test_should_not_modify_argument: .: (0.000069) Bio::TestLocationsRoundTrip: - test_locations_roundtrip: .: (0.002288) - test_locations_to_s: .: (0.000934) + test_locations_roundtrip: .: (0.002164) + test_locations_to_s: .: (0.000877) Bio::TestMEDLINE: - test_authors: .: (0.000597) - test_authors_with_last_name_all_caps: .: (0.000119) - test_authors_with_suffix: .: (0.000145) + test_authors: .: (0.000531) + test_authors_with_last_name_all_caps: .: (0.000071) + test_authors_with_suffix: .: (0.000060) Bio::TestMEDLINE_20146148: - test_ab: .: (0.001108) - test_ad: .: (0.000359) - test_au: .: (0.000263) - test_authors: .: (0.000272) - test_doi: .: (0.000259) - test_dp: .: (0.000256) - test_ip: .: (0.000286) - test_mh: .: (0.000290) - test_pages: .: (0.000303) - test_pg: .: (0.000259) - test_pii: .: (0.000258) - test_pmid: .: (0.000269) - test_pt: .: (0.000265) - test_reference: .: (0.000486) - test_self_new: .: (0.003460) - test_so: .: (0.000636) - test_ta: .: (0.000296) - test_ti: .: (0.000317) - test_ui: .: (0.000325) - test_vi: .: (0.000285) - test_year: .: (0.000323) + test_ab: .: (0.000415) + test_ad: .: (0.000893) + test_au: .: (0.000270) + test_authors: .: (0.000236) + test_doi: .: (0.000222) + test_dp: .: (0.000199) + test_ip: .: (0.000197) + test_mh: .: (0.000211) + test_pages: .: (0.000193) + test_pg: .: (0.000197) + test_pii: .: (0.000194) + test_pmid: .: (0.000193) + test_pt: .: (0.000203) + test_reference: .: (0.000432) + test_self_new: .: (0.000262) + test_so: .: (0.003376) + test_ta: .: (0.000575) + test_ti: .: (0.000246) + test_ui: .: (0.000209) + test_vi: .: (0.000216) + test_year: .: (0.000245) Bio::TestMapSimple: - test_attributes: .: (0.000924) + test_attributes: .: (0.000253) Bio::TestMapping: - test_add_mapping_as_map: .: (0.000332) - test_add_mapping_as_marker: .: (0.000155) - test_contains_marker?: .: (0.000129) - test_mapped_to?: .: (0.000121) - test_mapping_location_comparison: .: (0.000281) - test_mappings_as_map_each: .: (0.000126) - test_mappings_as_marker_each: .: (0.000193) - test_mappings_on: .: (0.000182) - test_multiple_mappings_between_same_marker_and_map: .: (0.000274) - test_positions_on: .: (0.000173) - test_raise_error_kind_of: .: (0.000464) + test_add_mapping_as_map: .: (0.000244) + test_add_mapping_as_marker: .: (0.000718) + test_contains_marker?: .: (0.000105) + test_mapped_to?: .: (0.000067) + test_mapping_location_comparison: .: (0.000367) + test_mappings_as_map_each: .: (0.000086) + test_mappings_as_marker_each: .: (0.000118) + test_mappings_on: .: (0.000111) + test_multiple_mappings_between_same_marker_and_map: .: (0.000211) + test_positions_on: .: (0.000114) + test_raise_error_kind_of: .: (0.000396) Bio::TestMast: - test_check_options_with_empty_opts: .: (0.000365) - test_check_options_with_invalid_opts: .: (0.000185) - test_check_options_with_valid_opts: .: (0.000156) - test_command_to_be_run: .: (0.000174) - test_config_defaults: .: (0.000141) - test_minimal_config: .: (0.000154) - test_more_config: .: (0.000136) - test_run: .: (0.000097) + test_check_options_with_empty_opts: .: (0.000299) + test_check_options_with_invalid_opts: .: (0.000117) + test_check_options_with_valid_opts: .: (0.000116) + test_command_to_be_run: .: (0.000115) + test_config_defaults: .: (0.000092) + test_minimal_config: .: (0.000101) + test_more_config: .: (0.000097) + test_run: .: (0.000061) Bio::TestMastReport: - test_parse_hit_list_with_bad_data: .: (0.000619) - test_report_has_motifs: .: (0.000246) + test_parse_hit_list_with_bad_data: .: (0.000362) + test_report_has_motifs: .: (0.000214) Bio::TestModel: - test_addChain: .: (0.000239) - test_comp: .: (0.000145) - test_each: .: (0.000118) - test_each_chain: .: (0.000102) - test_inspect: .: (0.000108) - test_rehash: .: (0.000101) - test_square_brace: .: (0.000110) - test_to_s: .: (0.000100) + test_addChain: .: (0.000166) + test_comp: .: (0.000085) + test_each: .: (0.000080) + test_each_chain: .: (0.000057) + test_inspect: .: (0.000057) + test_rehash: .: (0.000048) + test_square_brace: .: (0.000058) + test_to_s: .: (0.000059) Bio::TestModelFinder: - test_find_model: .: (0.000235) + test_find_model: .: (0.000167) Bio::TestMotif: - test_creation_and_attributes: .: (0.000215) - test_length: .: (0.000086) + test_creation_and_attributes: .: (0.000155) + test_length: .: (0.000050) Bio::TestMyGraph: - test_cliquishness: .: (0.000468) + test_cliquishness: .: (0.000416) Bio::TestNA: - test_accessor: .: (0.000171) - test_na: .: (0.000081) - test_name: .: (0.000094) - test_names: .: (0.000078) - test_to_re: .: (0.000191) - test_weight: .: (0.000104) - test_weight_rna: .: (0.000080) + test_accessor: .: (0.000121) + test_na: .: (0.000047) + test_name: .: (0.000043) + test_names: .: (0.000038) + test_to_re: .: (0.000166) + test_weight: .: (0.000060) + test_weight_rna: .: (0.000046) Bio::TestNAConstants: - test_NAMES: .: (0.000162) - test_NAMES_1_to_name: .: (0.000086) - test_WEIGHT: .: (0.000099) + test_NAMES: .: (0.000107) + test_NAMES_1_to_name: .: (0.000044) + test_WEIGHT: .: (0.000046) Bio::TestNATranslate: - test_translate: .: (0.000324) - test_translate_1: .: (0.000169) - test_translate_2: .: (0.000109) - test_translate_3: .: (0.000101) - test_translate_4: .: (0.000174) - test_translate_5: .: (0.000150) - test_translate_6: .: (0.000105) + test_translate: .: (0.000266) + test_translate_1: .: (0.000109) + test_translate_2: .: (0.000060) + test_translate_3: .: (0.000052) + test_translate_4: .: (0.000096) + test_translate_5: .: (0.000057) + test_translate_6: .: (0.000088) Bio::TestNCBIDB: - test_fetch: .: (0.000235) - test_p_entry2hash: .: (0.000083) - test_p_subtag2array: .: (0.000071) - test_p_toptag2array: .: (0.000081) + test_fetch: .: (0.000172) + test_p_entry2hash: .: (0.000042) + test_p_subtag2array: .: (0.000036) + test_p_toptag2array: .: (0.000035) Bio::TestNewick: - test_reparse: .: (0.000973) - test_reparse_before_lazy_parsing: .: (0.000320) - test_string_tree: .: (0.000536) + test_reparse: .: (0.000907) + test_reparse_before_lazy_parsing: .: (0.000272) + test_string_tree: .: (0.000474) Bio::TestNewick2: - test_string_tree: .: (0.000547) + test_string_tree: .: (0.000471) Bio::TestNewickPrivate: - test_parse_newick_get_tokens_for_leaf: .: (0.000183) - test_parse_newick_leaf: .: (0.000184) - test_parse_newick_tokenize: .: (0.000263) + test_parse_newick_get_tokens_for_leaf: .: (0.000177) + test_parse_newick_leaf: .: (0.000129) + test_parse_newick_tokenize: .: (0.000212) Bio::TestNexus: - test_nexus: .: (0.006207) + test_nexus: .: (0.006091) Bio::TestOSLine: - test_period_trancation_O63147: .: (0.000312) - test_uncapitalized_letter_Q32725_9POAL: .: (0.000138) + test_period_trancation_O63147: .: (0.000241) + test_uncapitalized_letter_Q32725_9POAL: .: (0.000076) Bio::TestPAMLCodeml::TestCodeml: - test_dump_parameters: .: (0.000240) - test_load_parameters: .: (0.000124) - test_parameters: .: (0.000087) - test_set_default_parameters: .: (0.000125) + test_dump_parameters: .: (0.000154) + test_load_parameters: .: (0.000076) + test_parameters: .: (0.000045) + test_set_default_parameters: .: (0.000059) Bio::TestPAMLCodeml::TestCodemlControlGeneration: - test_control_file_generated: .: (0.000568) - test_expected_parameters_set_in_control_file: .: (0.000457) + test_control_file_generated: .: (0.000506) + test_expected_parameters_set_in_control_file: .: (0.000387) Bio::TestPAMLCodeml::TestCodemlInitialize: - test_new_with_one_argument: .: (0.000216) - test_new_with_parameters: .: (0.000111) - test_new_with_two_argument: .: (0.000122) - test_new_without_argument: .: (0.000101) + test_new_with_one_argument: .: (0.000157) + test_new_with_parameters: .: (0.000069) + test_new_with_two_argument: .: (0.000061) + test_new_without_argument: .: (0.000049) Bio::TestPAMLCodeml::TestCodemlRates: - test_rates_first_position: .: (0.005601) - test_rates_hundred_and_fiftieth_position: .: (0.000926) - test_rates_last_position: .: (0.001454) + test_rates_first_position: .: (0.005608) + test_rates_hundred_and_fiftieth_position: .: (0.000844) + test_rates_last_position: .: (0.001431) Bio::TestPAMLCodeml::TestCodemlReport: - test_alpha: .: (0.000731) - test_tree: .: (0.000534) - test_tree_length: .: (0.000481) - test_tree_log_likelihood: .: (0.000471) + test_alpha: .: (0.000630) + test_tree: .: (0.000444) + test_tree_length: .: (0.000417) + test_tree_log_likelihood: .: (0.000403) Bio::TestPAMLCodeml::TestControlFileUsage: - test_correct_parameters_should_be_loaded: .: (0.000443) - test_parameters_should_be_loaded_from_control: .: (0.000249) + test_correct_parameters_should_be_loaded: .: (0.000397) + test_parameters_should_be_loaded_from_control: .: (0.000202) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: - test_error_thrown_if_seqfile_does_not_specified: .: (0.001295) + test_error_thrown_if_seqfile_does_not_specified: .: (0.001136) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: - test_alpha: .: (0.000329) - test_dN_dS: .: (0.000166) - test_kappa: .: (0.000165) - test_lnL: .: (0.000167) - test_m3_classes: .: (0.000238) - test_m3_lnL: .: (0.000154) - test_m3_to_s: .: (0.000149) - test_m3_tree: .: (0.000206) - test_omega: .: (0.000156) - test_to_s: .: (0.000156) - test_tree: .: (0.000207) - test_tree_length: .: (0.000164) + test_alpha: .: (0.000240) + test_dN_dS: .: (0.000116) + test_kappa: .: (0.000102) + test_lnL: .: (0.000098) + test_m3_classes: .: (0.000165) + test_m3_lnL: .: (0.000100) + test_m3_to_s: .: (0.000115) + test_m3_tree: .: (0.000174) + test_omega: .: (0.000108) + test_to_s: .: (0.000095) + test_tree: .: (0.000139) + test_tree_length: .: (0.000249) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: - test_dN_dS: .: (0.000508) - test_p: .: (0.000322) - test_position: .: (0.000298) - test_probability: .: (0.000319) - test_w: .: (0.000495) + test_dN_dS: .: (0.000428) + test_p: .: (0.000242) + test_position: .: (0.000232) + test_probability: .: (0.000230) + test_w: .: (0.000235) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: - test_graph: .: (0.000470) - test_graph_omega: .: (0.000349) + test_graph: .: (0.000547) + test_graph_omega: .: (0.000301) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: - test_descr: .: (0.000306) - test_footer: .: (0.000166) - test_header: .: (0.000163) - test_initialize: .: (0.000202) - test_models: .: (0.000189) - test_nb_sites: .: (0.001380) - test_num_codons: .: (0.000213) - test_num_sequences: .: (0.000194) - test_significant: .: (0.000205) + test_descr: .: (0.000209) + test_footer: .: (0.000099) + test_header: .: (0.000112) + test_initialize: .: (0.000119) + test_models: .: (0.000103) + test_nb_sites: .: (0.000482) + test_num_codons: .: (0.000131) + test_num_sequences: .: (0.000107) + test_significant: .: (0.000112) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: - test_models: .: (0.000349) - test_nb_sites: .: (0.000284) - test_significant: .: (0.000182) - test_sites: .: (0.000738) + test_models: .: (0.000240) + test_nb_sites: .: (0.000181) + test_significant: .: (0.000115) + test_sites: .: (0.001248) Bio::TestPDB: - test_accession: .: (0.000965) - test_addModel: .: (0.000594) - test_authors: .: (0.000524) - test_bracket: .: (0.000571) - test_classification: .: (0.000553) - test_dbref: .: (0.000609) - test_definition: .: (0.000523) - test_each: .: (0.000560) - test_each_model: .: (0.000506) - test_entry_id: .: (0.000508) - test_helix: .: (0.000574) - test_inspect: .: (0.000552) - test_jrnl: .: (0.000508) - test_keywords: .: (0.000515) - test_record: .: (0.000486) - test_remark: .: (0.000670) - test_seqres: .: (0.000738) - test_sheet: .: (0.000707) - test_ssbond: .: (0.000542) - test_to_s: .: (0.000687) - test_turn: .: (0.000533) - test_version: .: (0.000525) + test_accession: .: (0.000871) + test_addModel: .: (0.000485) + test_authors: .: (0.000445) + test_bracket: .: (0.000519) + test_classification: .: (0.000474) + test_dbref: .: (0.000521) + test_definition: .: (0.000480) + test_each: .: (0.000500) + test_each_model: .: (0.000503) + test_entry_id: .: (0.000472) + test_helix: .: (0.000531) + test_inspect: .: (0.000478) + test_jrnl: .: (0.000435) + test_keywords: .: (0.000448) + test_record: .: (0.000416) + test_remark: .: (0.000588) + test_seqres: .: (0.000646) + test_sheet: .: (0.000631) + test_ssbond: .: (0.000490) + test_to_s: .: (0.000599) + test_turn: .: (0.000472) + test_version: .: (0.000454) Bio::TestPDBRecord::TestANISOU: - test_U11: .: (0.000285) - test_U12: .: (0.006515) - test_U13: .: (0.000248) - test_U22: .: (0.000135) - test_U23: .: (0.000123) - test_U33: .: (0.000127) - test_altLoc: .: (0.000155) - test_chainID: .: (0.000159) - test_charge: .: (0.000119) - test_element: .: (0.000128) - test_iCode: .: (0.000129) - test_name: .: (0.000135) - test_resName: .: (0.000128) - test_resSeq: .: (0.000124) - test_segID: .: (0.000130) - test_serial: .: (0.000133) + test_U11: .: (0.000217) + test_U12: .: (0.000070) + test_U13: .: (0.000059) + test_U22: .: (0.000059) + test_U23: .: (0.000071) + test_U33: .: (0.000059) + test_altLoc: .: (0.006431) + test_chainID: .: (0.000107) + test_charge: .: (0.000070) + test_element: .: (0.000067) + test_iCode: .: (0.000065) + test_name: .: (0.000062) + test_resName: .: (0.000063) + test_resSeq: .: (0.000068) + test_segID: .: (0.000062) + test_serial: .: (0.000059) Bio::TestPDBRecord::TestATOM: - test_altLoc: .: (0.000275) - test_anisou: .: (0.000495) - test_chainID: .: (0.000120) - test_charge: .: (0.000107) - test_comparable: .: (0.000126) - test_do_parse: .: (0.000097) - test_element: .: (0.000121) - test_iCode: .: (0.000100) - test_name: .: (0.000098) - test_occupancy: .: (0.000137) - test_original_data: .: (0.000121) - test_record_name: .: (0.000110) - test_resName: .: (0.000098) - test_resSeq: .: (0.000092) - test_residue: .: (0.000094) - test_segID: .: (0.000098) - test_serial: .: (0.000097) - test_sigatm: .: (0.000095) - test_tempFactor: .: (0.000122) - test_ter: .: (0.000387) - test_to_a: .: (0.000114) - test_to_s: .: (0.000131) - test_x: .: (0.000163) - test_xyz: .: (0.000134) - test_y: .: (0.000106) - test_z: .: (0.000103) + test_altLoc: .: (0.000205) + test_anisou: .: (0.000055) + test_chainID: .: (0.000063) + test_charge: .: (0.000076) + test_comparable: .: (0.000095) + test_do_parse: .: (0.000068) + test_element: .: (0.000064) + test_iCode: .: (0.000059) + test_name: .: (0.000056) + test_occupancy: .: (0.000515) + test_original_data: .: (0.000092) + test_record_name: .: (0.000050) + test_resName: .: (0.000089) + test_resSeq: .: (0.000050) + test_residue: .: (0.000046) + test_segID: .: (0.000048) + test_serial: .: (0.000045) + test_sigatm: .: (0.000047) + test_tempFactor: .: (0.000067) + test_ter: .: (0.000046) + test_to_a: .: (0.000062) + test_to_s: .: (0.000085) + test_x: .: (0.000062) + test_xyz: .: (0.000094) + test_y: .: (0.000059) + test_z: .: (0.000060) Bio::TestPDBRecord::TestAUTHOR: - test_authorList: .: (0.000277) + test_authorList: .: (0.000216) Bio::TestPDBRecord::TestCAVEAT: - test_comment: .: (0.000227) - test_idcode: .: (0.000088) + test_comment: .: (0.000131) + test_idcode: .: (0.000056) Bio::TestPDBRecord::TestCISPEP: - test_chainID1: .: (0.000240) - test_chainID2: .: (0.000106) - test_icode1: .: (0.000117) - test_icode2: .: (0.000117) - test_measure: .: (0.000126) - test_modNum: .: (0.000325) - test_pep1: .: (0.000165) - test_pep2: .: (0.000119) - test_seqNum1: .: (0.000097) - test_seqNum2: .: (0.000094) - test_serNum: .: (0.000090) + test_chainID1: .: (0.000163) + test_chainID2: .: (0.000075) + test_icode1: .: (0.000063) + test_icode2: .: (0.000058) + test_measure: .: (0.000057) + test_modNum: .: (0.000065) + test_pep1: .: (0.000080) + test_pep2: .: (0.000070) + test_seqNum1: .: (0.000074) + test_seqNum2: .: (0.000066) + test_serNum: .: (0.000070) Bio::TestPDBRecord::TestCOMPND: - test_compound: .: (0.000232) + test_compound: .: (0.000409) Bio::TestPDBRecord::TestCONECT: - test_serial: .: (0.000185) + test_serial: .: (0.000157) Bio::TestPDBRecord::TestCRYST1: - test_a: .: (0.000230) - test_alpha: .: (0.000129) - test_b: .: (0.000116) - test_beta: .: (0.000098) - test_c: .: (0.000142) - test_gamma: .: (0.000095) - test_sGroup: .: (0.000100) - test_z: .: (0.000101) + test_a: .: (0.000158) + test_alpha: .: (0.000071) + test_b: .: (0.000067) + test_beta: .: (0.000062) + test_c: .: (0.000056) + test_gamma: .: (0.000051) + test_sGroup: .: (0.000054) + test_z: .: (0.000055) Bio::TestPDBRecord::TestDBREF: - test_chainID: .: (0.000264) - test_database: .: (0.000337) - test_dbAccession: .: (0.000157) - test_dbIdCode: .: (0.000129) - test_dbseqBegin: .: (0.000126) - test_dbseqEnd: .: (0.000120) - test_idCode: .: (0.000120) - test_idbnsBeg: .: (0.000128) - test_insertBegin: .: (0.000125) - test_insertEnd: .: (0.000119) - test_seqBegin: .: (0.000119) - test_seqEnd: .: (0.000132) + test_chainID: .: (0.000167) + test_database: .: (0.000079) + test_dbAccession: .: (0.000088) + test_dbIdCode: .: (0.000070) + test_dbseqBegin: .: (0.000067) + test_dbseqEnd: .: (0.000065) + test_idCode: .: (0.000072) + test_idbnsBeg: .: (0.000232) + test_insertBegin: .: (0.000085) + test_insertEnd: .: (0.000068) + test_seqBegin: .: (0.000065) + test_seqEnd: .: (0.000066) Bio::TestPDBRecord::TestDefault: - test_text: .: (0.002495) + test_text: .: (0.000148) Bio::TestPDBRecord::TestENDMDL: - test_serial: .: (0.001174) + test_serial: .: (0.000115) Bio::TestPDBRecord::TestEXPDTA: - test_technique: .: (0.001216) + test_technique: .: (0.002290) Bio::TestPDBRecord::TestEnd: - test_serial: .: (0.000231) + test_serial: .: (0.000979) Bio::TestPDBRecord::TestHEADER: - test_classification: .: (0.001411) - test_depDate: .: (0.000127) - test_idCode: .: (0.000104) + test_classification: .: (0.001777) + test_depDate: .: (0.000135) + test_idCode: .: (0.001171) Bio::TestPDBRecord::TestHET: - test_ChainID: .: (0.003406) - test_hetID: .: (0.000184) - test_iCode: .: (0.000227) - test_numHetAtoms: .: (0.000118) - test_seqNum: .: (0.000113) - test_text: .: (0.001223) + test_ChainID: .: (0.000209) + test_hetID: .: (0.001015) + test_iCode: .: (0.001201) + test_numHetAtoms: .: (0.000804) + test_seqNum: .: (0.001214) + test_text: .: (0.001170) Bio::TestPDBRecord::TestHETATM: - test_altLoc: .: (0.000246) - test_anisou: .: (0.001418) - test_chainID: .: (0.000135) - test_charge: .: (0.000089) - test_comparable: .: (0.001180) - test_do_parse: .: (0.000127) - test_element: .: (0.000154) - test_iCode: .: (0.001235) - test_name: .: (0.000118) - test_occupancy: .: (0.001307) - test_original_data: .: (0.000140) - test_record_name: .: (0.000106) - test_resName: .: (0.000099) - test_resSeq: .: (0.000167) - test_residue: .: (0.000097) - test_segID: .: (0.001169) - test_serial: .: (0.001255) - test_sigatm: .: (0.000147) - test_tempFactor: .: (0.001350) - test_ter: .: (0.000139) - test_to_a: .: (0.000116) - test_to_s: .: (0.000140) - test_x: .: (0.000154) - test_xyz: .: (0.002308) - test_y: .: (0.001370) - test_z: .: (0.000167) + test_altLoc: .: (0.000229) + test_anisou: .: (0.000071) + test_chainID: .: (0.000103) + test_charge: .: (0.001712) + test_comparable: .: (0.000116) + test_do_parse: .: (0.000065) + test_element: .: (0.000993) + test_iCode: .: (0.000087) + test_name: .: (0.000062) + test_occupancy: .: (0.001937) + test_original_data: .: (0.000113) + test_record_name: .: (0.000069) + test_resName: .: (0.001134) + test_resSeq: .: (0.000068) + test_residue: .: (0.000065) + test_segID: .: (0.001028) + test_serial: .: (0.000084) + test_sigatm: .: (0.000052) + test_tempFactor: .: (0.001063) + test_ter: .: (0.000093) + test_to_a: .: (0.000121) + test_to_s: .: (0.001010) + test_x: .: (0.000117) + test_xyz: .: (0.000096) + test_y: .: (0.001094) + test_z: .: (0.000107) Bio::TestPDBRecord::TestHYDBND: - test_Chain1: .: (0.001586) - test_ChainH: .: (0.000150) - test_ICode1: .: (0.001228) - test_altLoc1: .: (0.000877) - test_altLoc2: .: (0.000170) - test_altLocH: .: (0.000716) - test_chainID2: .: (0.001153) - test_iCode2: .: (0.001293) - test_iCodeH: .: (0.000162) - test_name1: .: (0.000881) - test_name2: .: (0.002910) - test_nameH: .: (0.001095) - test_resName1: .: (0.000184) - test_resName2: .: (0.001351) - test_resSeq1: .: (0.002071) - test_resSeq2: .: (0.000794) - test_resSeqH: .: (0.000690) - test_sym1: .: (0.000294) - test_sym2: .: (0.000151) + test_Chain1: .: (0.001311) + test_ChainH: .: (0.000138) + test_ICode1: .: (0.000103) + test_altLoc1: .: (0.000155) + test_altLoc2: .: (0.000163) + test_altLocH: .: (0.001096) + test_chainID2: .: (0.001060) + test_iCode2: .: (0.001220) + test_iCodeH: .: (0.002163) + test_name1: .: (0.000147) + test_name2: .: (0.000149) + test_nameH: .: (0.000162) + test_resName1: .: (0.000676) + test_resName2: .: (0.000124) + test_resSeq1: .: (0.000628) + test_resSeq2: .: (0.000100) + test_resSeqH: .: (0.001958) + test_sym1: .: (0.000129) + test_sym2: .: (0.001549) Bio::TestPDBRecord::TestKEYWDS: - test_keywds: .: (0.000258) + test_keywds: .: (0.003521) Bio::TestPDBRecord::TestLINK: - test_altLoc1: .: (0.000285) - test_altLoc2: .: (0.000137) - test_chainID1: .: (0.000125) - test_chainID2: .: (0.000131) - test_iCode1: .: (0.000141) - test_iCode2: .: (0.000133) - test_name1: .: (0.000129) - test_name2: .: (0.000129) - test_resName1: .: (0.000136) - test_resName2: .: (0.000828) - test_resSeq1: .: (0.000156) - test_resSeq2: .: (0.000135) - test_sym1: .: (0.000130) - test_sym2: .: (0.000121) + test_altLoc1: .: (0.003623) + test_altLoc2: .: (0.001729) + test_chainID1: .: (0.000155) + test_chainID2: .: (0.000086) + test_iCode1: .: (0.000100) + test_iCode2: .: (0.000083) + test_name1: .: (0.000078) + test_name2: .: (0.000071) + test_resName1: .: (0.000071) + test_resName2: .: (0.000071) + test_resSeq1: .: (0.000071) + test_resSeq2: .: (0.000072) + test_sym1: .: (0.000073) + test_sym2: .: (0.000074) Bio::TestPDBRecord::TestMASTER: - test_numConect: .: (0.000259) - test_numCoord: .: (0.000098) - test_numHelix: .: (0.000093) - test_numHet: .: (0.000096) - test_numRemark: .: (0.000097) - test_numSeq: .: (0.000089) - test_numSheet: .: (0.000091) - test_numSite: .: (0.000097) - test_numTer: .: (0.000096) - test_numTurn: .: (0.000101) - test_numXform: .: (0.000098) + test_numConect: .: (0.000217) + test_numCoord: .: (0.000075) + test_numHelix: .: (0.000118) + test_numHet: .: (0.000074) + test_numRemark: .: (0.000068) + test_numSeq: .: (0.000061) + test_numSheet: .: (0.000054) + test_numSite: .: (0.000055) + test_numTer: .: (0.000050) + test_numTurn: .: (0.000050) + test_numXform: .: (0.000051) Bio::TestPDBRecord::TestMODEL: - test_serial: .: (0.000253) + test_serial: .: (0.000247) Bio::TestPDBRecord::TestMODRES: - test_chainID: .: (0.000251) - test_comment: .: (0.000071) - test_iCode: .: (0.000060) - test_idCode: .: (0.000055) - test_resName: .: (0.000070) - test_seqNum: .: (0.000059) - test_stdRes: .: (0.000054) + test_chainID: .: (0.000177) + test_comment: .: (0.000080) + test_iCode: .: (0.000073) + test_idCode: .: (0.000068) + test_resName: .: (0.000066) + test_seqNum: .: (0.000060) + test_stdRes: .: (0.000107) Bio::TestPDBRecord::TestMTRIX1: - test_Mn1: .: (0.000150) - test_Mn2: .: (0.000050) - test_Mn3: .: (0.000046) - test_Vn: .: (0.000045) - test_iGiven: .: (0.000049) - test_serial: .: (0.000047) + test_Mn1: .: (0.000176) + test_Mn2: .: (0.000057) + test_Mn3: .: (0.000059) + test_Vn: .: (0.000052) + test_iGiven: .: (0.000051) + test_serial: .: (0.000049) Bio::TestPDBRecord::TestMTRIX2: - test_Mn1: .: (0.000122) - test_Mn2: .: (0.000047) - test_Mn3: .: (0.000061) - test_Vn: .: (0.000042) - test_iGiven: .: (0.000042) - test_serial: .: (0.000041) + test_Mn1: .: (0.000147) + test_Mn2: .: (0.000060) + test_Mn3: .: (0.000052) + test_Vn: .: (0.000050) + test_iGiven: .: (0.000053) + test_serial: .: (0.000050) Bio::TestPDBRecord::TestMTRIX3: - test_Mn1: .: (0.000123) - test_Mn2: .: (0.000046) - test_Mn3: .: (0.000043) - test_Vn: .: (0.000040) - test_iGiven: .: (0.000045) - test_serial: .: (0.000039) + test_Mn1: .: (0.000137) + test_Mn2: .: (0.000055) + test_Mn3: .: (0.000347) + test_Vn: .: (0.000075) + test_iGiven: .: (0.000052) + test_serial: .: (0.000062) Bio::TestPDBRecord::TestOBSLTE: - test_idCode: .: (0.000127) - test_rIdCode: .: (0.000058) - test_repDate: .: (0.000050) + test_idCode: .: (0.000166) + test_rIdCode: .: (0.000057) + test_repDate: .: (0.000057) Bio::TestPDBRecord::TestORIGX1: - test_On1: .: (0.000121) - test_On2: .: (0.000047) - test_On3: .: (0.000044) - test_Tn: .: (0.000178) + test_On1: .: (0.000130) + test_On2: .: (0.000051) + test_On3: .: (0.000047) + test_Tn: .: (0.000048) Bio::TestPDBRecord::TestREVDAT: - test_modDate: .: (0.000292) - test_modId: .: (0.000107) - test_modNum: .: (0.000101) - test_modType: .: (0.000109) - test_record: .: (0.000111) + test_modDate: .: (0.000139) + test_modId: .: (0.000065) + test_modNum: .: (0.000055) + test_modType: .: (0.000058) + test_record: .: (0.000067) Bio::TestPDBRecord::TestRemarkN: - test_remarkNum: .: (0.000196) - test_text: .: (0.000094) + test_remarkNum: .: (0.000313) + test_text: .: (0.000061) Bio::TestPDBRecord::TestSCALE1: - test_Sn1: .: (0.000207) - test_Sn2: .: (0.000130) - test_Sn3: .: (0.000088) - test_Un: .: (0.000085) + test_Sn1: .: (0.000139) + test_Sn2: .: (0.000070) + test_Sn3: .: (0.000053) + test_Un: .: (0.000056) Bio::TestPDBRecord::TestSCALE2: - test_Sn1: .: (0.000188) - test_Sn2: .: (0.000091) - test_Sn3: .: (0.000089) - test_Un: .: (0.000081) + test_Sn1: .: (0.000129) + test_Sn2: .: (0.000052) + test_Sn3: .: (0.000047) + test_Un: .: (0.000045) Bio::TestPDBRecord::TestSCALE3: - test_Sn1: .: (0.000381) - test_Sn2: .: (0.000102) - test_Sn3: .: (0.000090) - test_Un: .: (0.000086) + test_Sn1: .: (0.000115) + test_Sn2: .: (0.000051) + test_Sn3: .: (0.000043) + test_Un: .: (0.000043) Bio::TestPDBRecord::TestSEQADV: - test_chainID: .: (0.000231) - test_conflict: .: (0.000124) - test_database: .: (0.000110) - test_dbIdCode: .: (0.000106) - test_dbRes: .: (0.000109) - test_dbSeq: .: (0.000110) - test_iCode: .: (0.000113) - test_idCode: .: (0.000167) - test_resName: .: (0.000114) - test_seqNum: .: (0.000114) + test_chainID: .: (0.000155) + test_conflict: .: (0.000072) + test_database: .: (0.000218) + test_dbIdCode: .: (0.000085) + test_dbRes: .: (0.000063) + test_dbSeq: .: (0.000060) + test_iCode: .: (0.000057) + test_idCode: .: (0.000057) + test_resName: .: (0.000056) + test_seqNum: .: (0.000062) Bio::TestPDBRecord::TestSEQRES: - test_chainID: .: (0.000227) - test_numRes: .: (0.000110) - test_resName: .: (0.000136) + test_chainID: .: (0.000156) + test_numRes: .: (0.000069) + test_resName: .: (0.000073) Bio::TestPDBRecord::TestSHEET: - test_curAtom: .: (0.000262) - test_curChainId: .: (0.000140) - test_curICode: .: (0.000126) - test_curResName: .: (0.000226) - test_curResSeq: .: (0.000134) - test_endChainID: .: (0.000128) - test_endICode: .: (0.000121) - test_endResName: .: (0.000123) - test_endSeqNum: .: (0.000191) - test_initChainID: .: (0.000168) - test_initICode: .: (0.000139) - test_initResName: .: (0.000142) - test_initSeqNum: .: (0.000136) - test_numStrands: .: (0.000130) - test_prevAtom: .: (0.000147) - test_prevChainId: .: (0.000139) - test_prevICode: .: (0.000122) - test_prevResName: .: (0.000120) - test_prevResSeq: .: (0.000181) - test_sense: .: (0.000135) - test_sheetID: .: (0.000132) - test_strand: .: (0.000124) + test_curAtom: .: (0.000171) + test_curChainId: .: (0.000085) + test_curICode: .: (0.000085) + test_curResName: .: (0.000082) + test_curResSeq: .: (0.000082) + test_endChainID: .: (0.000100) + test_endICode: .: (0.000078) + test_endResName: .: (0.000077) + test_endSeqNum: .: (0.000079) + test_initChainID: .: (0.000074) + test_initICode: .: (0.000075) + test_initResName: .: (0.000076) + test_initSeqNum: .: (0.000097) + test_numStrands: .: (0.000083) + test_prevAtom: .: (0.000079) + test_prevChainId: .: (0.000077) + test_prevICode: .: (0.000077) + test_prevResName: .: (0.000078) + test_prevResSeq: .: (0.000078) + test_sense: .: (0.000106) + test_sheetID: .: (0.000077) + test_strand: .: (0.000070) Bio::TestPDBRecord::TestSIGATM: - test_altLoc: .: (0.000255) - test_chainID: .: (0.000124) - test_charge: .: (0.000120) - test_element: .: (0.000114) - test_iCode: .: (0.000108) - test_name: .: (0.000109) - test_resName: .: (0.000112) - test_resSeq: .: (0.000108) - test_segID: .: (0.000118) - test_serial: .: (0.000116) - test_sigOcc: .: (0.000119) - test_sigTemp: .: (0.000113) - test_sigX: .: (0.000107) - test_sigY: .: (0.000110) - test_sigZ: .: (0.000175) + test_altLoc: .: (0.000189) + test_chainID: .: (0.000105) + test_charge: .: (0.000084) + test_element: .: (0.000084) + test_iCode: .: (0.000080) + test_name: .: (0.000071) + test_resName: .: (0.000074) + test_resSeq: .: (0.000074) + test_segID: .: (0.000064) + test_serial: .: (0.000064) + test_sigOcc: .: (0.000064) + test_sigTemp: .: (0.000060) + test_sigX: .: (0.000055) + test_sigY: .: (0.000060) + test_sigZ: .: (0.000061) Bio::TestPDBRecord::TestSIGUIJ: - test_SigmaU11: .: (0.000289) - test_SigmaU12: .: (0.000120) - test_SigmaU13: .: (0.000117) - test_SigmaU22: .: (0.000110) - test_SigmaU23: .: (0.000139) - test_SigmaU33: .: (0.000111) - test_altLoc: .: (0.000106) - test_chainID: .: (0.000104) - test_charge: .: (0.000108) - test_element: .: (0.000107) - test_iCode: .: (0.000110) - test_name: .: (0.000114) - test_resName: .: (0.000107) - test_resSeq: .: (0.000124) - test_segID: .: (0.000113) - test_serial: .: (0.000105) + test_SigmaU11: .: (0.000166) + test_SigmaU12: .: (0.000074) + test_SigmaU13: .: (0.000062) + test_SigmaU22: .: (0.000058) + test_SigmaU23: .: (0.000059) + test_SigmaU33: .: (0.000059) + test_altLoc: .: (0.000062) + test_chainID: .: (0.000058) + test_charge: .: (0.000058) + test_element: .: (0.000058) + test_iCode: .: (0.000058) + test_name: .: (0.000060) + test_resName: .: (0.000060) + test_resSeq: .: (0.000059) + test_segID: .: (0.000060) + test_serial: .: (0.000057) Bio::TestPDBRecord::TestSITE: - test_chainID1: .: (0.000259) - test_chainID2: .: (0.000190) - test_chainID3: .: (0.000131) - test_chainID4: .: (0.000117) - test_iCode1: .: (0.000137) - test_iCode2: .: (0.000120) - test_iCode3: .: (0.000115) - test_iCode4: .: (0.000116) - test_numRes: .: (0.000136) - test_resName1: .: (0.000112) - test_resName2: .: (0.000113) - test_resName3: .: (0.000143) - test_resName4: .: (0.000114) - test_seq1: .: (0.000124) - test_seq2: .: (0.000140) - test_seq3: .: (0.000123) - test_seq4: .: (0.000112) - test_seqNum: .: (0.000114) - test_siteID: .: (0.000127) + test_chainID1: .: (0.000195) + test_chainID2: .: (0.000080) + test_chainID3: .: (0.000075) + test_chainID4: .: (0.000071) + test_iCode1: .: (0.000077) + test_iCode2: .: (0.000070) + test_iCode3: .: (0.000137) + test_iCode4: .: (0.000077) + test_numRes: .: (0.000067) + test_resName1: .: (0.000064) + test_resName2: .: (0.000061) + test_resName3: .: (0.000086) + test_resName4: .: (0.000080) + test_seq1: .: (0.000073) + test_seq2: .: (0.000063) + test_seq3: .: (0.000072) + test_seq4: .: (0.000079) + test_seqNum: .: (0.000081) + test_siteID: .: (0.000081) Bio::TestPDBRecord::TestSLTBRG: - test_altLoc1: .: (0.000248) - test_altLoc2: .: (0.000111) - test_atom1: .: (0.000105) - test_atom2: .: (0.000222) - test_chainID1: .: (0.000122) - test_chainID2: .: (0.000126) - test_iCode1: .: (0.000121) - test_iCode2: .: (0.000107) - test_resName1: .: (0.000102) - test_resName2: .: (0.000124) - test_resSeq1: .: (0.000100) - test_resSeq2: .: (0.000112) - test_sym1: .: (0.000106) - test_sym2: .: (0.000099) + test_altLoc1: .: (0.000173) + test_altLoc2: .: (0.000071) + test_atom1: .: (0.000060) + test_atom2: .: (0.000068) + test_chainID1: .: (0.000058) + test_chainID2: .: (0.000056) + test_iCode1: .: (0.000055) + test_iCode2: .: (0.000054) + test_resName1: .: (0.000125) + test_resName2: .: (0.000060) + test_resSeq1: .: (0.000056) + test_resSeq2: .: (0.000057) + test_sym1: .: (0.000057) + test_sym2: .: (0.000051) Bio::TestPDBRecord::TestSOURCE: - test_srcName: .: (0.000249) + test_srcName: .: (0.000153) Bio::TestPDBRecord::TestSPRSDE: - test_idCode: .: (0.000202) - test_sIdCode: .: (0.000107) - test_sprsdeDate: .: (0.000100) + test_idCode: .: (0.000117) + test_sIdCode: .: (0.000051) + test_sprsdeDate: .: (0.000047) Bio::TestPDBRecord::TestTER: - test_chainID: .: (0.000204) - test_iCode: .: (0.000104) - test_resName: .: (0.000105) - test_resSeq: .: (0.000098) - test_serial: .: (0.000113) + test_chainID: .: (0.000134) + test_iCode: .: (0.000050) + test_resName: .: (0.000047) + test_resSeq: .: (0.000045) + test_serial: .: (0.000046) Bio::TestPDBRecord::TestTITLE: - test_title: .: (0.000188) + test_title: .: (0.000117) Bio::TestPDBRecord::TestTVECT: - test_serial: .: (0.000217) - test_t1: .: (0.000123) - test_t2: .: (0.000106) - test_t3: .: (0.000094) - test_text: .: (0.000744) + test_serial: .: (0.000135) + test_t1: .: (0.000075) + test_t2: .: (0.000066) + test_t3: .: (0.000064) + test_text: .: (0.000139) Bio::TestPROSITE: - test_ac: .: (0.000968) - test_cc: .: (0.000815) - test_de: .: (0.000845) - test_division: .: (0.000840) - test_dr: .: (0.016753) - test_dt: .: (0.000890) - test_false_neg: .: (0.000913) - test_false_pos: .: (0.000896) - test_false_positive_sequences: .: (0.000867) - test_list_falsenegative: .: (0.020242) - test_list_falsepositive: .: (0.014144) - test_list_potentialhit: .: (0.015407) - test_list_truepositive: .: (0.013748) - test_list_unknown: .: (0.011935) - test_list_xref: .: (0.014627) - test_ma: .: (0.001070) - test_max_repeat: .: (0.000862) - test_name: .: (0.000847) - test_nr: .: (0.000889) - test_pa: .: (0.000819) - test_pa2re: .: (0.001019) - test_partial: .: (0.000849) - test_pdb_xref: .: (0.000952) - test_pdoc_xref: .: (0.000949) - test_positive: .: (0.001004) - test_positive_hits: .: (0.003134) - test_positive_sequences: .: (0.001738) - test_release: .: (0.001664) - test_ru: .: (0.000883) - test_self_pa2re: .: (0.001138) - test_site: .: (0.001407) - test_skip_flag: .: (0.001061) - test_swissprot_release_number: .: (0.001098) - test_swissprot_release_sequences: .: (0.001079) - test_taxon_range: .: (0.001006) - test_total: .: (0.002900) - test_total_hits: .: (0.001134) - test_total_sequences: .: (0.001435) - test_unknown: .: (0.000985) - test_unknown_hits: .: (0.001161) - test_unknown_sequences: .: (0.001251) + test_ac: .: (0.001531) + test_cc: .: (0.000762) + test_de: .: (0.000757) + test_division: .: (0.000778) + test_dr: .: (0.016297) + test_dt: .: (0.000815) + test_false_neg: .: (0.000743) + test_false_pos: .: (0.000739) + test_false_positive_sequences: .: (0.000765) + test_list_falsenegative: .: (0.019081) + test_list_falsepositive: .: (0.013283) + test_list_potentialhit: .: (0.014012) + test_list_truepositive: .: (0.012578) + test_list_unknown: .: (0.011371) + test_list_xref: .: (0.014179) + test_ma: .: (0.000813) + test_max_repeat: .: (0.000866) + test_name: .: (0.000832) + test_nr: .: (0.000868) + test_pa: .: (0.000892) + test_pa2re: .: (0.000991) + test_partial: .: (0.000888) + test_pdb_xref: .: (0.000954) + test_pdoc_xref: .: (0.001035) + test_positive: .: (0.001002) + test_positive_hits: .: (0.003022) + test_positive_sequences: .: (0.000863) + test_release: .: (0.001315) + test_ru: .: (0.000810) + test_self_pa2re: .: (0.001001) + test_site: .: (0.001059) + test_skip_flag: .: (0.000818) + test_swissprot_release_number: .: (0.000812) + test_swissprot_release_sequences: .: (0.000847) + test_taxon_range: .: (0.000817) + test_total: .: (0.002605) + test_total_hits: .: (0.000866) + test_total_sequences: .: (0.001133) + test_unknown: .: (0.000765) + test_unknown_hits: .: (0.000850) + test_unknown_sequences: .: (0.000940) Bio::TestPROSITEConst: - test_delimiter: .: (0.000192) - test_tagsize: .: (0.000041) + test_delimiter: .: (0.000177) + test_tagsize: .: (0.000048) Bio::TestPTS1: test_function_set: .: (0.000143) - test_function_set_number_1: .: (0.000053) - test_function_set_number_2: .: (0.000046) - test_function_set_number_3: .: (0.000048) - test_function_show: .: (0.000043) + test_function_set_number_1: .: (0.000370) + test_function_set_number_2: .: (0.000064) + test_function_set_number_3: .: (0.000050) + test_function_show: .: (0.000044) Bio::TestPTS1Constant: - test_FUNCTION: .: (0.000105) + test_FUNCTION: .: (0.000130) Bio::TestPTS1New: - test_fungi: .: (0.000427) - test_general: .: (0.000161) - test_metazoa: .: (0.000134) + test_fungi: .: (0.000111) + test_general: .: (0.000050) + test_metazoa: .: (0.000051) Bio::TestQualifier: - test_qualifier: .: (0.000252) - test_value: .: (0.000155) + test_qualifier: .: (0.000126) + test_value: .: (0.000042) Bio::TestREBASE: - test_methods: .: (0.000698) + test_methods: .: (0.000550) Bio::TestRPSBlast::TestRPSBlastHSP: - test_align_len: .: (0.000826) - test_bit_score: .: (0.000580) - test_evalue: .: (0.000536) - test_gaps: .: (0.000569) - test_hit_from: .: (0.000608) - test_hit_to: .: (0.000539) - test_hseq: .: (0.000546) - test_identity: .: (0.000511) - test_midline: .: (0.000562) - test_percent_identity: .: (0.000593) - test_positive: .: (0.000575) - test_qseq: .: (0.000522) - test_query_from: .: (0.000564) - test_query_to: .: (0.000516) - test_score: .: (0.000498) + test_align_len: .: (0.000761) + test_bit_score: .: (0.000460) + test_evalue: .: (0.000434) + test_gaps: .: (0.000423) + test_hit_from: .: (0.000444) + test_hit_to: .: (0.000448) + test_hseq: .: (0.000450) + test_identity: .: (0.000420) + test_midline: .: (0.000451) + test_percent_identity: .: (0.000416) + test_positive: .: (0.000395) + test_qseq: .: (0.000411) + test_query_from: .: (0.000409) + test_query_to: .: (0.000412) + test_score: .: (0.000406) Bio::TestRPSBlast::TestRPSBlastReport: - test_db: .: (0.000628) - test_hits_size: .: (0.001040) - test_iterations_size: .: (0.000977) - test_program: .: (0.000464) - test_query_def: .: (0.000989) - test_query_len: .: (0.000984) - test_version: .: (0.000458) - test_version_date: .: (0.003307) - test_version_number: .: (0.000630) + test_db: .: (0.000512) + test_hits_size: .: (0.000939) + test_iterations_size: .: (0.000801) + test_program: .: (0.000357) + test_query_def: .: (0.000827) + test_query_len: .: (0.000846) + test_version: .: (0.000375) + test_version_date: .: (0.002940) + test_version_number: .: (0.000420) Bio::TestRPSBlast::TestRPSBlastReportHit: - test_bit_score: .: (0.000868) - test_definition: .: (0.000636) - test_evalue: .: (0.000573) - test_hsps_size: .: (0.000473) - test_identity: .: (0.000446) - test_lap_at: .: (0.001008) - test_len: .: (0.000612) - test_midline: .: (0.000450) - test_overlap: .: (0.000730) - test_query_end: .: (0.000619) - test_query_seq: .: (0.000609) - test_query_start: .: (0.000558) - test_target_def: .: (0.000565) - test_target_end: .: (0.000606) - test_target_len: .: (0.000680) - test_target_seq: .: (0.000564) - test_target_start: .: (0.000538) + test_bit_score: .: (0.000591) + test_definition: .: (0.000476) + test_evalue: .: (0.000448) + test_hsps_size: .: (0.000414) + test_identity: .: (0.000431) + test_lap_at: .: (0.001088) + test_len: .: (0.000620) + test_midline: .: (0.000516) + test_overlap: .: (0.000462) + test_query_end: .: (0.000452) + test_query_seq: .: (0.000447) + test_query_start: .: (0.000440) + test_target_def: .: (0.000428) + test_target_end: .: (0.000474) + test_target_len: .: (0.000527) + test_target_seq: .: (0.000495) + test_target_start: .: (0.000477) Bio::TestRPSBlast::TestRPSBlastSplitter: - test_entry_pos: .: (0.000467) - test_get_entry: .: (0.000428) - test_rewind: .: (0.000146) - test_skip_leader: .: (0.000243) + test_entry_pos: .: (0.000395) + test_get_entry: .: (0.000313) + test_rewind: .: (0.000084) + test_skip_leader: .: (0.000130) Bio::TestReference: - test_abstract: .: (0.000256) - test_affiliations: .: (0.000110) - test_authors: .: (0.000113) - test_format_bibitem: .: (0.000156) - test_format_bibtex: .: (0.000265) - test_format_bibtex_with_arguments: .: (0.000193) - test_format_cell: .: (0.000142) - test_format_current: .: (0.000125) - test_format_endnote: .: (0.000151) - test_format_general: .: (0.000136) - test_format_genome_biol: .: (0.000130) - test_format_genome_res: .: (0.000131) - test_format_nar: .: (0.000121) - test_format_nature: .: (0.000132) - test_format_rd: .: (0.000141) - test_format_science: .: (0.000239) - test_format_trends: .: (0.000123) - test_issue: .: (0.000105) - test_journal: .: (0.000108) - test_mesh: .: (0.000114) - test_pages: .: (0.000105) - test_pubmed: .: (0.000093) - test_pubmed_url: .: (0.000104) - test_url: .: (0.000114) - test_volume: .: (0.000115) - test_year: .: (0.000103) + test_abstract: .: (0.000152) + test_affiliations: .: (0.000053) + test_authors: .: (0.000053) + test_format_bibitem: .: (0.000094) + test_format_bibtex: .: (0.000180) + test_format_bibtex_with_arguments: .: (0.000105) + test_format_cell: .: (0.000063) + test_format_current: .: (0.000081) + test_format_endnote: .: (0.000080) + test_format_general: .: (0.000075) + test_format_genome_biol: .: (0.000061) + test_format_genome_res: .: (0.000062) + test_format_nar: .: (0.000058) + test_format_nature: .: (0.000067) + test_format_rd: .: (0.000062) + test_format_science: .: (0.000087) + test_format_trends: .: (0.000049) + test_issue: .: (0.000041) + test_journal: .: (0.000043) + test_mesh: .: (0.000046) + test_pages: .: (0.000040) + test_pubmed: .: (0.000110) + test_pubmed_url: .: (0.000048) + test_url: .: (0.000043) + test_volume: .: (0.000042) + test_year: .: (0.000040) Bio::TestReference_noURL: - test_format_endnote: .: (0.000314) - test_url: .: (0.000111) + test_format_endnote: .: (0.000169) + test_url: .: (0.000045) Bio::TestReferences: - test_append: .: (0.000919) - test_each: .: (0.000139) + test_append: .: (0.000718) + test_each: .: (0.000074) Bio::TestRelation: - test_comparison_operator: .: (0.000251) - test_uniq: .: (0.000145) + test_comparison_operator: .: (0.000163) + test_uniq: .: (0.000089) Bio::TestResidue: - test_addAtom: .: (0.000362) - test_each: .: (0.000219) - test_each_atom: .: (0.000179) - test_get_residue_id_from_atom: .: (0.000193) - test_het_atom: .: (0.000163) - test_iCode: .: (0.000158) - test_inspect: .: (0.000203) - test_resSeq: .: (0.000149) - test_sort: .: (0.000215) - test_square_bracket: .: (0.000182) - test_to_s: .: (0.000212) - test_update_resudue_id: .: (0.000150) + test_addAtom: .: (0.000259) + test_each: .: (0.000137) + test_each_atom: .: (0.000106) + test_get_residue_id_from_atom: .: (0.000104) + test_het_atom: .: (0.000092) + test_iCode: .: (0.000096) + test_inspect: .: (0.000103) + test_resSeq: .: (0.000077) + test_sort: .: (0.000124) + test_square_bracket: .: (0.000097) + test_to_s: .: (0.000132) + test_update_resudue_id: .: (0.000080) Bio::TestResidueFinder: - test_each_residue: .: (0.000309) - test_find_residue: .: (0.000148) - test_residues: .: (0.000190) + test_each_residue: .: (0.000170) + test_find_residue: .: (0.000072) + test_residues: .: (0.000120) Bio::TestRestrictionEnzyme::TestAnalysis: - test_cut: .: (0.217167) - test_cut_from_bio_sequence_na: .: (0.036326) - test_cut_without_permutations: .: (0.017883) - test_view_ranges: .: (0.014239) + test_cut: .: (0.129644) + test_cut_from_bio_sequence_na: .: (0.024036) + test_cut_without_permutations: .: (0.017576) + test_view_ranges: .: (0.013672) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: - test_cuts: .: (0.001001) - test_cuts_after_remove_incomplete_cuts: .: (0.000528) - test_strands_for_display: .: (0.001739) - test_strands_for_display_current: .: (0.000601) + test_cuts: .: (0.000845) + test_cuts_after_remove_incomplete_cuts: .: (0.000418) + test_strands_for_display: .: (0.001496) + test_strands_for_display_current: .: (0.000447) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: - test_fragments: .: (0.003624) - test_fragments_for_display_1: .: (0.000661) - test_fragments_for_display_10: .: (0.000564) - test_fragments_for_display_2: .: (0.001046) - test_fragments_for_display_3: .: (0.000877) - test_fragments_for_display_4: .: (0.000953) - test_fragments_for_display_5: .: (0.000472) - test_fragments_for_display_6: .: (0.000461) - test_fragments_for_display_7: .: (0.000702) - test_fragments_for_display_8: .: (0.000457) - test_fragments_for_display_9: .: (0.000438) + test_fragments: .: (0.002844) + test_fragments_for_display_1: .: (0.000528) + test_fragments_for_display_10: .: (0.000541) + test_fragments_for_display_2: .: (0.000753) + test_fragments_for_display_3: .: (0.000615) + test_fragments_for_display_4: .: (0.000832) + test_fragments_for_display_5: .: (0.000373) + test_fragments_for_display_6: .: (0.000359) + test_fragments_for_display_7: .: (0.000884) + test_fragments_for_display_8: .: (0.000359) + test_fragments_for_display_9: .: (0.000365) Bio::TestRestrictionEnzyme::TestCutRanges: - test_obj_2: .: (0.000464) - test_obj_3: .: (0.000229) - test_obj_7: .: (0.000191) - test_obj_z: .: (0.000377) + test_obj_2: .: (0.000304) + test_obj_3: .: (0.000163) + test_obj_7: .: (0.000131) + test_obj_z: .: (0.000138) Bio::TestRestrictionEnzyme::TestCutSymbol: - test_methods: .: (0.000364) + test_methods: .: (0.000269) Bio::TestRestrictionEnzyme::TestDenseIntArray: - test_bracket: .: (0.000262) - test_bracket_eq: .: (0.000201) - test_concat: .: (0.000140) - test_delete: .: (0.000142) - test_dup: .: (0.000176) - test_each: .: (0.000151) - test_eqeq: .: (0.000146) - test_eqeq_false: .: (0.000156) - test_eqeq_other: .: (0.000114) - test_eqeq_self: .: (0.000360) - test_include?: .: (0.000131) - test_internal_data: .: (0.000156) - test_internal_data_eq: .: (0.000137) - test_length: .: (0.000112) - test_ltlt: .: (0.000163) - test_ltlt_larger: .: (0.000132) - test_ltlt_middle: .: (0.000125) - test_plus: .: (0.000156) - test_plus_error: .: (0.000174) - test_push: .: (0.000137) - test_reverse_each: .: (0.000165) - test_self_bracket: .: (0.000115) - test_self_new: .: (0.000134) - test_size: .: (0.000127) - test_sort!: .: (0.000118) - test_to_a: .: (0.000152) - test_uniq!: .: (0.000126) - test_unshift: .: (0.000184) + test_bracket: .: (0.000193) + test_bracket_eq: .: (0.000119) + test_concat: .: (0.000078) + test_delete: .: (0.000077) + test_dup: .: (0.000105) + test_each: .: (0.000237) + test_eqeq: .: (0.000098) + test_eqeq_false: .: (0.000054) + test_eqeq_other: .: (0.000046) + test_eqeq_self: .: (0.000312) + test_include?: .: (0.000067) + test_internal_data: .: (0.000058) + test_internal_data_eq: .: (0.000064) + test_length: .: (0.000049) + test_ltlt: .: (0.000053) + test_ltlt_larger: .: (0.000052) + test_ltlt_middle: .: (0.000052) + test_plus: .: (0.000069) + test_plus_error: .: (0.000100) + test_push: .: (0.000062) + test_reverse_each: .: (0.000081) + test_self_bracket: .: (0.000049) + test_self_new: .: (0.000071) + test_size: .: (0.000046) + test_sort!: .: (0.000047) + test_to_a: .: (0.000050) + test_uniq!: .: (0.000047) + test_unshift: .: (0.000074) Bio::TestRestrictionEnzyme::TestDoubleStranded: - test_argument_error: .: (0.003474) - test_complement: .: (0.003033) - test_complement_with_cut_symbols: .: (0.014978) - test_cut_locations: .: (0.021714) - test_cut_locations_in_enzyme_notation: .: (0.017772) - test_primary: .: (0.005604) - test_primary_with_cut_symbols: .: (0.003534) - test_to_re: .: (0.003293) + test_argument_error: .: (0.003296) + test_complement: .: (0.005254) + test_complement_with_cut_symbols: .: (0.017240) + test_cut_locations: .: (0.018208) + test_cut_locations_in_enzyme_notation: .: (0.014792) + test_primary: .: (0.006448) + test_primary_with_cut_symbols: .: (0.003379) + test_to_re: .: (0.003101) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: - test_align: .: (0.000939) - test_align_with_cuts: .: (0.000917) - test_argument_error: .: (0.000890) - test_ds: .: (0.000887) + test_align: .: (0.001081) + test_align_with_cuts: .: (0.000485) + test_argument_error: .: (0.000751) + test_ds: .: (0.000746) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: - test_argument_error: .: (0.000485) - test_complement: .: (0.000188) - test_contents: .: (0.000161) - test_primary: .: (0.000145) + test_argument_error: .: (0.000347) + test_complement: .: (0.000119) + test_contents: .: (0.000124) + test_primary: .: (0.000114) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: - test_argument_error: .: (0.000307) - test_complement: .: (0.000107) - test_contents: .: (0.000093) - test_primary: .: (0.000342) + test_argument_error: .: (0.000286) + test_complement: .: (0.000117) + test_contents: .: (0.000108) + test_primary: .: (0.000096) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: - test_complement: .: (0.000177) - test_contents: .: (0.000069) - test_primary: .: (0.000080) + test_complement: .: (0.000217) + test_contents: .: (0.000081) + test_primary: .: (0.000088) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: - test_complement: .: (0.000175) - test_complement_to_array_index: .: (0.000129) - test_complement_to_array_index_class: .: (0.000341) - test_contents: .: (0.000171) - test_primary: .: (0.000182) - test_primary_to_array_index: .: (0.000203) - test_primary_to_array_index_class: .: (0.000190) - test_to_array_index: .: (0.000553) - test_to_array_index_class: .: (0.000311) + test_complement: .: (0.000220) + test_complement_to_array_index: .: (0.000138) + test_complement_to_array_index_class: .: (0.000125) + test_contents: .: (0.000086) + test_primary: .: (0.000078) + test_primary_to_array_index: .: (0.000125) + test_primary_to_array_index_class: .: (0.000117) + test_to_array_index: .: (0.000384) + test_to_array_index_class: .: (0.000227) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: - test_enzyme_name: .: (0.000403) - test_rebase: .: (0.000162) + test_enzyme_name: .: (0.000318) + test_rebase: .: (0.000093) Bio::TestRestrictionEnzyme::TestSingleStrand: - test_argument_error: .: (0.000744) - test_creation_with_no_cuts: .: (0.000622) - test_cut_locations: .: (0.000365) - test_cut_locations_in_enzyme_notation: .: (0.000346) - test_orientation: .: (0.000331) - test_pattern: .: (0.000524) - test_pattern_palindromic?: .: (0.000414) - test_stripped: .: (0.000361) - test_to_re: .: (0.002065) - test_with_cut_symbols: .: (0.000428) - test_with_spaces: .: (0.000382) + test_argument_error: .: (0.000834) + test_creation_with_no_cuts: .: (0.000293) + test_cut_locations: .: (0.000256) + test_cut_locations_in_enzyme_notation: .: (0.000277) + test_orientation: .: (0.000480) + test_pattern: .: (0.000280) + test_pattern_palindromic?: .: (0.000331) + test_stripped: .: (0.000244) + test_to_re: .: (0.000300) + test_with_cut_symbols: .: (0.000265) + test_with_spaces: .: (0.000305) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: - test_argument_error: .: (0.000744) - test_creation_with_no_cuts: .: (0.000436) - test_cut_locations: .: (0.000409) - test_cut_locations_in_enzyme_notation: .: (0.000419) - test_orientation: .: (0.000373) - test_pattern: .: (0.000348) - test_pattern_palindromic?: .: (0.000447) - test_stripped: .: (0.000346) - test_to_re: .: (0.000362) - test_with_cut_symbols: .: (0.000388) - test_with_spaces: .: (0.000371) + test_argument_error: .: (0.000619) + test_creation_with_no_cuts: .: (0.000307) + test_cut_locations: .: (0.000270) + test_cut_locations_in_enzyme_notation: .: (0.000288) + test_orientation: .: (0.000239) + test_pattern: .: (0.000253) + test_pattern_palindromic?: .: (0.000304) + test_stripped: .: (0.000235) + test_to_re: .: (0.000201) + test_with_cut_symbols: .: (0.000248) + test_with_spaces: .: (0.000272) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: - test_argument_error: .: (0.000490) - test_initialize_with_pattern: .: (0.000279) - test_max: .: (0.000136) - test_min: .: (0.000135) - test_to_array_index: .: (0.000162) + test_argument_error: .: (0.000345) + test_initialize_with_pattern: .: (0.000219) + test_max: .: (0.000102) + test_min: .: (0.000089) + test_to_array_index: .: (0.000096) Bio::TestRestrictionEnzyme::TestSortedNumArray: - test_bracket: .: (0.000221) - test_bracket_eq: .: (0.000124) - test_concat: .: (0.000079) + test_bracket: .: (0.000180) + test_bracket_eq: .: (0.000092) + test_concat: .: (0.000066) test_delete: .: (0.000055) - test_dup: .: (0.000085) - test_each: .: (0.000081) - test_eqeq: .: (0.000053) - test_eqeq_false: .: (0.000047) - test_eqeq_other: .: (0.000043) - test_eqeq_self: .: (0.000040) - test_include?: .: (0.000049) - test_internal_data_hash: .: (0.000044) - test_internal_data_hash_eq: .: (0.000071) - test_length: .: (0.000042) - test_ltlt: .: (0.000047) - test_ltlt_noeffect: .: (0.000048) - test_plus: .: (0.000048) - test_plus_error: .: (0.000090) - test_private_push_element: .: (0.000051) - test_private_push_element_intermediate: .: (0.000048) - test_private_push_element_last: .: (0.000046) - test_private_push_element_noeffect: .: (0.000044) - test_private_sorted_keys: .: (0.000043) - test_private_unshift_element: .: (0.000048) - test_private_unshift_element_first: .: (0.000053) - test_private_unshift_element_intermediate: .: (0.000048) - test_private_unshift_element_noeffect: .: (0.000047) - test_push: .: (0.000050) - test_reverse_each: .: (0.000086) - test_self_bracket: .: (0.000041) - test_self_new: .: (0.000064) - test_size: .: (0.000039) - test_sort!: .: (0.000040) - test_to_a: .: (0.000039) - test_uniq!: .: (0.000036) - test_unshift: .: (0.000053) + test_dup: .: (0.000091) + test_each: .: (0.000086) + test_eqeq: .: (0.000055) + test_eqeq_false: .: (0.000076) + test_eqeq_other: .: (0.000049) + test_eqeq_self: .: (0.000046) + test_include?: .: (0.000051) + test_internal_data_hash: .: (0.000047) + test_internal_data_hash_eq: .: (0.000054) + test_length: .: (0.000043) + test_ltlt: .: (0.000049) + test_ltlt_noeffect: .: (0.000050) + test_plus: .: (0.000053) + test_plus_error: .: (0.000085) + test_private_push_element: .: (0.000052) + test_private_push_element_intermediate: .: (0.000055) + test_private_push_element_last: .: (0.000051) + test_private_push_element_noeffect: .: (0.000052) + test_private_sorted_keys: .: (0.000049) + test_private_unshift_element: .: (0.000050) + test_private_unshift_element_first: .: (0.000056) + test_private_unshift_element_intermediate: .: (0.000052) + test_private_unshift_element_noeffect: .: (0.000050) + test_push: .: (0.000057) + test_reverse_each: .: (0.000087) + test_self_bracket: .: (0.000048) + test_self_new: .: (0.000067) + test_size: .: (0.000047) + test_sort!: .: (0.000041) + test_to_a: .: (0.000043) + test_uniq!: .: (0.000041) + test_unshift: .: (0.000057) Bio::TestRestrictionEnzyme::TestStringFormatting: - test_add_spacing: .: (0.000188) - test_left_padding: .: (0.000077) - test_right_padding: .: (0.000069) + test_add_spacing: .: (0.000177) + test_left_padding: .: (0.000076) + test_right_padding: .: (0.000075) test_strip_padding: .: (0.000076) Bio::TestSOFT: - test_dataset: .: (0.009787) - test_series: .: (0.005013) + test_dataset: .: (0.009291) + test_series: .: (0.004755) Bio::TestSOSUIReport: - test_entry_id: .: (0.000396) - test_prediction: .: (0.000207) - test_tmh: .: (0.000193) - test_tmhs: .: (0.000219) + test_entry_id: .: (0.000258) + test_prediction: .: (0.000100) + test_tmh: .: (0.000088) + test_tmhs: .: (0.000106) Bio::TestSOSUIReportConst: - test_delimiter: .: (0.000264) - test_rs: .: (0.000164) + test_delimiter: .: (0.000119) + test_rs: .: (0.000045) Bio::TestSOSUITMH: - test_grade: .: (0.000322) - test_range: .: (0.000163) - test_sequence: .: (0.000150) + test_grade: .: (0.000155) + test_range: .: (0.000086) + test_sequence: .: (0.000090) Bio::TestSampleGraph: - test_bellman_ford: .: (0.000419) - test_bfs_shortest_path: .: (0.000196) - test_breadth_first_search: .: (0.000169) - test_depth_first_search: .: (0.000270) - test_dijkstra: .: (0.000212) - test_dump_list: .: (0.000410) - test_dump_matrix: .: (0.000335) - test_extract_subgraph_by_label: .: (0.000217) - test_extract_subgraph_by_list: .: (0.000183) - test_extract_subgraph_retains_disconnected_nodes: .: (0.000145) - test_small_world_aka_node_degree_histogram: .: (0.000146) - test_to_matrix: .: (0.000291) - test_to_matrix_fixed_index: .: (0.000225) - test_undirected_cliquishness: .: (0.000231) + test_bellman_ford: .: (0.000314) + test_bfs_shortest_path: .: (0.000133) + test_breadth_first_search: .: (0.000093) + test_depth_first_search: .: (0.000174) + test_dijkstra: .: (0.000135) + test_dump_list: .: (0.000148) + test_dump_matrix: .: (0.000220) + test_extract_subgraph_by_label: .: (0.000141) + test_extract_subgraph_by_list: .: (0.000168) + test_extract_subgraph_retains_disconnected_nodes: .: (0.000082) + test_small_world_aka_node_degree_histogram: .: (0.000081) + test_to_matrix: .: (0.000194) + test_to_matrix_fixed_index: .: (0.000139) + test_undirected_cliquishness: .: (0.000159) Bio::TestScf_version_2: - test_complement: .: (0.004622) - test_seq: .: (0.004352) - test_to_biosequence: .: (0.004375) + test_complement: .: (0.004494) + test_seq: .: (0.004238) + test_to_biosequence: .: (0.004231) Bio::TestScf_version_3: - test_complement: .: (0.012814) - test_seq: .: (0.013292) - test_to_biosequence: .: (0.013138) + test_complement: .: (0.012633) + test_seq: .: (0.012240) + test_to_biosequence: .: (0.012282) Bio::TestSequence: - test_AA_new_blank_sequence: .: (0.000326) - test_AA_new_sequence_all_legal_symbols: .: (0.000163) - test_AA_new_sequence_removes_whitespace: .: (0.000138) - test_AA_new_sequence_upcases_symbols: .: (0.000146) - test_DNA_new_blank_sequence: .: (0.000139) - test_DNA_new_sequence_downcases_symbols: .: (0.000112) - test_DNA_new_sequence_removes_whitespace: .: (0.000110) - test_NA_randomize_with_counts: .: (0.000637) - test_NA_randomize_with_counts_and_block: .: (0.001407) - test_RNA_new_sequence: .: (0.000147) - test_ambiguous_dna_sequence_complement: .: (0.000116) - test_ambiguous_rna_sequence_complement: .: (0.000106) - test_amino_acid_codes: .: (0.000145) - test_amino_acid_molecular_weight: .: (0.000226) - test_amino_acid_names: .: (0.000152) - test_amino_acid_randomize_can_be_chained: .: (0.001341) - test_amino_acid_randomize_has_same_composition: .: (0.000719) - test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000421) - test_dna_composition: .: (0.000143) - test_dna_gc_percent: .: (0.000175) - test_dna_molecular_weight: .: (0.000298) - test_dna_pikachu: .: (0.000155) - test_dna_sequence_complement: .: (0.000157) - test_dna_sequence_translate: .: (0.000609) - test_dna_to_re: .: (0.000424) - test_element_reference_operator_with_one_argument: .: (0.000141) - test_element_reference_operator_with_two_arguments: .: (0.000131) - test_invalid_nucleic_acid_illegal_bases: .: (0.000153) - test_invalid_nucleic_acid_illegal_bases_more: .: (0.000190) - test_nucleic_acid_names: .: (0.000165) - test_randomize_dna_can_be_chained: .: (0.000315) - test_randomize_dna_retains_composition: .: (0.000258) - test_randomize_dna_with_block: .: (0.000442) - test_rna_composition: .: (0.000141) - test_rna_gc_percent: .: (0.000145) - test_rna_molecular_weight: .: (0.000193) - test_rna_pikachu: .: (0.000128) - test_rna_sequence_complement: .: (0.000115) - test_rna_sequence_translate: .: (0.000386) - test_rna_to_re: .: (0.000239) - test_total: .: (0.000175) - test_two_consecutive_dna_randomizations_not_equal: .: (0.000261) - test_valid_dna_sequence_illegal_bases: .: (0.000163) + test_AA_new_blank_sequence: .: (0.000191) + test_AA_new_sequence_all_legal_symbols: .: (0.000081) + test_AA_new_sequence_removes_whitespace: .: (0.000054) + test_AA_new_sequence_upcases_symbols: .: (0.000050) + test_DNA_new_blank_sequence: .: (0.000050) + test_DNA_new_sequence_downcases_symbols: .: (0.000049) + test_DNA_new_sequence_removes_whitespace: .: (0.000047) + test_NA_randomize_with_counts: .: (0.000535) + test_NA_randomize_with_counts_and_block: .: (0.006697) + test_RNA_new_sequence: .: (0.000099) + test_ambiguous_dna_sequence_complement: .: (0.000070) + test_ambiguous_rna_sequence_complement: .: (0.000083) + test_amino_acid_codes: .: (0.000100) + test_amino_acid_molecular_weight: .: (0.000146) + test_amino_acid_names: .: (0.000087) + test_amino_acid_randomize_can_be_chained: .: (0.001028) + test_amino_acid_randomize_has_same_composition: .: (0.000609) + test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.000355) + test_dna_composition: .: (0.000092) + test_dna_gc_percent: .: (0.000123) + test_dna_molecular_weight: .: (0.000125) + test_dna_pikachu: .: (0.000343) + test_dna_sequence_complement: .: (0.000059) + test_dna_sequence_translate: .: (0.000483) + test_dna_to_re: .: (0.000162) + test_element_reference_operator_with_one_argument: .: (0.000069) + test_element_reference_operator_with_two_arguments: .: (0.000058) + test_invalid_nucleic_acid_illegal_bases: .: (0.000087) + test_invalid_nucleic_acid_illegal_bases_more: .: (0.000088) + test_nucleic_acid_names: .: (0.000078) + test_randomize_dna_can_be_chained: .: (0.000205) + test_randomize_dna_retains_composition: .: (0.000299) + test_randomize_dna_with_block: .: (0.000204) + test_rna_composition: .: (0.000077) + test_rna_gc_percent: .: (0.000084) + test_rna_molecular_weight: .: (0.000104) + test_rna_pikachu: .: (0.000065) + test_rna_sequence_complement: .: (0.000056) + test_rna_sequence_translate: .: (0.000231) + test_rna_to_re: .: (0.000124) + test_total: .: (0.000072) + test_two_consecutive_dna_randomizations_not_equal: .: (0.000366) + test_valid_dna_sequence_illegal_bases: .: (0.000069) Bio::TestSequenceAA: - test_codes: .: (0.000397) - test_molecular_weight: .: (0.000187) - test_names: .: (0.000133) - test_to_re: .: (0.000176) - test_to_s: .: (0.000104) + test_codes: .: (0.000173) + test_molecular_weight: .: (0.000088) + test_names: .: (0.000064) + test_to_re: .: (0.000097) + test_to_s: .: (0.000054) Bio::TestSequenceAACompat: - test_aa_self_randomize: .: (0.000291) + test_aa_self_randomize: .: (0.000190) Bio::TestSequenceAANew: - test_new: .: (0.000180) - test_new_n: .: (0.000108) - test_new_r: .: (0.000106) - test_new_t: .: (0.000102) + test_new: .: (0.000140) + test_new_n: .: (0.000056) + test_new_r: .: (0.000047) + test_new_t: .: (0.000045) Bio::TestSequenceCommon::TestSequenceCommon: - test_composition: .: (0.000229) - test_concat: .: (0.000105) - test_push: .: (0.000098) - test_seq: .: (0.000150) - test_splicing: .: (0.000206) - test_sum: .: (0.000107) - test_to_s: .: (0.000119) - test_to_str: .: (0.000098) - test_total: .: (0.000108) - test_window_search: .: (0.000189) + test_composition: .: (0.000151) + test_concat: .: (0.000056) + test_push: .: (0.000042) + test_seq: .: (0.000042) + test_splicing: .: (0.000282) + test_sum: .: (0.000047) + test_to_s: .: (0.000040) + test_to_str: .: (0.000039) + test_total: .: (0.000049) + test_window_search: .: (0.000140) Bio::TestSequenceCommon::TestSequenceCommonNormalize: - test_no_normalize: .: (0.000202) - test_normalize_A: .: (0.000103) - test_normalize_a: .: (0.000101) + test_no_normalize: .: (0.000112) + test_normalize_A: .: (0.000047) + test_normalize_a: .: (0.000042) Bio::TestSequenceCommon::TestSequenceCommonRandomize: - test_randomize: .: (0.000916) - test_randomize_with_block: .: (0.002703) - test_randomize_with_hash: .: (0.001012) - test_randomize_with_hash_block: .: (0.002962) + test_randomize: .: (0.000754) + test_randomize_with_block: .: (0.002113) + test_randomize_with_hash: .: (0.000677) + test_randomize_with_hash_block: .: (0.002735) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:325:in `test_randomize_equiprobability' =============================================================================== -: (0.001060) +: (0.000715) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.6/test/unit/bio/sequence/test_common.rb:331:in `test_randomize_with_hash_equiprobability' =============================================================================== -: (0.000875) +: (0.000531) Bio::TestSequenceCommon::TestSequenceCommonSubseq: - test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000286) - test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000124) - test_subseq_returns_subsequence: .: (0.000105) - test_to_s_returns_self_as_string: .: (0.000116) + test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000185) + test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000066) + test_subseq_returns_subsequence: .: (0.000055) + test_to_s_returns_self_as_string: .: (0.000063) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: - test_window_search_with_width_3_default_step_no_residual: .: (0.000235) - test_window_search_with_width_3_step_two_with_residual: .: (0.000141) + test_window_search_with_width_3_default_step_no_residual: .: (0.000118) + test_window_search_with_width_3_step_two_with_residual: .: (0.000057) Bio::TestSequenceCompat::TestSequenceCommonCompat: - test_to_fasta: .: (0.000261) + test_to_fasta: .: (0.000123) Bio::TestSequenceCompat::TestSequenceCompat: - test_to_s: .: (0.000325) + test_to_s: .: (0.000186) Bio::TestSequenceCompat::TestSequenceNACompat: - test_aa_self_randomize: .: (0.000324) - test_na_self_randomize: .: (0.000195) + test_aa_self_randomize: .: (0.000178) + test_na_self_randomize: .: (0.000099) Bio::TestSequenceDBLink: - test_database: .: (0.000202) - test_id: .: (0.000094) - test_secondary_ids: .: (0.000093) + test_database: .: (0.000123) + test_id: .: (0.000039) + test_secondary_ids: .: (0.000040) Bio::TestSequenceDBLinkClassMethods: - test_parse_embl_DR_line: .: (0.000209) - test_parse_uniprot_DR_line: .: (0.000136) + test_parse_embl_DR_line: .: (0.000122) + test_parse_uniprot_DR_line: .: (0.000062) Bio::TestSequenceFormatFormatterFasta_numeric: - test_output: .: (0.000578) - test_output_width_35: .: (0.000280) - test_output_width_nil: .: (0.000251) + test_output: .: (0.000570) + test_output_width_35: .: (0.000229) + test_output_width_nil: .: (0.000176) Bio::TestSequenceFormatFormatterQual: - test_output: .: (0.000480) - test_output_after_adding_sequence: .: (0.000259) - test_output_after_truncating_sequence: .: (0.000180) - test_output_from_error_probabilities: .: (0.001969) - test_output_width45: .: (0.000303) - test_output_with_converting_score_phred2solexa: .: (0.000443) - test_output_with_converting_score_solexa2phred: .: (0.000257) - test_output_with_default_score: .: (0.000191) + test_output: .: (0.000334) + test_output_after_adding_sequence: .: (0.000183) + test_output_after_truncating_sequence: .: (0.000105) + test_output_from_error_probabilities: .: (0.001583) + test_output_width45: .: (0.000219) + test_output_with_converting_score_phred2solexa: .: (0.000368) + test_output_with_converting_score_solexa2phred: .: (0.000191) + test_output_with_default_score: .: (0.000136) Bio::TestSequenceMasker: - test_mask: .: (0.000269) - test_mask_with_enumerator: .: (0.000145) - test_mask_with_enumerator_empty_mask_char: .: (0.000138) - test_mask_with_enumerator_excess: .: (0.000323) - test_mask_with_enumerator_longer_mask_char: .: (0.000129) - test_mask_with_enumerator_shorter: .: (0.000169) - test_mask_with_error_probability: .: (0.000178) - test_mask_with_quality_score: .: (0.000132) + test_mask: .: (0.000213) + test_mask_with_enumerator: .: (0.000104) + test_mask_with_enumerator_empty_mask_char: .: (0.000088) + test_mask_with_enumerator_excess: .: (0.000259) + test_mask_with_enumerator_longer_mask_char: .: (0.000082) + test_mask_with_enumerator_shorter: .: (0.000101) + test_mask_with_error_probability: .: (0.000072) + test_mask_with_quality_score: .: (0.000066) Bio::TestSequenceNA: - test_at_content: .: (0.000365) - test_at_skew: .: (0.000203) - test_codon_usage: .: (0.000136) - test_complement: .: (0.000114) - test_dna: .: (0.000138) - test_dna!: .: (0.000119) - test_forward_complement: .: (0.000141) - test_gc_content: .: (0.000201) - test_gc_percent: .: (0.000161) - test_gc_skew: .: (0.000257) - test_iliegal_bases: .: (0.000131) - test_molecular_weight: .: (0.000230) - test_names: .: (0.000238) - test_reverse_complement: .: (0.000160) - test_rna: .: (0.000108) - test_rna!: .: (0.000119) - test_splicing: .: (0.000210) - test_to_re: .: (0.000185) - test_to_s: .: (0.000110) + test_at_content: .: (0.000235) + test_at_skew: .: (0.000214) + test_codon_usage: .: (0.000097) + test_complement: .: (0.000065) + test_dna: .: (0.000056) + test_dna!: .: (0.000047) + test_forward_complement: .: (0.000104) + test_gc_content: .: (0.000138) + test_gc_percent: .: (0.000101) + test_gc_skew: .: (0.000160) + test_iliegal_bases: .: (0.000054) + test_molecular_weight: .: (0.000154) + test_names: .: (0.000114) + test_reverse_complement: .: (0.000079) + test_rna: .: (0.000049) + test_rna!: .: (0.000044) + test_splicing: .: (0.000101) + test_to_re: .: (0.000135) + test_to_s: .: (0.000045) Bio::TestSequenceNACommon: - test_composition: .: (0.000265) - test_concat: .: (0.000110) - test_push: .: (0.000108) - test_seq: .: (0.000173) - test_splicing: .: (0.000217) - test_sum: .: (0.000109) - test_to_s: .: (0.000092) - test_to_str: .: (0.000093) - test_total: .: (0.000105) - test_window_search: .: (0.000273) + test_composition: .: (0.000156) + test_concat: .: (0.000056) + test_push: .: (0.000052) + test_seq: .: (0.000051) + test_splicing: .: (0.000188) + test_sum: .: (0.000054) + test_to_s: .: (0.000042) + test_to_str: .: (0.000046) + test_total: .: (0.000050) + test_window_search: .: (0.000135) Bio::TestSequenceNANew: - test_new: .: (0.000253) - test_new_n: .: (0.000120) - test_new_r: .: (0.000096) - test_new_t: .: (0.000131) + test_new: .: (0.000122) + test_new_n: .: (0.000048) + test_new_r: .: (0.000039) + test_new_t: .: (0.000039) Bio::TestSequenceNATranslation: - test_translate: .: (0.000461) - test_translate_0: .: (0.000656) - test_translate_1: .: (0.000212) - test_translate_2: .: (0.000192) - test_translate_3: .: (0.000234) - test_translate_4: .: (0.000221) - test_translate_5: .: (0.000324) - test_translate_6: .: (0.000223) - test_translate_7: .: (0.000356) - test_translate_given_codon_table: .: (0.034649) - test_translate_n1: .: (0.000574) - test_translate_n2: .: (0.000458) - test_translate_n3: .: (0.000432) - test_translate_unknown_o: .: (0.000288) - test_translate_unknown_x: .: (0.000340) + test_translate: .: (0.000370) + test_translate_0: .: (0.000438) + test_translate_1: .: (0.000170) + test_translate_2: .: (0.000130) + test_translate_3: .: (0.000125) + test_translate_4: .: (0.000128) + test_translate_5: .: (0.000202) + test_translate_6: .: (0.000124) + test_translate_7: .: (0.000263) + test_translate_given_codon_table: .: (0.031509) + test_translate_n1: .: (0.000389) + test_translate_n2: .: (0.000334) + test_translate_n3: .: (0.000419) + test_translate_unknown_o: .: (0.000164) + test_translate_unknown_x: .: (0.000135) Bio::TestSequenceQualityScore::TestConverter: - test_convert_nothing: .: (0.000347) - test_convert_scores_from_phred_to_solexa: .: (0.000345) - test_convert_scores_from_solexa_to_phred: .: (0.000161) + test_convert_nothing: .: (0.000173) + test_convert_scores_from_phred_to_solexa: .: (0.000238) + test_convert_scores_from_solexa_to_phred: .: (0.000091) Bio::TestSequenceQualityScore::TestPhred: - test_convert_nothing: .: (0.000228) - test_convert_scores_from_phred: .: (0.000109) - test_convert_scores_from_phred_to_solexa: .: (0.000305) - test_convert_scores_from_solexa: .: (0.000149) - test_convert_scores_from_solexa_to_phred: .: (0.000171) - test_convert_scores_to_phred: .: (0.000113) - test_convert_scores_to_solexa: .: (0.000499) - test_p2q: .: (0.000164) - test_phred_p2q: .: (0.000131) - test_phred_q2p: .: (0.001539) - test_q2p: .: (0.001684) - test_quality_score_type: .: (0.000080) - test_self_convert_scores_to_solexa: .: (0.000357) - test_self_p2q: .: (0.000102) - test_self_q2p: .: (0.001313) + test_convert_nothing: .: (0.000113) + test_convert_scores_from_phred: .: (0.000045) + test_convert_scores_from_phred_to_solexa: .: (0.000202) + test_convert_scores_from_solexa: .: (0.000251) + test_convert_scores_from_solexa_to_phred: .: (0.000087) + test_convert_scores_to_phred: .: (0.000038) + test_convert_scores_to_solexa: .: (0.000220) + test_p2q: .: (0.000085) + test_phred_p2q: .: (0.000069) + test_phred_q2p: .: (0.001370) + test_q2p: .: (0.001251) + test_quality_score_type: .: (0.000058) + test_self_convert_scores_to_solexa: .: (0.000222) + test_self_p2q: .: (0.000079) + test_self_q2p: .: (0.001258) Bio::TestSequenceQualityScore::TestSolexa: - test_convert_nothing: .: (0.000258) - test_convert_scores_from_phred: .: (0.000223) - test_convert_scores_from_phred_to_solexa: .: (0.000227) - test_convert_scores_from_solexa: .: (0.000041) - test_convert_scores_from_solexa_to_phred: .: (0.000079) - test_convert_scores_to_phred: .: (0.000092) + test_convert_nothing: .: (0.000245) + test_convert_scores_from_phred: .: (0.000266) + test_convert_scores_from_phred_to_solexa: .: (0.000200) + test_convert_scores_from_solexa: .: (0.000043) + test_convert_scores_from_solexa_to_phred: .: (0.000080) + test_convert_scores_to_phred: .: (0.000082) test_convert_scores_to_solexa: .: (0.000038) - test_p2q: .: (0.000112) - test_q2p: .: (0.002414) - test_quality_score_type: .: (0.000131) - test_self_convert_scores_to_phred: .: (0.000180) - test_self_p2q: .: (0.000180) - test_self_q2p: .: (0.001359) - test_solexa_p2q: .: (0.000199) - test_solexa_q2p: .: (0.001434) + test_p2q: .: (0.000107) + test_q2p: .: (0.002073) + test_quality_score_type: .: (0.000062) + test_self_convert_scores_to_phred: .: (0.000103) + test_self_p2q: .: (0.000105) + test_self_q2p: .: (0.001208) + test_solexa_p2q: .: (0.000114) + test_solexa_q2p: .: (0.001210) Bio::TestSequenceRuby3::TestSequenceCommon: - test_capitalize: .: (0.000336) - test_center: .: (0.000128) - test_chomp: .: (0.000177) - test_chop: .: (0.000157) - test_delete: .: (0.000118) - test_delete_prefix: .: (0.000113) - test_delete_suffix: .: (0.000111) - test_downcase: .: (0.000140) - test_each_char: .: (0.000183) - test_each_char_enum: .: (0.000288) - test_each_grapheme_cluster: .: (0.000858) - test_each_grapheme_cluster_enum: .: (0.000214) - test_each_line: .: (0.000194) - test_each_line_enum: .: (0.000151) - test_gsub: .: (0.000144) - test_gsub_with_block: .: (0.000373) - test_ljust: .: (0.000125) - test_lstrip: .: (0.000133) - test_multiply: .: (0.000126) - test_next: .: (0.000123) - test_reverse: .: (0.000119) - test_rjust: .: (0.000129) - test_rstrip: .: (0.000147) - test_slice: .: (0.000144) - test_slice2: .: (0.000130) - test_split: .: (0.000155) - test_squeeze: .: (0.000126) - test_strip: .: (0.000113) - test_sub: .: (0.000140) - test_sub_with_block: .: (0.000501) - test_succ: .: (0.000154) - test_swapcase: .: (0.000160) - test_tr: .: (0.000151) - test_tr_s: .: (0.000143) - test_upcase: .: (0.000128) + test_capitalize: .: (0.000197) + test_center: .: (0.000062) + test_chomp: .: (0.000070) + test_chop: .: (0.000070) + test_delete: .: (0.000051) + test_delete_prefix: .: (0.000054) + test_delete_suffix: .: (0.000050) + test_downcase: .: (0.000051) + test_each_char: .: (0.000114) + test_each_char_enum: .: (0.000089) + test_each_grapheme_cluster: .: (0.000609) + test_each_grapheme_cluster_enum: .: (0.000098) + test_each_line: .: (0.000080) + test_each_line_enum: .: (0.000072) + test_gsub: .: (0.000074) + test_gsub_with_block: .: (0.000319) + test_ljust: .: (0.000077) + test_lstrip: .: (0.000070) + test_multiply: .: (0.000055) + test_next: .: (0.000055) + test_reverse: .: (0.000057) + test_rjust: .: (0.000054) + test_rstrip: .: (0.000053) + test_slice: .: (0.000056) + test_slice2: .: (0.000052) + test_split: .: (0.000073) + test_squeeze: .: (0.000052) + test_strip: .: (0.000052) + test_sub: .: (0.000059) + test_sub_with_block: .: (0.006308) + test_succ: .: (0.000091) + test_swapcase: .: (0.000070) + test_tr: .: (0.000066) + test_tr_s: .: (0.000080) + test_upcase: .: (0.000062) Bio::TestSequenceRuby3::TestSequenceCommonPartition: - test_partition: .: (0.000312) - test_partition_nomatch: .: (0.000152) - test_partition_sep_TSeq: .: (0.000146) - test_partition_sep_regexp: .: (0.000154) + test_partition: .: (0.000212) + test_partition_nomatch: .: (0.000094) + test_partition_sep_TSeq: .: (0.000089) + test_partition_sep_regexp: .: (0.000090) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: - test_rpartition: .: (0.000280) - test_rpartition_nomatch: .: (0.000778) - test_rpartition_sep_TSeq: .: (0.000153) - test_rpartition_sep_regexp: .: (0.000144) + test_rpartition: .: (0.000177) + test_rpartition_nomatch: .: (0.000666) + test_rpartition_sep_TSeq: .: (0.000095) + test_rpartition_sep_regexp: .: (0.000091) Bio::TestShRNA: - test_blocK_it: .: (0.026745) - test_blocK_it_: .: (0.021801) - test_blocK_it_BLOCK_IT: .: (0.020978) - test_blocK_it_BLOCK_iT: .: (0.020438) - test_blocK_it_piGene: .: (0.023509) - test_bottom_strand: .: (0.021320) - test_bottom_strand_class: .: (0.020217) - test_bottom_strand_nil: .: (0.019959) - test_design: .: (0.021164) - test_design_BLOCK_IT: .: (0.020833) - test_report: .: (0.020794) - test_report_before_design: .: (0.020972) - test_top_strand: .: (0.020137) - test_top_strand_class: .: (0.021144) - test_top_strand_nil: .: (0.020283) + test_blocK_it: .: (0.025297) + test_blocK_it_: .: (0.020350) + test_blocK_it_BLOCK_IT: .: (0.019710) + test_blocK_it_BLOCK_iT: .: (0.018822) + test_blocK_it_piGene: .: (0.019186) + test_bottom_strand: .: (0.019858) + test_bottom_strand_class: .: (0.019026) + test_bottom_strand_nil: .: (0.018410) + test_design: .: (0.019682) + test_design_BLOCK_IT: .: (0.019440) + test_report: .: (0.019496) + test_report_before_design: .: (0.019864) + test_top_strand: .: (0.018987) + test_top_strand_class: .: (0.019858) + test_top_strand_nil: .: (0.019191) Bio::TestShRNANew: - test_new: .: (0.000715) + test_new: .: (0.000584) Bio::TestSiRNA: - test_antisense_size: .: (0.000265) - test_design: .: (0.022066) - test_design_reynolds: .: (0.051561) - test_design_uitei: .: (0.039842) - test_max_gc_percent: .: (0.000195) - test_min_gc_percent: .: (0.000159) - test_reynolds: .: (0.057109) - test_reynolds?: .: (0.000233) - test_uitei: .: (0.049786) - test_uitei?: .: (0.003441) + test_antisense_size: .: (0.000156) + test_design: .: (0.021023) + test_design_reynolds: .: (0.025327) + test_design_uitei: .: (0.019544) + test_max_gc_percent: .: (0.000093) + test_min_gc_percent: .: (0.000050) + test_reynolds: .: (0.024551) + test_reynolds?: .: (0.000135) + test_uitei: .: (0.020352) + test_uitei?: .: (0.000104) Bio::TestSiRNANew: - test_new: .: (0.001289) + test_new: .: (0.000799) Bio::TestSiRNAPair: - test_antisense: .: (0.049175) - test_gc_percent: .: (0.048279) - test_report: .: (0.043570) - test_rule: .: (0.043424) - test_sense: .: (0.044478) - test_start: .: (0.046073) - test_stop: .: (0.045781) - test_target: .: (0.042492) + test_antisense: .: (0.019618) + test_gc_percent: .: (0.020720) + test_report: .: (0.021166) + test_rule: .: (0.020342) + test_sense: .: (0.020823) + test_start: .: (0.021105) + test_stop: .: (0.020629) + test_target: .: (0.020834) Bio::TestSiRNAPairNew: - test_new: .: (0.004189) + test_new: .: (0.001017) Bio::TestSim4Report: - test_all_hits: .: (0.000866) - test_each: .: (0.000426) - test_each_hit: .: (0.000281) - test_hits: .: (0.000290) - test_num_hits: .: (0.000242) - test_query_def: .: (0.000209) - test_query_id: .: (0.000193) - test_query_len: .: (0.000210) - test_seq1: .: (0.000253) + test_all_hits: .: (0.000394) + test_each: .: (0.000166) + test_each_hit: .: (0.000129) + test_hits: .: (0.000136) + test_num_hits: .: (0.000129) + test_query_def: .: (0.000126) + test_query_id: .: (0.000114) + test_query_len: .: (0.000111) + test_seq1: .: (0.000156) Bio::TestSim4Report2: - test_all_hits: .: (0.007131) - test_each: .: (0.000404) - test_each_hit: .: (0.000249) - test_hits: .: (0.000237) - test_num_hits: .: (0.000354) - test_query_def: .: (0.000201) - test_query_id: .: (0.000192) - test_query_len: .: (0.000198) - test_seq1: .: (0.000254) + test_all_hits: .: (0.000263) + test_each: .: (0.000321) + test_each_hit: .: (0.000165) + test_hits: .: (0.000139) + test_num_hits: .: (0.000118) + test_query_def: .: (0.000106) + test_query_id: .: (0.000104) + test_query_len: .: (0.000099) + test_seq1: .: (0.000136) Bio::TestSim4Report4: - test_all_hits: .: (0.000378) - test_each: .: (0.000289) - test_each_hit: .: (0.000237) - test_hits: .: (0.000290) - test_num_hits: .: (0.000236) - test_query_def: .: (0.000218) - test_query_id: .: (0.000207) - test_query_len: .: (0.000195) - test_seq1: .: (0.000250) + test_all_hits: .: (0.000291) + test_each: .: (0.000157) + test_each_hit: .: (0.000137) + test_hits: .: (0.000135) + test_num_hits: .: (0.000116) + test_query_def: .: (0.000221) + test_query_id: .: (0.000121) + test_query_len: .: (0.000107) + test_seq1: .: (0.000148) Bio::TestSim4ReportHit: - test_align: .: (0.000404) - test_complement?: .: (0.000200) - test_definition: .: (0.000194) - test_each: .: (0.000532) - test_exons: .: (0.003568) - test_hit_id: .: (0.000928) - test_hsps: .: (0.000452) - test_introns: .: (0.000394) - test_len: .: (0.000242) - test_query_def: .: (0.000240) - test_query_id: .: (0.000202) - test_query_len: .: (0.000191) - test_segmentpairs: .: (0.004162) - test_seq1: .: (0.000373) - test_seq2: .: (0.000256) - test_target_def: .: (0.000197) - test_target_id: .: (0.000182) - test_target_len: .: (0.000192) + test_align: .: (0.000323) + test_complement?: .: (0.000682) + test_definition: .: (0.000175) + test_each: .: (0.000290) + test_exons: .: (0.000224) + test_hit_id: .: (0.000117) + test_hsps: .: (0.000185) + test_introns: .: (0.000222) + test_len: .: (0.000137) + test_query_def: .: (0.000117) + test_query_id: .: (0.000115) + test_query_len: .: (0.000118) + test_segmentpairs: .: (0.000218) + test_seq1: .: (0.000145) + test_seq2: .: (0.000134) + test_target_def: .: (0.000102) + test_target_id: .: (0.000099) + test_target_len: .: (0.000101) Bio::TestSim4ReportHit2: - test_align: .: (0.000419) - test_complement?: .: (0.000206) - test_definition: .: (0.000191) - test_each: .: (0.000324) - test_exons: .: (0.000325) - test_hit_id: .: (0.000194) - test_hsps: .: (0.000308) - test_introns: .: (0.003208) - test_len: .: (0.000363) - test_query_def: .: (0.000230) - test_query_id: .: (0.000185) - test_query_len: .: (0.000175) - test_segmentpairs: .: (0.000272) - test_seq1: .: (0.000147) - test_seq2: .: (0.000145) - test_target_def: .: (0.000091) - test_target_id: .: (0.000084) - test_target_len: .: (0.000079) + test_align: .: (0.000289) + test_complement?: .: (0.000115) + test_definition: .: (0.000108) + test_each: .: (0.000208) + test_exons: .: (0.000232) + test_hit_id: .: (0.000125) + test_hsps: .: (0.000187) + test_introns: .: (0.000178) + test_len: .: (0.000104) + test_query_def: .: (0.000097) + test_query_id: .: (0.000096) + test_query_len: .: (0.000089) + test_segmentpairs: .: (0.000212) + test_seq1: .: (0.000160) + test_seq2: .: (0.000136) + test_target_def: .: (0.000099) + test_target_id: .: (0.000093) + test_target_len: .: (0.000091) Bio::TestSim4ReportHit4: - test_align: .: (0.000311) - test_complement?: .: (0.000109) - test_definition: .: (0.000092) - test_each: .: (0.000268) - test_exons: .: (0.000242) - test_hit_id: .: (0.000100) - test_hsps: .: (0.004700) - test_introns: .: (0.000481) - test_len: .: (0.000254) - test_query_def: .: (0.000233) - test_query_id: .: (0.000240) - test_query_len: .: (0.000230) - test_segmentpairs: .: (0.000406) - test_seq1: .: (0.000238) - test_seq2: .: (0.005662) - test_target_def: .: (0.000563) - test_target_id: .: (0.000218) - test_target_len: .: (0.005508) + test_align: .: (0.000339) + test_complement?: .: (0.000136) + test_definition: .: (0.000124) + test_each: .: (0.000297) + test_exons: .: (0.000275) + test_hit_id: .: (0.000122) + test_hsps: .: (0.000241) + test_introns: .: (0.000272) + test_len: .: (0.000130) + test_query_def: .: (0.000122) + test_query_id: .: (0.000109) + test_query_len: .: (0.000114) + test_segmentpairs: .: (0.000272) + test_seq1: .: (0.002457) + test_seq2: .: (0.000458) + test_target_def: .: (0.000141) + test_target_id: .: (0.000111) + test_target_len: .: (0.000110) Bio::TestSim4ReportSegment: - test_from: .: (0.000355) - test_self_new: .: (0.000163) - test_seq: .: (0.000112) - test_to: .: (0.000102) + test_from: .: (0.000175) + test_self_new: .: (0.000077) + test_seq: .: (0.000048) + test_to: .: (0.000046) Bio::TestSim4ReportSegmentPair2_exon: - test_align_len: .: (0.000499) - test_direction: .: (0.000302) - test_hit_from: .: (0.000286) - test_hit_to: .: (0.000282) - test_hseq: .: (0.000313) - test_midline: .: (0.001049) - test_percent_identity: .: (0.000595) - test_qseq: .: (0.000324) - test_query_from: .: (0.000280) - test_query_to: .: (0.000558) - test_seq1: .: (0.000471) - test_seq2: .: (0.000410) + test_align_len: .: (0.000376) + test_direction: .: (0.000213) + test_hit_from: .: (0.000187) + test_hit_to: .: (0.000418) + test_hseq: .: (0.000192) + test_midline: .: (0.000173) + test_percent_identity: .: (0.000175) + test_qseq: .: (0.000170) + test_query_from: .: (0.000202) + test_query_to: .: (0.000194) + test_seq1: .: (0.000224) + test_seq2: .: (0.000528) Bio::TestSim4ReportSegmentPair2_intron: - test_align_len: .: (0.000454) - test_direction: .: (0.000585) - test_hit_from: .: (0.000305) - test_hit_to: .: (0.000284) - test_hseq: .: (0.000300) - test_midline: .: (0.000290) - test_percent_identity: .: (0.000263) - test_qseq: .: (0.000268) - test_query_from: .: (0.000292) - test_query_to: .: (0.000270) - test_seq1: .: (0.005337) - test_seq2: .: (0.000553) + test_align_len: .: (0.000394) + test_direction: .: (0.000197) + test_hit_from: .: (0.000185) + test_hit_to: .: (0.000175) + test_hseq: .: (0.000170) + test_midline: .: (0.000162) + test_percent_identity: .: (0.000167) + test_qseq: .: (0.000160) + test_query_from: .: (0.000168) + test_query_to: .: (0.000456) + test_seq1: .: (0.000247) + test_seq2: .: (0.000248) Bio::TestSim4ReportSegmentPair4_exon: - test_align_len: .: (0.000950) - test_direction: .: (0.000416) - test_hit_from: .: (0.000399) - test_hit_to: .: (0.000388) - test_hseq: .: (0.000369) - test_midline: .: (0.000355) - test_percent_identity: .: (0.000325) - test_qseq: .: (0.000536) - test_query_from: .: (0.006061) - test_query_to: .: (0.000588) - test_seq1: .: (0.000373) - test_seq2: .: (0.000268) + test_align_len: .: (0.000398) + test_direction: .: (0.000243) + test_hit_from: .: (0.000228) + test_hit_to: .: (0.000259) + test_hseq: .: (0.000259) + test_midline: .: (0.000248) + test_percent_identity: .: (0.000492) + test_qseq: .: (0.000270) + test_query_from: .: (0.000247) + test_query_to: .: (0.000244) + test_seq1: .: (0.000290) + test_seq2: .: (0.000290) Bio::TestSim4ReportSegmentPair4_intron: - test_align_len: .: (0.000360) - test_direction: .: (0.000225) - test_hit_from: .: (0.000512) - test_hit_to: .: (0.000385) - test_hseq: .: (0.000334) - test_midline: .: (0.000331) - test_percent_identity: .: (0.000331) - test_qseq: .: (0.000314) - test_query_from: .: (0.001071) - test_query_to: .: (0.000400) - test_seq1: .: (0.000511) - test_seq2: .: (0.000403) + test_align_len: .: (0.000378) + test_direction: .: (0.000234) + test_hit_from: .: (0.000227) + test_hit_to: .: (0.000327) + test_hseq: .: (0.000233) + test_midline: .: (0.000232) + test_percent_identity: .: (0.000226) + test_qseq: .: (0.000239) + test_query_from: .: (0.000244) + test_query_to: .: (0.000234) + test_seq1: .: (0.001015) + test_seq2: .: (0.000373) Bio::TestSim4ReportSegmentPair4_intron1: - test_align_len: .: (0.000695) - test_direction: .: (0.000411) - test_hit_from: .: (0.000371) - test_hit_to: .: (0.000350) - test_hseq: .: (0.000315) - test_midline: .: (0.004899) - test_percent_identity: .: (0.000511) - test_qseq: .: (0.000385) - test_query_from: .: (0.000324) - test_query_to: .: (0.000302) - test_seq1: .: (0.000346) - test_seq2: .: (0.000348) + test_align_len: .: (0.000382) + test_direction: .: (0.000251) + test_hit_from: .: (0.000267) + test_hit_to: .: (0.000239) + test_hseq: .: (0.000222) + test_midline: .: (0.000234) + test_percent_identity: .: (0.000223) + test_qseq: .: (0.000224) + test_query_from: .: (0.000222) + test_query_to: .: (0.000218) + test_seq1: .: (0.000271) + test_seq2: .: (0.000261) Bio::TestSim4ReportSegmentPair_exon: - test_align_len: .: (0.000424) - test_direction: .: (0.000334) - test_hit_from: .: (0.000302) - test_hit_to: .: (0.000259) - test_hseq: .: (0.000241) - test_midline: .: (0.000237) - test_percent_identity: .: (0.000236) - test_qseq: .: (0.000588) - test_query_from: .: (0.000338) - test_query_to: .: (0.000278) - test_seq1: .: (0.000331) - test_seq2: .: (0.000288) + test_align_len: .: (0.000358) + test_direction: .: (0.000191) + test_hit_from: .: (0.000176) + test_hit_to: .: (0.000174) + test_hseq: .: (0.000170) + test_midline: .: (0.000203) + test_percent_identity: .: (0.000183) + test_qseq: .: (0.000177) + test_query_from: .: (0.000177) + test_query_to: .: (0.000179) + test_seq1: .: (0.000209) + test_seq2: .: (0.000207) Bio::TestSim4ReportSegmentPair_intron: - test_align_len: .: (0.000426) - test_direction: .: (0.000307) - test_hit_from: .: (0.000269) - test_hit_to: .: (0.007965) - test_hseq: .: (0.000825) - test_midline: .: (0.000352) - test_percent_identity: .: (0.000318) - test_qseq: .: (0.000221) - test_query_from: .: (0.000170) - test_query_to: .: (0.000167) - test_seq1: .: (0.000205) - test_seq2: .: (0.000190) + test_align_len: .: (0.000320) + test_direction: .: (0.000176) + test_hit_from: .: (0.003053) + test_hit_to: .: (0.000466) + test_hseq: .: (0.000214) + test_midline: .: (0.000195) + test_percent_identity: .: (0.000185) + test_qseq: .: (0.000196) + test_query_from: .: (0.000232) + test_query_to: .: (0.000229) + test_seq1: .: (0.000258) + test_seq2: .: (0.000233) Bio::TestSim4ReportSeqDesc: - test_definition: .: (0.000183) - test_entry_id: .: (0.000161) - test_filename: .: (0.000118) - test_len: .: (0.000113) - test_self_new: .: (0.000144) - test_self_parse: .: (0.000150) + test_definition: .: (0.000209) + test_entry_id: .: (0.000893) + test_filename: .: (0.000061) + test_len: .: (0.000053) + test_self_new: .: (0.000079) + test_self_parse: .: (0.000075) Bio::TestTMHMMReport: - test_entry_id: .: (0.000618) - test_exp_aas_in_tmhs: .: (0.000390) - test_exp_first_60aa: .: (0.000351) - test_helix: .: (0.000374) - test_predicted_tmhs: .: (0.000319) - test_query_len: .: (0.000296) - test_tmhs: .: (0.000668) - test_to_s: .: (0.000387) - test_total_prob_of_N_in: .: (0.000292) + test_entry_id: .: (0.000387) + test_exp_aas_in_tmhs: .: (0.000207) + test_exp_first_60aa: .: (0.000209) + test_helix: .: (0.000232) + test_predicted_tmhs: .: (0.000226) + test_query_len: .: (0.000212) + test_tmhs: .: (0.000543) + test_to_s: .: (0.000293) + test_total_prob_of_N_in: .: (0.000220) Bio::TestTMHMMReport_reports: - test_reports: .: (0.000271) + test_reports: .: (0.000205) Bio::TestTMHMMTMH: - test_entry_id: .: (0.000391) - test_pos: .: (0.001648) - test_range: .: (0.000301) - test_status: .: (0.000325) - test_version: .: (0.000301) + test_entry_id: .: (0.000293) + test_pos: .: (0.001573) + test_range: .: (0.000233) + test_status: .: (0.000213) + test_version: .: (0.000194) Bio::TestTargetPReport: - test_cleavage_site_prediction: .: (0.000375) - test_cutoff: .: (0.000262) - test_entry_id: .: (0.000206) - test_length: .: (0.000237) - test_loc: .: (0.000210) - test_name: .: (0.000179) - test_networks: .: (0.000183) - test_prediction: .: (0.000204) - test_query_len: .: (0.000215) - test_query_sequences: .: (0.000200) - test_rc: .: (0.000193) - test_version: .: (0.000198) + test_cleavage_site_prediction: .: (0.000303) + test_cutoff: .: (0.000133) + test_entry_id: .: (0.000194) + test_length: .: (0.000143) + test_loc: .: (0.000126) + test_name: .: (0.000123) + test_networks: .: (0.000117) + test_prediction: .: (0.000129) + test_query_len: .: (0.000115) + test_query_sequences: .: (0.000125) + test_rc: .: (0.000118) + test_version: .: (0.000118) Bio::TestTargetPReportConst: - test_delimiter: .: (0.000251) - test_rs: .: (0.000105) + test_delimiter: .: (0.000157) + test_rs: .: (0.000042) Bio::TestTogoWSAccessWait: - test_reset_togows_access_wait: .: (0.000196) - test_togows_access_wait: .: (2.005542) + test_reset_togows_access_wait: .: (0.000113) + test_togows_access_wait: .: (2.000421) Bio::TestTogoWSREST: - test_debug: .: (0.000610) - test_debug_default: .: (0.000275) - test_internal_http: .: (0.000211) + test_debug: .: (0.000518) + test_debug_default: .: (0.000141) + test_internal_http: .: (0.000115) Bio::TestTogoWSRESTclassMethod: - test_convert: .: (0.000224) - test_entry: .: (0.000066) - test_entry_database_list: .: (0.000046) - test_new: .: (0.000138) - test_new_with_uri_object: .: (0.000119) - test_new_with_uri_string: .: (0.000098) - test_retrieve: .: (0.000040) - test_search: .: (0.000039) - test_search_database_list: .: (0.000039) + test_convert: .: (0.000146) + test_entry: .: (0.000055) + test_entry_database_list: .: (0.000049) + test_new: .: (0.000129) + test_new_with_uri_object: .: (0.000166) + test_new_with_uri_string: .: (0.000123) + test_retrieve: .: (0.000048) + test_search: .: (0.000041) + test_search_database_list: .: (0.000038) Bio::TestTogoWSRESTprivate: - test_make_path: .: (0.000225) - test_prepare_return_value: .: (0.000119) + test_make_path: .: (0.000232) + test_prepare_return_value: .: (0.000151) Bio::TestTopologicalSort: - test_dfs_topological_sort: .: (0.004700) + test_dfs_topological_sort: .: (0.000270) Bio::TestTree: - test_get_edge_distance: .: (0.000306) - test_get_edge_distance_string: .: (0.000157) - test_get_node_name: .: (0.000119) - test_initialize: .: (0.000334) - test_options: .: (0.000145) - test_root: .: (0.000113) - test_root=: .: (0.000124) + test_get_edge_distance: .: (0.000164) + test_get_edge_distance_string: .: (0.000082) + test_get_node_name: .: (0.000058) + test_initialize: .: (0.000065) + test_options: .: (0.000055) + test_root: .: (0.000041) + test_root=: .: (0.000049) Bio::TestTree2: - test_add_edge: .: (0.000417) - test_add_node: .: (0.006097) - test_adjacency_matrix: .: (0.000512) - test_adjacency_matrix_with_block: .: (0.000232) - test_adjacent_nodes: .: (0.000258) - test_adjacent_nodes_nonexistent: .: (0.000199) - test_ancestors: .: (0.000209) - test_children: .: (0.000127) - test_clear: .: (0.009677) - test_clear_node: .: (0.000380) - test_clear_node_nonexistent: .: (0.000576) - test_collect_edge!: .: (0.000314) - test_collect_node!: .: (0.000265) - test_concat: .: (0.000264) - test_descendents: .: (0.000197) - test_distance_matrix: .: (0.000426) - test_each_edge: .: (0.000225) - test_each_node: .: (0.000248) - test_each_out_edge: .: (0.000974) - test_each_out_edge_chimpanzee: .: (0.000188) - test_each_out_edge_human: .: (0.000179) - test_each_out_edge_mammals: .: (0.000204) - test_each_out_edge_nonexistent: .: (0.000172) - test_each_out_edge_primates: .: (0.005665) - test_each_out_edge_rat: .: (0.000334) - test_each_out_edge_rodents: .: (0.000279) - test_edges: .: (0.000213) - test_get_edge: .: (0.000604) - test_get_edge_indirect: .: (0.000202) - test_get_edge_merged: .: (0.000185) - test_get_edge_nonexistent: .: (0.000162) - test_get_node_bootstrap: .: (0.000178) - test_get_node_bootstrap_string=: .: (0.000166) - test_get_node_by_name: .: (0.000232) - test_get_node_by_name_noexistent: .: (0.000172) - test_include?: .: (0.000199) - test_include_nonexistent: .: (0.000192) - test_insert_node: .: (0.000242) - test_leaves: .: (0.000197) - test_leaves_noargs: .: (0.000167) - test_lowest_common_ancestor: .: (0.000184) - test_nodes: .: (0.000168) - test_number_of_edges: .: (0.000341) - test_number_of_nodes: .: (0.000166) - test_out_degree: .: (0.000191) - test_out_degree_nonexistent: .: (0.004751) - test_out_edges: .: (0.000511) - test_out_edges_mammals: .: (0.000260) - test_out_edges_nonexistent: .: (0.000180) - test_out_edges_primates: .: (0.000221) - test_out_edges_rodents: .: (0.000214) - test_parent: .: (0.000197) - test_path: .: (0.000168) - test_remove_edge: .: (0.000177) - test_remove_edge_if: .: (0.000343) - test_remove_edge_if_nothing_removed: .: (0.000220) - test_remove_edge_nonexistent: .: (0.000263) - test_remove_node: .: (0.000172) - test_remove_node_if: .: (0.000097) - test_remove_node_if_false: .: (0.000116) - test_remove_node_nonexistent: .: (0.000160) - test_remove_nonsense_nodes: .: (0.000134) - test_subtree: .: (0.000154) - test_subtree_with_all_paths: .: (0.000197) - test_total_distance: .: (0.000096) + test_add_edge: .: (0.000255) + test_add_node: .: (0.000130) + test_adjacency_matrix: .: (0.000397) + test_adjacency_matrix_with_block: .: (0.000198) + test_adjacent_nodes: .: (0.000139) + test_adjacent_nodes_nonexistent: .: (0.000081) + test_ancestors: .: (0.000108) + test_children: .: (0.004145) + test_clear: .: (0.000132) + test_clear_node: .: (0.000156) + test_clear_node_nonexistent: .: (0.000377) + test_collect_edge!: .: (0.000194) + test_collect_node!: .: (0.000186) + test_concat: .: (0.000183) + test_descendents: .: (0.000132) + test_distance_matrix: .: (0.000356) + test_each_edge: .: (0.000159) + test_each_node: .: (0.000139) + test_each_out_edge: .: (0.000786) + test_each_out_edge_chimpanzee: .: (0.000117) + test_each_out_edge_human: .: (0.000104) + test_each_out_edge_mammals: .: (0.000122) + test_each_out_edge_nonexistent: .: (0.000095) + test_each_out_edge_primates: .: (0.000144) + test_each_out_edge_rat: .: (0.000103) + test_each_out_edge_rodents: .: (0.000136) + test_edges: .: (0.000099) + test_get_edge: .: (0.000450) + test_get_edge_indirect: .: (0.000104) + test_get_edge_merged: .: (0.000101) + test_get_edge_nonexistent: .: (0.000081) + test_get_node_bootstrap: .: (0.000089) + test_get_node_bootstrap_string=: .: (0.000087) + test_get_node_by_name: .: (0.000127) + test_get_node_by_name_noexistent: .: (0.000078) + test_include?: .: (0.000113) + test_include_nonexistent: .: (0.000082) + test_insert_node: .: (0.000155) + test_leaves: .: (0.000130) + test_leaves_noargs: .: (0.000090) + test_lowest_common_ancestor: .: (0.000099) + test_nodes: .: (0.000226) + test_number_of_edges: .: (0.000082) + test_number_of_nodes: .: (0.000074) + test_out_degree: .: (0.000107) + test_out_degree_nonexistent: .: (0.000265) + test_out_edges: .: (0.000129) + test_out_edges_mammals: .: (0.000128) + test_out_edges_nonexistent: .: (0.000086) + test_out_edges_primates: .: (0.000136) + test_out_edges_rodents: .: (0.000130) + test_parent: .: (0.000114) + test_path: .: (0.000092) + test_remove_edge: .: (0.000294) + test_remove_edge_if: .: (0.000124) + test_remove_edge_if_nothing_removed: .: (0.000114) + test_remove_edge_nonexistent: .: (0.000138) + test_remove_node: .: (0.000121) + test_remove_node_if: .: (0.000091) + test_remove_node_if_false: .: (0.000098) + test_remove_node_nonexistent: .: (0.000108) + test_remove_nonsense_nodes: .: (0.000117) + test_subtree: .: (0.000143) + test_subtree_with_all_paths: .: (0.000204) + test_total_distance: .: (0.000099) Bio::TestTreeEdge: - test_distance: .: (0.000209) - test_distance=: .: (0.000069) - test_distance_string: .: (0.000040) - test_distance_string=: .: (0.000059) - test_initialize: .: (0.000064) - test_inspect: .: (0.000042) - test_to_s: .: (0.000040) + test_distance: .: (0.000162) + test_distance=: .: (0.000075) + test_distance_string: .: (0.000048) + test_distance_string=: .: (0.000067) + test_initialize: .: (0.000122) + test_inspect: .: (0.000049) + test_to_s: .: (0.000043) Bio::TestTreeNode: - test_bootstrap: .: (0.000108) - test_bootstrap=: .: (0.000064) - test_bootstrap_string: .: (0.000036) - test_bootstrap_string=: .: (0.000074) - test_initialize: .: (0.000058) - test_inspect: .: (0.000060) - test_name: .: (0.000043) - test_to_s: .: (0.000036) + test_bootstrap: .: (0.000127) + test_bootstrap=: .: (0.000069) + test_bootstrap_string: .: (0.000039) + test_bootstrap_string=: .: (0.000076) + test_initialize: .: (0.000060) + test_inspect: .: (0.000062) + test_name: .: (0.000047) + test_to_s: .: (0.000040) Bio::TestUniProt: - test_gene_name: .: (0.008164) + test_gene_name: .: (0.002581) Bio::TestUniProtKB: - test_ac: .: (0.004815) - test_accession: .: (0.007972) - test_cc: .: (0.011139) - test_cc_alternative_products: .: (0.046090) - test_cc_database: .: (0.005015) - test_cc_mass_spectrometry: .: (0.003873) - test_de: .: (0.003900) - test_dr: .: (0.005965) - test_dr_with_key: .: (0.004880) - test_dr_with_key_empty: .: (0.004529) - test_dt: .: (0.004475) - test_dt_annotation: .: (0.003423) - test_dt_created: .: (0.002589) - test_dt_sequence: .: (0.002196) - test_entry: .: (0.002057) - test_ft: .: (0.009343) - test_gene_name: .: (0.003009) - test_gene_names: .: (0.002319) - test_gn: .: (0.002733) - test_gn_old_parser: .: (0.002030) - test_gn_uniprot_parser: .: (0.002130) - test_id_line: .: (0.004693) - test_id_line_data_class: .: (0.003457) - test_id_line_entry_name: .: (0.002557) - test_id_line_molecule_type: .: (0.002064) - test_id_line_sequence_length: .: (0.002626) - test_kw: .: (0.001944) - test_molecule: .: (0.001877) - test_oc: .: (0.005482) - test_og_1: .: (0.003038) - test_og_2: .: (0.002383) - test_og_3: .: (0.002264) - test_og_4: .: (0.002623) - test_og_5: .: (0.002091) - test_og_6: .: (0.004208) - test_os: .: (0.003526) - test_os_access: .: (0.002495) - test_os_access2: .: (0.002355) - test_ox: .: (0.002763) - test_protein_name: .: (0.002046) - test_ref: .: (0.008422) - test_seq: .: (0.002896) - test_sequence_length: .: (0.002238) - test_sq: .: (0.002630) - test_sq_crc64: .: (0.002045) - test_sq_len: .: (0.004119) - test_sq_mw: .: (0.003529) - test_synonyms: .: (0.002936) + test_ac: .: (0.001987) + test_accession: .: (0.007192) + test_cc: .: (0.012213) + test_cc_alternative_products: .: (0.042266) + test_cc_database: .: (0.004521) + test_cc_mass_spectrometry: .: (0.003592) + test_de: .: (0.003629) + test_dr: .: (0.005359) + test_dr_with_key: .: (0.004406) + test_dr_with_key_empty: .: (0.003954) + test_dt: .: (0.003952) + test_dt_annotation: .: (0.002509) + test_dt_created: .: (0.002687) + test_dt_sequence: .: (0.001961) + test_entry: .: (0.001820) + test_ft: .: (0.008324) + test_gene_name: .: (0.002729) + test_gene_names: .: (0.002115) + test_gn: .: (0.002423) + test_gn_old_parser: .: (0.001821) + test_gn_uniprot_parser: .: (0.001893) + test_id_line: .: (0.004153) + test_id_line_data_class: .: (0.003146) + test_id_line_entry_name: .: (0.002192) + test_id_line_molecule_type: .: (0.001840) + test_id_line_sequence_length: .: (0.002278) + test_kw: .: (0.001861) + test_molecule: .: (0.001828) + test_oc: .: (0.004551) + test_og_1: .: (0.002639) + test_og_2: .: (0.002305) + test_og_3: .: (0.001949) + test_og_4: .: (0.002399) + test_og_5: .: (0.001804) + test_og_6: .: (0.003673) + test_os: .: (0.003003) + test_os_access: .: (0.002107) + test_os_access2: .: (0.001995) + test_ox: .: (0.002305) + test_protein_name: .: (0.001834) + test_ref: .: (0.007403) + test_seq: .: (0.002465) + test_sequence_length: .: (0.001863) + test_sq: .: (0.002341) + test_sq_crc64: .: (0.001803) + test_sq_len: .: (0.003616) + test_sq_mw: .: (0.003406) + test_synonyms: .: (0.002281) Bio::TestUniProtKB_CC: - test_allergen: .: (0.000463) - test_alternative_products_access_as_hash: .: (0.000315) - test_alternative_products_ai: .: (0.000333) - test_alternative_products_apu: .: (0.000705) - test_alternative_products_as: .: (0.000383) - test_alternative_products_rf: .: (0.000127) - test_biophysicochemical_properties: .: (0.000456) - test_biotechnology: .: (0.000263) - test_catalytic_activity: .: (0.000206) - test_caution: .: (0.000264) - test_cofactor: .: (0.000227) - test_developmental_stage: .: (0.000232) - test_disease: .: (0.000309) - test_domain: .: (0.000318) - test_enzyme_regulation: .: (0.000258) - test_function: .: (0.000246) - test_induction: .: (0.000199) - test_interaction: .: (0.000280) - test_mass_spectrometry: .: (0.000304) - test_miscellaneous: .: (0.000205) - test_pathway: .: (0.000232) - test_pharmaceutical: .: (0.000233) - test_polymorphism: .: (0.000285) - test_ptm: .: (0.000205) - test_rna_editing: .: (0.000292) - test_similarity: .: (0.000217) - test_subcellular_location: .: (0.000258) - test_subunit: .: (0.000191) - test_tissue_specificity: .: (0.000228) - test_toxic_dose: .: (0.000188) - test_web_resource: .: (0.000280) + test_allergen: .: (0.000284) + test_alternative_products_access_as_hash: .: (0.000363) + test_alternative_products_ai: .: (0.000221) + test_alternative_products_apu: .: (0.000326) + test_alternative_products_as: .: (0.000210) + test_alternative_products_rf: .: (0.000062) + test_biophysicochemical_properties: .: (0.000297) + test_biotechnology: .: (0.000170) + test_catalytic_activity: .: (0.000140) + test_caution: .: (0.000148) + test_cofactor: .: (0.000122) + test_developmental_stage: .: (0.000127) + test_disease: .: (0.000190) + test_domain: .: (0.000222) + test_enzyme_regulation: .: (0.000228) + test_function: .: (0.000149) + test_induction: .: (0.000118) + test_interaction: .: (0.000164) + test_mass_spectrometry: .: (0.000173) + test_miscellaneous: .: (0.000101) + test_pathway: .: (0.000128) + test_pharmaceutical: .: (0.000118) + test_polymorphism: .: (0.000173) + test_ptm: .: (0.000104) + test_rna_editing: .: (0.000174) + test_similarity: .: (0.000111) + test_subcellular_location: .: (0.000134) + test_subunit: .: (0.000085) + test_tissue_specificity: .: (0.000138) + test_toxic_dose: .: (0.000099) + test_web_resource: .: (0.000177) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: - test_cc_web_resource: .: (0.000449) + test_cc_web_resource: .: (0.000332) Bio::TestUniProtKB_DE_since_rel14_0: - test_private_parse_DE_line_rel14: .: (0.000452) - test_protein_name: .: (0.000942) - test_synonyms: .: (0.000368) + test_private_parse_DE_line_rel14: .: (0.000315) + test_protein_name: .: (0.000725) + test_synonyms: .: (0.000250) Bio::TestUniProtKB_ID_since_rel9_0: - test_aalen: .: (0.000282) - test_entry: .: (0.000142) - test_entry_id: .: (0.000143) - test_entry_name: .: (0.000140) - test_id_line: .: (0.000147) - test_molecule: .: (0.000148) - test_sequence_length: .: (0.000141) + test_aalen: .: (0.000169) + test_entry: .: (0.000065) + test_entry_id: .: (0.000056) + test_entry_name: .: (0.000055) + test_id_line: .: (0.000058) + test_molecule: .: (0.000055) + test_sequence_length: .: (0.000051) Bio::TestUniProtKB_P03589: - test_ac: .: (0.000560) - test_accession: .: (0.000413) - test_cc: .: (0.000563) - test_cc_alternative_products: .: (0.000506) - test_cc_database: .: (0.000500) - test_cc_mass_spectrometry: .: (0.000536) - test_de: .: (0.000416) - test_dr: .: (0.000571) - test_dr_with_key: .: (0.000580) - test_dr_with_key_empty: .: (0.000576) - test_dt: .: (0.000389) - test_dt_annotation: .: (0.000360) - test_dt_created: .: (0.000330) - test_dt_sequence: .: (0.000353) - test_entry: .: (0.000365) - test_ft: .: (0.000561) - test_gene_name: .: (0.000454) - test_gene_names: .: (0.000397) - test_gn: .: (0.000369) - test_gn_old_parser: .: (0.000413) - test_gn_uniprot_parser: .: (0.000404) - test_id_line: .: (0.000357) - test_id_line_data_class: .: (0.000350) - test_id_line_entry_name: .: (0.000370) - test_id_line_sequence_length: .: (0.003206) - test_kw: .: (0.000558) - test_oc: .: (0.000492) - test_oh: .: (0.000720) - test_os: .: (0.000436) - test_os_access: .: (0.000416) - test_os_access2: .: (0.001479) - test_ox: .: (0.000502) - test_protein_name: .: (0.000461) - test_protein_name_after_calling_de: .: (0.000448) - test_ref: .: (0.000455) - test_seq: .: (0.001143) - test_sequence_length: .: (0.000437) - test_sq: .: (0.000469) - test_sq_crc64: .: (0.000451) - test_sq_len: .: (0.000460) - test_sq_mw: .: (0.000432) - test_synonyms: .: (0.000531) + test_ac: .: (0.000401) + test_accession: .: (0.000278) + test_cc: .: (0.000413) + test_cc_alternative_products: .: (0.000383) + test_cc_database: .: (0.000389) + test_cc_mass_spectrometry: .: (0.000375) + test_de: .: (0.000276) + test_dr: .: (0.000407) + test_dr_with_key: .: (0.000437) + test_dr_with_key_empty: .: (0.000413) + test_dt: .: (0.000253) + test_dt_annotation: .: (0.000262) + test_dt_created: .: (0.000236) + test_dt_sequence: .: (0.000225) + test_entry: .: (0.000249) + test_ft: .: (0.000398) + test_gene_name: .: (0.000299) + test_gene_names: .: (0.000262) + test_gn: .: (0.000260) + test_gn_old_parser: .: (0.000296) + test_gn_uniprot_parser: .: (0.000305) + test_id_line: .: (0.000260) + test_id_line_data_class: .: (0.000235) + test_id_line_entry_name: .: (0.000220) + test_id_line_sequence_length: .: (0.002737) + test_kw: .: (0.000372) + test_oc: .: (0.000311) + test_oh: .: (0.000538) + test_os: .: (0.000339) + test_os_access: .: (0.000946) + test_os_access2: .: (0.000297) + test_ox: .: (0.000271) + test_protein_name: .: (0.000319) + test_protein_name_after_calling_de: .: (0.000831) + test_ref: .: (0.000471) + test_seq: .: (0.000511) + test_sequence_length: .: (0.000295) + test_sq: .: (0.000298) + test_sq_crc64: .: (0.000290) + test_sq_len: .: (0.000565) + test_sq_mw: .: (0.000303) + test_synonyms: .: (0.000331) Bio::TestUniProtKB_P28907: - test_ac: .: (0.001182) - test_accession: .: (0.001243) - test_cc: .: (0.001413) - test_cc_alternative_products: .: (0.001739) - test_cc_database: .: (0.002190) - test_cc_mass_spectrometry: .: (0.001362) - test_de: .: (0.000921) - test_dr: .: (0.005490) - test_dr_with_key: .: (0.003327) - test_dr_with_key_empty: .: (0.004024) - test_dt: .: (0.001056) - test_dt_annotation: .: (0.000953) - test_dt_created: .: (0.000967) - test_dt_sequence: .: (0.004056) - test_entry: .: (0.001199) - test_ft: .: (0.003206) - test_gene_name: .: (0.001344) - test_gene_names: .: (0.001221) - test_gn: .: (0.001204) - test_gn_old_parser: .: (0.001081) - test_gn_uniprot_parser: .: (0.001052) - test_id_line: .: (0.000950) - test_id_line_data_class: .: (0.001498) - test_id_line_entry_name: .: (0.000875) - test_id_line_sequence_length: .: (0.000858) - test_kw: .: (0.001061) - test_oc: .: (0.000980) - test_os: .: (0.000884) - test_os_access: .: (0.000970) - test_os_access2: .: (0.000996) - test_ox: .: (0.003947) - test_protein_name: .: (0.001894) - test_protein_name_after_calling_de: .: (0.001438) - test_ref: .: (0.002025) - test_seq: .: (0.001377) - test_sequence_length: .: (0.000964) - test_sq: .: (0.001094) - test_sq_crc64: .: (0.001104) - test_sq_len: .: (0.001603) - test_sq_mw: .: (0.000953) - test_synonyms: .: (0.001027) - test_synonyms_after_calling_de: .: (0.001024) + test_ac: .: (0.001238) + test_accession: .: (0.000791) + test_cc: .: (0.001374) + test_cc_alternative_products: .: (0.001216) + test_cc_database: .: (0.001896) + test_cc_mass_spectrometry: .: (0.001069) + test_de: .: (0.000760) + test_dr: .: (0.004849) + test_dr_with_key: .: (0.002837) + test_dr_with_key_empty: .: (0.003658) + test_dt: .: (0.000827) + test_dt_annotation: .: (0.000729) + test_dt_created: .: (0.000777) + test_dt_sequence: .: (0.003524) + test_entry: .: (0.001621) + test_ft: .: (0.002012) + test_gene_name: .: (0.001000) + test_gene_names: .: (0.000917) + test_gn: .: (0.000902) + test_gn_old_parser: .: (0.000787) + test_gn_uniprot_parser: .: (0.000844) + test_id_line: .: (0.000737) + test_id_line_data_class: .: (0.001188) + test_id_line_entry_name: .: (0.000715) + test_id_line_sequence_length: .: (0.000726) + test_kw: .: (0.000787) + test_oc: .: (0.000778) + test_os: .: (0.000720) + test_os_access: .: (0.000779) + test_os_access2: .: (0.000807) + test_ox: .: (0.003420) + test_protein_name: .: (0.001624) + test_protein_name_after_calling_de: .: (0.000881) + test_ref: .: (0.001780) + test_seq: .: (0.001107) + test_sequence_length: .: (0.000766) + test_sq: .: (0.000765) + test_sq_crc64: .: (0.000784) + test_sq_len: .: (0.001432) + test_sq_mw: .: (0.000742) + test_synonyms: .: (0.000840) + test_synonyms_after_calling_de: .: (0.000822) Bio::TestUniProtKB_P49144: - test_ac: .: (0.000700) - test_accession: .: (0.000517) - test_cc: .: (0.000893) - test_cc_alternative_products: .: (0.000875) - test_cc_database: .: (0.000845) - test_cc_mass_spectrometry: .: (0.003634) - test_de: .: (0.000668) - test_dr: .: (0.001075) - test_dr_with_key: .: (0.001817) - test_dr_with_key_empty: .: (0.001127) - test_dt: .: (0.000625) - test_dt_annotation: .: (0.001129) - test_dt_created: .: (0.000669) - test_dt_sequence: .: (0.000595) - test_entry: .: (0.000607) - test_ft: .: (0.001523) - test_gene_name: .: (0.000599) - test_gene_names: .: (0.000713) - test_gn: .: (0.001269) - test_gn_old_parser: .: (0.000588) - test_gn_uniprot_parser: .: (0.000541) - test_id_line: .: (0.000464) - test_id_line_data_class: .: (0.000444) - test_id_line_entry_name: .: (0.000427) - test_id_line_sequence_length: .: (0.000491) - test_kw: .: (0.000607) - test_oc: .: (0.000558) - test_os: .: (0.000501) - test_os_access: .: (0.000495) - test_os_access2: .: (0.000521) - test_ox: .: (0.000493) - test_protein_name: .: (0.000575) - test_protein_name_after_calling_de: .: (0.000611) - test_ref: .: (0.000672) - test_seq: .: (0.000645) - test_sequence_length: .: (0.003230) - test_sq: .: (0.000881) - test_sq_crc64: .: (0.000633) - test_sq_len: .: (0.000715) - test_sq_mw: .: (0.001430) - test_synonyms: .: (0.000706) - test_synonyms_after_calling_de: .: (0.000674) + test_ac: .: (0.000597) + test_accession: .: (0.000403) + test_cc: .: (0.000735) + test_cc_alternative_products: .: (0.000746) + test_cc_database: .: (0.000749) + test_cc_mass_spectrometry: .: (0.003085) + test_de: .: (0.000472) + test_dr: .: (0.000836) + test_dr_with_key: .: (0.001412) + test_dr_with_key_empty: .: (0.000814) + test_dt: .: (0.000422) + test_dt_annotation: .: (0.000892) + test_dt_created: .: (0.000393) + test_dt_sequence: .: (0.000405) + test_entry: .: (0.000464) + test_ft: .: (0.001253) + test_gene_name: .: (0.000457) + test_gene_names: .: (0.000604) + test_gn: .: (0.001042) + test_gn_old_parser: .: (0.000433) + test_gn_uniprot_parser: .: (0.000379) + test_id_line: .: (0.000370) + test_id_line_data_class: .: (0.000351) + test_id_line_entry_name: .: (0.000339) + test_id_line_sequence_length: .: (0.000372) + test_kw: .: (0.000444) + test_oc: .: (0.000408) + test_os: .: (0.000371) + test_os_access: .: (0.000420) + test_os_access2: .: (0.000397) + test_ox: .: (0.000393) + test_protein_name: .: (0.000432) + test_protein_name_after_calling_de: .: (0.000426) + test_ref: .: (0.000554) + test_seq: .: (0.000547) + test_sequence_length: .: (0.002787) + test_sq: .: (0.000665) + test_sq_crc64: .: (0.000478) + test_sq_len: .: (0.000483) + test_sq_mw: .: (0.001213) + test_synonyms: .: (0.000513) + test_synonyms_after_calling_de: .: (0.000472) Bio::TestUniProtKB_Ref: - test_RA: .: (0.000517) - test_RC: .: (0.000431) - test_RG: .: (0.000289) - test_RL: .: (0.000257) - test_RN: .: (0.000248) - test_RP: .: (0.000268) - test_RT: .: (0.000252) - test_RX: .: (0.000259) - test_ref: .: (0.000263) + test_RA: .: (0.000342) + test_RC: .: (0.000620) + test_RG: .: (0.000168) + test_RL: .: (0.000147) + test_RN: .: (0.000163) + test_RP: .: (0.000163) + test_RT: .: (0.000176) + test_RX: .: (0.000162) + test_ref: .: (0.000162) Bio::TestUniProtKB_SwissProtRel41_0: - test_multiple_RP_lines: .: (0.000583) + test_multiple_RP_lines: .: (0.000433) Bio::TestUniProtKB_SwissProtRel41_1: - test_alternative_products: .: (0.000523) - test_alternative_products_with_ft: .: (0.000653) + test_alternative_products: .: (0.000395) + test_alternative_products_with_ft: .: (0.000481) Bio::TestUniProtKB_SwissProtRel41_10: - test_RC_lines: .: (0.000374) + test_RC_lines: .: (0.000236) Bio::TestUniProtKB_SwissProtRel41_20: - test_CC_allergen: .: (0.000314) - test_RL_lines: .: (0.000177) + test_CC_allergen: .: (0.000211) + test_RL_lines: .: (0.000095) Bio::TestUniProtKB_SwissProtRel42_6: - test_CC_rna_editing: .: (0.000560) + test_CC_rna_editing: .: (0.000344) Bio::TestUniProtKB_UniProtRel1_12: - test_DOI_in_RX_line: .: (0.000283) - test_RG_line: .: (0.000187) + test_DOI_in_RX_line: .: (0.000300) + test_RG_line: .: (0.000085) Bio::TestUniProtKB_UniProtRel2_0: - test_GN_line: .: (0.000472) + test_GN_line: .: (0.000358) Bio::TestUniProtKB_UniProtRel2_1: - test_CC_mass_spectrometry: .: (0.000320) + test_CC_mass_spectrometry: .: (0.000199) Bio::TestUniProtKB_UniProtRel2_3: - test_DR_PDB: .: (0.000237) - test_RL_line: .: (0.000171) + test_DR_PDB: .: (0.000137) + test_RL_line: .: (0.000080) Bio::TestUniProtKB_UniProtRel3_4: - test_CC_biophysiochemical_properties: .: (0.000680) - test_RP_line: .: (0.000265) + test_CC_biophysiochemical_properties: .: (0.000423) + test_RP_line: .: (0.000201) Bio::TestUniProtKB_UniProtRel3_5: - test_entry_name_format: .: (0.000177) + test_entry_name_format: .: (0.000092) Bio::TestUniProtKB_UniProtRel4_0: - test_CC_interaction: .: (0.000317) - test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000273) - test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000222) - test_CC_interaction_isoform: .: (0.000197) - test_CC_interaction_no_gene_name: .: (0.000234) - test_CC_interaction_self_association: .: (0.000280) + test_CC_interaction: .: (0.000182) + test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000127) + test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000105) + test_CC_interaction_isoform: .: (0.000099) + test_CC_interaction_no_gene_name: .: (0.000098) + test_CC_interaction_self_association: .: (0.000124) Bio::TestUniProtKB_UniProtRel5_0: - test_DR_line: .: (0.000343) + test_DR_line: .: (0.000191) Bio::TestUniProtKB_UniProtRel5_4: - test_multiple_cofactors: .: (0.000350) + test_multiple_cofactors: .: (0.000203) Bio::TestUniProtKB_UniProtRel6_0: - test_OG_line: .: (0.000368) + test_OG_line: .: (0.000245) Bio::TestUniProtKB_UniProtRel6_1: - test_FT_metal: .: (0.000300) + test_FT_metal: .: (0.000213) Bio::TestUniProtKB_UniProtRel6_5: - test_HI_line: .: (0.000298) + test_HI_line: .: (0.000211) Bio::TestUniProtKB_UniProtRel7_0: - test_CC_copyright_statement: .: (0.000292) - test_DT_line: .: (0.000224) + test_CC_copyright_statement: .: (0.000159) + test_DT_line: .: (0.000102) Bio::TestUniProtKB_UniProtRel7_6: - test_10000aa: .: (0.003142) + test_10000aa: .: (0.002794) Bio::TestUniProtKB_UniProtRel8_0: - test_CC_alternative_products: .: (0.000751) - test_CC_web_resource: .: (0.000126) - test_FT_VER_SEQ: .: (0.000239) - test_OH_line_exception: .: (0.000283) - test_OH_lines: .: (0.000308) + test_CC_alternative_products: .: (0.000476) + test_CC_web_resource: .: (0.000072) + test_FT_VER_SEQ: .: (0.000111) + test_OH_line_exception: .: (0.000178) + test_OH_lines: .: (0.000211) Bio::TestUtils: - test_centreOfGravity: .: (0.000481) - test_dihedral_angle: .: (0.000421) - test_distance: .: (0.000327) - test_geometricCentre: .: (0.000306) - test_rad2deg: .: (0.000192) + test_centreOfGravity: .: (0.000366) + test_dihedral_angle: .: (0.000321) + test_distance: .: (0.000236) + test_geometricCentre: .: (0.000161) + test_rad2deg: .: (0.000114) Bio::TestWeightedGraph: - test_bellman_ford_on_negative_weighted_graph: .: (0.000330) - test_dijkstra_on_weighted_graph: .: (0.000174) + test_bellman_ford_on_negative_weighted_graph: .: (0.000204) + test_dijkstra_on_weighted_graph: .: (0.000082) -Finished in 12.490327617 seconds. +Finished in 9.9363554 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- -315.52 tests/s, 1729.42 assertions/s +396.62 tests/s, 2173.94 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ @@ -5480,12 +5516,14 @@ 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/526850/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/526850/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/515837 and its subdirectories -I: Current time: Mon Sep 29 00:43:56 -12 2025 -I: pbuilder-time-stamp: 1759149836 +I: removing directory /srv/workspace/pbuilder/526850 and its subdirectories +I: Current time: Mon Nov 2 09:07:58 +14 2026 +I: pbuilder-time-stamp: 1793560078