Diff of the two buildlogs: -- --- b1/build.log 2023-06-01 06:52:06.694817735 +0000 +++ b2/build.log 2023-06-01 06:56:26.447435815 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 31 18:48:58 -12 2023 -I: pbuilder-time-stamp: 1685602138 +I: Current time: Thu Jun 1 20:52:33 +14 2023 +I: pbuilder-time-stamp: 1685602353 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./ruby-bio_2.0.4.orig.tar.gz] I: copying [./ruby-bio_2.0.4-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Oct 8 20:31:23 2022 -12 +gpgv: Signature made Sun Oct 9 22:31:23 2022 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,167 @@ 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/13379/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28272/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 Jun 1 20:52 /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/28272/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28272/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='30d95107082b4826bcb397135af0bd00' - 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='13379' - PS1='# ' - PS2='> ' + INVOCATION_ID=94c9113b5d134c9facd7b691652d2542 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=28272 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.9JVao602/pbuilderrc_52qe --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9JVao602/b1 --logfile b1/build.log ruby-bio_2.0.4-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9JVao602/pbuilderrc_vroP --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9JVao602/b2 --logfile b2/build.log --extrapackages usrmerge ruby-bio_2.0.4-1.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32c 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/13379/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Jun 1 20:52 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/28272/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -338,7 +370,7 @@ Get: 133 http://deb.debian.org/debian bookworm/main armhf ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 134 http://deb.debian.org/debian bookworm/main armhf rdtool all 0.6.38-4.1 [44.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main armhf ruby-libxml armhf 3.2.4-2 [71.9 kB] -Fetched 46.1 MB in 1s (36.4 MB/s) +Fetched 46.1 MB in 1s (35.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19324 files and directories currently installed.) @@ -904,8 +936,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/ruby-bio-2.0.4/ && 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_2.0.4-1_source.changes +I: user script /srv/workspace/pbuilder/28272/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/28272/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/ruby-bio-2.0.4/ && 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_2.0.4-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.4-1 dpkg-buildpackage: info: source distribution unstable @@ -1163,4306 +1206,4306 @@ Loaded suite /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader Started Bio::External2go: - test_db_ids: .: (0.001058) - test_dbs: .: (0.000844) - test_go_ids: .: (0.000525) - test_go_terms: .: (0.000498) - test_parser: .: (0.001516) - test_set_date: .: (0.000688) - test_set_desc: .: (0.000535) - test_to_str: .: (0.000683) + test_db_ids: .: (0.001254) + test_dbs: .: (0.000625) + test_go_ids: .: (0.000583) + test_go_terms: .: (0.000991) + test_parser: .: (0.001606) + test_set_date: .: (0.000668) + test_set_desc: .: (0.000598) + test_to_str: .: (0.000923) Bio::FuncTestCommandBackports: - test_mktmpdir_with_block: .: (0.001856) - test_mktmpdir_without_block: .: (0.001622) - test_remove_entry_secure: .: (0.000911) + test_mktmpdir_with_block: .: (0.002158) + test_mktmpdir_without_block: .: (0.001876) + test_remove_entry_secure: .: (0.001100) Bio::FuncTestCommandCallMisc1: - test_call_command: .: (0.004091) - test_call_command_fork: .: (0.000876) - test_call_command_open3: .: (0.005620) - test_call_command_popen: .: (0.003381) + test_call_command: .: (0.006208) + test_call_command_fork: .: (0.000450) + test_call_command_open3: .: (0.005479) + test_call_command_popen: .: (0.004689) Bio::FuncTestCommandCallSimple: - test_call_command: .: (0.003574) - test_call_command_fork: .: (0.000287) - test_call_command_open3: .: (0.003505) - test_call_command_popen: .: (0.003286) + test_call_command: .: (0.005233) + test_call_command_fork: .: (0.000381) + test_call_command_open3: .: (0.004752) + test_call_command_popen: .: (0.005173) Bio::FuncTestCommandCallWithSpace: - test_call_command: .: (0.003557) - test_call_command_fork: .: (0.000296) - test_call_command_open3: .: (0.003544) - test_call_command_popen: .: (0.003237) + test_call_command: .: (0.005494) + test_call_command_fork: .: (0.000421) + test_call_command_open3: .: (0.004969) + test_call_command_popen: .: (0.004938) Bio::FuncTestCommandChdir: - test_call_command_chdir: .: (0.004068) - test_call_command_fork_chdir: .: (0.000632) - test_call_command_popen_chdir: .: (0.003190) - test_query_command_chdir: .: (0.003023) - test_query_command_fork_chdir: .: (0.000671) - test_query_command_popen_chdir: .: (0.005617) + test_call_command_chdir: .: (0.004214) + test_call_command_fork_chdir: .: (0.000896) + test_call_command_popen_chdir: .: (0.003276) + test_query_command_chdir: .: (0.003276) + test_query_command_fork_chdir: .: (0.000711) + test_query_command_popen_chdir: .: (0.003842) Bio::FuncTestCommandQuery: - test_query_command: .: (0.006849) - test_query_command_fork: .: (0.002190) - test_query_command_open3: .: (0.007087) - test_query_command_popen: .: (0.009632) + test_query_command: .: (0.007495) + test_query_command_fork: .: (0.003817) + test_query_command_open3: .: (0.007372) + test_query_command_popen: .: (0.006694) Bio::FuncTestCommandTmpdir: - test_close!: .: (0.002110) - test_initialize: .: (0.001108) - test_path: .: (0.000650) - test_path_after_close: .: (0.001278) + test_close!: .: (0.002316) + test_initialize: .: (0.000895) + test_path: .: (0.000628) + test_path_after_close: .: (0.001180) Bio::FuncTestSequenceOutputEMBL: - test_output_embl: .: (0.053966) - test_output_fasta: .: (0.021708) + test_output_embl: .: (0.057490) + test_output_fasta: .: (0.023261) Bio::NCBIDB::TestCommon: - test_acc_version: .: (0.001030) - test_accession: .: (0.000425) - test_accessions: .: (0.000534) - test_comment: .: (0.000351) - test_common_name: .: (0.001066) - test_definition: .: (0.000513) - test_features: .: (0.000987) - test_gi: .: (0.000525) - test_keywords: .: (0.000408) - test_locus: .: (0.000311) - test_nid: .: (0.000394) - test_organism: .: (0.000428) - test_origin: .: (0.000348) - test_references: .: (0.001800) - test_segment: .: (0.000591) - test_source: .: (0.000687) - test_taxonomy: .: (0.000629) - test_version: .: (0.000463) - test_versions: .: (0.000409) + test_acc_version: .: (0.000868) + test_accession: .: (0.000534) + test_accessions: .: (0.000532) + test_comment: .: (0.000475) + test_common_name: .: (0.000645) + test_definition: .: (0.001084) + test_features: .: (0.000982) + test_gi: .: (0.000504) + test_keywords: .: (0.000592) + test_locus: .: (0.000382) + test_nid: .: (0.000548) + test_organism: .: (0.000629) + test_origin: .: (0.000434) + test_references: .: (0.001982) + test_segment: .: (0.000517) + test_source: .: (0.000844) + test_taxonomy: .: (0.000535) + test_version: .: (0.000494) + test_versions: .: (0.000496) Bio::TestAA: - test_13: .: (0.000507) - test_1n: .: (0.000234) - test_name2one: .: (0.000313) - test_name2three: .: (0.000278) - test_one2name: .: (0.000736) - test_one2three: .: (0.000234) - test_three2name: .: (0.000196) - test_three2one: .: (0.000291) - test_to_1_1: .: (0.000367) - test_to_1_3: .: (0.000287) - test_to_1_name: .: (0.000304) - test_to_3_1: .: (0.000214) - test_to_3_3: .: (0.000193) - test_to_3_name: .: (0.000265) - test_to_re: .: (0.000500) + test_13: .: (0.000621) + test_1n: .: (0.000303) + test_name2one: .: (0.000444) + test_name2three: .: (0.000370) + test_one2name: .: (0.000331) + test_one2three: .: (0.000642) + test_three2name: .: (0.000313) + test_three2one: .: (0.000378) + test_to_1_1: .: (0.000280) + test_to_1_3: .: (0.000397) + test_to_1_name: .: (0.000357) + test_to_3_1: .: (0.000293) + test_to_3_3: .: (0.000278) + test_to_3_name: .: (0.000416) + test_to_re: .: (0.000383) Bio::TestAAConstants: - test_bio_aminoacid: .: (0.000479) + test_bio_aminoacid: .: (0.000555) Bio::TestAAindex: - test_api: .: (0.000386) - test_auto_aax1: .: (0.000679) - test_auto_aax2: .: (0.000532) + test_api: .: (0.000449) + test_auto_aax1: .: (0.000701) + test_auto_aax2: .: (0.000693) Bio::TestAAindex1: - test_author: .: (0.001137) - test_comment: .: (0.000672) - test_correlation_coefficient: .: (0.001088) - test_dblinks: .: (0.000532) - test_definition: .: (0.000520) - test_entry_id: .: (0.000524) - test_index: .: (0.000835) - test_journal: .: (0.000632) - test_title: .: (0.001248) + test_author: .: (0.001013) + test_comment: .: (0.000642) + test_correlation_coefficient: .: (0.001121) + test_dblinks: .: (0.000608) + test_definition: .: (0.000617) + test_entry_id: .: (0.000598) + test_index: .: (0.000823) + test_journal: .: (0.000720) + test_title: .: (0.001229) Bio::TestAAindex2: - test_access_A_R: .: (0.002160) - test_access_R_A: .: (0.001898) - test_author: .: (0.000651) - test_cols: .: (0.000536) - test_comment: .: (0.000628) - test_dblinks: .: (0.000736) - test_definition: .: (0.000554) - test_entry_id: .: (0.000587) - test_journal: .: (0.000619) - test_matrix: .: (0.002395) - test_matrix_1_2: .: (0.001847) - test_matrix_2_2: .: (0.001963) - test_matrix_A_R: .: (0.002254) - test_matrix_R_A: .: (0.002014) - test_matrix_determinant: .: (0.025415) - test_matrix_rank: .: (0.015826) - test_matrix_transpose: .: (0.003873) - test_rows: .: (0.000515) - test_title: .: (0.000867) + test_access_A_R: .: (0.002190) + test_access_R_A: .: (0.001708) + test_author: .: (0.000752) + test_cols: .: (0.000679) + test_comment: .: (0.000634) + test_dblinks: .: (0.000607) + test_definition: .: (0.000646) + test_entry_id: .: (0.000616) + test_journal: .: (0.000749) + test_matrix: .: (0.002358) + test_matrix_1_2: .: (0.001913) + test_matrix_2_2: .: (0.001753) + test_matrix_A_R: .: (0.002345) + test_matrix_R_A: .: (0.001870) + test_matrix_determinant: .: (0.025480) + test_matrix_rank: .: (0.015665) + test_matrix_transpose: .: (0.003611) + test_rows: .: (0.000669) + test_title: .: (0.000646) Bio::TestAAindexConstant: - test_delimiter: .: (0.000522) - test_tagsize: .: (0.000227) + test_delimiter: .: (0.000647) + test_tagsize: .: (0.000307) Bio::TestAbif: - test_complement: .: (0.022358) - test_seq: .: (0.023294) - test_to_biosequence: .: (0.022613) + test_complement: .: (0.021368) + test_seq: .: (0.021282) + test_to_biosequence: .: (0.021701) Bio::TestActsLikeMap: - test_mixin: .: (0.000695) + test_mixin: .: (0.000822) Bio::TestActsLikeMapAndMarker: - test_mixin: .: (0.000832) + test_mixin: .: (0.000922) Bio::TestActsLikeMarker: - test_mixin: .: (0.000599) + test_mixin: .: (0.000651) Bio::TestAlignment: - test_add_seq_no_key: .: (0.000992) - test_add_seq_using_seq_with_aaseq_method: .: (0.000374) - test_add_seq_using_seq_with_definition_method: .: (0.000280) - test_add_seq_using_seq_with_entry_id_method: .: (0.000442) - test_add_seq_using_seq_with_naseq_method: .: (0.000343) - test_add_seq_using_seq_with_seq_method: .: (0.000360) - test_consensus_iupac_gap_modes: .: (0.001061) - test_consensus_iupac_missing_char: .: (0.000735) - test_consensus_iupac_missing_char_option: .: (0.000568) - test_consensus_iupac_no_gaps: .: (0.020533) - test_consensus_iupac_of_ambiguous_bases: .: (0.001171) - test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.092507) - test_consensus_opt_gap_mode: .: (0.002221) - test_consensus_opt_missing_char: .: (0.000784) - test_consensus_string_no_gaps: .: (0.000641) - test_consensus_threshold_four_sequences: .: (0.001254) - test_consensus_threshold_two_sequences: .: (0.001558) - test_convert_match: .: (0.000608) - test_convert_unmatch: .: (0.000637) - test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000446) - test_convert_unmatch_different_match_char: .: (0.000384) - test_convert_unmatch_multiple_sequences: .: (0.000551) - test_default_gap_char: .: (0.000371) - test_default_gap_regexp_matches_default_gap_char: .: (0.000253) - test_default_missing_char: .: (0.000220) - test_each_site_equal_length: .: (0.000808) - test_each_site_unequal_length: .: (0.000458) - test_equals: .: (0.000500) - test_match_line_protein: .: (0.001371) - test_normalizebang_extends_sequences_with_gaps: .: (0.000396) - test_seq_length_is_max_seq_length: .: (0.000600) - test_seq_length_when_one_sequence: .: (0.000271) - test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000247) - test_seqclass_when_seqclass_set: .: (0.000256) - test_seqclass_when_sequence_used: .: (0.000243) - test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000250) - test_set_and_get_gap_char: .: (0.000261) - test_store_cannot_override_key: .: (0.000261) - test_store_with_default_keys_and_user_defined_keys: .: (0.000279) - test_store_with_nil_key_uses_next_number_for_key: .: (0.000425) + test_add_seq_no_key: .: (0.000779) + test_add_seq_using_seq_with_aaseq_method: .: (0.000882) + test_add_seq_using_seq_with_definition_method: .: (0.000372) + test_add_seq_using_seq_with_entry_id_method: .: (0.000578) + test_add_seq_using_seq_with_naseq_method: .: (0.000445) + test_add_seq_using_seq_with_seq_method: .: (0.000416) + test_consensus_iupac_gap_modes: .: (0.001199) + test_consensus_iupac_missing_char: .: (0.000575) + test_consensus_iupac_missing_char_option: .: (0.000712) + test_consensus_iupac_no_gaps: .: (0.000782) + test_consensus_iupac_of_ambiguous_bases: .: (0.001370) + test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.089169) + test_consensus_opt_gap_mode: .: (0.002174) + test_consensus_opt_missing_char: .: (0.000792) + test_consensus_string_no_gaps: .: (0.000773) + test_consensus_threshold_four_sequences: .: (0.001160) + test_consensus_threshold_two_sequences: .: (0.001802) + test_convert_match: .: (0.000749) + test_convert_unmatch: .: (0.000608) + test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000539) + test_convert_unmatch_different_match_char: .: (0.000478) + test_convert_unmatch_multiple_sequences: .: (0.000674) + test_default_gap_char: .: (0.000320) + test_default_gap_regexp_matches_default_gap_char: .: (0.000350) + test_default_missing_char: .: (0.000312) + test_each_site_equal_length: .: (0.000790) + test_each_site_unequal_length: .: (0.000528) + test_equals: .: (0.000621) + test_match_line_protein: .: (0.001338) + test_normalizebang_extends_sequences_with_gaps: .: (0.000528) + test_seq_length_is_max_seq_length: .: (0.000366) + test_seq_length_when_one_sequence: .: (0.000333) + test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000332) + test_seqclass_when_seqclass_set: .: (0.000374) + test_seqclass_when_sequence_used: .: (0.000328) + test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000885) + test_set_and_get_gap_char: .: (0.000334) + test_store_cannot_override_key: .: (0.000350) + test_store_with_default_keys_and_user_defined_keys: .: (0.000391) + test_store_with_nil_key_uses_next_number_for_key: .: (0.000362) Bio::TestAlignmentEnumerableExtension: - test_alignment_collect: .: (0.000604) - test_alignment_concat: .: (0.000369) - test_alignment_length: .: (0.000237) - test_alignment_lstrip!: .: (0.000416) - test_alignment_lstrip_nil: .: (0.000306) - test_alignment_normalize!: .: (0.000248) - test_alignment_rstrip!: .: (0.000463) - test_alignment_rstrip_nil: .: (0.000298) - test_alignment_site: .: (0.000380) - test_alignment_slice: .: (0.000257) - test_alignment_strip!: .: (0.000803) - test_alignment_strip_nil: .: (0.000464) - test_alignment_subseq: .: (0.000552) - test_alignment_window: .: (0.000273) - test_collect_each_site: .: (0.000345) - test_consensus_each_site_default: .: (0.000480) - test_consensus_each_site_gap_mode_1: .: (0.000408) - test_consensus_each_site_gap_mode_minus1: .: (0.000454) - test_consensus_iupac: .: (0.001122) - test_consensus_string_default: .: (0.000438) - test_consensus_string_half: .: (0.000659) - test_convert_match: .: (0.000324) - test_convert_unmatch: .: (0.000432) - test_each_seq: .: (0.000304) - test_each_site: .: (0.000472) - test_each_site_step: .: (0.000346) - test_each_window: .: (0.000593) - test_match_line: .: (0.002541) - test_match_line_amino: .: (0.004040) - test_match_line_nuc: .: (0.000829) - test_private_alignment_site: .: (0.000287) - test_remove_all_gaps!: .: (0.000702) - test_seqclass: .: (0.000253) - test_seqclass=: .: (0.000342) - test_seqclass_default: .: (0.000211) + test_alignment_collect: .: (0.000697) + test_alignment_concat: .: (0.000451) + test_alignment_length: .: (0.000319) + test_alignment_lstrip!: .: (0.000515) + test_alignment_lstrip_nil: .: (0.000394) + test_alignment_normalize!: .: (0.000336) + test_alignment_rstrip!: .: (0.000560) + test_alignment_rstrip_nil: .: (0.000368) + test_alignment_site: .: (0.000499) + test_alignment_slice: .: (0.000283) + test_alignment_strip!: .: (0.000584) + test_alignment_strip_nil: .: (0.000330) + test_alignment_subseq: .: (0.000348) + test_alignment_window: .: (0.000269) + test_collect_each_site: .: (0.000352) + test_consensus_each_site_default: .: (0.000402) + test_consensus_each_site_gap_mode_1: .: (0.000578) + test_consensus_each_site_gap_mode_minus1: .: (0.000549) + test_consensus_iupac: .: (0.001454) + test_consensus_string_default: .: (0.000494) + test_consensus_string_half: .: (0.000445) + test_convert_match: .: (0.000417) + test_convert_unmatch: .: (0.000285) + test_each_seq: .: (0.000299) + test_each_site: .: (0.000484) + test_each_site_step: .: (0.000357) + test_each_window: .: (0.000463) + test_match_line: .: (0.002746) + test_match_line_amino: .: (0.003959) + test_match_line_nuc: .: (0.001124) + test_private_alignment_site: .: (0.000392) + test_remove_all_gaps!: .: (0.000495) + test_seqclass: .: (0.000339) + test_seqclass=: .: (0.000410) + test_seqclass_default: .: (0.000278) Bio::TestAlignmentMultiFastaFormat: - test_alignment: .: (0.009518) - test_determine_seq_method: .: (0.005781) - test_entries: .: (0.000894) + test_alignment: .: (0.009081) + test_determine_seq_method: .: (0.005446) + test_entries: .: (0.000977) Bio::TestAlignmentOutput: - test_avoid_same_name: .: (0.000721) - test_avoid_same_name_numbering: .: (0.000387) - test_clustal_have_same_name_true: .: (0.000301) - test_have_same_name_false: .: (0.000434) + test_avoid_same_name: .: (0.000795) + test_avoid_same_name_numbering: .: (0.000545) + test_clustal_have_same_name_true: .: (0.000897) + test_have_same_name_false: .: (0.000372) Bio::TestAlignmentPropertyMethods: - test_gap_char=: .: (0.001302) - test_gap_char_default: .: (0.000302) - test_gap_char_never_nil: .: (0.000391) - test_gap_regexp: .: (0.000275) - test_gap_regexp=: .: (0.000272) - test_gap_regexp_never_nil: .: (0.000302) - test_get_all_property_default: .: (0.000269) - test_get_all_property_nodefault: .: (0.000434) - test_is_gap_default_false: .: (0.000290) - test_is_gap_default_true: .: (0.000320) - test_is_gap_nodefault_false: .: (0.000282) - test_is_gap_nodefault_true: .: (0.000275) - test_missing_char=: .: (0.000288) - test_missing_char_default: .: (0.000262) - test_missing_char_never_nil: .: (0.000277) - test_seqclass=: .: (0.000408) - test_seqclass_default: .: (0.000269) - test_seqclass_never_nil: .: (0.000477) - test_set_all_property: .: (0.000300) + test_gap_char=: .: (0.000609) + test_gap_char_default: .: (0.000333) + test_gap_char_never_nil: .: (0.000323) + test_gap_regexp: .: (0.000388) + test_gap_regexp=: .: (0.000360) + test_gap_regexp_never_nil: .: (0.000332) + test_get_all_property_default: .: (0.000334) + test_get_all_property_nodefault: .: (0.000373) + test_is_gap_default_false: .: (0.000329) + test_is_gap_default_true: .: (0.000341) + test_is_gap_nodefault_false: .: (0.000352) + test_is_gap_nodefault_true: .: (0.000712) + test_missing_char=: .: (0.000344) + test_missing_char_default: .: (0.000323) + test_missing_char_never_nil: .: (0.000305) + test_seqclass=: .: (0.000345) + test_seqclass_default: .: (0.000313) + test_seqclass_never_nil: .: (0.000303) + test_set_all_property: .: (0.000338) Bio::TestAlignmentSite: - test_consensus_iupac: .: (0.001635) - test_consensus_string_50percent: .: (0.000286) - test_consensus_string_50percent_nil: .: (0.000413) - test_consensus_string_default: .: (0.000449) - test_consensus_string_default_nil: .: (0.000287) - test_has_gap_false: .: (0.000368) - test_has_gap_true: .: (0.000243) - test_match_line_amino_100percent: .: (0.000361) - test_match_line_amino_missing: .: (0.000464) + test_consensus_iupac: .: (0.001737) + test_consensus_string_50percent: .: (0.000395) + test_consensus_string_50percent_nil: .: (0.000344) + test_consensus_string_default: .: (0.000276) + test_consensus_string_default_nil: .: (0.000392) + test_has_gap_false: .: (0.000313) + test_has_gap_true: .: (0.000273) + test_match_line_amino_100percent: .: (0.000396) + test_match_line_amino_missing: .: (0.000582) test_match_line_amino_strong: .: (0.000419) - test_match_line_amino_weak: .: (0.000616) - test_match_line_nuc_100percent: .: (0.000333) - test_match_line_nuc_missing: .: (0.000313) - test_remove_gaps!: .: (0.000390) - test_remove_gaps_bang_not_removed: .: (0.000226) + test_match_line_amino_weak: .: (0.000483) + test_match_line_nuc_100percent: .: (0.000414) + test_match_line_nuc_missing: .: (0.000358) + test_remove_gaps!: .: (0.000267) + test_remove_gaps_bang_not_removed: .: (0.000220) Bio::TestAtomFinder: - test_atoms: .: (0.061154) - test_each_atom: .: (0.001050) - test_find_atom: .: (0.000552) + test_atoms: .: (0.060454) + test_each_atom: .: (0.000741) + test_find_atom: .: (0.000647) Bio::TestBioFastaDefline: - test_acc_version: .: (0.001323) - test_accession: .: (0.001902) - test_accessions: .: (0.001037) - test_description: .: (0.000904) - test_descriptions: .: (0.001040) - test_entry_id: .: (0.000802) - test_get: .: (0.001373) - test_get_all_by_type: .: (0.000863) - test_get_by_type: .: (0.000961) - test_gi: .: (0.000733) - test_id_strings: .: (0.002420) - test_locus: .: (0.000743) - test_method_missing: .: (0.001110) - test_to_s: .: (0.000909) - test_words: .: (0.002611) + test_acc_version: .: (0.001345) + test_accession: .: (0.001272) + test_accessions: .: (0.001263) + test_description: .: (0.001072) + test_descriptions: .: (0.001034) + test_entry_id: .: (0.001127) + test_get: .: (0.001528) + test_get_all_by_type: .: (0.000846) + test_get_by_type: .: (0.000975) + test_gi: .: (0.000821) + test_id_strings: .: (0.002158) + test_locus: .: (0.000876) + test_method_missing: .: (0.001059) + test_to_s: .: (0.000992) + test_words: .: (0.002366) Bio::TestBioGOOntology: - test_dag_edit_format_parser: .: (0.002405) - test_goid2term: .: (0.000975) - test_parse_goids: .: (0.001836) + test_dag_edit_format_parser: .: (0.002240) + test_goid2term: .: (0.001015) + test_parse_goids: .: (0.001950) Bio::TestBioGenBank: - test_basecount: .: (0.000877) - test_circular: .: (0.000714) - test_classification: .: (0.000751) - test_date: .: (0.000781) - test_date_modified: .: (0.001762) - test_division: .: (0.000617) - test_each_cds_feature: .: (0.003628) - test_each_cds_qualifiers: .: (0.002421) - test_each_gene: .: (0.003411) - test_entry_id: .: (0.000658) - test_length: .: (0.000795) - test_locus_circular: .: (0.000754) - test_locus_class: .: (0.000954) - test_locus_date: .: (0.000730) - test_locus_division: .: (0.000728) - test_locus_entry_id: .: (0.000736) - test_locus_length: .: (0.001279) - test_locus_natype: .: (0.000736) - test_locus_strand: .: (0.000871) - test_natype: .: (0.000660) - test_seq: .: (0.001095) - test_seq_len: .: (0.000758) - test_strand: .: (0.000792) - test_strandedness: .: (0.000641) - test_to_biosequence: .: (0.006373) + test_basecount: .: (0.001011) + test_circular: .: (0.000733) + test_classification: .: (0.000859) + test_date: .: (0.000722) + test_date_modified: .: (0.001765) + test_division: .: (0.000707) + test_each_cds_feature: .: (0.003099) + test_each_cds_qualifiers: .: (0.002227) + test_each_gene: .: (0.002219) + test_entry_id: .: (0.000921) + test_length: .: (0.000723) + test_locus_circular: .: (0.000841) + test_locus_class: .: (0.000811) + test_locus_date: .: (0.000804) + test_locus_division: .: (0.000822) + test_locus_entry_id: .: (0.000836) + test_locus_length: .: (0.000792) + test_locus_natype: .: (0.000831) + test_locus_strand: .: (0.001401) + test_natype: .: (0.000711) + test_seq: .: (0.000888) + test_seq_len: .: (0.000823) + test_strand: .: (0.000720) + test_strandedness: .: (0.000735) + test_to_biosequence: .: (0.006071) Bio::TestBioGenPept: - test_circular: .: (0.001320) - test_date: .: (0.000985) - test_dbsource: .: (0.000508) - test_division: .: (0.000533) - test_entry_id: .: (0.000548) - test_length: .: (0.000543) - test_locus: .: (0.000869) - test_seq: .: (0.000591) - test_seq_len: .: (0.000569) + test_circular: .: (0.001044) + test_date: .: (0.000617) + test_dbsource: .: (0.001195) + test_division: .: (0.000606) + test_entry_id: .: (0.000623) + test_length: .: (0.000643) + test_locus: .: (0.000630) + test_seq: .: (0.000671) + test_seq_len: .: (0.000642) Bio::TestBioKEGGGENES_b0529: - test_aalen: .: (0.001240) - test_aaseq: .: (0.001698) - test_chromosome: .: (0.000753) - test_codon_usage: .: (0.000939) - test_cu_list: .: (0.000758) - test_dblinks_as_hash: .: (0.000720) - test_dblinks_as_strings: .: (0.000718) - test_definition: .: (0.000667) - test_division: .: (0.000561) - test_eclinks: .: (0.000991) - test_entry: .: (0.001430) - test_entry_id: .: (0.000695) - test_gbposition: .: (0.000589) - test_gene: .: (0.000920) - test_genes: .: (0.000607) - test_keggclass: .: (0.000671) - test_keggclasses: .: (0.000848) - test_locations: .: (0.001092) - test_motifs_as_hash: .: (0.000989) - test_motifs_as_strings: .: (0.000569) - test_name: .: (0.000615) - test_names_as_array: .: (0.000773) - test_new: .: (0.000817) - test_ntlen: .: (0.000883) - test_ntseq: .: (0.001023) - test_organism: .: (0.000605) - test_orthologs_as_hash: .: (0.000938) - test_orthologs_as_strings: .: (0.000567) - test_pathway: .: (0.000632) - test_pathway_after_pathways_as_strings: .: (0.000845) - test_pathway_before_pathways_as_strings: .: (0.000755) - test_pathways_as_hash: .: (0.000721) - test_pathways_as_strings: .: (0.000556) - test_position: .: (0.000722) - test_structure: .: (0.000591) + test_aalen: .: (0.001188) + test_aaseq: .: (0.000868) + test_chromosome: .: (0.001623) + test_codon_usage: .: (0.001115) + test_cu_list: .: (0.000687) + test_dblinks_as_hash: .: (0.000805) + test_dblinks_as_strings: .: (0.000729) + test_definition: .: (0.000763) + test_division: .: (0.000699) + test_eclinks: .: (0.000797) + test_entry: .: (0.001538) + test_entry_id: .: (0.000665) + test_gbposition: .: (0.000753) + test_gene: .: (0.000689) + test_genes: .: (0.000706) + test_keggclass: .: (0.000753) + test_keggclasses: .: (0.000761) + test_locations: .: (0.001004) + test_motifs_as_hash: .: (0.000928) + test_motifs_as_strings: .: (0.000648) + test_name: .: (0.000652) + test_names_as_array: .: (0.000800) + test_new: .: (0.000734) + test_ntlen: .: (0.000908) + test_ntseq: .: (0.000994) + test_organism: .: (0.000842) + test_orthologs_as_hash: .: (0.000692) + test_orthologs_as_strings: .: (0.000671) + test_pathway: .: (0.000814) + test_pathway_after_pathways_as_strings: .: (0.001155) + test_pathway_before_pathways_as_strings: .: (0.001001) + test_pathways_as_hash: .: (0.000994) + test_pathways_as_strings: .: (0.000674) + test_position: .: (0.000774) + test_structure: .: (0.000758) Bio::TestBioKEGGGENOME_T00005: - test_chromosomes: .: (0.003929) - test_comment: .: (0.001409) - test_data_source: .: (0.001766) - test_definition: .: (0.001250) - test_disease: .: (0.001020) - test_entry_id: .: (0.001227) - test_lineage: .: (0.001482) - test_nalen: .: (0.001152) - test_name: .: (0.001138) - test_new: .: (0.001381) - test_num_gene: .: (0.001014) - test_num_rna: .: (0.001095) - test_original_databases: .: (0.001326) - test_original_db: .: (0.004751) - test_plasmids: .: (0.001066) - test_references: .: (0.007637) - test_statistics: .: (0.001187) - test_taxid: .: (0.001449) - test_taxonomy: .: (0.001891) + test_chromosomes: .: (0.003980) + test_comment: .: (0.001361) + test_data_source: .: (0.001246) + test_definition: .: (0.001204) + test_disease: .: (0.001106) + test_entry_id: .: (0.001302) + test_lineage: .: (0.001364) + test_nalen: .: (0.001135) + test_name: .: (0.001341) + test_new: .: (0.001329) + test_num_gene: .: (0.001219) + test_num_rna: .: (0.001185) + test_original_databases: .: (0.001149) + test_original_db: .: (0.001236) + test_plasmids: .: (0.001097) + test_references: .: (0.007415) + test_statistics: .: (0.001164) + test_taxid: .: (0.001198) + test_taxonomy: .: (0.001267) Bio::TestBioKEGGGENOME_T00070: - test_chromosomes: .: (0.001292) - test_comment: .: (0.000686) - test_data_source: .: (0.000764) - test_definition: .: (0.000703) - test_disease: .: (0.000623) - test_entry_id: .: (0.000888) - test_lineage: .: (0.000897) - test_nalen: .: (0.000634) - test_name: .: (0.000628) - test_new: .: (0.000865) - test_num_gene: .: (0.000622) - test_num_rna: .: (0.000715) - test_original_databases: .: (0.000696) - test_original_db: .: (0.000608) - test_plasmids: .: (0.001175) - test_references: .: (0.001108) - test_statistics: .: (0.000715) - test_taxid: .: (0.000689) - test_taxonomy: .: (0.000905) + test_chromosomes: .: (0.001409) + test_comment: .: (0.000827) + test_data_source: .: (0.000701) + test_definition: .: (0.000772) + test_disease: .: (0.000735) + test_entry_id: .: (0.000714) + test_lineage: .: (0.000916) + test_nalen: .: (0.000684) + test_name: .: (0.000747) + test_new: .: (0.000721) + test_num_gene: .: (0.000754) + test_num_rna: .: (0.000668) + test_original_databases: .: (0.000734) + test_original_db: .: (0.000734) + test_plasmids: .: (0.001032) + test_references: .: (0.001050) + test_statistics: .: (0.000742) + test_taxid: .: (0.000775) + test_taxonomy: .: (0.000764) Bio::TestBioKEGGPATHWAY_ec00072: - test_compounds_as_hash: .: (0.001150) - test_compounds_as_strings: .: (0.000596) - test_dblinks_as_hash: .: (0.000616) - test_dblinks_as_strings: .: (0.000722) - test_description: .: (0.000539) - test_diseases_as_hash: .: (0.000603) - test_diseases_as_strings: .: (0.000455) - test_entry_id: .: (0.000600) - test_enzymes_as_strings: .: (0.000532) - test_genes_as_hash: .: (0.000807) - test_genes_as_strings: .: (0.000481) - test_keggclass: .: (0.000583) - test_ko_pathway: .: (0.000645) - test_modules_as_hash: .: (0.000515) - test_modules_as_strings: .: (0.000542) - test_name: .: (0.001371) - test_new: .: (0.000522) - test_organism: .: (0.000546) - test_orthologs_as_hash: .: (0.000552) - test_orthologs_as_strings: .: (0.000476) - test_pathways_as_hash: .: (0.000836) - test_pathways_as_strings: .: (0.000477) - test_reactions_as_hash: .: (0.000543) - test_reactions_as_strings: .: (0.000502) - test_references: .: (0.000471) - test_rel_pathways_as_hash: .: (0.000560) - test_rel_pathways_as_strings: .: (0.000821) + test_compounds_as_hash: .: (0.001088) + test_compounds_as_strings: .: (0.000641) + test_dblinks_as_hash: .: (0.000571) + test_dblinks_as_strings: .: (0.000607) + test_description: .: (0.000638) + test_diseases_as_hash: .: (0.000566) + test_diseases_as_strings: .: (0.000591) + test_entry_id: .: (0.000687) + test_enzymes_as_strings: .: (0.000614) + test_genes_as_hash: .: (0.000599) + test_genes_as_strings: .: (0.000550) + test_keggclass: .: (0.000704) + test_ko_pathway: .: (0.000631) + test_modules_as_hash: .: (0.000614) + test_modules_as_strings: .: (0.000819) + test_name: .: (0.000678) + test_new: .: (0.000687) + test_organism: .: (0.000697) + test_orthologs_as_hash: .: (0.000669) + test_orthologs_as_strings: .: (0.000638) + test_pathways_as_hash: .: (0.000620) + test_pathways_as_strings: .: (0.000575) + test_reactions_as_hash: .: (0.000673) + test_reactions_as_strings: .: (0.000559) + test_references: .: (0.000569) + test_rel_pathways_as_hash: .: (0.000650) + test_rel_pathways_as_strings: .: (0.000661) Bio::TestBioKEGGPATHWAY_hsa00790: - test_compounds_as_hash: .: (0.001545) - test_compounds_as_strings: .: (0.000802) - test_dblinks_as_hash: .: (0.000784) - test_dblinks_as_strings: .: (0.000627) - test_description: .: (0.000581) + test_compounds_as_hash: .: (0.001592) + test_compounds_as_strings: .: (0.000995) + test_dblinks_as_hash: .: (0.000676) + test_dblinks_as_strings: .: (0.000710) + test_description: .: (0.000667) test_diseases_as_hash: .: (0.000748) - test_diseases_as_strings: .: (0.000639) - test_entry_id: .: (0.000828) - test_enzymes_as_strings: .: (0.000536) - test_genes_as_hash: .: (0.000829) - test_genes_as_strings: .: (0.000683) - test_keggclass: .: (0.000607) - test_ko_pathway: .: (0.000876) - test_modules_as_hash: .: (0.000599) - test_modules_as_strings: .: (0.000702) - test_name: .: (0.000645) - test_new: .: (0.000586) - test_organism: .: (0.000816) - test_orthologs_as_hash: .: (0.000541) - test_orthologs_as_strings: .: (0.000588) - test_pathways_as_hash: .: (0.000728) - test_pathways_as_strings: .: (0.000551) - test_reactions_as_hash: .: (0.000545) - test_reactions_as_strings: .: (0.000600) - test_references: .: (0.000539) - test_rel_pathways_as_hash: .: (0.000663) - test_rel_pathways_as_strings: .: (0.000647) + test_diseases_as_strings: .: (0.000729) + test_entry_id: .: (0.000667) + test_enzymes_as_strings: .: (0.000686) + test_genes_as_hash: .: (0.001069) + test_genes_as_strings: .: (0.000949) + test_keggclass: .: (0.000810) + test_ko_pathway: .: (0.000929) + test_modules_as_hash: .: (0.000722) + test_modules_as_strings: .: (0.000772) + test_name: .: (0.000726) + test_new: .: (0.000713) + test_organism: .: (0.000699) + test_orthologs_as_hash: .: (0.000693) + test_orthologs_as_strings: .: (0.000690) + test_pathways_as_hash: .: (0.000669) + test_pathways_as_strings: .: (0.000722) + test_reactions_as_hash: .: (0.000642) + test_reactions_as_strings: .: (0.000744) + test_references: .: (0.000613) + test_rel_pathways_as_hash: .: (0.000729) + test_rel_pathways_as_strings: .: (0.000795) Bio::TestBioKEGGPATHWAY_ko00312: - test_compounds_as_hash: .: (0.001170) - test_compounds_as_strings: .: (0.000491) - test_dblinks_as_hash: .: (0.000517) - test_dblinks_as_strings: .: (0.000478) - test_description: .: (0.000617) - test_diseases_as_hash: .: (0.000461) - test_diseases_as_strings: .: (0.000716) - test_entry_id: .: (0.000524) - test_enzymes_as_strings: .: (0.000451) - test_genes_as_hash: .: (0.000476) - test_genes_as_strings: .: (0.000503) - test_keggclass: .: (0.000637) - test_ko_pathway: .: (0.000702) - test_modules_as_hash: .: (0.000466) - test_modules_as_strings: .: (0.000452) - test_name: .: (0.000527) - test_new: .: (0.000476) - test_organism: .: (0.000499) - test_orthologs_as_hash: .: (0.000885) - test_orthologs_as_strings: .: (0.000704) - test_pathways_as_hash: .: (0.000501) - test_pathways_as_strings: .: (0.000494) - test_reactions_as_hash: .: (0.002866) - test_reactions_as_strings: .: (0.000565) - test_references: .: (0.000608) - test_rel_pathways_as_hash: .: (0.000504) - test_rel_pathways_as_strings: .: (0.000763) + test_compounds_as_hash: .: (0.001081) + test_compounds_as_strings: .: (0.000608) + test_dblinks_as_hash: .: (0.000669) + test_dblinks_as_strings: .: (0.000601) + test_description: .: (0.000581) + test_diseases_as_hash: .: (0.000530) + test_diseases_as_strings: .: (0.000595) + test_entry_id: .: (0.000609) + test_enzymes_as_strings: .: (0.000532) + test_genes_as_hash: .: (0.000560) + test_genes_as_strings: .: (0.000538) + test_keggclass: .: (0.000670) + test_ko_pathway: .: (0.000590) + test_modules_as_hash: .: (0.000528) + test_modules_as_strings: .: (0.000642) + test_name: .: (0.000618) + test_new: .: (0.000672) + test_organism: .: (0.000635) + test_orthologs_as_hash: .: (0.000827) + test_orthologs_as_strings: .: (0.000689) + test_pathways_as_hash: .: (0.000620) + test_pathways_as_strings: .: (0.000650) + test_reactions_as_hash: .: (0.000611) + test_reactions_as_strings: .: (0.000517) + test_references: .: (0.000590) + test_rel_pathways_as_hash: .: (0.000582) + test_rel_pathways_as_strings: .: (0.000606) Bio::TestBioKEGGPATHWAY_map00030: - test_compounds_as_hash: .: (0.000833) - test_compounds_as_strings: .: (0.000549) - test_dblinks_as_hash: .: (0.000653) - test_dblinks_as_strings: .: (0.000563) - test_description: .: (0.001282) - test_diseases_as_hash: .: (0.000639) - test_diseases_as_strings: .: (0.000587) - test_entry_id: .: (0.000606) - test_enzymes_as_strings: .: (0.000590) - test_genes_as_hash: .: (0.000561) - test_genes_as_strings: .: (0.000828) - test_keggclass: .: (0.000774) - test_ko_pathway: .: (0.000640) - test_modules_as_hash: .: (0.001014) - test_modules_as_strings: .: (0.000690) - test_name: .: (0.000608) - test_new: .: (0.000598) - test_organism: .: (0.000593) - test_orthologs_as_hash: .: (0.000798) - test_orthologs_as_strings: .: (0.000538) - test_pathways_as_hash: .: (0.000716) - test_pathways_as_strings: .: (0.000655) - test_reactions_as_hash: .: (0.000542) - test_reactions_as_strings: .: (0.000526) - test_references: .: (0.002140) - test_rel_pathways_as_hash: .: (0.000762) - test_rel_pathways_as_strings: .: (0.000591) + test_compounds_as_hash: .: (0.000980) + test_compounds_as_strings: .: (0.000713) + test_dblinks_as_hash: .: (0.000772) + test_dblinks_as_strings: .: (0.000743) + test_description: .: (0.001038) + test_diseases_as_hash: .: (0.000710) + test_diseases_as_strings: .: (0.000603) + test_entry_id: .: (0.000730) + test_enzymes_as_strings: .: (0.000798) + test_genes_as_hash: .: (0.000687) + test_genes_as_strings: .: (0.000716) + test_keggclass: .: (0.000732) + test_ko_pathway: .: (0.000795) + test_modules_as_hash: .: (0.000923) + test_modules_as_strings: .: (0.000834) + test_name: .: (0.000726) + test_new: .: (0.000640) + test_organism: .: (0.000718) + test_orthologs_as_hash: .: (0.000707) + test_orthologs_as_strings: .: (0.000651) + test_pathways_as_hash: .: (0.000728) + test_pathways_as_strings: .: (0.000784) + test_reactions_as_hash: .: (0.000607) + test_reactions_as_strings: .: (0.000630) + test_references: .: (0.002251) + test_rel_pathways_as_hash: .: (0.000864) + test_rel_pathways_as_strings: .: (0.000671) Bio::TestBioKeggDRUG: - test_activity: .: (0.001143) - test_comment: .: (0.000670) - test_dblinks_as_hash: .: (0.000802) - test_dblinks_as_strings: .: (0.000890) - test_entry_id: .: (0.000761) - test_formula: .: (0.000626) - test_kcf: .: (0.000669) - test_mass: .: (0.000615) - test_name: .: (0.000880) - test_names: .: (0.000792) - test_pathways_as_hash: .: (0.000670) - test_pathways_as_strings: .: (0.000606) - test_products: .: (0.000682) - test_remark: .: (0.001036) + test_activity: .: (0.001147) + test_comment: .: (0.000793) + test_dblinks_as_hash: .: (0.000961) + test_dblinks_as_strings: .: (0.000916) + test_entry_id: .: (0.000752) + test_formula: .: (0.000771) + test_kcf: .: (0.000714) + test_mass: .: (0.000775) + test_name: .: (0.000810) + test_names: .: (0.000829) + test_pathways_as_hash: .: (0.000883) + test_pathways_as_strings: .: (0.000621) + test_products: .: (0.000838) + test_remark: .: (0.000799) Bio::TestBioKeggGLYCAN: - test_comment: .: (0.000911) - test_composition: .: (0.000719) - test_compounds: .: (0.000570) - test_dblinks_as_hash: .: (0.001406) - test_dblinks_as_strings: .: (0.000693) - test_entry_id: .: (0.000629) - test_enzymes: .: (0.000681) - test_kcf: .: (0.000856) - test_keggclass: .: (0.000608) - test_mass: .: (0.000670) - test_name: .: (0.000625) - test_orthologs_as_hash: .: (0.000795) - test_orthologs_as_strings: .: (0.001071) - test_pathways_as_hash: .: (0.000656) - test_pathways_as_strings: .: (0.000550) - test_reactions: .: (0.000681) - test_references: .: (0.000703) - test_remark: .: (0.000900) + test_comment: .: (0.001187) + test_composition: .: (0.000925) + test_compounds: .: (0.000803) + test_dblinks_as_hash: .: (0.001361) + test_dblinks_as_strings: .: (0.000824) + test_entry_id: .: (0.000792) + test_enzymes: .: (0.000915) + test_kcf: .: (0.000638) + test_keggclass: .: (0.000695) + test_mass: .: (0.000820) + test_name: .: (0.000751) + test_orthologs_as_hash: .: (0.000970) + test_orthologs_as_strings: .: (0.000861) + test_pathways_as_hash: .: (0.000762) + test_pathways_as_strings: .: (0.000770) + test_reactions: .: (0.000988) + test_references: .: (0.001109) + test_remark: .: (0.000881) Bio::TestBioKeggGLYCAN_G01366: - test_comment: .: (0.000851) - test_composition: .: (0.000574) - test_compounds: .: (0.000489) - test_dblinks_as_hash: .: (0.001018) - test_dblinks_as_strings: .: (0.000496) - test_entry_id: .: (0.000517) - test_enzymes: .: (0.000536) - test_kcf: .: (0.000464) - test_keggclass: .: (0.000623) - test_mass: .: (0.000715) - test_name: .: (0.000504) - test_orthologs_as_hash: .: (0.000480) - test_orthologs_as_strings: .: (0.000476) - test_pathways_as_hash: .: (0.000486) - test_pathways_as_strings: .: (0.000575) - test_reactions: .: (0.000857) - test_references: .: (0.000454) - test_remark: .: (0.000481) + test_comment: .: (0.001177) + test_composition: .: (0.000764) + test_compounds: .: (0.000700) + test_dblinks_as_hash: .: (0.000839) + test_dblinks_as_strings: .: (0.000617) + test_entry_id: .: (0.000641) + test_enzymes: .: (0.000642) + test_kcf: .: (0.000558) + test_keggclass: .: (0.000648) + test_mass: .: (0.000631) + test_name: .: (0.000643) + test_orthologs_as_hash: .: (0.000598) + test_orthologs_as_strings: .: (0.000566) + test_pathways_as_hash: .: (0.000592) + test_pathways_as_strings: .: (0.000585) + test_reactions: .: (0.000654) + test_references: .: (0.000571) + test_remark: .: (0.000652) Bio::TestBioKeggPathway_rn00250: - test_compounds_as_hash: .: (0.001377) - test_compounds_as_strings: .: (0.001217) - test_dblinks_as_hash: .: (0.000651) - test_dblinks_as_strings: .: (0.000590) - test_description: .: (0.000650) - test_diseases_as_hash: .: (0.000717) - test_diseases_as_strings: .: (0.000627) - test_entry_id: .: (0.000638) - test_enzymes_as_strings: .: (0.000685) - test_genes_as_hash: .: (0.000588) - test_genes_as_strings: .: (0.000568) - test_keggclass: .: (0.000663) - test_ko_pathway: .: (0.000634) - test_modules_as_hash: .: (0.000957) - test_modules_as_strings: .: (0.000768) - test_name: .: (0.000868) - test_new: .: (0.000648) - test_organism: .: (0.000636) - test_orthologs_as_hash: .: (0.000729) - test_orthologs_as_strings: .: (0.000585) - test_pathways_as_hash: .: (0.000816) - test_pathways_as_strings: .: (0.000668) - test_reactions_as_hash: .: (0.001506) - test_reactions_as_strings: .: (0.001147) - test_references: .: (0.001334) - test_rel_pathways_as_hash: .: (0.001174) - test_rel_pathways_as_strings: .: (0.000820) + test_compounds_as_hash: .: (0.001651) + test_compounds_as_strings: .: (0.000953) + test_dblinks_as_hash: .: (0.000710) + test_dblinks_as_strings: .: (0.000667) + test_description: .: (0.000774) + test_diseases_as_hash: .: (0.000795) + test_diseases_as_strings: .: (0.000765) + test_entry_id: .: (0.000746) + test_enzymes_as_strings: .: (0.000763) + test_genes_as_hash: .: (0.000659) + test_genes_as_strings: .: (0.000681) + test_keggclass: .: (0.000806) + test_ko_pathway: .: (0.000902) + test_modules_as_hash: .: (0.000967) + test_modules_as_strings: .: (0.000908) + test_name: .: (0.000722) + test_new: .: (0.000796) + test_organism: .: (0.000724) + test_orthologs_as_hash: .: (0.000658) + test_orthologs_as_strings: .: (0.000701) + test_pathways_as_hash: .: (0.000750) + test_pathways_as_strings: .: (0.000853) + test_reactions_as_hash: .: (0.001602) + test_reactions_as_strings: .: (0.001126) + test_references: .: (0.001664) + test_rel_pathways_as_hash: .: (0.001261) + test_rel_pathways_as_strings: .: (0.001001) Bio::TestBioLITDB: - test_author: .: (0.000937) - test_entry_id: .: (0.000516) - test_field: .: (0.000520) - test_journal: .: (0.000490) - test_keyword: .: (0.000874) - test_reference: .: (0.000899) - test_title: .: (0.000552) - test_volume: .: (0.000602) + test_author: .: (0.001053) + test_entry_id: .: (0.000653) + test_field: .: (0.000615) + test_journal: .: (0.000651) + test_keyword: .: (0.000783) + test_reference: .: (0.001093) + test_title: .: (0.000668) + test_volume: .: (0.000700) Bio::TestBioNBRF: - test_aalen: .: (0.000870) - test_aaseq: .: (0.000431) - test_entry: .: (0.000364) - test_length: .: (0.014393) - test_nalen: .: (0.000888) - test_naseq: .: (0.000471) - test_seq: .: (0.000413) - test_seq_class: .: (0.000375) - test_to_nbrf: .: (0.000452) + test_aalen: .: (0.000854) + test_aaseq: .: (0.000500) + test_entry: .: (0.000459) + test_length: .: (0.014180) + test_nalen: .: (0.000775) + test_naseq: .: (0.000607) + test_seq: .: (0.000512) + test_seq_class: .: (0.000497) + test_to_nbrf: .: (0.000567) Bio::TestBioTreeOutputPrivate: - test_to_newick_format_label: .: (0.001052) - test_to_newick_format_leaf: .: (0.000751) - test_to_newick_format_leaf_NHX: .: (0.000489) + test_to_newick_format_label: .: (0.000953) + test_to_newick_format_leaf: .: (0.000877) + test_to_newick_format_leaf_NHX: .: (0.000641) Bio::TestBl2seqReport: - test_db_len: .: (0.002787) - test_db_num: .: (0.001444) - test_new: .: (0.000762) - test_undefed_methods: .: (0.003065) - test_undefed_methods_for_iteration: .: (0.002891) + test_db_len: .: (0.002760) + test_db_num: .: (0.001437) + test_new: .: (0.000862) + test_undefed_methods: .: (0.002973) + test_undefed_methods_for_iteration: .: (0.002829) Bio::TestBl2seqReportConstants: - test_rs: .: (0.001036) + test_rs: .: (0.001094) Bio::TestBl2seqReportHit: - test_empty_hits: .: (0.001454) - test_hits: .: (0.000766) + test_empty_hits: .: (0.001179) + test_hits: .: (0.000907) Bio::TestBlast: - test_blast_reports_format0: .: (0.017695) - test_blast_reports_format0_with_block: .: (0.002917) - test_blast_reports_format7: .: (0.043921) - test_blast_reports_format7_with_block: .: (0.041261) - test_blast_reports_format7_with_parser: .: (0.039638) - test_blast_reports_format7_with_parser_with_block: .: (0.039765) - test_blast_reports_format8: .: (0.002362) - test_blast_reports_format8_with_block: .: (0.001201) - test_blast_reports_format8_with_parser: .: (0.000980) - test_blast_reports_format8_with_parser_with_block: .: (0.000615) - test_blast_reports_xml: .: (0.038879) - test_blast_reports_xml_with_block: .: (0.050953) - test_blastll: .: (0.000465) - test_db: .: (0.000385) - test_exec_genomenet: .: (0.000335) - test_exec_local: .: (0.000337) - test_exec_ncbi: .: (0.000382) - test_filter: .: (0.000436) - test_format: .: (0.000565) - test_make_command_line: .: (0.001710) - test_make_command_line_2: .: (0.001363) - test_matrix: .: (0.000537) - test_new: .: (0.000901) - test_new_opt_string: .: (0.000675) - test_option: .: (0.000446) - test_option_set: .: (0.000842) - test_option_set_m0: .: (0.001102) - test_options: .: (0.000407) - test_output: .: (0.000384) - test_parse_result: .: (0.038867) - test_parser: .: (0.000482) - test_program: .: (0.000393) - test_query: .: (0.000345) - test_self_local: .: (0.000787) - test_self_remote: .: (0.009767) - test_server: .: (0.000590) + test_blast_reports_format0: .: (0.015107) + test_blast_reports_format0_with_block: .: (0.002738) + test_blast_reports_format7: .: (0.042954) + test_blast_reports_format7_with_block: .: (0.040763) + test_blast_reports_format7_with_parser: .: (0.038449) + test_blast_reports_format7_with_parser_with_block: .: (0.039724) + test_blast_reports_format8: .: (0.002576) + test_blast_reports_format8_with_block: .: (0.001341) + test_blast_reports_format8_with_parser: .: (0.000809) + test_blast_reports_format8_with_parser_with_block: .: (0.000708) + test_blast_reports_xml: .: (0.038165) + test_blast_reports_xml_with_block: .: (0.048837) + test_blastll: .: (0.000623) + test_db: .: (0.000483) + test_exec_genomenet: .: (0.000424) + test_exec_local: .: (0.000418) + test_exec_ncbi: .: (0.000452) + test_filter: .: (0.000459) + test_format: .: (0.000532) + test_make_command_line: .: (0.001632) + test_make_command_line_2: .: (0.001458) + test_matrix: .: (0.000477) + test_new: .: (0.000776) + test_new_opt_string: .: (0.000758) + test_option: .: (0.000563) + test_option_set: .: (0.000764) + test_option_set_m0: .: (0.000733) + test_options: .: (0.000749) + test_output: .: (0.000475) + test_parse_result: .: (0.039489) + test_parser: .: (0.000575) + test_program: .: (0.000496) + test_query: .: (0.000437) + test_self_local: .: (0.000905) + test_self_remote: .: (0.005063) + test_server: .: (0.000585) Bio::TestBlastNCBIOptions: - test_add_options: .: (0.001180) - test_delete: .: (0.001456) - test_equal_equal: .: (0.001089) - test_get: .: (0.001406) - test_make_command_line_options: .: (0.001216) - test_normalize!: .: (0.000640) - test_parse: .: (0.000725) - test_set: .: (0.001849) + test_add_options: .: (0.001091) + test_delete: .: (0.001134) + test_equal_equal: .: (0.001140) + test_get: .: (0.001374) + test_make_command_line_options: .: (0.000950) + test_normalize!: .: (0.000663) + test_parse: .: (0.000689) + test_set: .: (0.001522) Bio::TestBlastReport: - test_db: .: (0.046856) - test_db_len: .: (0.045796) - test_db_num: .: (0.047014) - test_each_hit: .: (0.051719) - test_each_iteration: .: (0.048553) - test_eff_space: .: (0.047712) - test_entrez_query: .: (0.046973) - test_entropy: .: (0.045025) - test_expect: .: (0.045454) - test_filter: .: (0.048459) - test_gap_extend: .: (0.046095) - test_gap_open: .: (0.045631) - test_hits: .: (0.045629) - test_hsp_len: .: (0.045100) - test_inclusion: .: (0.047250) - test_iterations: .: (0.046535) - test_kappa: .: (0.044840) - test_lambda: .: (0.045351) - test_matrix: .: (0.045182) - test_message: .: (0.046243) - test_parameters: .: (0.048840) - test_pattern: .: (0.046657) - test_program: .: (0.045899) - test_query_def: .: (0.046640) - test_query_id: .: (0.046006) - test_query_len: .: (0.045268) - test_reference: .: (0.047751) - test_sc_match: .: (0.046622) - test_sc_mismatch: .: (0.046625) - test_statistics: .: (0.047431) - test_version: .: (0.046383) + test_db: .: (0.041970) + test_db_len: .: (0.042421) + test_db_num: .: (0.043400) + test_each_hit: .: (0.049901) + test_each_iteration: .: (0.044603) + test_eff_space: .: (0.043246) + test_entrez_query: .: (0.042087) + test_entropy: .: (0.037390) + test_expect: .: (0.037960) + test_filter: .: (0.040765) + test_gap_extend: .: (0.040564) + test_gap_open: .: (0.042979) + test_hits: .: (0.039446) + test_hsp_len: .: (0.037600) + test_inclusion: .: (0.040951) + test_iterations: .: (0.039787) + test_kappa: .: (0.039993) + test_lambda: .: (0.038799) + test_matrix: .: (0.042085) + test_message: .: (0.042599) + test_parameters: .: (0.042678) + test_pattern: .: (0.037651) + test_program: .: (0.040711) + test_query_def: .: (0.043127) + test_query_id: .: (0.040330) + test_query_len: .: (0.037306) + test_reference: .: (0.042406) + test_sc_match: .: (0.040012) + test_sc_mismatch: .: (0.041558) + test_statistics: .: (0.043565) + test_version: .: (0.041294) Bio::TestBlastReportDefault: - test_db: .: (0.001900) - test_db_len: .: (0.006045) - test_db_num: .: (0.001168) - test_each_hit: .: (0.001132) - test_each_iteration: .: (0.001166) - test_eff_space: .: (0.001296) - test_entropy: .: (0.008016) - test_expect: .: (0.001289) - test_gap_extend: .: (0.001507) - test_gap_open: .: (0.001298) - test_gapped_entropy: .: (0.008091) - test_gapped_kappa: .: (0.001298) - test_gapped_lambda: .: (0.001072) - test_hits: .: (0.001079) - test_iterations: .: (0.001122) - test_kappa: .: (0.007813) - test_lambda: .: (0.001128) - test_matrix: .: (0.001312) - test_message: .: (0.001128) - test_pattern: .: (0.000956) - test_program: .: (0.008422) - test_query_def: .: (0.001215) - test_query_len: .: (0.001177) - test_reference: .: (0.016590) - test_sc_match: .: (0.001323) - test_sc_mismatch: .: (0.005709) - test_version: .: (0.001005) + test_db: .: (0.001945) + test_db_len: .: (0.005923) + test_db_num: .: (0.001226) + test_each_hit: .: (0.001130) + test_each_iteration: .: (0.001003) + test_eff_space: .: (0.001316) + test_entropy: .: (0.008054) + test_expect: .: (0.001331) + test_gap_extend: .: (0.001281) + test_gap_open: .: (0.001295) + test_gapped_entropy: .: (0.008002) + test_gapped_kappa: .: (0.001127) + test_gapped_lambda: .: (0.001291) + test_hits: .: (0.001152) + test_iterations: .: (0.001032) + test_kappa: .: (0.007913) + test_lambda: .: (0.001156) + test_matrix: .: (0.001318) + test_message: .: (0.000983) + test_pattern: .: (0.001039) + test_program: .: (0.008238) + test_query_def: .: (0.001152) + test_query_len: .: (0.001030) + test_reference: .: (0.001130) + test_sc_match: .: (0.001257) + test_sc_mismatch: .: (0.005426) + test_version: .: (0.001045) Bio::TestBlastReportHit: - test_Hit_accession: .: (0.112848) - test_Hit_bit_score: .: (0.047645) - test_Hit_definition: .: (0.046932) - test_Hit_evalue: .: (0.046003) - test_Hit_hit_id: .: (0.045551) - test_Hit_hsps: .: (0.046993) - test_Hit_identity: .: (0.048551) - test_Hit_lap_at: .: (0.050950) - test_Hit_len: .: (0.052084) - test_Hit_midline: .: (0.057335) - test_Hit_num: .: (0.083140) - test_Hit_overlap: .: (0.060257) - test_Hit_query_def: .: (0.046208) - test_Hit_query_end: .: (0.048531) - test_Hit_query_id: .: (0.048847) - test_Hit_query_len: .: (0.047482) - test_Hit_query_seq: .: (0.047170) - test_Hit_query_start: .: (0.046555) - test_Hit_taeget_def: .: (0.046010) - test_Hit_target_end: .: (0.046289) - test_Hit_target_id: .: (0.048627) - test_Hit_target_len: .: (0.047022) - test_Hit_target_seq: .: (0.047994) - test_Hit_target_start: .: (0.047111) + test_Hit_accession: .: (0.112391) + test_Hit_bit_score: .: (0.043830) + test_Hit_definition: .: (0.043415) + test_Hit_evalue: .: (0.043197) + test_Hit_hit_id: .: (0.045751) + test_Hit_hsps: .: (0.041081) + test_Hit_identity: .: (0.039438) + test_Hit_lap_at: .: (0.047195) + test_Hit_len: .: (0.042755) + test_Hit_midline: .: (0.038344) + test_Hit_num: .: (0.041436) + test_Hit_overlap: .: (0.044886) + test_Hit_query_def: .: (0.048831) + test_Hit_query_end: .: (0.048379) + test_Hit_query_id: .: (0.045679) + test_Hit_query_len: .: (0.046348) + test_Hit_query_seq: .: (0.044480) + test_Hit_query_start: .: (0.045702) + test_Hit_taeget_def: .: (0.044696) + test_Hit_target_end: .: (0.044439) + test_Hit_target_id: .: (0.048889) + test_Hit_target_len: .: (0.044085) + test_Hit_target_seq: .: (0.046288) + test_Hit_target_start: .: (0.046636) Bio::TestBlastReportHitDefault: - test_Hit_bit_score: .: (0.001870) - test_Hit_definition: .: (0.001469) - test_Hit_evalue: .: (0.001131) - test_Hit_hsps: .: (0.001083) - test_Hit_identity: .: (0.001375) - test_Hit_lap_at: .: (0.001650) - test_Hit_len: .: (0.001118) - test_Hit_midline: .: (0.002208) - test_Hit_overlap: .: (0.001163) - test_Hit_query_end: .: (0.001836) - test_Hit_query_seq: .: (0.001647) - test_Hit_query_start: .: (0.001863) - test_Hit_taeget_def: .: (0.001136) - test_Hit_target_end: .: (0.002132) - test_Hit_target_id: .: (0.001093) - test_Hit_target_len: .: (0.001121) - test_Hit_target_seq: .: (0.001807) - test_Hit_target_start: .: (0.001634) + test_Hit_bit_score: .: (0.002370) + test_Hit_definition: .: (0.001217) + test_Hit_evalue: .: (0.001180) + test_Hit_hsps: .: (0.001181) + test_Hit_identity: .: (0.001289) + test_Hit_lap_at: .: (0.001910) + test_Hit_len: .: (0.001279) + test_Hit_midline: .: (0.002200) + test_Hit_overlap: .: (0.001221) + test_Hit_query_end: .: (0.001868) + test_Hit_query_seq: .: (0.001777) + test_Hit_query_start: .: (0.001716) + test_Hit_taeget_def: .: (0.001349) + test_Hit_target_end: .: (0.001944) + test_Hit_target_id: .: (0.001299) + test_Hit_target_len: .: (0.001083) + test_Hit_target_seq: .: (0.001540) + test_Hit_target_start: .: (0.001605) Bio::TestBlastReportHitMulti: - test_Hit_accession: .: (0.142518) - test_Hit_bit_score: .: (0.139498) - test_Hit_definition: .: (0.176861) - test_Hit_evalue: .: (0.140667) - test_Hit_hit_id: .: (0.138108) - test_Hit_hsps: .: (0.202244) - test_Hit_identity: .: (0.135552) - test_Hit_lap_at: .: (0.141387) - test_Hit_len: .: (0.136202) - test_Hit_midline: .: (0.206171) - test_Hit_num: .: (0.140901) - test_Hit_overlap: .: (0.139538) - test_Hit_query_def: .: (0.129355) - test_Hit_query_end: .: (0.135950) - test_Hit_query_id: .: (0.136187) - test_Hit_query_len: .: (0.193148) - test_Hit_query_seq: .: (0.135964) - test_Hit_query_start: .: (0.170246) - test_Hit_taeget_def: .: (0.139420) - test_Hit_target_end: .: (0.139741) - test_Hit_target_id: .: (0.134814) - test_Hit_target_len: .: (0.139101) - test_Hit_target_seq: .: (0.217623) - test_Hit_target_start: .: (0.142604) + test_Hit_accession: .: (0.116963) + test_Hit_bit_score: .: (0.114778) + test_Hit_definition: .: (0.116185) + test_Hit_evalue: .: (0.140934) + test_Hit_hit_id: .: (0.137634) + test_Hit_hsps: .: (0.136675) + test_Hit_identity: .: (0.136905) + test_Hit_lap_at: .: (0.139139) + test_Hit_len: .: (0.133435) + test_Hit_midline: .: (0.139480) + test_Hit_num: .: (0.136026) + test_Hit_overlap: .: (0.139672) + test_Hit_query_def: .: (0.133913) + test_Hit_query_end: .: (0.142321) + test_Hit_query_id: .: (0.123263) + test_Hit_query_len: .: (0.119398) + test_Hit_query_seq: .: (0.120357) + test_Hit_query_start: .: (0.120052) + test_Hit_taeget_def: .: (0.125859) + test_Hit_target_end: .: (0.131688) + test_Hit_target_id: .: (0.126472) + test_Hit_target_len: .: (0.122712) + test_Hit_target_seq: .: (0.117006) + test_Hit_target_start: .: (0.123633) Bio::TestBlastReportHitMultiREXML: - test_Hit_accession: .: (0.139424) - test_Hit_bit_score: .: (0.141255) - test_Hit_definition: .: (0.161787) - test_Hit_evalue: .: (0.135450) - test_Hit_hit_id: .: (0.136590) - test_Hit_hsps: .: (0.138984) - test_Hit_identity: .: (0.133543) - test_Hit_lap_at: .: (0.136526) - test_Hit_len: .: (0.163498) - test_Hit_midline: .: (0.139255) - test_Hit_num: .: (0.137957) - test_Hit_overlap: .: (0.139255) - test_Hit_query_def: .: (0.142617) - test_Hit_query_end: .: (0.139150) - test_Hit_query_id: .: (0.210726) - test_Hit_query_len: .: (0.109857) - test_Hit_query_seq: .: (0.113416) - test_Hit_query_start: .: (0.119813) - test_Hit_taeget_def: .: (0.138892) - test_Hit_target_end: .: (0.113816) - test_Hit_target_id: .: (0.112920) - test_Hit_target_len: .: (0.108386) - test_Hit_target_seq: .: (0.112104) - test_Hit_target_start: .: (0.108172) + test_Hit_accession: .: (0.121847) + test_Hit_bit_score: .: (0.130272) + test_Hit_definition: .: (0.127093) + test_Hit_evalue: .: (0.142346) + test_Hit_hit_id: .: (0.138222) + test_Hit_hsps: .: (0.141681) + test_Hit_identity: .: (0.143944) + test_Hit_lap_at: .: (0.131074) + test_Hit_len: .: (0.145597) + test_Hit_midline: .: (0.124272) + test_Hit_num: .: (0.124597) + test_Hit_overlap: .: (0.130075) + test_Hit_query_def: .: (0.144195) + test_Hit_query_end: .: (0.135163) + test_Hit_query_id: .: (0.135928) + test_Hit_query_len: .: (0.138643) + test_Hit_query_seq: .: (0.143590) + test_Hit_query_start: .: (0.127969) + test_Hit_taeget_def: .: (0.128293) + test_Hit_target_end: .: (0.124625) + test_Hit_target_id: .: (0.138309) + test_Hit_target_len: .: (0.134236) + test_Hit_target_seq: .: (0.139671) + test_Hit_target_start: .: (0.134118) Bio::TestBlastReportHitREXML: - test_Hit_accession: .: (0.038616) - test_Hit_bit_score: .: (0.039316) - test_Hit_definition: .: (0.036807) - test_Hit_evalue: .: (0.038113) - test_Hit_hit_id: .: (0.036360) - test_Hit_hsps: .: (0.036289) - test_Hit_identity: .: (0.037079) - test_Hit_lap_at: .: (0.037460) - test_Hit_len: .: (0.039613) - test_Hit_midline: .: (0.036903) - test_Hit_num: .: (0.037018) - test_Hit_overlap: .: (0.037140) - test_Hit_query_def: .: (0.036615) - test_Hit_query_end: .: (0.039210) - test_Hit_query_id: .: (0.040093) - test_Hit_query_len: .: (0.037533) - test_Hit_query_seq: .: (0.037509) - test_Hit_query_start: .: (0.036674) - test_Hit_taeget_def: .: (0.036623) - test_Hit_target_end: .: (0.036727) - test_Hit_target_id: .: (0.036891) - test_Hit_target_len: .: (0.039239) - test_Hit_target_seq: .: (0.037396) - test_Hit_target_start: .: (0.036668) + test_Hit_accession: .: (0.045249) + test_Hit_bit_score: .: (0.047172) + test_Hit_definition: .: (0.045455) + test_Hit_evalue: .: (0.046578) + test_Hit_hit_id: .: (0.046155) + test_Hit_hsps: .: (0.044782) + test_Hit_identity: .: (0.045527) + test_Hit_lap_at: .: (0.047501) + test_Hit_len: .: (0.049366) + test_Hit_midline: .: (0.040617) + test_Hit_num: .: (0.040799) + test_Hit_overlap: .: (0.038629) + test_Hit_query_def: .: (0.040062) + test_Hit_query_end: .: (0.041340) + test_Hit_query_id: .: (0.045025) + test_Hit_query_len: .: (0.043321) + test_Hit_query_seq: .: (0.039893) + test_Hit_query_start: .: (0.042911) + test_Hit_taeget_def: .: (0.041600) + test_Hit_target_end: .: (0.042928) + test_Hit_target_id: .: (0.046447) + test_Hit_target_len: .: (0.050230) + test_Hit_target_seq: .: (0.045070) + test_Hit_target_start: .: (0.040281) Bio::TestBlastReportHitTabular: - test_Hit_accession: .: (0.000936) - test_Hit_bit_score: .: (0.000437) - test_Hit_definition: .: (0.000416) - test_Hit_evalue: .: (0.000434) - test_Hit_hit_id: .: (0.000410) - test_Hit_hsps: .: (0.000394) - test_Hit_identity: .: (0.000387) - test_Hit_lap_at: .: (0.000452) - test_Hit_len: .: (0.000654) - test_Hit_midline: .: (0.000481) - test_Hit_num: .: (0.000596) - test_Hit_overlap: .: (0.000405) - test_Hit_query_def: .: (0.000415) - test_Hit_query_end: .: (0.000392) - test_Hit_query_id: .: (0.000446) - test_Hit_query_len: .: (0.000394) - test_Hit_query_seq: .: (0.000384) - test_Hit_query_start: .: (0.000574) - test_Hit_taeget_def: .: (0.000416) - test_Hit_target_end: .: (0.000400) - test_Hit_target_id: .: (0.000391) - test_Hit_target_len: .: (0.000454) - test_Hit_target_seq: .: (0.000682) - test_Hit_target_start: .: (0.000422) + test_Hit_accession: .: (0.001075) + test_Hit_bit_score: .: (0.000843) + test_Hit_definition: .: (0.000571) + test_Hit_evalue: .: (0.000464) + test_Hit_hit_id: .: (0.000540) + test_Hit_hsps: .: (0.000487) + test_Hit_identity: .: (0.000485) + test_Hit_lap_at: .: (0.000502) + test_Hit_len: .: (0.000474) + test_Hit_midline: .: (0.000501) + test_Hit_num: .: (0.000548) + test_Hit_overlap: .: (0.000507) + test_Hit_query_def: .: (0.000610) + test_Hit_query_end: .: (0.000547) + test_Hit_query_id: .: (0.000535) + test_Hit_query_len: .: (0.000839) + test_Hit_query_seq: .: (0.000598) + test_Hit_query_start: .: (0.000556) + test_Hit_taeget_def: .: (0.000513) + test_Hit_target_end: .: (0.000482) + test_Hit_target_id: .: (0.000475) + test_Hit_target_len: .: (0.000510) + test_Hit_target_seq: .: (0.000467) + test_Hit_target_start: .: (0.000473) Bio::TestBlastReportHsp: - test_Hsp_align_len: .: (0.037487) - test_Hsp_bit_score: .: (0.036773) - test_Hsp_density: .: (0.036855) - test_Hsp_evalue: .: (0.039755) - test_Hsp_gaps: .: (0.037406) - test_Hsp_hit_frame: .: (0.036762) - test_Hsp_hit_from: .: (0.037781) - test_Hsp_hit_to: .: (0.036524) - test_Hsp_hseq: .: (0.036413) - test_Hsp_identity: .: (0.039064) - test_Hsp_midline: .: (0.037234) - test_Hsp_mismatch_count: .: (0.037270) - test_Hsp_num: .: (0.036790) - test_Hsp_pattern_from: .: (0.037174) - test_Hsp_pattern_to: .: (0.036707) - test_Hsp_percent_identity: .: (0.036810) - test_Hsp_positive: .: (0.039280) - test_Hsp_qseq: .: (0.037702) - test_Hsp_query_frame: .: (0.037078) - test_Hsp_query_from: .: (0.036424) - test_Hsp_query_to: .: (0.036793) - test_Hsp_score: .: (0.037032) + test_Hsp_align_len: .: (0.043110) + test_Hsp_bit_score: .: (0.041031) + test_Hsp_density: .: (0.040748) + test_Hsp_evalue: .: (0.046033) + test_Hsp_gaps: .: (0.047341) + test_Hsp_hit_frame: .: (0.047713) + test_Hsp_hit_from: .: (0.045411) + test_Hsp_hit_to: .: (0.038620) + test_Hsp_hseq: .: (0.039982) + test_Hsp_identity: .: (0.040707) + test_Hsp_midline: .: (0.042466) + test_Hsp_mismatch_count: .: (0.042247) + test_Hsp_num: .: (0.038903) + test_Hsp_pattern_from: .: (0.041108) + test_Hsp_pattern_to: .: (0.039115) + test_Hsp_percent_identity: .: (0.046637) + test_Hsp_positive: .: (0.049384) + test_Hsp_qseq: .: (0.046535) + test_Hsp_query_frame: .: (0.047265) + test_Hsp_query_from: .: (0.038269) + test_Hsp_query_to: .: (0.039598) + test_Hsp_score: .: (0.039839) Bio::TestBlastReportHspDefault: - test_Hsp_align_len: .: (0.001695) - test_Hsp_bit_score: .: (0.001015) - test_Hsp_evalue: .: (0.001176) - test_Hsp_gaps: .: (0.001005) - test_Hsp_hit_frame: .: (0.001322) - test_Hsp_hit_from: .: (0.001629) - test_Hsp_hit_to: .: (0.001448) - test_Hsp_hseq: .: (0.001578) - test_Hsp_identity: .: (0.000996) - test_Hsp_midline: .: (0.001484) - test_Hsp_percent_identity: .: (0.001040) - test_Hsp_positive: .: (0.001104) - test_Hsp_qseq: .: (0.001455) - test_Hsp_query_frame: .: (0.001157) - test_Hsp_query_from: .: (0.001389) - test_Hsp_query_to: .: (0.001437) - test_Hsp_score: .: (0.001188) + test_Hsp_align_len: .: (0.002122) + test_Hsp_bit_score: .: (0.001203) + test_Hsp_evalue: .: (0.001081) + test_Hsp_gaps: .: (0.001489) + test_Hsp_hit_frame: .: (0.001253) + test_Hsp_hit_from: .: (0.002187) + test_Hsp_hit_to: .: (0.001612) + test_Hsp_hseq: .: (0.001864) + test_Hsp_identity: .: (0.001150) + test_Hsp_midline: .: (0.001679) + test_Hsp_percent_identity: .: (0.001185) + test_Hsp_positive: .: (0.001369) + test_Hsp_qseq: .: (0.001631) + test_Hsp_query_frame: .: (0.001074) + test_Hsp_query_from: .: (0.001493) + test_Hsp_query_to: .: (0.001569) + test_Hsp_score: .: (0.001131) Bio::TestBlastReportHspMulti: - test_Hsp_align_len: .: (0.125035) - test_Hsp_bit_score: .: (0.108905) - test_Hsp_density: .: (0.112479) - test_Hsp_evalue: .: (0.108895) - test_Hsp_gaps: .: (0.112099) - test_Hsp_hit_frame: .: (0.107758) - test_Hsp_hit_from: .: (0.112099) - test_Hsp_hit_to: .: (0.111884) - test_Hsp_hseq: .: (0.120098) - test_Hsp_identity: .: (0.110770) - test_Hsp_midline: .: (0.139406) - test_Hsp_mismatch_count: .: (0.138852) - test_Hsp_num: .: (0.160522) - test_Hsp_pattern_from: .: (0.174687) - test_Hsp_pattern_to: .: (0.141154) - test_Hsp_percent_identity: .: (0.137148) - test_Hsp_positive: .: (0.143786) - test_Hsp_qseq: .: (0.150606) - test_Hsp_query_frame: .: (0.142605) - test_Hsp_query_from: .: (0.137296) - test_Hsp_query_to: .: (0.143681) - test_Hsp_score: .: (0.139973) + test_Hsp_align_len: .: (0.124194) + test_Hsp_bit_score: .: (0.134646) + test_Hsp_density: .: (0.138257) + test_Hsp_evalue: .: (0.123469) + test_Hsp_gaps: .: (0.134969) + test_Hsp_hit_frame: .: (0.122271) + test_Hsp_hit_from: .: (0.124255) + test_Hsp_hit_to: .: (0.122081) + test_Hsp_hseq: .: (0.122971) + test_Hsp_identity: .: (0.123301) + test_Hsp_midline: .: (0.128542) + test_Hsp_mismatch_count: .: (0.120502) + test_Hsp_num: .: (0.120981) + test_Hsp_pattern_from: .: (0.114740) + test_Hsp_pattern_to: .: (0.118279) + test_Hsp_percent_identity: .: (0.121783) + test_Hsp_positive: .: (0.124625) + test_Hsp_qseq: .: (0.113086) + test_Hsp_query_frame: .: (0.118841) + test_Hsp_query_from: .: (0.113040) + test_Hsp_query_to: .: (0.121118) + test_Hsp_score: .: (0.119004) Bio::TestBlastReportHspMultiREXML: - test_Hsp_align_len: .: (0.140760) - test_Hsp_bit_score: .: (0.133177) - test_Hsp_density: .: (0.142204) - test_Hsp_evalue: .: (0.142740) - test_Hsp_gaps: .: (0.138105) - test_Hsp_hit_frame: .: (0.129602) - test_Hsp_hit_from: .: (0.112000) - test_Hsp_hit_to: .: (0.107353) - test_Hsp_hseq: .: (0.125592) - test_Hsp_identity: .: (0.108177) - test_Hsp_midline: .: (0.111425) - test_Hsp_mismatch_count: .: (0.106880) - test_Hsp_num: .: (0.111563) - test_Hsp_pattern_from: .: (0.107285) - test_Hsp_pattern_to: .: (0.111148) - test_Hsp_percent_identity: .: (0.106702) - test_Hsp_positive: .: (0.117198) - test_Hsp_qseq: .: (0.112602) - test_Hsp_query_frame: .: (0.112725) - test_Hsp_query_from: .: (0.109504) - test_Hsp_query_to: .: (0.114683) - test_Hsp_score: .: (0.109481) + test_Hsp_align_len: .: (0.120081) + test_Hsp_bit_score: .: (0.115741) + test_Hsp_density: .: (0.120617) + test_Hsp_evalue: .: (0.126563) + test_Hsp_gaps: .: (0.123011) + test_Hsp_hit_frame: .: (0.117474) + test_Hsp_hit_from: .: (0.125951) + test_Hsp_hit_to: .: (0.134128) + test_Hsp_hseq: .: (0.125874) + test_Hsp_identity: .: (0.115805) + test_Hsp_midline: .: (0.131988) + test_Hsp_mismatch_count: .: (0.121735) + test_Hsp_num: .: (0.127206) + test_Hsp_pattern_from: .: (0.115454) + test_Hsp_pattern_to: .: (0.133131) + test_Hsp_percent_identity: .: (0.123690) + test_Hsp_positive: .: (0.142925) + test_Hsp_qseq: .: (0.127529) + test_Hsp_query_frame: .: (0.120991) + test_Hsp_query_from: .: (0.120892) + test_Hsp_query_to: .: (0.126358) + test_Hsp_score: .: (0.128333) Bio::TestBlastReportHspREXML: - test_Hsp_align_len: .: (0.038795) - test_Hsp_bit_score: .: (0.039740) - test_Hsp_density: .: (0.036558) - test_Hsp_evalue: .: (0.038161) - test_Hsp_gaps: .: (0.037246) - test_Hsp_hit_frame: .: (0.036424) - test_Hsp_hit_from: .: (0.040400) - test_Hsp_hit_to: .: (0.040912) - test_Hsp_hseq: .: (0.038327) - test_Hsp_identity: .: (0.038056) - test_Hsp_midline: .: (0.038135) - test_Hsp_mismatch_count: .: (0.038059) - test_Hsp_num: .: (0.037891) - test_Hsp_pattern_from: .: (0.044779) - test_Hsp_pattern_to: .: (0.042267) - test_Hsp_percent_identity: .: (0.078927) - test_Hsp_positive: .: (0.069527) - test_Hsp_qseq: .: (0.045794) - test_Hsp_query_frame: .: (0.045838) - test_Hsp_query_from: .: (0.049654) - test_Hsp_query_to: .: (0.048366) - test_Hsp_score: .: (0.047046) + test_Hsp_align_len: .: (0.044668) + test_Hsp_bit_score: .: (0.046872) + test_Hsp_density: .: (0.042304) + test_Hsp_evalue: .: (0.040831) + test_Hsp_gaps: .: (0.037917) + test_Hsp_hit_frame: .: (0.037887) + test_Hsp_hit_from: .: (0.042124) + test_Hsp_hit_to: .: (0.047562) + test_Hsp_hseq: .: (0.044411) + test_Hsp_identity: .: (0.042791) + test_Hsp_midline: .: (0.044905) + test_Hsp_mismatch_count: .: (0.043736) + test_Hsp_num: .: (0.043470) + test_Hsp_pattern_from: .: (0.046476) + test_Hsp_pattern_to: .: (0.043475) + test_Hsp_percent_identity: .: (0.044217) + test_Hsp_positive: .: (0.042900) + test_Hsp_qseq: .: (0.044076) + test_Hsp_query_frame: .: (0.044324) + test_Hsp_query_from: .: (0.045630) + test_Hsp_query_to: .: (0.045331) + test_Hsp_score: .: (0.043250) Bio::TestBlastReportHspTabular: - test_Hsp_align_len: .: (0.000924) - test_Hsp_bit_score: .: (0.000492) - test_Hsp_density: .: (0.000478) - test_Hsp_evalue: .: (0.000470) - test_Hsp_gaps: .: (0.000494) - test_Hsp_hit_frame: .: (0.000449) - test_Hsp_hit_from: .: (0.000459) - test_Hsp_hit_to: .: (0.000500) - test_Hsp_hseq: .: (0.000541) - test_Hsp_identity: .: (0.000485) - test_Hsp_midline: .: (0.000449) - test_Hsp_mismatch_count: .: (0.000449) - test_Hsp_num: .: (0.000717) - test_Hsp_pattern_from: .: (0.000458) - test_Hsp_pattern_to: .: (0.000443) - test_Hsp_percent_identity: .: (0.000443) - test_Hsp_positive: .: (0.000476) - test_Hsp_qseq: .: (0.000447) - test_Hsp_query_frame: .: (0.000443) - test_Hsp_query_from: .: (0.000466) - test_Hsp_query_to: .: (0.000454) - test_Hsp_score: .: (0.000450) + test_Hsp_align_len: .: (0.001137) + test_Hsp_bit_score: .: (0.000524) + test_Hsp_density: .: (0.000500) + test_Hsp_evalue: .: (0.000520) + test_Hsp_gaps: .: (0.000488) + test_Hsp_hit_frame: .: (0.000498) + test_Hsp_hit_from: .: (0.000557) + test_Hsp_hit_to: .: (0.000495) + test_Hsp_hseq: .: (0.000477) + test_Hsp_identity: .: (0.000479) + test_Hsp_midline: .: (0.000494) + test_Hsp_mismatch_count: .: (0.000607) + test_Hsp_num: .: (0.000481) + test_Hsp_pattern_from: .: (0.000480) + test_Hsp_pattern_to: .: (0.000491) + test_Hsp_percent_identity: .: (0.000518) + test_Hsp_positive: .: (0.000470) + test_Hsp_qseq: .: (0.000445) + test_Hsp_query_frame: .: (0.000471) + test_Hsp_query_from: .: (0.000443) + test_Hsp_query_to: .: (0.000446) + test_Hsp_score: .: (0.000479) Bio::TestBlastReportIteration: - test_hits: .: (0.045816) - test_message: .: (0.046315) - test_num: .: (0.046180) - test_statistics: .: (0.048109) + test_hits: .: (0.038794) + test_message: .: (0.039788) + test_num: .: (0.042091) + test_statistics: .: (0.042901) Bio::TestBlastReportIterationDefault: - test_hits: .: (0.001482) - test_message: .: (0.001323) - test_num: .: (0.001053) + test_hits: .: (0.001745) + test_message: .: (0.001067) + test_num: .: (0.001067) Bio::TestBlastReportIterationMulti: - test_each: .: (0.153281) - test_hits: .: (0.266842) - test_message: .: (0.142544) - test_num: .: (0.111913) - test_query_def: .: (0.149707) - test_query_id: .: (0.135931) - test_query_len: .: (0.115491) - test_statistics: .: (0.116012) + test_each: .: (0.126880) + test_hits: .: (0.184365) + test_message: .: (0.160004) + test_num: .: (0.121151) + test_query_def: .: (0.120457) + test_query_id: .: (0.123387) + test_query_len: .: (0.123531) + test_statistics: .: (0.116638) Bio::TestBlastReportIterationMultiREXML: - test_each: .: (0.130164) - test_hits: .: (0.121071) - test_message: .: (0.140614) - test_num: .: (0.127067) - test_query_def: .: (0.155684) - test_query_id: .: (0.163155) - test_query_len: .: (0.148077) - test_statistics: .: (0.185416) + test_each: .: (0.123747) + test_hits: .: (0.128081) + test_message: .: (0.119901) + test_num: .: (0.122068) + test_query_def: .: (0.119782) + test_query_id: .: (0.121680) + test_query_len: .: (0.125766) + test_statistics: .: (0.123400) Bio::TestBlastReportIterationREXML: - test_hits: .: (0.076208) - test_message: .: (0.074381) - test_num: .: (0.051498) - test_statistics: .: (0.093881) + test_hits: .: (0.042589) + test_message: .: (0.039749) + test_num: .: (0.044494) + test_statistics: .: (0.044855) Bio::TestBlastReportIterationTabular: - test_hits: .: (0.002985) - test_message: .: (0.000792) - test_num: .: (0.000841) - test_statistics: .: (0.000811) + test_hits: .: (0.001285) + test_message: .: (0.000582) + test_num: .: (0.000555) + test_statistics: .: (0.001138) Bio::TestBlastReportMulti: - test_db: .: (0.185233) - test_db_len: .: (0.157667) - test_db_num: .: (0.177458) - test_each_hit: .: (0.142975) - test_each_iteration: .: (0.170738) - test_eff_space: .: (0.204695) - test_entropy: .: (0.121432) - test_expect: .: (0.200295) - test_filter: .: (0.168828) - test_gap_extend: .: (0.174694) - test_gap_open: .: (0.137511) - test_hits: .: (0.143484) - test_hsp_len: .: (0.140155) - test_iterations: .: (0.152101) - test_kappa: .: (0.114151) - test_lambda: .: (0.127605) - test_matrix: .: (0.137340) - test_message: .: (0.117963) - test_parameters: .: (0.127571) - test_pattern: .: (0.222164) - test_program: .: (0.115310) - test_query_def: .: (0.118067) - test_query_id: .: (0.111354) - test_query_len: .: (0.116877) - test_reference: .: (0.124193) - test_reports: .: (0.132911) - test_statistics: .: (0.211827) - test_version: .: (0.227385) + test_db: .: (0.116877) + test_db_len: .: (0.121001) + test_db_num: .: (0.121531) + test_each_hit: .: (0.127469) + test_each_iteration: .: (0.126345) + test_eff_space: .: (0.134644) + test_entropy: .: (0.121006) + test_expect: .: (0.125503) + test_filter: .: (0.120427) + test_gap_extend: .: (0.137036) + test_gap_open: .: (0.121955) + test_hits: .: (0.123156) + test_hsp_len: .: (0.121144) + test_iterations: .: (0.125954) + test_kappa: .: (0.117862) + test_lambda: .: (0.122677) + test_matrix: .: (0.113879) + test_message: .: (0.117006) + test_parameters: .: (0.113859) + test_pattern: .: (0.120880) + test_program: .: (0.115426) + test_query_def: .: (0.115972) + test_query_id: .: (0.119642) + test_query_len: .: (0.136221) + test_reference: .: (0.132591) + test_reports: .: (0.130371) + test_statistics: .: (0.129346) + test_version: .: (0.135245) Bio::TestBlastReportMultiREXML: - test_db: .: (0.249002) - test_db_len: .: (0.158344) - test_db_num: .: (0.234278) - test_each_hit: .: (0.244932) - test_each_iteration: .: (0.169116) - test_eff_space: .: (0.158934) - test_entropy: .: (0.248761) - test_expect: .: (0.306974) - test_filter: .: (0.149547) - test_gap_extend: .: (0.117257) - test_gap_open: .: (0.127302) - test_hits: .: (0.120504) - test_hsp_len: .: (0.113149) - test_iterations: .: (0.116632) - test_kappa: .: (0.113565) - test_lambda: .: (0.121289) - test_matrix: .: (0.113712) - test_message: .: (0.233368) - test_parameters: .: (0.191467) - test_pattern: .: (0.170139) - test_program: .: (0.202439) - test_query_def: .: (0.141902) - test_query_id: .: (0.130429) - test_query_len: .: (0.137514) - test_reference: .: (0.146227) - test_reports: .: (0.173884) - test_statistics: .: (0.167966) - test_version: .: (0.168356) + test_db: .: (0.119658) + test_db_len: .: (0.127017) + test_db_num: .: (0.126419) + test_each_hit: .: (0.118560) + test_each_iteration: .: (0.114341) + test_eff_space: .: (0.121321) + test_entropy: .: (0.116159) + test_expect: .: (0.122597) + test_filter: .: (0.117904) + test_gap_extend: .: (0.123089) + test_gap_open: .: (0.116899) + test_hits: .: (0.121814) + test_hsp_len: .: (0.113739) + test_iterations: .: (0.123256) + test_kappa: .: (0.117350) + test_lambda: .: (0.123727) + test_matrix: .: (0.124336) + test_message: .: (0.117003) + test_parameters: .: (0.114574) + test_pattern: .: (0.130290) + test_program: .: (0.138867) + test_query_def: .: (0.136766) + test_query_id: .: (0.112462) + test_query_len: .: (0.119966) + test_reference: .: (0.121100) + test_reports: .: (0.136449) + test_statistics: .: (0.112038) + test_version: .: (0.116180) Bio::TestBlastReportREXML: - test_db: .: (0.055940) - test_db_len: .: (0.045409) - test_db_num: .: (0.046058) - test_each_hit: .: (0.051088) - test_each_iteration: .: (0.046646) - test_eff_space: .: (0.045469) - test_entrez_query: .: (0.047448) - test_entropy: .: (0.047084) - test_expect: .: (0.046560) - test_filter: .: (0.060828) - test_gap_extend: .: (0.047534) - test_gap_open: .: (0.071115) - test_hits: .: (0.047555) - test_hsp_len: .: (0.046660) - test_inclusion: .: (0.047604) - test_iterations: .: (0.049596) - test_kappa: .: (0.047976) - test_lambda: .: (0.046784) - test_matrix: .: (0.048111) - test_message: .: (0.047938) - test_parameters: .: (0.046414) - test_pattern: .: (0.050413) - test_program: .: (0.047298) - test_query_def: .: (0.043501) - test_query_id: .: (0.045537) - test_query_len: .: (0.047441) - test_reference: .: (0.047494) - test_sc_match: .: (0.047051) - test_sc_mismatch: .: (0.045111) - test_statistics: .: (0.045353) - test_version: .: (0.045528) + test_db: .: (0.039728) + test_db_len: .: (0.037074) + test_db_num: .: (0.041449) + test_each_hit: .: (0.046832) + test_each_iteration: .: (0.043280) + test_eff_space: .: (0.041856) + test_entrez_query: .: (0.042913) + test_entropy: .: (0.043351) + test_expect: .: (0.044846) + test_filter: .: (0.047997) + test_gap_extend: .: (0.044661) + test_gap_open: .: (0.039720) + test_hits: .: (0.039004) + test_hsp_len: .: (0.038662) + test_inclusion: .: (0.038011) + test_iterations: .: (0.041273) + test_kappa: .: (0.038290) + test_lambda: .: (0.038414) + test_matrix: .: (0.037554) + test_message: .: (0.038624) + test_parameters: .: (0.038247) + test_pattern: .: (0.040597) + test_program: .: (0.038912) + test_query_def: .: (0.037965) + test_query_id: .: (0.038834) + test_query_len: .: (0.037321) + test_reference: .: (0.038422) + test_sc_match: .: (0.040061) + test_sc_mismatch: .: (0.039327) + test_statistics: .: (0.037588) + test_version: .: (0.038919) Bio::TestBlastReportTabular: - test_db: .: (0.000984) - test_db_len: .: (0.000451) - test_db_num: .: (0.000746) - test_each_hit: .: (0.000987) - test_each_iteration: .: (0.000600) - test_eff_space: .: (0.000412) - test_entrez_query: .: (0.000462) - test_entropy: .: (0.000713) - test_expect: .: (0.000466) - test_filter: .: (0.000411) - test_gap_extend: .: (0.000394) - test_gap_open: .: (0.000472) - test_hits: .: (0.000464) - test_hsp_len: .: (0.000448) - test_inclusion: .: (0.000677) - test_iterations: .: (0.000453) - test_kappa: .: (0.000411) - test_lambda: .: (0.000408) - test_matrix: .: (0.000464) - test_message: .: (0.000554) - test_parameters: .: (0.000481) - test_pattern: .: (0.000455) - test_program: .: (0.000443) - test_query_def: .: (0.000454) - test_query_id: .: (0.000453) - test_query_len: .: (0.000444) - test_reference: .: (0.000728) - test_sc_match: .: (0.000414) - test_sc_mismatch: .: (0.000399) - test_statistics: .: (0.000458) - test_version: .: (0.000414) + test_db: .: (0.001157) + test_db_len: .: (0.000477) + test_db_num: .: (0.000468) + test_each_hit: .: (0.000510) + test_each_iteration: .: (0.000474) + test_eff_space: .: (0.000464) + test_entrez_query: .: (0.000470) + test_entropy: .: (0.000449) + test_expect: .: (0.000439) + test_filter: .: (0.000473) + test_gap_extend: .: (0.000440) + test_gap_open: .: (0.001004) + test_hits: .: (0.000652) + test_hsp_len: .: (0.000471) + test_inclusion: .: (0.000491) + test_iterations: .: (0.000464) + test_kappa: .: (0.000461) + test_lambda: .: (0.000510) + test_matrix: .: (0.000448) + test_message: .: (0.000458) + test_parameters: .: (0.000458) + test_pattern: .: (0.000474) + test_program: .: (0.000467) + test_query_def: .: (0.000470) + test_query_id: .: (0.000465) + test_query_len: .: (0.000440) + test_reference: .: (0.000780) + test_sc_match: .: (0.000560) + test_sc_mismatch: .: (0.000469) + test_statistics: .: (0.000517) + test_version: .: (0.000477) Bio::TestChain: - test_aaseq: .: (0.001152) - test_addLigand: .: (0.000322) - test_addResidue: .: (0.000529) - test_atom_seq: .: (0.000341) - test_comp: .: (0.000429) - test_each: .: (0.000391) - test_each_heterogen: .: (0.000363) - test_each_residue: .: (0.000329) - test_get_heterogen_by_id: .: (0.000385) - test_get_residue_by_id: .: (0.000326) - test_inspect: .: (0.000391) - test_rehash: .: (0.000358) - test_rehash_heterogens: .: (0.000337) - test_rehash_residues: .: (0.000275) - test_square_brace: .: (0.000349) - test_to_s: .: (0.000901) + test_aaseq: .: (0.000940) + test_addLigand: .: (0.000405) + test_addResidue: .: (0.000397) + test_atom_seq: .: (0.000398) + test_comp: .: (0.000459) + test_each: .: (0.000406) + test_each_heterogen: .: (0.000375) + test_each_residue: .: (0.000396) + test_get_heterogen_by_id: .: (0.000368) + test_get_residue_by_id: .: (0.000376) + test_inspect: .: (0.000698) + test_rehash: .: (0.000390) + test_rehash_heterogens: .: (0.000356) + test_rehash_residues: .: (0.000364) + test_square_brace: .: (0.000451) + test_to_s: .: (0.000424) Bio::TestChainFinder: - test_chains: .: (0.000700) - test_each_chain: .: (0.000333) - test_find_chain: .: (0.000396) + test_chains: .: (0.000775) + test_each_chain: .: (0.000425) + test_find_chain: .: (0.000408) Bio::TestClustalWReport::TestClustalWReport: - test_alignment: .: (0.031578) - test_header: .: (0.002487) - test_match_line: .: (0.001660) - test_sequence0: .: (0.002014) - test_sequence1: .: (0.001812) + test_alignment: .: (0.027580) + test_header: .: (0.002380) + test_match_line: .: (0.001754) + test_sequence0: .: (0.001669) + test_sequence1: .: (0.001538) Bio::TestClustalWReport::TestClustalWReportSeqnos: - test_alignment: .: (0.032805) - test_header: .: (0.002906) - test_match_line: .: (0.002445) - test_sequence0: .: (0.002498) - test_sequence1: .: (0.002356) + test_alignment: .: (0.026485) + test_header: .: (0.003169) + test_match_line: .: (0.002251) + test_sequence0: .: (0.002198) + test_sequence1: .: (0.002369) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: - test_alignment: .: (0.045097) - test_header: .: (0.002473) - test_match_line: .: (0.002458) - test_sequence0: .: (0.002074) - test_sequence1: .: (0.001810) + test_alignment: .: (0.037995) + test_header: .: (0.002338) + test_match_line: .: (0.001850) + test_sequence0: .: (0.001722) + test_sequence1: .: (0.001570) Bio::TestCodonTable: - test_Tables: .: (0.000646) - test_accessor: .: (0.000919) - test_definition: .: (0.000301) - test_each: .: (0.000341) - test_revtrans: .: (0.000521) - test_self_accessor: .: (0.000310) - test_self_copy: .: (0.002219) - test_set_accessor: .: (0.291794) - test_start: .: (0.000320) - test_start_codon?: .: (0.000337) - test_stop: .: (0.000316) - test_stop_codon?: .: (0.000326) - test_table: .: (0.000265) + test_Tables: .: (0.000657) + test_accessor: .: (0.000428) + test_definition: .: (0.000331) + test_each: .: (0.000349) + test_revtrans: .: (0.000512) + test_self_accessor: .: (0.000342) + test_self_copy: .: (0.002101) + test_set_accessor: .: (0.272681) + test_start: .: (0.000371) + test_start_codon?: .: (0.000375) + test_stop: .: (0.000315) + test_stop_codon?: .: (0.000348) + test_table: .: (0.000327) Bio::TestCodonTableConstants: - test_Definitions: .: (0.000972) - test_Starts: .: (0.000323) - test_Tables: .: (0.000262) - test_stops: .: (0.000321) + test_Definitions: .: (0.000630) + test_Starts: .: (0.000362) + test_Tables: .: (0.000320) + test_stops: .: (0.000338) Bio::TestColorScheme: - test_buried: .: (0.003234) + test_buried: .: (0.002919) Bio::TestCommand: - test_command_constants: .: (0.000677) - test_escape_shell: .: (0.000427) - test_escape_shell_unix: .: (0.000379) - test_escape_shell_windows: .: (0.000450) - test_make_cgi_params_by_array_of_array: .: (0.000918) - test_make_cgi_params_by_array_of_hash: .: (0.001144) - test_make_cgi_params_by_array_of_string: .: (0.000490) - test_make_cgi_params_by_hash_in_string: .: (0.001685) - test_make_cgi_params_by_hash_in_symbol: .: (0.001427) - test_make_cgi_params_by_string: .: (0.000463) - test_make_command_line: .: (0.000381) - test_make_command_line_unix: .: (0.000369) - test_make_command_line_windows: .: (0.000362) - test_safe_command_line_array: .: (0.000415) - test_safe_command_line_array_passthrough: .: (0.000431) + test_command_constants: .: (0.000642) + test_escape_shell: .: (0.000480) + test_escape_shell_unix: .: (0.000413) + test_escape_shell_windows: .: (0.000418) + test_make_cgi_params_by_array_of_array: .: (0.000928) + test_make_cgi_params_by_array_of_hash: .: (0.001201) + test_make_cgi_params_by_array_of_string: .: (0.000598) + test_make_cgi_params_by_hash_in_string: .: (0.001282) + test_make_cgi_params_by_hash_in_symbol: .: (0.001289) + test_make_cgi_params_by_string: .: (0.000556) + test_make_command_line: .: (0.000436) + test_make_command_line_unix: .: (0.000392) + test_make_command_line_windows: .: (0.000403) + test_safe_command_line_array: .: (0.000905) + test_safe_command_line_array_passthrough: .: (0.000406) Bio::TestContingencyTable: - test_lite_example: .: (0.518730) + test_lite_example: .: (0.496170) Bio::TestDB: - test_entry_id: .: (0.000802) - test_exists: .: (0.000294) - test_fetch: .: (0.000510) - test_get: .: (0.000281) - test_open: .: (0.000286) - test_tags: .: (0.000288) + test_entry_id: .: (0.000738) + test_exists: .: (0.000254) + test_fetch: .: (0.000408) + test_get: .: (0.000261) + test_open: .: (0.000239) + test_tags: .: (0.000224) Bio::TestDataType: - test_const_like_method: .: (0.001687) - test_pdb_achar: .: (0.000644) - test_pdb_atom: .: (0.000628) - test_pdb_character: .: (0.000546) - test_pdb_date: .: (0.000570) - test_pdb_idcode: .: (0.001833) - test_pdb_integer: .: (0.000280) - test_pdb_list: .: (0.000349) - test_pdb_lstring: .: (0.000556) - test_pdb_real: .: (0.000446) - test_pdb_resudue_name: .: (0.000700) - test_pdb_slist: .: (0.000334) - test_pdb_string: .: (0.000597) - test_pdb_stringrj: .: (0.000658) - test_pdb_symop: .: (0.000574) - test_specification_list: .: (0.000343) + test_const_like_method: .: (0.001550) + test_pdb_achar: .: (0.000810) + test_pdb_atom: .: (0.000576) + test_pdb_character: .: (0.000585) + test_pdb_date: .: (0.000612) + test_pdb_idcode: .: (0.000564) + test_pdb_integer: .: (0.000289) + test_pdb_list: .: (0.000366) + test_pdb_lstring: .: (0.000628) + test_pdb_real: .: (0.000521) + test_pdb_resudue_name: .: (0.000668) + test_pdb_slist: .: (0.000363) + test_pdb_string: .: (0.000611) + test_pdb_stringrj: .: (0.000320) + test_pdb_symop: .: (0.000579) + test_specification_list: .: (0.000404) Bio::TestEMBL: - test_ac: .: (0.001596) - test_accession: .: (0.001953) - test_cc: .: (0.001014) - test_de: .: (0.002635) - test_division: .: (0.001121) - test_dr: .: (0.001471) - test_dt: .: (0.000922) - test_dt_created: .: (0.000956) - test_dt_iterator: .: (0.000924) - test_dt_updated: .: (0.002242) - test_each_cds: .: (0.001775) - test_each_gene: .: (0.001380) - test_entry: .: (0.001110) - test_fh: .: (0.000904) - test_ft: .: (0.001528) - test_ft_accessor: .: (0.001428) - test_ft_iterator: .: (0.001808) - test_id_line: .: (0.001166) - test_id_line_data_class: .: (0.000985) - test_id_line_division: .: (0.001166) - test_id_line_entry_name: .: (0.000976) - test_id_line_iterator: .: (0.001183) - test_id_line_molecule_type: .: (0.001159) - test_id_line_sequence_length: .: (0.000976) - test_kw: .: (0.001010) - test_molecule: .: (0.001318) - test_oc: .: (0.001187) - test_og: .: (0.000970) - test_os: .: (0.001110) - test_ref: .: (0.001613) - test_references: .: (0.001791) - test_seq: .: (0.001794) - test_sequence_length: .: (0.001229) - test_sq: .: (0.000988) - test_sq_get: .: (0.001229) - test_sv: .: (0.000964) - test_version: .: (0.001143) -Bio::TestEMBL89: - test_ac: .: (0.001296) - test_accession: .: (0.000979) - test_cc: .: (0.000855) - test_de: .: (0.001247) - test_division: .: (0.001265) - test_dr: .: (0.000982) - test_dt: .: (0.001164) - test_dt_created: .: (0.000925) - test_dt_iterator: .: (0.000954) - test_dt_updated: .: (0.001262) - test_each_cds: .: (0.001337) - test_each_gene: .: (0.001281) - test_entry: .: (0.001486) - test_fh: .: (0.000948) - test_ft: .: (0.001433) - test_ft_accessor: .: (0.001592) - test_ft_iterator: .: (0.001489) - test_id_line: .: (0.000939) - test_id_line_data_class: .: (0.001216) - test_id_line_division: .: (0.001008) - test_id_line_entry_name: .: (0.001035) - test_id_line_iterator: .: (0.001546) - test_id_line_molecule_type: .: (0.001016) - test_id_line_sequence_length: .: (0.001067) - test_id_line_sequence_version: .: (0.001291) - test_kw: .: (0.001104) - test_molecule: .: (0.001165) - test_oc: .: (0.001347) - test_og: .: (0.000896) - test_os: .: (0.001133) - test_ref: .: (0.001353) - test_references: .: (0.001552) - test_seq: .: (0.001480) - test_sequence_length: .: (0.001340) - test_sq: .: (0.001065) - test_sq_get: .: (0.001044) - test_sv: .: (0.001261) + test_ac: .: (0.001787) + test_accession: .: (0.001044) + test_cc: .: (0.000987) + test_de: .: (0.000994) + test_division: .: (0.001010) + test_dr: .: (0.001034) + test_dt: .: (0.001139) + test_dt_created: .: (0.000937) + test_dt_iterator: .: (0.000962) + test_dt_updated: .: (0.000954) + test_each_cds: .: (0.001535) + test_each_gene: .: (0.001362) + test_entry: .: (0.001157) + test_fh: .: (0.000946) + test_ft: .: (0.001379) + test_ft_accessor: .: (0.001359) + test_ft_iterator: .: (0.001419) + test_id_line: .: (0.001027) + test_id_line_data_class: .: (0.001171) + test_id_line_division: .: (0.000998) + test_id_line_entry_name: .: (0.001022) + test_id_line_iterator: .: (0.001057) + test_id_line_molecule_type: .: (0.001241) + test_id_line_sequence_length: .: (0.001080) + test_kw: .: (0.001109) + test_molecule: .: (0.001049) + test_oc: .: (0.001260) + test_og: .: (0.001005) + test_os: .: (0.001030) + test_ref: .: (0.001303) + test_references: .: (0.001841) + test_seq: .: (0.001591) + test_sequence_length: .: (0.001061) + test_sq: .: (0.001035) + test_sq_get: .: (0.001121) + test_sv: .: (0.000970) test_version: .: (0.000990) +Bio::TestEMBL89: + test_ac: .: (0.001276) + test_accession: .: (0.001041) + test_cc: .: (0.001123) + test_de: .: (0.001043) + test_division: .: (0.001128) + test_dr: .: (0.000950) + test_dt: .: (0.000928) + test_dt_created: .: (0.001115) + test_dt_iterator: .: (0.000901) + test_dt_updated: .: (0.000981) + test_each_cds: .: (0.001420) + test_each_gene: .: (0.001502) + test_entry: .: (0.001133) + test_fh: .: (0.000983) + test_ft: .: (0.001536) + test_ft_accessor: .: (0.001315) + test_ft_iterator: .: (0.001431) + test_id_line: .: (0.001154) + test_id_line_data_class: .: (0.001222) + test_id_line_division: .: (0.001145) + test_id_line_entry_name: .: (0.001205) + test_id_line_iterator: .: (0.001253) + test_id_line_molecule_type: .: (0.001226) + test_id_line_sequence_length: .: (0.001131) + test_id_line_sequence_version: .: (0.001009) + test_kw: .: (0.001035) + test_molecule: .: (0.001295) + test_oc: .: (0.001145) + test_og: .: (0.000961) + test_os: .: (0.001073) + test_ref: .: (0.001426) + test_references: .: (0.001650) + test_seq: .: (0.001790) + test_sequence_length: .: (0.001099) + test_sq: .: (0.001265) + test_sq_get: .: (0.000969) + test_sv: .: (0.001131) + test_version: .: (0.001090) Bio::TestEMBLAPI: - test_ac: .: (0.000976) - test_accessions: .: (0.000694) + test_ac: .: (0.000877) + test_accessions: .: (0.000505) Bio::TestEMBLCommon: - test_ac: .: (0.000565) - test_accession: .: (0.000241) - test_accessions: .: (0.000246) - test_de: .: (0.000267) - test_definition: .: (0.000269) - test_description: .: (0.000252) - test_dr: .: (0.000248) - test_keywords: .: (0.000247) - test_kw: .: (0.000488) - test_oc: .: (0.000255) - test_og: .: (0.000227) - test_os: .: (0.000252) - test_ref: .: (0.000447) - test_references: .: (0.000319) + test_ac: .: (0.000739) + test_accession: .: (0.000330) + test_accessions: .: (0.000327) + test_de: .: (0.000308) + test_definition: .: (0.000318) + test_description: .: (0.000320) + test_dr: .: (0.000300) + test_keywords: .: (0.000319) + test_kw: .: (0.000290) + test_oc: .: (0.000288) + test_og: .: (0.000300) + test_os: .: (0.000357) + test_ref: .: (0.000303) + test_references: .: (0.000297) Bio::TestEMBLDB: - test_fetch: .: (0.000763) - test_p_entry2hash: .: (0.000228) + test_fetch: .: (0.000924) + test_p_entry2hash: .: (0.000305) Bio::TestEMBLToBioSequence: - test_classification: .: (0.009604) - test_date_created: .: (0.001579) - test_date_modified: .: (0.001543) - test_definition: .: (0.001388) - test_division: .: (0.001494) - test_entry_id: .: (0.001111) - test_entry_version: .: (0.001099) - test_features: .: (0.001901) - test_keywords: .: (0.001196) - test_molecule_type: .: (0.001226) - test_primary_accession: .: (0.001076) - test_references: .: (0.001948) - test_release_created: .: (0.001302) - test_release_modified: .: (0.001177) - test_secondary_accessions: .: (0.001304) - test_sequence_version: .: (0.001486) - test_species: .: (0.001125) - test_topology: .: (0.001091) + test_classification: .: (0.010623) + test_date_created: .: (0.001624) + test_date_modified: .: (0.001374) + test_definition: .: (0.001382) + test_division: .: (0.001317) + test_entry_id: .: (0.001252) + test_entry_version: .: (0.001334) + test_features: .: (0.001975) + test_keywords: .: (0.001297) + test_molecule_type: .: (0.001323) + test_primary_accession: .: (0.001217) + test_references: .: (0.002304) + test_release_created: .: (0.001187) + test_release_modified: .: (0.001226) + test_secondary_accessions: .: (0.001392) + test_sequence_version: .: (0.001345) + test_species: .: (0.001321) + test_topology: .: (0.001246) Bio::TestEMBLToBioSequenceRoundTrip: - test_classification: .: (0.015689) - test_date_created: .: (0.008196) - test_date_modified: .: (0.007872) - test_definition: .: (0.008101) - test_division: .: (0.007802) - test_entry_id: .: (0.007673) - test_entry_version: .: (0.007885) - test_features: .: (0.009071) - test_keywords: .: (0.008215) - test_molecule_type: .: (0.008638) - test_primary_accession: .: (0.008039) - test_references: .: (0.008965) - test_release_created: .: (0.008442) - test_release_modified: .: (0.007877) - test_secondary_accessions: .: (0.017008) - test_sequence_version: .: (0.017605) - test_species: .: (0.008863) - test_topology: .: (0.009614) + test_classification: .: (0.017023) + test_date_created: .: (0.007783) + test_date_modified: .: (0.007637) + test_definition: .: (0.007887) + test_division: .: (0.007749) + test_entry_id: .: (0.008190) + test_entry_version: .: (0.009015) + test_features: .: (0.010208) + test_keywords: .: (0.009981) + test_molecule_type: .: (0.009827) + test_primary_accession: .: (0.009588) + test_references: .: (0.009271) + test_release_created: .: (0.008304) + test_release_modified: .: (0.008314) + test_secondary_accessions: .: (0.009332) + test_sequence_version: .: (0.008823) + test_species: .: (0.008690) + test_topology: .: (0.008109) Bio::TestFasta: - test_db: .: (0.000603) - test_format: .: (0.000260) - test_format_arg_integer: .: (0.000653) - test_format_arg_str: .: (0.000277) - test_ktup: .: (0.000244) - test_matrix: .: (0.000265) - test_option: .: (0.000375) + test_db: .: (0.000655) + test_format: .: (0.000310) + test_format_arg_integer: .: (0.000364) + test_format_arg_str: .: (0.000403) + test_ktup: .: (0.000338) + test_matrix: .: (0.000317) + test_option: .: (0.000427) test_options: .: (0.000331) - test_output: .: (0.000216) - test_program: .: (0.000252) - test_server: .: (0.000255) + test_output: .: (0.000272) + test_program: .: (0.000307) + test_server: .: (0.000304) Bio::TestFastaDeflineEmb: - test_acc_version: .: (0.000715) - test_accession: .: (0.000310) - test_accessions: .: (0.000311) - test_description: .: (0.000596) - test_descriptions: .: (0.000306) - test_entry_id: .: (0.000278) - test_get_all_by_type: .: (0.000284) - test_gi: .: (0.008277) - test_id_strings: .: (0.000571) - test_list_ids: .: (0.000301) - test_locus: .: (0.000292) - test_words: .: (0.000640) + test_acc_version: .: (0.006817) + test_accession: .: (0.000429) + test_accessions: .: (0.000425) + test_description: .: (0.000363) + test_descriptions: .: (0.000370) + test_entry_id: .: (0.000350) + test_get_all_by_type: .: (0.000370) + test_gi: .: (0.008329) + test_id_strings: .: (0.000545) + test_list_ids: .: (0.000352) + test_locus: .: (0.000383) + test_words: .: (0.000459) Bio::TestFastaDeflineGI1: - test_acc_version: .: (0.000656) - test_accession: .: (0.000440) - test_accessions: .: (0.000398) - test_description: .: (0.000325) - test_descriptions: .: (0.000328) - test_emb: .: (0.000349) - test_entry_id: .: (0.000626) - test_get_all_by_type: .: (0.000366) - test_get_emb: .: (0.008948) - test_gi: .: (0.000477) - test_id_strings: .: (0.000503) - test_list_ids: .: (0.000365) - test_locus: .: (0.000658) - test_words: .: (0.000446) + test_acc_version: .: (0.000733) + test_accession: .: (0.000393) + test_accessions: .: (0.000395) + test_description: .: (0.000456) + test_descriptions: .: (0.000413) + test_emb: .: (0.000505) + test_entry_id: .: (0.000428) + test_get_all_by_type: .: (0.000505) + test_get_emb: .: (0.000469) + test_gi: .: (0.000398) + test_id_strings: .: (0.010204) + test_list_ids: .: (0.000489) + test_locus: .: (0.000434) + test_words: .: (0.000502) Bio::TestFastaDeflineGI2: - test_acc_version: .: (0.000603) - test_accession: .: (0.006035) - test_accessions: .: (0.000347) - test_description: .: (0.000280) - test_descriptions: .: (0.000278) - test_entry_id: .: (0.000276) - test_get_all_by_type: .: (0.000281) - test_gi: .: (0.000315) - test_id_strings: .: (0.006691) - test_list_ids: .: (0.000328) - test_locus: .: (0.000285) - test_sp: .: (0.000328) - test_words: .: (0.000377) + test_acc_version: .: (0.000726) + test_accession: .: (0.000426) + test_accessions: .: (0.000459) + test_description: .: (0.000502) + test_descriptions: .: (0.000440) + test_entry_id: .: (0.000379) + test_get_all_by_type: .: (0.000383) + test_gi: .: (0.000405) + test_id_strings: .: (0.000464) + test_list_ids: .: (0.000335) + test_locus: .: (0.000427) + test_sp: .: (0.000416) + test_words: .: (0.000438) Bio::TestFastaDeflineGIMultiple: - test_acc_version: .: (0.000975) - test_accession: .: (0.007281) - test_accessions: .: (0.000486) - test_description: .: (0.000437) - test_descriptions: .: (0.000439) - test_entry_id: .: (0.000444) - test_get_all_by_type: .: (0.000431) - test_gi: .: (0.000401) - test_id_strings: .: (0.007619) - test_list_ids: .: (0.000449) - test_locus: .: (0.000700) - test_words: .: (0.000729) + test_acc_version: .: (0.000766) + test_accession: .: (0.000485) + test_accessions: .: (0.007474) + test_description: .: (0.000484) + test_descriptions: .: (0.000505) + test_entry_id: .: (0.000480) + test_get_all_by_type: .: (0.000452) + test_gi: .: (0.000437) + test_id_strings: .: (0.005979) + test_list_ids: .: (0.000543) + test_locus: .: (0.000472) + test_words: .: (0.000759) Bio::TestFastaDeflineSce: - test_acc_version: .: (0.006144) - test_accession: .: (0.000430) - test_accessions: .: (0.000374) - test_description: .: (0.000344) - test_descriptions: .: (0.000334) - test_entry_id: .: (0.000398) - test_get_all_by_type: .: (0.000350) - test_gi: .: (0.006623) - test_id_strings: .: (0.000636) - test_list_ids: .: (0.000355) - test_locus: .: (0.000331) - test_words: .: (0.007354) + test_acc_version: .: (0.006923) + test_accession: .: (0.000472) + test_accessions: .: (0.000429) + test_description: .: (0.000395) + test_descriptions: .: (0.000393) + test_entry_id: .: (0.000405) + test_get_all_by_type: .: (0.000429) + test_gi: .: (0.000377) + test_id_strings: .: (0.000745) + test_list_ids: .: (0.000472) + test_locus: .: (0.000481) + test_words: .: (0.000754) Bio::TestFastaDeflineSimple: - test_acc_version: .: (0.000564) - test_accession: .: (0.000504) - test_accessions: .: (0.000274) - test_description: .: (0.000295) - test_descriptions: .: (0.000281) - test_entry_id: .: (0.007143) - test_get_all_by_type: .: (0.000307) - test_gi: .: (0.000253) - test_id_strings: .: (0.000331) - test_list_ids: .: (0.000306) - test_locus: .: (0.000273) - test_words: .: (0.000314) + test_acc_version: .: (0.000767) + test_accession: .: (0.000415) + test_accessions: .: (0.000405) + test_description: .: (0.000347) + test_descriptions: .: (0.000344) + test_entry_id: .: (0.000316) + test_get_all_by_type: .: (0.006179) + test_gi: .: (0.000368) + test_id_strings: .: (0.000401) + test_list_ids: .: (0.000313) + test_locus: .: (0.000309) + test_words: .: (0.000423) Bio::TestFastaDeflineSwissProt: - test_acc_version: .: (0.004281) - test_accession: .: (0.000551) - test_accessions: .: (0.000313) - test_description: .: (0.023211) + test_acc_version: .: (0.005660) + test_accession: .: (0.000393) + test_accessions: .: (0.000364) + test_description: .: (0.019005) test_descriptions: .: (0.000352) - test_entry_id: .: (0.000284) - test_get: .: (0.000300) - test_get_all_by_type: .: (0.000269) - test_id_strings: .: (0.000504) - test_list_ids: .: (0.000286) - test_locus: .: (0.000285) - test_sp: .: (0.000310) - test_words: .: (0.000782) + test_entry_id: .: (0.000339) + test_get: .: (0.000395) + test_get_all_by_type: .: (0.000336) + test_id_strings: .: (0.000588) + test_list_ids: .: (0.000376) + test_locus: .: (0.000357) + test_sp: .: (0.000369) + test_words: .: (0.000529) Bio::TestFastaDeflineTrembl: - test_acc_version: .: (0.000579) - test_accession: .: (0.000334) - test_accessions: .: (0.000924) - test_description: .: (0.000285) - test_descriptions: .: (0.000269) - test_entry_id: .: (0.000530) - test_get: .: (0.000309) - test_get_all_by_type: .: (0.000269) - test_id_strings: .: (0.000512) - test_list_ids: .: (0.000281) - test_locus: .: (0.000294) - test_tr: .: (0.000300) - test_words: .: (0.000540) + test_acc_version: .: (0.000667) + test_accession: .: (0.000447) + test_accessions: .: (0.001003) + test_description: .: (0.000369) + test_descriptions: .: (0.000332) + test_entry_id: .: (0.000337) + test_get: .: (0.000390) + test_get_all_by_type: .: (0.000367) + test_id_strings: .: (0.000628) + test_list_ids: .: (0.000399) + test_locus: .: (0.000356) + test_tr: .: (0.000385) + test_words: .: (0.000610) Bio::TestFastaFirstName: - test_first_name1: .: (0.000566) - test_first_name_multi_identifier: .: (0.000291) - test_first_name_single_worded_defintion: .: (0.000243) - test_no_definition: .: (0.000289) - test_space_before_first_name: .: (0.000289) - test_tabbed_defintion: .: (0.000284) + test_first_name1: .: (0.000636) + test_first_name_multi_identifier: .: (0.000872) + test_first_name_single_worded_defintion: .: (0.000321) + test_no_definition: .: (0.000304) + test_space_before_first_name: .: (0.000314) + test_tabbed_defintion: .: (0.000330) Bio::TestFastaFormat: - test_aalen: .: (0.000783) - test_aaseq: .: (0.000313) - test_acc_version: .: (0.000435) - test_accession: .: (0.000396) - test_accessions: .: (0.000433) - test_data: .: (0.000270) - test_definition: .: (0.000262) - test_entry: .: (0.000269) - test_entry_id: .: (0.001019) - test_entry_overrun: .: (0.000279) - test_first_name: .: (0.000271) - test_gi: .: (0.000371) - test_identifiers: .: (0.000427) - test_length: .: (0.000298) - test_query: .: (0.000331) - test_seq: .: (0.000321) + test_aalen: .: (0.000684) + test_aaseq: .: (0.000369) + test_acc_version: .: (0.000501) + test_accession: .: (0.000501) + test_accessions: .: (0.000461) + test_data: .: (0.000329) + test_definition: .: (0.000306) + test_entry: .: (0.000368) + test_entry_id: .: (0.000418) + test_entry_overrun: .: (0.000378) + test_first_name: .: (0.000344) + test_gi: .: (0.000441) + test_identifiers: .: (0.000484) + test_length: .: (0.000349) + test_query: .: (0.000453) + test_seq: .: (0.000423) Bio::TestFastaFormatConst: - test_delimiter: .: (0.000557) + test_delimiter: .: (0.000577) Bio::TestFastaFormatKeggGenesAA: - test_acc_version: .: (0.000672) - test_data: .: (0.000284) - test_definition: .: (0.000309) - test_entry: .: (0.000277) - test_entry_id: .: (0.005170) - test_first_name: .: (0.000328) + test_acc_version: .: (0.000733) + test_data: .: (0.000360) + test_definition: .: (0.000320) + test_entry: .: (0.000393) + test_entry_id: .: (0.001196) + test_first_name: .: (0.000370) Bio::TestFastaFormatKeggGenesNT: - test_nalen: .: (0.000543) - test_naseq: .: (0.000283) - test_naseq_class: .: (0.000303) + test_nalen: .: (0.000712) + test_naseq: .: (0.000353) + test_naseq_class: .: (0.000375) Bio::TestFastaFormatSwissProt: - test_locus: .: (0.000586) + test_locus: .: (0.000682) Bio::TestFastaInitialize: - test_new_1: .: (0.005439) - test_option: .: (0.000264) - test_option_backward_compatibility: .: (0.000936) + test_new_1: .: (0.001492) + test_option: .: (0.000345) + test_option_backward_compatibility: .: (0.001145) Bio::TestFastaNumericFormat: - test_arg: .: (0.000650) - test_data: .: (0.000354) - test_definition: .: (0.000272) - test_each: .: (0.000347) - test_entry: .: (0.000254) - test_entry_id: .: (0.000290) - test_length: .: (0.000339) - test_to_biosequence: .: (0.006086) + test_arg: .: (0.000742) + test_data: .: (0.000443) + test_definition: .: (0.000321) + test_each: .: (0.000448) + test_entry: .: (0.000364) + test_entry_id: .: (0.000345) + test_length: .: (0.000427) + test_to_biosequence: .: (0.002353) Bio::TestFastaQuery: - test_query: .: (0.000424) - test_self_local: .: (0.000162) - test_self_parser: .: (0.000151) - test_self_remote: .: (0.000732) + test_query: .: (0.000560) + test_self_local: .: (0.000260) + test_self_parser: .: (0.000259) + test_self_remote: .: (0.000212) Bio::TestFastacmd: - test_database: .: (0.000485) - test_fastacmd: .: (0.000212) - test_methods: .: (0.004482) + test_database: .: (0.000762) + test_fastacmd: .: (0.000301) + test_methods: .: (0.000382) Bio::TestFastq::TestFastq_error_diff_ids: - test_validate_format: .: (0.001538) + test_validate_format: .: (0.001707) Bio::TestFastq::TestFastq_error_double_qual: - test_validate_format: .: (0.001281) + test_validate_format: .: (0.001512) Bio::TestFastq::TestFastq_error_double_seq: - test_validate_format: .: (0.001231) + test_validate_format: .: (0.001419) Bio::TestFastq::TestFastq_error_long_qual: - test_validate_format: .: (0.001319) + test_validate_format: .: (0.001576) Bio::TestFastq::TestFastq_error_no_qual: - test_validate_format: .: (0.001360) + test_validate_format: .: (0.001655) Bio::TestFastq::TestFastq_error_qual_del: - test_validate_format: .: (0.001285) + test_validate_format: .: (0.001460) Bio::TestFastq::TestFastq_error_qual_escape: - test_validate_format: .: (0.005887) + test_validate_format: .: (0.002139) Bio::TestFastq::TestFastq_error_qual_null: - test_validate_format: .: (0.001345) + test_validate_format: .: (0.001339) Bio::TestFastq::TestFastq_error_qual_space: - test_validate_format: .: (0.001485) + test_validate_format: .: (0.001400) Bio::TestFastq::TestFastq_error_qual_tab: - test_validate_format: .: (0.001241) + test_validate_format: .: (0.001335) Bio::TestFastq::TestFastq_error_qual_unit_sep: - test_validate_format: .: (0.005471) + test_validate_format: .: (0.002066) Bio::TestFastq::TestFastq_error_qual_vtab: - test_validate_format: .: (0.001254) + test_validate_format: .: (0.001441) Bio::TestFastq::TestFastq_error_short_qual: - test_validate_format: .: (0.001162) + test_validate_format: .: (0.001448) Bio::TestFastq::TestFastq_error_spaces: - test_validate_format: .: (0.003468) + test_validate_format: .: (0.003810) Bio::TestFastq::TestFastq_error_tabs: - test_validate_format: .: (0.003586) + test_validate_format: .: (0.004306) Bio::TestFastq::TestFastq_error_trunc_at_plus: - test_validate_format: .: (0.001297) + test_validate_format: .: (0.001571) Bio::TestFastq::TestFastq_error_trunc_at_qual: - test_validate_format: .: (0.001179) + test_validate_format: .: (0.001326) Bio::TestFastq::TestFastq_error_trunc_at_seq: - test_validate_format: .: (0.005988) + test_validate_format: .: (0.001921) Bio::TestFastq::TestFastq_illumina_full_range: - test_error_probabilities_as_illumina: .: (0.030260) - test_error_probabilities_as_sanger: .: (0.028846) - test_error_probabilities_as_solexa: .: (0.028985) - test_quality_scores_as_illumina: .: (0.001482) - test_quality_scores_as_sanger: .: (0.000877) - test_quality_scores_as_solexa: .: (0.000969) - test_validate_format: .: (0.001542) + test_error_probabilities_as_illumina: .: (0.018886) + test_error_probabilities_as_sanger: .: (0.018176) + test_error_probabilities_as_solexa: .: (0.019620) + test_quality_scores_as_illumina: .: (0.001532) + test_quality_scores_as_sanger: .: (0.000939) + test_quality_scores_as_solexa: .: (0.001837) + test_validate_format: .: (0.001848) Bio::TestFastq::TestFastq_longreads_original_sanger: - test_definition: .: (0.003424) - test_entry_id: .: (0.007430) - test_error_probabilities: .: (0.511847) - test_nalen: .: (0.007387) - test_naseq: .: (0.006771) - test_quality_scores: .: (0.010318) - test_quality_string: .: (0.002303) - test_roundtrip: .: (0.486921) - test_seq: .: (0.006937) - test_sequence_string: .: (0.002784) - test_to_biosequence: .: (0.686911) - test_to_biosequence_and_output: .: (0.014110) - test_to_s: .: (0.002847) - test_validate_format: .: (0.002512) - test_validate_format_with_array: .: (0.003266) + test_definition: .: (0.003889) + test_entry_id: .: (0.003361) + test_error_probabilities: .: (0.473756) + test_nalen: .: (0.003166) + test_naseq: .: (0.003232) + test_quality_scores: .: (0.005387) + test_quality_string: .: (0.002943) + test_roundtrip: .: (0.479791) + test_seq: .: (0.003604) + test_sequence_string: .: (0.002883) + test_to_biosequence: .: (0.461511) + test_to_biosequence_and_output: .: (0.015601) + test_to_s: .: (0.002927) + test_validate_format: .: (0.003361) + test_validate_format_with_array: .: (0.003547) Bio::TestFastq::TestFastq_mask: - test_mask_20: .: (0.001350) - test_mask_20_with_empty_string: .: (0.001064) - test_mask_20_with_longer_string: .: (0.001019) - test_mask_20_with_x: .: (0.000991) - test_mask_60: .: (0.001788) + test_mask_20: .: (0.001486) + test_mask_20_with_empty_string: .: (0.001144) + test_mask_20_with_longer_string: .: (0.001154) + test_mask_20_with_x: .: (0.001069) + test_mask_60: .: (0.001347) Bio::TestFastq::TestFastq_sanger_full_range: - test_error_probabilities_as_illumina: .: (0.021481) - test_error_probabilities_as_sanger: .: (0.021443) - test_error_probabilities_as_solexa: .: (0.024958) - test_quality_scores_as_illumina: .: (0.001072) - test_quality_scores_as_sanger: .: (0.001082) - test_quality_scores_as_solexa: .: (0.001690) - test_validate_format: .: (0.001824) + test_error_probabilities_as_illumina: .: (0.023612) + test_error_probabilities_as_sanger: .: (0.023483) + test_error_probabilities_as_solexa: .: (0.026935) + test_quality_scores_as_illumina: .: (0.001182) + test_quality_scores_as_sanger: .: (0.000929) + test_quality_scores_as_solexa: .: (0.001696) + test_validate_format: .: (0.001913) Bio::TestFastq::TestFastq_solexa_full_range: - test_error_probabilities_as_illumina: .: (0.016705) - test_error_probabilities_as_sanger: .: (0.016296) - test_error_probabilities_as_solexa: .: (0.016868) - test_quality_scores_as_illumina: .: (0.001508) - test_quality_scores_as_sanger: .: (0.001034) - test_quality_scores_as_solexa: .: (0.000795) - test_validate_format: .: (0.002456) + test_error_probabilities_as_illumina: .: (0.018109) + test_error_probabilities_as_sanger: .: (0.017735) + test_error_probabilities_as_solexa: .: (0.018104) + test_quality_scores_as_illumina: .: (0.002060) + test_quality_scores_as_sanger: .: (0.001168) + test_quality_scores_as_solexa: .: (0.000914) + test_validate_format: .: (0.001770) Bio::TestFeature: - test_append: .: (0.000587) - test_append_nil: .: (0.000306) - test_assoc: .: (0.000271) - test_each: .: (0.000218) - test_feature: .: (0.000204) - test_locations: .: (0.000557) - test_new: .: (0.000243) - test_position: .: (0.000213) - test_qualifiers: .: (0.000211) + test_append: .: (0.001221) + test_append_nil: .: (0.000360) + test_assoc: .: (0.000353) + test_each: .: (0.000300) + test_feature: .: (0.000279) + test_locations: .: (0.000488) + test_new: .: (0.000294) + test_position: .: (0.000278) + test_qualifiers: .: (0.000323) Bio::TestFeatures: - test_append: .: (0.000640) - test_arg: .: (0.000316) - test_each: .: (0.000253) - test_features: .: (0.000257) + test_append: .: (0.000751) + test_arg: .: (0.000354) + test_each: .: (0.000359) + test_features: .: (0.000354) Bio::TestFlatFile::TestDefaultAutoDetect: - test_aaindex1: .: (0.002953) - test_aaindex2: .: (0.000569) - test_blast: .: (0.000479) - test_blastxml: .: (0.001420) - test_embl: .: (0.000610) - test_embl_oldrelease: .: (0.000607) - test_fastaformat: .: (0.000889) - test_fastanumericformat: .: (0.000603) - test_fastq: .: (0.000483) - test_genbank: .: (0.000494) - test_genpept: .: (0.000869) - test_hmmer: .: (0.000670) - test_maxml_cluster: .: (0.007632) - test_maxml_sequence: .: (0.000623) - test_medline: .: (0.000630) - test_prosite: .: (0.006475) + test_aaindex1: .: (0.002958) + test_aaindex2: .: (0.000662) + test_blast: .: (0.000565) + test_blastxml: .: (0.001370) + test_embl: .: (0.000706) + test_embl_oldrelease: .: (0.000666) + test_fastaformat: .: (0.001069) + test_fastanumericformat: .: (0.000476) + test_fastq: .: (0.000573) + test_genbank: .: (0.000617) + test_genpept: .: (0.000622) + test_hmmer: .: (0.000681) + test_maxml_cluster: .: (0.008824) + test_maxml_sequence: .: (0.000422) + test_medline: .: (0.000510) + test_prosite: .: (0.006457) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. -.: (0.005744) - test_transfac: .: (0.004160) +.: (0.005687) + test_transfac: .: (0.004520) Bio::TestFlatFile::TestFlatFileClassMethod: - test_auto_0arg: .: (0.000692) - test_auto_1arg_filename: .: (0.001349) - test_auto_1arg_io: .: (0.000865) - test_auto_1arg_io_with_block: .: (0.001808) - test_auto_1arg_with_block: .: (0.001781) - test_auto_2arg_filename_mode: .: (0.001130) - test_auto_2arg_filename_mode_with_block: .: (0.001690) - test_auto_3arg: .: (0.000850) - test_auto_3arg_with_block: .: (0.001580) - test_foreach: .: (0.001793) - test_new_2arg_class: .: (0.000549) - test_new_2arg_nil: .: (0.000774) - test_open_0arg: .: (0.000372) - test_open_1arg_class: .: (0.000297) - test_open_1arg_filename: .: (0.000814) - test_open_1arg_io: .: (0.000826) - test_open_1arg_io_with_block: .: (0.001678) - test_open_1arg_nil: .: (0.000639) - test_open_1arg_with_block: .: (0.001800) - test_open_2arg_autodetect: .: (0.000835) - test_open_2arg_autodetect_io: .: (0.000800) - test_open_2arg_autodetect_io_with_block: .: (0.001773) - test_open_2arg_autodetect_with_block: .: (0.001972) - test_open_2arg_class: .: (0.000762) - test_open_2arg_class_io: .: (0.000488) - test_open_2arg_class_io_with_block: .: (0.001254) - test_open_2arg_class_with_block: .: (0.001222) - test_open_2arg_filename_mode: .: (0.001059) - test_open_2arg_filename_mode_with_block: .: (0.001577) - test_open_3arg: .: (0.002291) - test_open_3arg_with_block: .: (0.004123) - test_open_4arg: .: (0.003947) - test_to_a: .: (0.001351) + test_auto_0arg: .: (0.000790) + test_auto_1arg_filename: .: (0.001142) + test_auto_1arg_io: .: (0.000982) + test_auto_1arg_io_with_block: .: (0.002025) + test_auto_1arg_with_block: .: (0.001789) + test_auto_2arg_filename_mode: .: (0.000978) + test_auto_2arg_filename_mode_with_block: .: (0.002220) + test_auto_3arg: .: (0.001004) + test_auto_3arg_with_block: .: (0.001816) + test_foreach: .: (0.001551) + test_new_2arg_class: .: (0.000556) + test_new_2arg_nil: .: (0.001263) + test_open_0arg: .: (0.000504) + test_open_1arg_class: .: (0.000395) + test_open_1arg_filename: .: (0.000969) + test_open_1arg_io: .: (0.000923) + test_open_1arg_io_with_block: .: (0.001954) + test_open_1arg_nil: .: (0.000393) + test_open_1arg_with_block: .: (0.001812) + test_open_2arg_autodetect: .: (0.001351) + test_open_2arg_autodetect_io: .: (0.000915) + test_open_2arg_autodetect_io_with_block: .: (0.001840) + test_open_2arg_autodetect_with_block: .: (0.001823) + test_open_2arg_class: .: (0.000555) + test_open_2arg_class_io: .: (0.000948) + test_open_2arg_class_io_with_block: .: (0.001633) + test_open_2arg_class_with_block: .: (0.001445) + test_open_2arg_filename_mode: .: (0.000969) + test_open_2arg_filename_mode_with_block: .: (0.001871) + test_open_3arg: .: (0.002366) + test_open_3arg_with_block: .: (0.004630) + test_open_4arg: .: (0.004388) + test_to_a: .: (0.001508) Bio::TestFlatFile::TestFlatFileFastaFormat: - test_autodetect: .: (0.001256) - test_close: .: (0.000417) - test_dbclass: .: (0.000374) - test_dbclass_eq: .: (0.000452) - test_dbclass_nil: .: (0.000957) - test_each: .: (0.000742) - test_each_entry: .: (0.001248) - test_ended_pos: .: (0.000665) - test_entry_pos_flag: .: (0.000489) - test_entry_raw: .: (0.000855) - test_eof?: .: (0.000966) - test_next_entry: .: (0.001273) - test_path: .: (0.000516) - test_pos: .: (0.000569) - test_raw: .: (0.001024) - test_rewind: .: (0.000604) - test_start_pos: .: (0.000638) - test_start_pos_ended_pos_not_recorded: .: (0.000759) - test_to_io: .: (0.000423) + test_autodetect: .: (0.001283) + test_close: .: (0.000482) + test_dbclass: .: (0.000479) + test_dbclass_eq: .: (0.000569) + test_dbclass_nil: .: (0.001125) + test_each: .: (0.000876) + test_each_entry: .: (0.001276) + test_ended_pos: .: (0.000792) + test_entry_pos_flag: .: (0.000581) + test_entry_raw: .: (0.000999) + test_eof?: .: (0.000917) + test_next_entry: .: (0.001648) + test_path: .: (0.000474) + test_pos: .: (0.000658) + test_raw: .: (0.001012) + test_rewind: .: (0.000689) + test_start_pos: .: (0.000761) + test_start_pos_ended_pos_not_recorded: .: (0.000826) + test_to_io: .: (0.000533) Bio::TestFlatFile::TestFlatFileWithCustomClass: - test_simpleformat: .: (0.000951) - test_simpleformat2: .: (0.000519) + test_simpleformat: .: (0.000860) + test_simpleformat2: .: (0.000599) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: - test_close: .: (0.000533) - test_eof_false_after_prefetch: .: (0.000925) - test_eof_false_first: .: (0.000284) - test_eof_true: .: (0.000474) - test_getc: .: (0.000324) - test_getc_after_prefetch: .: (0.000300) - test_gets: .: (0.000295) - test_gets_equal_prefetch_gets: .: (0.000327) - test_gets_paragraph_mode: .: (0.000463) - test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000693) - test_gets_paragraph_mode_within_buffer: .: (0.001047) - test_gets_rs: .: (0.000422) - test_gets_rs_equal_prefetch_gets: .: (0.000428) - test_gets_rs_within_buffer: .: (0.001010) - test_pos: .: (0.000344) - test_pos=: .: (0.000337) - test_prefetch_buffer: .: (0.000295) - test_prefetch_gets: .: (0.000556) - test_prefetch_gets_with_arg: .: (0.000388) - test_rewind: .: (0.000294) - test_skip_spaces: .: (0.000334) - test_to_io: .: (0.000319) - test_ungetc: .: (0.000379) - test_ungetc_after_prefetch: .: (0.000349) - test_ungets: .: (0.000401) + test_close: .: (0.000636) + test_eof_false_after_prefetch: .: (0.000961) + test_eof_false_first: .: (0.000370) + test_eof_true: .: (0.000650) + test_getc: .: (0.000381) + test_getc_after_prefetch: .: (0.000363) + test_gets: .: (0.000371) + test_gets_equal_prefetch_gets: .: (0.000446) + test_gets_paragraph_mode: .: (0.000507) + test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000766) + test_gets_paragraph_mode_within_buffer: .: (0.000962) + test_gets_rs: .: (0.000508) + test_gets_rs_equal_prefetch_gets: .: (0.000560) + test_gets_rs_within_buffer: .: (0.000919) + test_pos: .: (0.000457) + test_pos=: .: (0.000711) + test_prefetch_buffer: .: (0.000440) + test_prefetch_gets: .: (0.000439) + test_prefetch_gets_with_arg: .: (0.000473) + test_rewind: .: (0.000391) + test_skip_spaces: .: (0.000419) + test_to_io: .: (0.000392) + test_ungetc: .: (0.000396) + test_ungetc_after_prefetch: .: (0.000422) + test_ungets: .: (0.000501) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: - test_self_for_io: .: (0.000808) - test_self_open_file: .: (0.000352) - test_self_open_file_with_block: .: (0.000401) + test_self_for_io: .: (0.000713) + test_self_open_file: .: (0.000478) + test_self_open_file_with_block: .: (0.000527) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: - test_parse_file_open_arg_int_opt: .: (0.000611) - test_parse_file_open_arg_int_perm: .: (0.000236) - test_parse_file_open_arg_int_perm_opt: .: (0.000222) - test_parse_file_open_arg_integer: .: (0.000227) - test_parse_file_open_arg_nil: .: (0.000243) - test_parse_file_open_arg_opt: .: (0.000314) - test_parse_file_open_arg_opt_with_integer_mode: .: (0.000271) - test_parse_file_open_arg_str: .: (0.000252) - test_parse_file_open_arg_str_opt: .: (0.000285) - test_parse_file_open_arg_str_perm: .: (0.000297) - test_parse_file_open_arg_str_perm_opt: .: (0.000280) - test_parse_file_open_arg_str_with_enc: .: (0.000273) - test_parse_file_open_arg_str_with_ext_enc: .: (0.000258) - test_parse_file_open_mode_integer: .: (0.000217) - test_parse_file_open_mode_nil: .: (0.000473) - test_parse_file_open_mode_str: .: (0.000263) - test_parse_file_open_mode_str_with_enc: .: (0.000641) - test_parse_file_open_mode_str_with_ext_enc: .: (0.000359) + test_parse_file_open_arg_int_opt: .: (0.000924) + test_parse_file_open_arg_int_perm: .: (0.000314) + test_parse_file_open_arg_int_perm_opt: .: (0.000319) + test_parse_file_open_arg_integer: .: (0.000299) + test_parse_file_open_arg_nil: .: (0.000295) + test_parse_file_open_arg_opt: .: (0.000460) + test_parse_file_open_arg_opt_with_integer_mode: .: (0.000356) + test_parse_file_open_arg_str: .: (0.000326) + test_parse_file_open_arg_str_opt: .: (0.000359) + test_parse_file_open_arg_str_perm: .: (0.000337) + test_parse_file_open_arg_str_perm_opt: .: (0.000337) + test_parse_file_open_arg_str_with_enc: .: (0.000350) + test_parse_file_open_arg_str_with_ext_enc: .: (0.000373) + test_parse_file_open_mode_integer: .: (0.000295) + test_parse_file_open_mode_nil: .: (0.000324) + test_parse_file_open_mode_str: .: (0.000325) + test_parse_file_open_mode_str_with_enc: .: (0.000733) + test_parse_file_open_mode_str_with_ext_enc: .: (0.000354) Bio::TestFlatFileSplitter::TestTemplate: - test_dbclass: .: (0.000528) - test_entry: .: (0.000275) - test_entry_ended_pos: .: (0.000252) - test_entry_pos_flag: .: (0.000473) - test_entry_start_pos: .: (0.000271) - test_get_entry: .: (0.000336) - test_rewind: .: (0.000289) - test_skip_leader: .: (0.000299) - test_stream: .: (0.000232) - test_stream_pos: .: (0.000354) + test_dbclass: .: (0.000627) + test_entry: .: (0.000363) + test_entry_ended_pos: .: (0.000345) + test_entry_pos_flag: .: (0.000384) + test_entry_start_pos: .: (0.000335) + test_get_entry: .: (0.000457) + test_rewind: .: (0.000357) + test_skip_leader: .: (0.000374) + test_stream: .: (0.000328) + test_stream_pos: .: (0.000379) Bio::TestFlatFileSplitter::TestDefault: - test_delimiter: .: (0.000543) - test_delimiter_overrun: .: (0.000236) - test_entry: .: (0.000593) - test_entry_ended_pos: .: (0.000327) - test_entry_ended_pos_default_nil: .: (0.000358) - test_entry_start_pos: .: (0.000575) - test_entry_start_pos_default_nil: .: (0.000357) - test_get_entry: .: (0.000574) - test_get_parsed_entry: .: (0.000600) - test_header: .: (0.000262) - test_skip_leader: .: (0.000362) - test_skip_leader_without_header: .: (0.000363) + test_delimiter: .: (0.000649) + test_delimiter_overrun: .: (0.000651) + test_entry: .: (0.000447) + test_entry_ended_pos: .: (0.000398) + test_entry_ended_pos_default_nil: .: (0.000424) + test_entry_start_pos: .: (0.000399) + test_entry_start_pos_default_nil: .: (0.000367) + test_get_entry: .: (0.000688) + test_get_parsed_entry: .: (0.000729) + test_header: .: (0.000325) + test_skip_leader: .: (0.000489) + test_skip_leader_without_header: .: (0.000465) Bio::TestFlatFileSplitter::TestLineOriented: - test_dbclass: .: (0.000783) - test_entry_ended_pos: .: (0.000605) - test_entry_start_pos: .: (0.001082) - test_flag_to_fetch_header: .: (0.000530) - test_get_entry: .: (0.000775) - test_get_parsed_entry: .: (0.000812) - test_rewind: .: (0.000610) - test_skip_leader: .: (0.000861) + test_dbclass: .: (0.001192) + test_entry_ended_pos: .: (0.000717) + test_entry_start_pos: .: (0.000744) + test_flag_to_fetch_header: .: (0.000635) + test_get_entry: .: (0.000912) + test_get_parsed_entry: .: (0.000919) + test_rewind: .: (0.000855) + test_skip_leader: .: (0.000440) Bio::TestGCGMsf: - test_alignment: .: (0.002463) - test_checksum: .: (0.000848) - test_compcheck: .: (0.000575) - test_date: .: (0.007535) - test_description: .: (0.000639) - test_entry_id: .: (0.000602) - test_gap_length_weight: .: (0.000600) - test_gap_weight: .: (0.000599) - test_heading: .: (0.000869) - test_length: .: (0.001078) - test_seq_type: .: (0.000658) - test_symbol_comparison_table: .: (0.000591) - test_validate_checksum: .: (0.004434) + test_alignment: .: (0.002860) + test_checksum: .: (0.000712) + test_compcheck: .: (0.000729) + test_date: .: (0.000710) + test_description: .: (0.001249) + test_entry_id: .: (0.000673) + test_gap_length_weight: .: (0.000723) + test_gap_weight: .: (0.000692) + test_heading: .: (0.000697) + test_length: .: (0.000661) + test_seq_type: .: (0.001140) + test_symbol_comparison_table: .: (0.000717) + test_validate_checksum: .: (0.004497) Bio::TestGFF: - test_record_class: .: (0.001636) - test_records: .: (0.000891) + test_record_class: .: (0.001439) + test_records: .: (0.001047) Bio::TestGFF2: - test_const_version: .: (0.001606) - test_gff_version: .: (0.001544) - test_metadata: .: (0.001072) - test_metadata_size: .: (0.001034) - test_records_size: .: (0.001461) - test_to_s: .: (0.002050) + test_const_version: .: (0.001576) + test_gff_version: .: (0.001243) + test_metadata: .: (0.001747) + test_metadata_size: .: (0.001209) + test_records_size: .: (0.001141) + test_to_s: .: (0.002522) Bio::TestGFF2ComplexAttributes: - test_attributes_case1: .: (0.000618) - test_attributes_case2: .: (0.000494) - test_attributes_incompatible_backslash_semicolon: .: (0.000874) + test_attributes_case1: .: (0.000721) + test_attributes_case2: .: (0.000537) + test_attributes_incompatible_backslash_semicolon: .: (0.000627) Bio::TestGFF2MetaData: - test_data: .: (0.000682) - test_directive: .: (0.000222) - test_parse: .: (0.000250) + test_data: .: (0.000606) + test_directive: .: (0.000302) + test_parse: .: (0.000372) Bio::TestGFF2Record: - test_attribute: .: (0.001181) - test_attribute_nonexistent: .: (0.000632) - test_attributes: .: (0.000903) - test_attributes_to_hash: .: (0.001129) - test_comment_only?: .: (0.000668) - test_delete_attribute: .: (0.000716) - test_delete_attribute_multiple: .: (0.000927) - test_delete_attribute_multiple2: .: (0.000834) - test_delete_attribute_multiple_nil: .: (0.000734) - test_delete_attribute_nil: .: (0.000764) - test_delete_attribute_nonexistent: .: (0.000861) - test_delete_attributes: .: (0.000859) - test_delete_attributes_multiple: .: (0.000784) - test_delete_attributes_nonexistent: .: (0.000775) - test_end: .: (0.000760) - test_eqeq: .: (0.001934) - test_eqeq_false: .: (0.001420) - test_feature: .: (0.000838) - test_frame: .: (0.000986) - test_get_attribute: .: (0.000902) - test_get_attribute_nonexistent: .: (0.000621) - test_get_attributes: .: (0.001118) - test_get_attributes_nonexistent: .: (0.000641) - test_replace_attributes: .: (0.001266) - test_replace_attributes_multiple_multiple_over: .: (0.000774) - test_replace_attributes_multiple_multiple_same: .: (0.001113) - test_replace_attributes_multiple_multiple_two: .: (0.000751) - test_replace_attributes_multiple_single: .: (0.000770) - test_replace_attributes_nonexistent: .: (0.000728) - test_replace_attributes_nonexistent_multiple: .: (0.001259) - test_replace_attributes_single_multiple: .: (0.000741) - test_score: .: (0.000649) - test_self_parse: .: (0.001650) - test_seqname: .: (0.000977) - test_set_attribute: .: (0.000717) - test_set_attribute_multiple: .: (0.000883) - test_set_attribute_nonexistent: .: (0.000712) - test_sort_attributes_by_tag!: .: (0.000955) - test_sort_attributes_by_tag_bang_test2: .: (0.001301) - test_sort_attributes_by_tag_bang_with_block: .: (0.000858) - test_source: .: (0.000860) - test_start: .: (0.000617) - test_strand: .: (0.000604) - test_to_s: .: (0.001055) + test_attribute: .: (0.001344) + test_attribute_nonexistent: .: (0.000791) + test_attributes: .: (0.000802) + test_attributes_to_hash: .: (0.000828) + test_comment_only?: .: (0.000711) + test_delete_attribute: .: (0.001253) + test_delete_attribute_multiple: .: (0.000879) + test_delete_attribute_multiple2: .: (0.000976) + test_delete_attribute_multiple_nil: .: (0.000849) + test_delete_attribute_nil: .: (0.000868) + test_delete_attribute_nonexistent: .: (0.000852) + test_delete_attributes: .: (0.001441) + test_delete_attributes_multiple: .: (0.000869) + test_delete_attributes_nonexistent: .: (0.000860) + test_end: .: (0.000754) + test_eqeq: .: (0.002270) + test_eqeq_false: .: (0.001657) + test_feature: .: (0.000722) + test_frame: .: (0.000780) + test_get_attribute: .: (0.000961) + test_get_attribute_nonexistent: .: (0.000746) + test_get_attributes: .: (0.001691) + test_get_attributes_nonexistent: .: (0.000696) + test_replace_attributes: .: (0.000849) + test_replace_attributes_multiple_multiple_over: .: (0.000860) + test_replace_attributes_multiple_multiple_same: .: (0.001042) + test_replace_attributes_multiple_multiple_two: .: (0.000864) + test_replace_attributes_multiple_single: .: (0.001388) + test_replace_attributes_nonexistent: .: (0.000904) + test_replace_attributes_nonexistent_multiple: .: (0.000830) + test_replace_attributes_single_multiple: .: (0.000828) + test_score: .: (0.000769) + test_self_parse: .: (0.001717) + test_seqname: .: (0.001237) + test_set_attribute: .: (0.000825) + test_set_attribute_multiple: .: (0.001084) + test_set_attribute_nonexistent: .: (0.000815) + test_sort_attributes_by_tag!: .: (0.001044) + test_sort_attributes_by_tag_bang_test2: .: (0.000999) + test_sort_attributes_by_tag_bang_with_block: .: (0.000954) + test_source: .: (0.001204) + test_start: .: (0.000711) + test_strand: .: (0.000784) + test_to_s: .: (0.001110) Bio::TestGFF2RecordEmpty: - test_comment: .: (0.000901) - test_comment_eq: .: (0.000255) - test_comment_only?: .: (0.000238) - test_comment_only_false: .: (0.000235) - test_to_s: .: (0.000267) - test_to_s_not_empty: .: (0.000444) + test_comment: .: (0.000663) + test_comment_eq: .: (0.000335) + test_comment_only?: .: (0.000340) + test_comment_only_false: .: (0.000363) + test_to_s: .: (0.000345) + test_to_s_not_empty: .: (0.000514) Bio::TestGFF3: - test_const_version: .: (0.002416) - test_gff_version: .: (0.001407) - test_records: .: (0.002364) - test_sequence_regions: .: (0.001449) - test_sequences: .: (0.001708) - test_to_s: .: (0.002721) + test_const_version: .: (0.002568) + test_gff_version: .: (0.001482) + test_records: .: (0.002382) + test_sequence_regions: .: (0.001969) + test_sequences: .: (0.001972) + test_to_s: .: (0.003360) Bio::TestGFF3MetaData: - test_data: .: (0.000479) - test_directive: .: (0.000212) - test_parse: .: (0.000249) + test_data: .: (0.000592) + test_directive: .: (0.000300) + test_parse: .: (0.000349) Bio::TestGFF3Record: - test_attributes: .: (0.002240) - test_end: .: (0.000591) - test_feature: .: (0.000571) - test_frame: .: (0.000611) - test_id: .: (0.000583) - test_score: .: (0.000590) - test_seqname: .: (0.001111) - test_source: .: (0.000573) - test_start: .: (0.000623) - test_strand: .: (0.000593) - test_to_s: .: (0.001714) - test_to_s_attr_order_changed: .: (0.001179) + test_attributes: .: (0.001047) + test_end: .: (0.001521) + test_feature: .: (0.000698) + test_frame: .: (0.000664) + test_id: .: (0.000774) + test_score: .: (0.000702) + test_seqname: .: (0.000688) + test_source: .: (0.001286) + test_start: .: (0.000727) + test_strand: .: (0.000663) + test_to_s: .: (0.001086) + test_to_s_attr_order_changed: .: (0.001336) Bio::TestGFF3RecordEscape: - test_escape: .: (0.000611) - test_escape_attribute: .: (0.000592) - test_escape_seqid: .: (0.000410) - test_unescape: .: (0.000380) + test_escape: .: (0.000738) + test_escape_attribute: .: (0.000492) + test_escape_seqid: .: (0.000501) + test_unescape: .: (0.000563) Bio::TestGFF3RecordGap: - test___scan_gap: .: (0.001449) - test_eqeq: .: (0.000537) - test_new_from_sequences_na: .: (0.000770) - test_new_from_sequences_na_aa: .: (0.000860) - test_new_from_sequences_na_aa_boundary_gap: .: (0.001540) - test_new_from_sequences_na_aa_example: .: (0.000946) - test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000774) - test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000683) - test_process_sequences_na: .: (0.000770) - test_process_sequences_na_aa: .: (0.000744) - test_process_sequences_na_aa_reverse_frameshift: .: (0.000546) - test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000558) - test_process_sequences_na_aa_tooshort: .: (0.000896) - test_process_sequences_na_tooshort: .: (0.000686) - test_to_s: .: (0.000749) + test___scan_gap: .: (0.001010) + test_eqeq: .: (0.000675) + test_new_from_sequences_na: .: (0.000749) + test_new_from_sequences_na_aa: .: (0.001041) + test_new_from_sequences_na_aa_boundary_gap: .: (0.002058) + test_new_from_sequences_na_aa_example: .: (0.001018) + test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000934) + test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.000882) + test_process_sequences_na: .: (0.000737) + test_process_sequences_na_aa: .: (0.000610) + test_process_sequences_na_aa_reverse_frameshift: .: (0.000598) + test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000627) + test_process_sequences_na_aa_tooshort: .: (0.001738) + test_process_sequences_na_tooshort: .: (0.000736) + test_to_s: .: (0.000619) Bio::TestGFF3RecordMisc: - test_attributes_none: .: (0.000655) - test_attributes_one: .: (0.000361) - test_attributes_with_escaping: .: (0.000390) - test_id_multiple: .: (0.000628) - test_id_multiple2: .: (0.000829) - test_id_replace: .: (0.000403) - test_id_set: .: (0.000525) - test_initialize_9: .: (0.000237) - test_phase: .: (0.000439) - test_score: .: (0.000872) - test_to_s_void: .: (0.000312) + test_attributes_none: .: (0.000829) + test_attributes_one: .: (0.000451) + test_attributes_with_escaping: .: (0.000465) + test_id_multiple: .: (0.000718) + test_id_multiple2: .: (0.001262) + test_id_replace: .: (0.000516) + test_id_set: .: (0.000536) + test_initialize_9: .: (0.000289) + test_phase: .: (0.000458) + test_score: .: (0.000465) + test_to_s_void: .: (0.000363) Bio::TestGFF3RecordTarget: - test_end: .: (0.000586) - test_parse: .: (0.000471) - test_start: .: (0.000270) - test_strand: .: (0.000321) - test_target_id: .: (0.000281) - test_to_s: .: (0.000457) + test_end: .: (0.000714) + test_parse: .: (0.000553) + test_start: .: (0.001087) + test_strand: .: (0.000416) + test_target_id: .: (0.000438) + test_to_s: .: (0.000755) Bio::TestGFF3SequenceRegion: - test_end: .: (0.000760) - test_parse: .: (0.000503) - test_seqid: .: (0.000289) - test_start: .: (0.000883) - test_to_s: .: (0.000447) + test_end: .: (0.000756) + test_parse: .: (0.000713) + test_seqid: .: (0.000396) + test_start: .: (0.000391) + test_to_s: .: (0.000608) Bio::TestGFFRecord: - test_attributes: .: (0.000820) - test_comment: .: (0.000327) - test_end: .: (0.000300) - test_feature: .: (0.000307) - test_frame: .: (0.000302) - test_score: .: (0.000348) - test_seqname: .: (0.000313) - test_source: .: (0.000305) - test_start: .: (0.000305) - test_strand: .: (0.000524) + test_attributes: .: (0.000742) + test_comment: .: (0.000442) + test_end: .: (0.000405) + test_feature: .: (0.001128) + test_frame: .: (0.000400) + test_score: .: (0.000395) + test_seqname: .: (0.000417) + test_source: .: (0.000400) + test_start: .: (0.000419) + test_strand: .: (0.000391) Bio::TestGFFRecordConstruct: - test_add_seqname: .: (0.000511) + test_add_seqname: .: (0.000632) Bio::TestGeneAssociation: - test_aspect: .: (0.000775) - test_assigned_by: .: (0.000307) - test_date: .: (0.000283) - test_db: .: (0.000480) - test_db_object_id: .: (0.000306) - test_db_object_name: .: (0.000284) - test_db_object_symbol: .: (0.000281) - test_db_object_synonym: .: (0.000282) - test_db_object_type: .: (0.000285) - test_db_reference: .: (0.000311) - test_evidence: .: (0.000287) - test_goid: .: (0.000323) - test_parser: .: (0.001840) - test_qualifier: .: (0.000305) - test_taxon: .: (0.000274) - test_to_str: .: (0.000358) - test_with: .: (0.000282) + test_aspect: .: (0.000736) + test_assigned_by: .: (0.000392) + test_date: .: (0.000423) + test_db: .: (0.000421) + test_db_object_id: .: (0.000404) + test_db_object_name: .: (0.000404) + test_db_object_symbol: .: (0.000375) + test_db_object_synonym: .: (0.000378) + test_db_object_type: .: (0.000390) + test_db_reference: .: (0.000451) + test_evidence: .: (0.000365) + test_goid: .: (0.000400) + test_parser: .: (0.001453) + test_qualifier: .: (0.000423) + test_taxon: .: (0.000407) + test_to_str: .: (0.000402) + test_with: .: (0.000356) Bio::TestGenscanReport: - test_date_run: .: (0.002860) - test_gccontent: .: (0.002003) - test_genscan_version: .: (0.001696) - test_isochore: .: (0.002429) - test_length: .: (0.001725) - test_matrix: .: (0.001874) - test_predictions_size: .: (0.002464) - test_query_name: .: (0.001923) - test_time: .: (0.007483) + test_date_run: .: (0.003127) + test_gccontent: .: (0.002057) + test_genscan_version: .: (0.002589) + test_isochore: .: (0.002122) + test_length: .: (0.002116) + test_matrix: .: (0.002778) + test_predictions_size: .: (0.002076) + test_query_name: .: (0.008374) + test_time: .: (0.010354) Bio::TestGenscanReportExon: - test_acceptor_score: .: (0.002093) - test_donor_score: .: (0.002019) - test_exon_type: .: (0.009394) - test_exon_type_long: .: (0.008873) - test_first: .: (0.009729) - test_initiation_score: .: (0.001823) - test_last: .: (0.006606) - test_number: .: (0.007446) - test_p_value: .: (0.001934) - test_phase: .: (0.008239) - test_range: .: (0.007937) - test_score: .: (0.001952) - test_strand: .: (0.006171) - test_t_score: .: (0.007901) - test_termination_score: .: (0.008041) + test_acceptor_score: .: (0.010192) + test_donor_score: .: (0.010422) + test_exon_type: .: (0.002024) + test_exon_type_long: .: (0.008725) + test_first: .: (0.007713) + test_initiation_score: .: (0.008763) + test_last: .: (0.002210) + test_number: .: (0.009489) + test_p_value: .: (0.002143) + test_phase: .: (0.008494) + test_range: .: (0.007161) + test_score: .: (0.002154) + test_strand: .: (0.008728) + test_t_score: .: (0.009117) + test_termination_score: .: (0.009536) Bio::TestGenscanReportGene: - test_aaseq: .: (0.008421) - test_naseq: .: (0.033004) - test_number: .: (0.002098) - test_polyA: .: (0.002582) - test_promoter: .: (0.002116) + test_aaseq: .: (0.029904) + test_naseq: .: (0.002085) + test_number: .: (0.002687) + test_polyA: .: (0.002246) + test_promoter: .: (0.002770) Bio::TestHMMERReportClassMethods: - test_reports_ary: .: (0.002469) - test_reports_ary_contents: .: (0.002394) + test_reports_ary: .: (0.002611) + test_reports_ary_contents: .: (0.001947) Bio::TestHMMERReportConstants: - test_rs: .: (0.000538) + test_rs: .: (0.001282) Bio::TestHMMERReportHit: - test_accession: .: (0.001953) - test_append_hsp: .: (0.001865) - test_bit_score: .: (0.002255) - test_definition: .: (0.001899) - test_description: .: (0.001706) - test_each: .: (0.002432) - test_each_hsp: .: (0.001853) - test_entry_id: .: (0.001944) - test_evalue: .: (0.001720) - test_hit: .: (0.002214) - test_hit_id: .: (0.001723) - test_hsps: .: (0.001771) - test_num: .: (0.002025) - test_score: .: (0.001964) - test_target_def: .: (0.001670) - test_target_id: .: (0.001886) + test_accession: .: (0.002131) + test_append_hsp: .: (0.001712) + test_bit_score: .: (0.001784) + test_definition: .: (0.002202) + test_description: .: (0.001918) + test_each: .: (0.001888) + test_each_hsp: .: (0.001919) + test_entry_id: .: (0.002085) + test_evalue: .: (0.001844) + test_hit: .: (0.001774) + test_hit_id: .: (0.001784) + test_hsps: .: (0.002191) + test_num: .: (0.001769) + test_score: .: (0.001727) + test_target_def: .: (0.001794) + test_target_id: .: (0.002113) Bio::TestHMMERReportHmmpfam: - test_domain_top_hits: .: (0.002393) - test_each: .: (0.001943) - test_each_hit: .: (0.001689) - test_histogram: .: (0.002045) + test_domain_top_hits: .: (0.002089) + test_each: .: (0.001739) + test_each_hit: .: (0.002155) + test_histogram: .: (0.001743) test_hits: .: (0.001716) - test_hsps: .: (0.001691) - test_parameter: .: (0.001763) - test_program: .: (0.002323) - test_query_info: .: (0.001779) - test_statistical_detail: .: (0.001860) - test_total_seq_searched: .: (0.002001) - test_whole_seq_top_hits: .: (0.001960) + test_hsps: .: (0.001720) + test_parameter: .: (0.002187) + test_program: .: (0.001879) + test_query_info: .: (0.001767) + test_statistical_detail: .: (0.001741) + test_total_seq_searched: .: (0.002139) + test_whole_seq_top_hits: .: (0.001713) Bio::TestHMMERReportHmmsearch: - test_domain_top_hits: .: (0.002374) - test_histogram: .: (0.002223) - test_statistical_detail: .: (0.002179) - test_total_seq_searched: .: (0.001873) - test_whole_seq_top_hit: .: (0.002094) + test_domain_top_hits: .: (0.002424) + test_histogram: .: (0.002316) + test_statistical_detail: .: (0.002079) + test_total_seq_searched: .: (0.001888) + test_whole_seq_top_hit: .: (0.002280) Bio::TestHMMERReportHsp: - test_accession: .: (0.002306) - test_bit_score: .: (0.001612) - test_csline: .: (0.001633) - test_domain: .: (0.002126) - test_evalue: .: (0.001675) - test_flatseq: .: (0.001813) - test_hmm_f: .: (0.001639) - test_hmm_t: .: (0.001958) - test_hmmseq: .: (0.001664) - test_hsp: .: (0.001631) - test_midline: .: (0.001613) - test_query_frame: .: (0.001880) - test_query_from: .: (0.001613) - test_query_seq: .: (0.001632) - test_query_to: .: (0.001907) - test_rfline: .: (0.001660) - test_score: .: (0.001596) - test_seq_f: .: (0.001614) - test_seq_ft: .: (0.002037) - test_seq_t: .: (0.001655) - test_set_alignment: .: (0.001591) - test_targat_to: .: (0.001626) - test_target_frame: .: (0.002153) - test_target_from: .: (0.001631) - test_target_seq: .: (0.001781) + test_accession: .: (0.002625) + test_bit_score: .: (0.001830) + test_csline: .: (0.001803) + test_domain: .: (0.002220) + test_evalue: .: (0.001910) + test_flatseq: .: (0.001733) + test_hmm_f: .: (0.001861) + test_hmm_t: .: (0.002096) + test_hmmseq: .: (0.001939) + test_hsp: .: (0.001964) + test_midline: .: (0.002160) + test_query_frame: .: (0.001944) + test_query_from: .: (0.002144) + test_query_seq: .: (0.001837) + test_query_to: .: (0.001877) + test_rfline: .: (0.002217) + test_score: .: (0.001892) + test_seq_f: .: (0.001963) + test_seq_ft: .: (0.001852) + test_seq_t: .: (0.002279) + test_set_alignment: .: (0.001875) + test_targat_to: .: (0.001843) + test_target_frame: .: (0.001872) + test_target_from: .: (0.001965) + test_target_seq: .: (0.002223) Bio::TestHetatmFinder: - test_each_hetatm: .: (0.001198) - test_find_hetatm: .: (0.001008) - test_hetatms: .: (0.001118) + test_each_hetatm: .: (0.001557) + test_find_hetatm: .: (0.000838) + test_hetatms: .: (0.001521) Bio::TestHeterogen: - test_addAtom: .: (0.000893) - test_each: .: (0.000613) - test_each_hetatm: .: (0.000830) - test_get_residue_id_from_atom: .: (0.000617) - test_het_atom: .: (0.000422) - test_iCode: .: (0.000415) - test_inspect: .: (0.000485) - test_resSeq: .: (0.000445) - test_sort: .: (0.000505) - test_square_bracket: .: (0.000941) - test_to_s: .: (0.000786) - test_update_resudue_id: .: (0.000444) + test_addAtom: .: (0.001095) + test_each: .: (0.000721) + test_each_hetatm: .: (0.000677) + test_get_residue_id_from_atom: .: (0.000719) + test_het_atom: .: (0.000539) + test_iCode: .: (0.000961) + test_inspect: .: (0.000680) + test_resSeq: .: (0.000606) + test_sort: .: (0.000642) + test_square_bracket: .: (0.000595) + test_to_s: .: (0.000855) + test_update_resudue_id: .: (0.000563) Bio::TestHeterogenFinder: - test_each_heterogen: .: (0.000665) - test_find_heterogen: .: (0.000340) - test_heterogens: .: (0.000370) + test_each_heterogen: .: (0.000766) + test_find_heterogen: .: (0.000798) + test_heterogens: .: (0.000527) Bio::TestIprscanPTxtReport: - test_match_accession: .: (0.000906) - test_match_description: .: (0.000406) - test_match_evalue: .: (0.000388) - test_match_ipr_description: .: (0.000844) - test_match_ipr_id: .: (0.000415) - test_match_match_end: .: (0.000385) - test_match_match_start: .: (0.000536) - test_match_method: .: (0.000406) - test_matches_size: .: (0.000387) - test_query_id: .: (0.000383) - test_query_length: .: (0.000384) + test_match_accession: .: (0.000867) + test_match_description: .: (0.000509) + test_match_evalue: .: (0.000566) + test_match_ipr_description: .: (0.000512) + test_match_ipr_id: .: (0.000493) + test_match_match_end: .: (0.000494) + test_match_match_start: .: (0.000514) + test_match_method: .: (0.000949) + test_matches_size: .: (0.000496) + test_query_id: .: (0.000509) + test_query_length: .: (0.000498) Bio::TestIprscanRawReport: - test_entry_id: .: (0.005999) - test_match_accession: .: (0.005675) - test_match_crc64: .: (0.005614) - test_match_date: .: (0.005309) - test_match_description: .: (0.005688) - test_match_evalue: .: (0.006150) - test_match_go_terms: .: (0.006171) - test_match_ipr_description: .: (0.005621) - test_match_ipr_id: .: (0.011924) - test_match_match_end: .: (0.006320) - test_match_match_start: .: (0.006699) - test_match_method: .: (0.006151) - test_match_query_id: .: (0.006214) - test_match_query_length: .: (0.006088) - test_match_status: .: (0.006569) - test_obj: .: (0.005531) - test_query_id: .: (0.005696) - test_query_length: .: (0.005623) - test_self_reports_in_raw: .: (0.011177) + test_entry_id: .: (0.007319) + test_match_accession: .: (0.006652) + test_match_crc64: .: (0.006215) + test_match_date: .: (0.006082) + test_match_description: .: (0.006469) + test_match_evalue: .: (0.006709) + test_match_go_terms: .: (0.007464) + test_match_ipr_description: .: (0.006481) + test_match_ipr_id: .: (0.014376) + test_match_match_end: .: (0.007291) + test_match_match_start: .: (0.007192) + test_match_method: .: (0.007692) + test_match_query_id: .: (0.006996) + test_match_query_length: .: (0.007012) + test_match_status: .: (0.006805) + test_obj: .: (0.006907) + test_query_id: .: (0.006727) + test_query_length: .: (0.006565) + test_self_reports_in_raw: .: (0.013438) Bio::TestIprscanReport: - test_output_raw: .: (0.001687) - test_to_raw: .: (0.001412) + test_output_raw: .: (0.001920) + test_to_raw: .: (0.001531) Bio::TestIprscanTxtEntry: - test_iprscan_report_class: .: (0.001969) - test_match_accession: .: (0.001385) - test_match_date: .: (0.001237) - test_match_description: .: (0.001212) - test_match_evalue: .: (0.001334) - test_match_go_terms: .: (0.001347) - test_match_ipr_description: .: (0.001248) - test_match_ipr_id: .: (0.001192) - test_match_match_end: .: (0.001235) - test_match_match_start: .: (0.001734) - test_match_method: .: (0.001252) - test_match_status: .: (0.001212) - test_matches_size: .: (0.001335) - test_query_id: .: (0.001747) - test_query_length: .: (0.001266) + test_iprscan_report_class: .: (0.002279) + test_match_accession: .: (0.001493) + test_match_date: .: (0.001436) + test_match_description: .: (0.001477) + test_match_evalue: .: (0.001404) + test_match_go_terms: .: (0.001958) + test_match_ipr_description: .: (0.001420) + test_match_ipr_id: .: (0.001442) + test_match_match_end: .: (0.001548) + test_match_match_start: .: (0.001970) + test_match_method: .: (0.001565) + test_match_status: .: (0.001463) + test_matches_size: .: (0.001455) + test_query_id: .: (0.001389) + test_query_length: .: (0.001865) Bio::TestIprscanTxtEntryList: - test_to_hash: .: (0.001666) - test_to_hash_match?: .: (0.001830) + test_to_hash: .: (0.001993) + test_to_hash_match?: .: (0.001893) Bio::TestIprscanTxtReport: - test_parse_txt: .: (0.004023) + test_parse_txt: .: (0.004105) Bio::TestKeggCompound: - test_comment: .: (0.001062) - test_dblinks_as_hash: .: (0.000900) - test_dblinks_as_strings: .: (0.001180) - test_entry_id: .: (0.000781) - test_enzymes: .: (0.001446) - test_formula: .: (0.000681) - test_kcf: .: (0.000752) - test_mass: .: (0.000682) - test_name: .: (0.001142) - test_names: .: (0.000826) - test_pathways_as_hash: .: (0.001353) - test_pathways_as_strings: .: (0.000842) - test_reactions: .: (0.001499) - test_remark: .: (0.000956) - test_rpairs: .: (0.000663) + test_comment: .: (0.001286) + test_dblinks_as_hash: .: (0.001193) + test_dblinks_as_strings: .: (0.001319) + test_entry_id: .: (0.000968) + test_enzymes: .: (0.001718) + test_formula: .: (0.000821) + test_kcf: .: (0.000840) + test_mass: .: (0.000891) + test_name: .: (0.001279) + test_names: .: (0.001123) + test_pathways_as_hash: .: (0.001576) + test_pathways_as_strings: .: (0.001019) + test_reactions: .: (0.001643) + test_remark: .: (0.001362) + test_rpairs: .: (0.000939) Bio::TestKeggEnzyme: - test_all_reac: .: (0.001482) - test_classes: .: (0.001124) - test_cofactors: .: (0.001026) - test_comment: .: (0.001141) - test_dblinks_as_hash: .: (0.001736) - test_dblinks_as_strings: .: (0.001115) - test_diseases: .: (0.000976) - test_entry: .: (0.001152) - test_entry_id: .: (0.001028) - test_genes: .: (0.040637) - test_genes_as_hash: .: (0.035233) - test_genes_as_strings: .: (0.010751) - test_inhibitors: .: (0.001410) - test_iubmb_reactions: .: (0.002273) - test_kegg_reactions: .: (0.001625) - test_motifs: .: (0.001273) - test_name: .: (0.001819) - test_names: .: (0.001518) - test_obsolete?: .: (0.001566) - test_orthologs_as_hash: .: (0.001436) - test_orthologs_as_strings: .: (0.002350) - test_pathways_as_hash: .: (0.001628) - test_pathways_as_strings: .: (0.001611) - test_products: .: (0.001387) - test_reaction: .: (0.001371) - test_structures: .: (0.002781) - test_substrates: .: (0.001676) - test_sysname: .: (0.001361) + test_all_reac: .: (0.001731) + test_classes: .: (0.001239) + test_cofactors: .: (0.001197) + test_comment: .: (0.001313) + test_dblinks_as_hash: .: (0.001741) + test_dblinks_as_strings: .: (0.001308) + test_diseases: .: (0.001126) + test_entry: .: (0.001180) + test_entry_id: .: (0.001292) + test_genes: .: (0.047693) + test_genes_as_hash: .: (0.041116) + test_genes_as_strings: .: (0.012659) + test_inhibitors: .: (0.001598) + test_iubmb_reactions: .: (0.001634) + test_kegg_reactions: .: (0.001637) + test_motifs: .: (0.001416) + test_name: .: (0.001751) + test_names: .: (0.001941) + test_obsolete?: .: (0.001491) + test_orthologs_as_hash: .: (0.001550) + test_orthologs_as_strings: .: (0.001439) + test_pathways_as_hash: .: (0.001700) + test_pathways_as_strings: .: (0.002595) + test_products: .: (0.001548) + test_reaction: .: (0.001631) + test_structures: .: (0.002027) + test_substrates: .: (0.001598) + test_sysname: .: (0.001462) Bio::TestKeggGenesDblinks: - test_data: .: (0.000791) - test_dblinks_0: .: (0.000366) - test_dblinks_1: .: (0.000326) - test_dblinks_2: .: (0.000606) + test_data: .: (0.001743) + test_dblinks_0: .: (0.000500) + test_dblinks_1: .: (0.000463) + test_dblinks_2: .: (0.000480) Bio::TestKeggGenesStructure: - test_data: .: (0.000598) - test_ids: .: (0.000443) - test_ids_in_array: .: (0.001059) + test_data: .: (0.000761) + test_ids: .: (0.000619) + test_ids_in_array: .: (0.000524) Bio::TestKeggKGML::TestKGMLEntry1: - test_components: .: (0.024762) - test_graphics__size: .: (0.030160) - test_id: .: (0.023543) - test_link: .: (0.022741) - test_name: .: (0.022852) - test_reaction: .: (0.023484) - test_type: .: (0.022430) + test_components: .: (0.040411) + test_graphics__size: .: (0.034064) + test_id: .: (0.031275) + test_link: .: (0.032367) + test_name: .: (0.031827) + test_reaction: .: (0.027709) + test_type: .: (0.025011) Bio::TestKeggKGML::TestKGMLEntry1234: - test_components: .: (0.024404) - test_graphics__size: .: (0.021658) - test_id: .: (0.021479) - test_link: .: (0.021380) - test_name: .: (0.021399) - test_reaction: .: (0.021954) - test_type: .: (0.023438) + test_components: .: (0.026899) + test_graphics__size: .: (0.023873) + test_id: .: (0.024071) + test_link: .: (0.023297) + test_name: .: (0.022896) + test_reaction: .: (0.023074) + test_type: .: (0.024746) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: - test_bgcolor=: .: (0.022322) - test_category: .: (0.022193) - test_entry_id: .: (0.021392) - test_fgcolor=: .: (0.021976) - test_height=: .: (0.021982) - test_label=: .: (0.022481) - test_shape=: .: (0.025394) - test_width=: .: (0.022706) - test_x=: .: (0.021963) - test_y=: .: (0.021569) + test_bgcolor=: .: (0.023615) + test_category: .: (0.023278) + test_entry_id: .: (0.023385) + test_fgcolor=: .: (0.024358) + test_height=: .: (0.024340) + test_label=: .: (0.024814) + test_shape=: .: (0.027575) + test_width=: .: (0.024026) + test_x=: .: (0.024182) + test_y=: .: (0.023624) Bio::TestKeggKGML::TestKGMLEntry567: - test_components: .: (0.021851) - test_graphics__size: .: (0.021625) - test_id: .: (0.024035) - test_link: .: (0.021939) - test_name: .: (0.021999) - test_reaction: .: (0.021225) - test_type: .: (0.021353) + test_components: .: (0.023005) + test_graphics__size: .: (0.023544) + test_id: .: (0.026045) + test_link: .: (0.023095) + test_name: .: (0.023832) + test_reaction: .: (0.022980) + test_type: .: (0.025388) Bio::TestKeggKGML::TestKGMLEntrySetter: - test_components=: .: (0.000645) - test_graphics=: .: (0.000307) - test_id=: .: (0.000320) - test_link=: .: (0.000749) - test_name=: .: (0.000332) - test_reaction=: .: (0.000308) - test_type=: .: (0.000298) + test_components=: .: (0.000781) + test_graphics=: .: (0.000465) + test_id=: .: (0.000444) + test_link=: .: (0.000385) + test_name=: .: (0.000404) + test_reaction=: .: (0.000403) + test_type=: .: (0.000396) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: - test_bgcolor=: .: (0.000697) - test_category=: .: (0.000394) - test_entry_id=: .: (0.000372) - test_fgcolor=: .: (0.000455) - test_height=: .: (0.000378) - test_label=: .: (0.000849) - test_pathway=: .: (0.000338) - test_shape=: .: (0.000424) - test_width=: .: (0.000381) - test_x=: .: (0.000364) - test_y=: .: (0.000561) + test_bgcolor=: .: (0.001482) + test_category=: .: (0.000560) + test_entry_id=: .: (0.000532) + test_fgcolor=: .: (0.000504) + test_height=: .: (0.000475) + test_label=: .: (0.000568) + test_pathway=: .: (0.000455) + test_shape=: .: (0.000466) + test_width=: .: (0.000412) + test_x=: .: (0.000403) + test_y=: .: (0.000447) Bio::TestKeggKGML::TestKGMLGraphics1234: - test_bgcolor: .: (0.021881) - test_coords: .: (0.024700) - test_fgcolor: .: (0.022162) - test_height: .: (0.021721) - test_name: .: (0.021831) - test_type: .: (0.021809) - test_width: .: (0.022013) - test_x: .: (0.024121) - test_y: .: (0.022979) + test_bgcolor: .: (0.023350) + test_coords: .: (0.028038) + test_fgcolor: .: (0.023869) + test_height: .: (0.024307) + test_name: .: (0.024299) + test_type: .: (0.022834) + test_width: .: (0.026124) + test_x: .: (0.025341) + test_y: .: (0.025075) Bio::TestKeggKGML::TestKGMLGraphics1_0: - test_bgcolor: .: (0.022222) - test_coords: .: (0.021973) - test_fgcolor: .: (0.021641) - test_height: .: (0.021591) - test_name: .: (0.021466) - test_type: .: (0.024460) - test_width: .: (0.021969) - test_x: .: (0.021740) - test_y: .: (0.021711) + test_bgcolor: .: (0.024562) + test_coords: .: (0.023266) + test_fgcolor: .: (0.024919) + test_height: .: (0.025449) + test_name: .: (0.027611) + test_type: .: (0.023756) + test_width: .: (0.023999) + test_x: .: (0.023543) + test_y: .: (0.022744) Bio::TestKeggKGML::TestKGMLGraphicsSetter: - test_bgcolor=: .: (0.000636) - test_coords=: .: (0.000306) - test_fgcolor=: .: (0.000617) - test_height=: .: (0.000357) - test_name=: .: (0.000309) - test_type=: .: (0.000320) - test_width=: .: (0.000344) - test_x=: .: (0.000321) - test_y=: .: (0.000411) + test_bgcolor=: .: (0.000737) + test_coords=: .: (0.000439) + test_fgcolor=: .: (0.000512) + test_height=: .: (0.000391) + test_name=: .: (0.000405) + test_type=: .: (0.000441) + test_width=: .: (0.000386) + test_x=: .: (0.000386) + test_y=: .: (0.000467) Bio::TestKeggKGML::TestKGMLPathway: - test_entries=: .: (0.023008) - test_entries__size: .: (0.021637) - test_image: .: (0.026842) - test_link: .: (0.024306) - test_name: .: (0.022185) - test_number: .: (0.022106) - test_org: .: (0.022258) - test_reactions=: .: (0.022298) - test_reactions__size: .: (0.024524) - test_relations=: .: (0.023069) - test_relations__size: .: (0.022386) - test_title: .: (0.022299) + test_entries=: .: (0.025674) + test_entries__size: .: (0.027746) + test_image: .: (0.025214) + test_link: .: (0.023337) + test_name: .: (0.023591) + test_number: .: (0.024636) + test_org: .: (0.022889) + test_reactions=: .: (0.025496) + test_reactions__size: .: (0.027703) + test_relations=: .: (0.026553) + test_relations__size: .: (0.023829) + test_title: .: (0.022992) Bio::TestKeggKGML::TestKGMLProduct: - test_id: .: (0.065576) - test_name: .: (0.099199) + test_id: .: (0.051131) + test_name: .: (0.064768) Bio::TestKeggKGML::TestKGMLProductSetter: - test_id=: .: (0.000694) - test_initialize_0: .: (0.000236) - test_initialize_1: .: (0.000248) - test_initialize_2: .: (0.000310) - test_name=: .: (0.000346) + test_id=: .: (0.000753) + test_initialize_0: .: (0.000282) + test_initialize_1: .: (0.000306) + test_initialize_2: .: (0.000339) + test_name=: .: (0.000397) Bio::TestKeggKGML::TestKGMLReaction: - test_id: .: (0.045610) - test_name: .: (0.044328) - test_products: .: (0.038888) - test_substrates: .: (0.035565) - test_type: .: (0.025850) + test_id: .: (0.023755) + test_name: .: (0.023494) + test_products: .: (0.022941) + test_substrates: .: (0.024043) + test_type: .: (0.025733) Bio::TestKeggKGML::TestKGMLReactionSetter: - test_id=: .: (0.000695) - test_name=: .: (0.000354) - test_products=: .: (0.000738) - test_substraces=: .: (0.000326) - test_type=: .: (0.000330) + test_id=: .: (0.001315) + test_name=: .: (0.000447) + test_products=: .: (0.000449) + test_substraces=: .: (0.000425) + test_type=: .: (0.000431) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: - test_direction=: .: (0.000723) - test_entry_id=: .: (0.000884) + test_direction=: .: (0.000752) + test_entry_id=: .: (0.000523) Bio::TestKeggKGML::TestKGMLRelation: - test_entry1: .: (0.023649) - test_entry2: .: (0.022879) - test_name: .: (0.023493) - test_type: .: (0.023038) - test_value: .: (0.090744) + test_entry1: .: (0.024526) + test_entry2: .: (0.026010) + test_name: .: (0.023987) + test_type: .: (0.023790) + test_value: .: (0.108909) Bio::TestKeggKGML::TestKGMLRelationDeprecated: - test_edge: .: (0.000543) - test_node1=: .: (0.000465) - test_node2=: .: (0.013880) - test_rel=: .: (0.000487) + test_edge: .: (0.000806) + test_node1=: .: (0.011153) + test_node2=: .: (0.000562) + test_rel=: .: (0.000548) Bio::TestKeggKGML::TestKGMLRelationSetter: - test_entry1=: .: (0.000644) - test_entry2=: .: (0.000397) - test_name=: .: (0.010579) - test_type=: .: (0.000369) - test_value=: .: (0.000333) + test_entry1=: .: (0.000781) + test_entry2=: .: (0.000570) + test_name=: .: (0.000452) + test_type=: .: (0.005669) + test_value=: .: (0.000582) Bio::TestKeggKGML::TestKGMLSubstrate: - test_id: .: (0.078681) - test_name: .: (0.083361) + test_id: .: (0.049708) + test_name: .: (0.049606) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: - test_id=: .: (0.000699) - test_initialize_0: .: (0.000253) - test_initialize_1: .: (0.000222) - test_initialize_2: .: (0.000224) - test_name=: .: (0.000312) + test_id=: .: (0.000935) + test_initialize_0: .: (0.000363) + test_initialize_1: .: (0.000395) + test_initialize_2: .: (0.000383) + test_name=: .: (0.000431) Bio::TestKeggKGML::TestKGMLSubstrateSetter: - test_id=: .: (0.004782) - test_initialize_0: .: (0.000232) - test_initialize_1: .: (0.000224) - test_initialize_2: .: (0.000273) - test_name=: .: (0.000378) + test_id=: .: (0.001018) + test_initialize_0: .: (0.000361) + test_initialize_1: .: (0.000379) + test_initialize_2: .: (0.000378) + test_name=: .: (0.000547) Bio::TestKeggModule: - test_compounds: .: (0.005270) - test_compounds_as_hash: .: (0.000762) - test_compounds_as_strings: .: (0.000599) - test_definition: .: (0.000643) - test_entry_id: .: (0.000542) - test_keggclass: .: (0.004688) - test_name: .: (0.000619) - test_new: .: (0.001042) - test_orthologs: .: (0.000776) - test_orthologs_as_array: .: (0.000784) - test_orthologs_as_hash: .: (0.000809) - test_orthologs_as_strings: .: (0.000653) - test_pathways: .: (0.000574) - test_pathways_as_hash: .: (0.000505) - test_pathways_as_strings: .: (0.000487) - test_reactions: .: (0.004914) - test_reactions_as_hash: .: (0.001089) - test_reactions_as_strings: .: (0.000667) + test_compounds: .: (0.001472) + test_compounds_as_hash: .: (0.000906) + test_compounds_as_strings: .: (0.000703) + test_definition: .: (0.000717) + test_entry_id: .: (0.000667) + test_keggclass: .: (0.000679) + test_name: .: (0.001125) + test_new: .: (0.000624) + test_orthologs: .: (0.000860) + test_orthologs_as_array: .: (0.000961) + test_orthologs_as_hash: .: (0.000843) + test_orthologs_as_strings: .: (0.000971) + test_pathways: .: (0.000731) + test_pathways_as_hash: .: (0.000618) + test_pathways_as_strings: .: (0.000593) + test_reactions: .: (0.001198) + test_reactions_as_hash: .: (0.000966) + test_reactions_as_strings: .: (0.000812) Bio::TestKeggOrthology: - test_dblinks: .: (0.005516) - test_dblinks_as_hash: .: (0.000997) - test_dblinks_as_strings: .: (0.000913) - test_definition: .: (0.000937) - test_entry_id: .: (0.005568) - test_genes_as_hash: .: (0.041542) - test_genes_as_strings: .: (0.012010) - test_keggclass: .: (0.001927) - test_keggclasses: .: (0.001229) - test_modules: .: (0.000876) - test_modules_as_hash: .: (0.001131) - test_modules_as_strings: .: (0.000841) - test_name: .: (0.000916) - test_names: .: (0.000870) - test_pathways_as_strings: .: (0.000910) - test_pathways_in_keggclass: .: (0.001296) - test_references: .: (0.001908) + test_dblinks: .: (0.001547) + test_dblinks_as_hash: .: (0.001129) + test_dblinks_as_strings: .: (0.000994) + test_definition: .: (0.001057) + test_entry_id: .: (0.001029) + test_genes_as_hash: .: (0.037136) + test_genes_as_strings: .: (0.012423) + test_keggclass: .: (0.001382) + test_keggclasses: .: (0.001421) + test_modules: .: (0.001021) + test_modules_as_hash: .: (0.001063) + test_modules_as_strings: .: (0.001013) + test_name: .: (0.001567) + test_names: .: (0.001031) + test_pathways_as_strings: .: (0.001230) + test_pathways_in_keggclass: .: (0.001471) + test_references: .: (0.001616) Bio::TestKeggPathway_map00052: - test_compounds_as_hash: .: (0.000916) - test_compounds_as_strings: .: (0.000559) - test_dblinks_as_hash: .: (0.000552) - test_dblinks_as_strings: .: (0.000841) - test_description: .: (0.000612) - test_diseases_as_hash: .: (0.000539) - test_diseases_as_strings: .: (0.000567) - test_entry_id: .: (0.001445) - test_enzymes_as_strings: .: (0.000764) - test_genes_as_hash: .: (0.000533) - test_genes_as_strings: .: (0.000567) - test_keggclass: .: (0.000599) - test_ko_pathway: .: (0.000578) - test_modules_as_hash: .: (0.001059) - test_modules_as_strings: .: (0.000599) - test_name: .: (0.000633) - test_organism: .: (0.000572) - test_orthologs_as_hash: .: (0.000538) - test_orthologs_as_strings: .: (0.001350) - test_pathways_as_hash: .: (0.000577) - test_pathways_as_strings: .: (0.000595) - test_reactions_as_hash: .: (0.000532) - test_reactions_as_strings: .: (0.000521) - test_references: .: (0.000558) - test_rel_pathways_as_hash: .: (0.000658) - test_rel_pathways_as_strings: .: (0.000608) + test_compounds_as_hash: .: (0.000952) + test_compounds_as_strings: .: (0.000615) + test_dblinks_as_hash: .: (0.000606) + test_dblinks_as_strings: .: (0.000649) + test_description: .: (0.000901) + test_diseases_as_hash: .: (0.000598) + test_diseases_as_strings: .: (0.000577) + test_entry_id: .: (0.000700) + test_enzymes_as_strings: .: (0.000630) + test_genes_as_hash: .: (0.000586) + test_genes_as_strings: .: (0.000582) + test_keggclass: .: (0.000702) + test_ko_pathway: .: (0.000684) + test_modules_as_hash: .: (0.000875) + test_modules_as_strings: .: (0.001337) + test_name: .: (0.000691) + test_organism: .: (0.000648) + test_orthologs_as_hash: .: (0.000592) + test_orthologs_as_strings: .: (0.000586) + test_pathways_as_hash: .: (0.000678) + test_pathways_as_strings: .: (0.000620) + test_reactions_as_hash: .: (0.000607) + test_reactions_as_strings: .: (0.000587) + test_references: .: (0.000596) + test_rel_pathways_as_hash: .: (0.001190) + test_rel_pathways_as_strings: .: (0.000855) Bio::TestKeggReaction: - test_definition: .: (0.000986) - test_entry_id: .: (0.000894) - test_enzymes: .: (0.000994) - test_equation: .: (0.000689) - test_name: .: (0.000642) - test_orthologs_as_hash: .: (0.001019) - test_orthologs_as_strings: .: (0.000615) - test_pathways_as_hash: .: (0.000640) - test_pathways_as_strings: .: (0.000609) - test_rpairs_as_hash: .: (0.006069) - test_rpairs_as_strings: .: (0.000615) - test_rpairs_as_tokens: .: (0.000751) + test_definition: .: (0.001060) + test_entry_id: .: (0.000707) + test_enzymes: .: (0.000693) + test_equation: .: (0.000736) + test_name: .: (0.005921) + test_orthologs_as_hash: .: (0.001026) + test_orthologs_as_strings: .: (0.000762) + test_pathways_as_hash: .: (0.000761) + test_pathways_as_strings: .: (0.000673) + test_rpairs_as_hash: .: (0.000860) + test_rpairs_as_strings: .: (0.000729) + test_rpairs_as_tokens: .: (0.000858) Bio::TestLasergene: - test_methods: .: (0.018149) + test_methods: .: (0.018912) Bio::TestLocations: - test_complement: .: (0.000724) - test_hat: .: (0.000438) - test_normal: .: (0.000841) - test_replace_single_base: .: (0.000314) - test_should_not_modify_argument: .: (0.000314) + test_complement: .: (0.000834) + test_hat: .: (0.000456) + test_normal: .: (0.000421) + test_replace_single_base: .: (0.000421) + test_should_not_modify_argument: .: (0.000361) Bio::TestLocationsRoundTrip: - test_locations_roundtrip: .: (0.009975) - test_locations_to_s: .: (0.004815) + test_locations_roundtrip: .: (0.010765) + test_locations_to_s: .: (0.005023) Bio::TestMEDLINE: - test_authors: .: (0.001896) - test_authors_with_last_name_all_caps: .: (0.000314) - test_authors_with_suffix: .: (0.000292) + test_authors: .: (0.002007) + test_authors_with_last_name_all_caps: .: (0.000406) + test_authors_with_suffix: .: (0.000878) Bio::TestMEDLINE_20146148: - test_ab: .: (0.001681) - test_ad: .: (0.001567) - test_au: .: (0.001210) - test_authors: .: (0.001063) - test_doi: .: (0.001330) - test_dp: .: (0.001286) - test_ip: .: (0.000973) - test_mh: .: (0.001059) - test_pages: .: (0.000975) - test_pg: .: (0.001433) - test_pii: .: (0.001040) - test_pmid: .: (0.000954) - test_pt: .: (0.001215) - test_reference: .: (0.001823) - test_self_new: .: (0.001006) - test_so: .: (0.001199) - test_ta: .: (0.001443) - test_ti: .: (0.001152) - test_ui: .: (0.000993) - test_vi: .: (0.000998) - test_year: .: (0.000970) + test_ab: .: (0.001594) + test_ad: .: (0.001147) + test_au: .: (0.001062) + test_authors: .: (0.001600) + test_doi: .: (0.001265) + test_dp: .: (0.001098) + test_ip: .: (0.001091) + test_mh: .: (0.001451) + test_pages: .: (0.001349) + test_pg: .: (0.001167) + test_pii: .: (0.001127) + test_pmid: .: (0.001397) + test_pt: .: (0.001269) + test_reference: .: (0.001668) + test_self_new: .: (0.001133) + test_so: .: (0.001525) + test_ta: .: (0.001200) + test_ti: .: (0.001145) + test_ui: .: (0.001081) + test_vi: .: (0.001532) + test_year: .: (0.001197) Bio::TestMapSimple: - test_attributes: .: (0.001381) + test_attributes: .: (0.000833) Bio::TestMapping: - test_add_mapping_as_map: .: (0.000820) - test_add_mapping_as_marker: .: (0.000449) - test_contains_marker?: .: (0.000343) - test_mapped_to?: .: (0.000322) - test_mapping_location_comparison: .: (0.001052) - test_mappings_as_map_each: .: (0.000341) - test_mappings_as_marker_each: .: (0.000437) - test_mappings_on: .: (0.000779) - test_multiple_mappings_between_same_marker_and_map: .: (0.000848) - test_positions_on: .: (0.000763) - test_raise_error_kind_of: .: (0.000945) + test_add_mapping_as_map: .: (0.000953) + test_add_mapping_as_marker: .: (0.000576) + test_contains_marker?: .: (0.000476) + test_mapped_to?: .: (0.000420) + test_mapping_location_comparison: .: (0.001282) + test_mappings_as_map_each: .: (0.000430) + test_mappings_as_marker_each: .: (0.000496) + test_mappings_on: .: (0.000577) + test_multiple_mappings_between_same_marker_and_map: .: (0.000976) + test_positions_on: .: (0.000584) + test_raise_error_kind_of: .: (0.000969) Bio::TestMast: - test_check_options_with_empty_opts: .: (0.000832) - test_check_options_with_invalid_opts: .: (0.000490) - test_check_options_with_valid_opts: .: (0.000674) - test_command_to_be_run: .: (0.000498) - test_config_defaults: .: (0.000367) - test_minimal_config: .: (0.000474) - test_more_config: .: (0.000666) - test_run: .: (0.000275) + test_check_options_with_empty_opts: .: (0.000941) + test_check_options_with_invalid_opts: .: (0.000569) + test_check_options_with_valid_opts: .: (0.000496) + test_command_to_be_run: .: (0.000852) + test_config_defaults: .: (0.000478) + test_minimal_config: .: (0.000494) + test_more_config: .: (0.000443) + test_run: .: (0.000323) Bio::TestMastReport: - test_parse_hit_list_with_bad_data: .: (0.001311) - test_report_has_motifs: .: (0.000631) + test_parse_hit_list_with_bad_data: .: (0.001147) + test_report_has_motifs: .: (0.000802) Bio::TestModel: - test_addChain: .: (0.000560) - test_comp: .: (0.000320) - test_each: .: (0.000306) - test_each_chain: .: (0.000281) - test_inspect: .: (0.000473) - test_rehash: .: (0.000251) - test_square_brace: .: (0.000690) - test_to_s: .: (0.000263) + test_addChain: .: (0.000629) + test_comp: .: (0.000368) + test_each: .: (0.000662) + test_each_chain: .: (0.000392) + test_inspect: .: (0.000316) + test_rehash: .: (0.000324) + test_square_brace: .: (0.000329) + test_to_s: .: (0.000333) Bio::TestModelFinder: test_find_model: .: (0.000623) Bio::TestMotif: - test_creation_and_attributes: .: (0.000621) - test_length: .: (0.000497) + test_creation_and_attributes: .: (0.000718) + test_length: .: (0.000281) Bio::TestMyGraph: - test_cliquishness: .: (0.001247) + test_cliquishness: .: (0.001932) Bio::TestNA: - test_accessor: .: (0.000526) - test_na: .: (0.000230) - test_name: .: (0.000215) - test_names: .: (0.000211) - test_to_re: .: (0.001291) - test_weight: .: (0.000299) - test_weight_rna: .: (0.000242) + test_accessor: .: (0.000576) + test_na: .: (0.000282) + test_name: .: (0.000322) + test_names: .: (0.000278) + test_to_re: .: (0.000659) + test_weight: .: (0.000334) + test_weight_rna: .: (0.000310) Bio::TestNAConstants: - test_NAMES: .: (0.000462) - test_NAMES_1_to_name: .: (0.000216) - test_WEIGHT: .: (0.000235) + test_NAMES: .: (0.000574) + test_NAMES_1_to_name: .: (0.000281) + test_WEIGHT: .: (0.000341) Bio::TestNATranslate: - test_translate: .: (0.001039) - test_translate_1: .: (0.000415) - test_translate_2: .: (0.000270) - test_translate_3: .: (0.000261) - test_translate_4: .: (0.000466) - test_translate_5: .: (0.000280) - test_translate_6: .: (0.000264) + test_translate: .: (0.000908) + test_translate_1: .: (0.001110) + test_translate_2: .: (0.000370) + test_translate_3: .: (0.000332) + test_translate_4: .: (0.000548) + test_translate_5: .: (0.000401) + test_translate_6: .: (0.000340) Bio::TestNCBIDB: - test_fetch: .: (0.000612) - test_p_entry2hash: .: (0.000212) - test_p_subtag2array: .: (0.000184) - test_p_toptag2array: .: (0.000179) + test_fetch: .: (0.000658) + test_p_entry2hash: .: (0.000258) + test_p_subtag2array: .: (0.000258) + test_p_toptag2array: .: (0.000242) Bio::TestNewick: - test_reparse: .: (0.003514) - test_reparse_before_lazy_parsing: .: (0.002368) - test_string_tree: .: (0.002545) + test_reparse: .: (0.004107) + test_reparse_before_lazy_parsing: .: (0.001243) + test_string_tree: .: (0.002304) Bio::TestNewick2: - test_string_tree: .: (0.002009) + test_string_tree: .: (0.002990) Bio::TestNewickPrivate: - test_parse_newick_get_tokens_for_leaf: .: (0.000592) - test_parse_newick_leaf: .: (0.000499) - test_parse_newick_tokenize: .: (0.001699) + test_parse_newick_get_tokens_for_leaf: .: (0.000687) + test_parse_newick_leaf: .: (0.000575) + test_parse_newick_tokenize: .: (0.000935) Bio::TestNexus: - test_nexus: .: (0.032327) + test_nexus: .: (0.033798) Bio::TestOSLine: - test_period_trancation_O63147: .: (0.000736) - test_uncapitalized_letter_Q32725_9POAL: .: (0.000354) + test_period_trancation_O63147: .: (0.000837) + test_uncapitalized_letter_Q32725_9POAL: .: (0.000500) Bio::TestPAMLCodeml::TestCodeml: - test_dump_parameters: .: (0.000836) - test_load_parameters: .: (0.000312) - test_parameters: .: (0.000235) - test_set_default_parameters: .: (0.000297) + test_dump_parameters: .: (0.001336) + test_load_parameters: .: (0.000377) + test_parameters: .: (0.000305) + test_set_default_parameters: .: (0.000363) Bio::TestPAMLCodeml::TestCodemlControlGeneration: - test_control_file_generated: .: (0.002765) - test_expected_parameters_set_in_control_file: .: (0.002092) + test_control_file_generated: .: (0.007442) + test_expected_parameters_set_in_control_file: .: (0.002355) Bio::TestPAMLCodeml::TestCodemlInitialize: - test_new_with_one_argument: .: (0.000558) - test_new_with_parameters: .: (0.000358) - test_new_with_two_argument: .: (0.000309) - test_new_without_argument: .: (0.000270) + test_new_with_one_argument: .: (0.000651) + test_new_with_parameters: .: (0.000392) + test_new_with_two_argument: .: (0.001081) + test_new_without_argument: .: (0.000351) Bio::TestPAMLCodeml::TestCodemlRates: - test_rates_first_position: .: (0.004398) - test_rates_hundred_and_fiftieth_position: .: (0.004491) - test_rates_last_position: .: (0.004174) + test_rates_first_position: .: (0.004599) + test_rates_hundred_and_fiftieth_position: .: (0.004737) + test_rates_last_position: .: (0.004498) Bio::TestPAMLCodeml::TestCodemlReport: - test_alpha: .: (0.024381) - test_tree: .: (0.024244) - test_tree_length: .: (0.023966) - test_tree_log_likelihood: .: (0.023992) + test_alpha: .: (0.026354) + test_tree: .: (0.025719) + test_tree_length: .: (0.024688) + test_tree_log_likelihood: .: (0.026711) Bio::TestPAMLCodeml::TestControlFileUsage: - test_correct_parameters_should_be_loaded: .: (0.001246) - test_parameters_should_be_loaded_from_control: .: (0.000723) + test_correct_parameters_should_be_loaded: .: (0.001346) + test_parameters_should_be_loaded_from_control: .: (0.001490) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: - test_error_thrown_if_seqfile_does_not_specified: .: (0.004091) + test_error_thrown_if_seqfile_does_not_specified: .: (0.004042) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: - test_alpha: .: (0.001484) - test_dN_dS: .: (0.000471) - test_kappa: .: (0.000430) - test_lnL: .: (0.000422) - test_m3_classes: .: (0.000908) - test_m3_lnL: .: (0.000434) - test_m3_to_s: .: (0.000416) - test_m3_tree: .: (0.001762) - test_omega: .: (0.000661) - test_to_s: .: (0.000416) - test_tree: .: (0.001534) - test_tree_length: .: (0.000424) + test_alpha: .: (0.000852) + test_dN_dS: .: (0.000499) + test_kappa: .: (0.000489) + test_lnL: .: (0.000475) + test_m3_classes: .: (0.001412) + test_m3_lnL: .: (0.000697) + test_m3_to_s: .: (0.000471) + test_m3_tree: .: (0.001780) + test_omega: .: (0.000490) + test_to_s: .: (0.000513) + test_tree: .: (0.001611) + test_tree_length: .: (0.000505) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: - test_dN_dS: .: (0.002167) - test_p: .: (0.000994) - test_position: .: (0.000938) - test_probability: .: (0.001795) - test_w: .: (0.001016) + test_dN_dS: .: (0.001446) + test_p: .: (0.001760) + test_position: .: (0.001020) + test_probability: .: (0.001045) + test_w: .: (0.001094) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: - test_graph: .: (0.001696) - test_graph_omega: .: (0.001876) + test_graph: .: (0.002192) + test_graph_omega: .: (0.001284) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: - test_descr: .: (0.000691) - test_footer: .: (0.000662) - test_header: .: (0.000454) - test_initialize: .: (0.000451) - test_models: .: (0.000477) - test_nb_sites: .: (0.001991) - test_num_codons: .: (0.000467) - test_num_sequences: .: (0.000446) - test_significant: .: (0.011023) + test_descr: .: (0.000763) + test_footer: .: (0.000802) + test_header: .: (0.000586) + test_initialize: .: (0.000497) + test_models: .: (0.000559) + test_nb_sites: .: (0.012107) + test_num_codons: .: (0.000594) + test_num_sequences: .: (0.000560) + test_significant: .: (0.000536) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: - test_models: .: (0.000821) - test_nb_sites: .: (0.000741) - test_significant: .: (0.000470) - test_sites: .: (0.004346) + test_models: .: (0.000897) + test_nb_sites: .: (0.000774) + test_significant: .: (0.000569) + test_sites: .: (0.005140) Bio::TestPDB: - test_accession: .: (0.004379) - test_addModel: .: (0.002095) - test_authors: .: (0.002882) - test_bracket: .: (0.002319) - test_classification: .: (0.002535) - test_dbref: .: (0.002589) - test_definition: .: (0.002750) - test_each: .: (0.002198) - test_each_model: .: (0.002623) - test_entry_id: .: (0.002079) - test_helix: .: (0.003497) - test_inspect: .: (0.002267) - test_jrnl: .: (0.002907) - test_keywords: .: (0.002143) - test_record: .: (0.002216) - test_remark: .: (0.003767) - test_seqres: .: (0.003660) - test_sheet: .: (0.003207) - test_ssbond: .: (0.002928) - test_to_s: .: (0.003067) - test_turn: .: (0.002801) - test_version: .: (0.002158) + test_accession: .: (0.003324) + test_addModel: .: (0.003085) + test_authors: .: (0.002135) + test_bracket: .: (0.002665) + test_classification: .: (0.002233) + test_dbref: .: (0.002879) + test_definition: .: (0.002254) + test_each: .: (0.002692) + test_each_model: .: (0.002212) + test_entry_id: .: (0.002909) + test_helix: .: (0.002989) + test_inspect: .: (0.002965) + test_jrnl: .: (0.002174) + test_keywords: .: (0.002837) + test_record: .: (0.002229) + test_remark: .: (0.002739) + test_seqres: .: (0.003393) + test_sheet: .: (0.004194) + test_ssbond: .: (0.002413) + test_to_s: .: (0.003692) + test_turn: .: (0.002238) + test_version: .: (0.002596) Bio::TestPDBRecord::TestANISOU: - test_U11: .: (0.000713) - test_U12: .: (0.000372) - test_U13: .: (0.000412) - test_U22: .: (0.000359) - test_U23: .: (0.000350) - test_U33: .: (0.000350) - test_altLoc: .: (0.000670) - test_chainID: .: (0.000365) - test_charge: .: (0.000350) - test_element: .: (0.000356) - test_iCode: .: (0.000397) - test_name: .: (0.000359) - test_resName: .: (0.000410) - test_resSeq: .: (0.000358) - test_segID: .: (0.000386) - test_serial: .: (0.000361) + test_U11: .: (0.000773) + test_U12: .: (0.000472) + test_U13: .: (0.000417) + test_U22: .: (0.000413) + test_U23: .: (0.000414) + test_U33: .: (0.000497) + test_altLoc: .: (0.000421) + test_chainID: .: (0.000457) + test_charge: .: (0.000461) + test_element: .: (0.000844) + test_iCode: .: (0.000421) + test_name: .: (0.000445) + test_resName: .: (0.000510) + test_resSeq: .: (0.000444) + test_segID: .: (0.000454) + test_serial: .: (0.000446) Bio::TestPDBRecord::TestATOM: - test_altLoc: .: (0.001073) - test_anisou: .: (0.000284) - test_chainID: .: (0.000261) - test_charge: .: (0.000261) - test_comparable: .: (0.000619) - test_do_parse: .: (0.000275) - test_element: .: (0.000287) - test_iCode: .: (0.000269) - test_name: .: (0.000250) - test_occupancy: .: (0.000436) - test_original_data: .: (0.000287) - test_record_name: .: (0.000263) - test_resName: .: (0.000254) - test_resSeq: .: (0.000929) - test_residue: .: (0.000270) - test_segID: .: (0.000250) - test_serial: .: (0.000244) - test_sigatm: .: (0.000243) - test_tempFactor: .: (0.000386) - test_ter: .: (0.000263) - test_to_a: .: (0.000276) - test_to_s: .: (0.000346) - test_x: .: (0.000624) - test_xyz: .: (0.000452) - test_y: .: (0.000346) - test_z: .: (0.000333) + test_altLoc: .: (0.000627) + test_anisou: .: (0.000356) + test_chainID: .: (0.000328) + test_charge: .: (0.000327) + test_comparable: .: (0.000405) + test_do_parse: .: (0.000356) + test_element: .: (0.000757) + test_iCode: .: (0.000328) + test_name: .: (0.000343) + test_occupancy: .: (0.000465) + test_original_data: .: (0.000325) + test_record_name: .: (0.000318) + test_resName: .: (0.000369) + test_resSeq: .: (0.000309) + test_residue: .: (0.000310) + test_segID: .: (0.000309) + test_serial: .: (0.000300) + test_sigatm: .: (0.000344) + test_tempFactor: .: (0.000451) + test_ter: .: (0.000352) + test_to_a: .: (0.000352) + test_to_s: .: (0.000403) + test_x: .: (0.000814) + test_xyz: .: (0.000644) + test_y: .: (0.000414) + test_z: .: (0.000423) Bio::TestPDBRecord::TestAUTHOR: - test_authorList: .: (0.001027) + test_authorList: .: (0.000741) Bio::TestPDBRecord::TestCAVEAT: - test_comment: .: (0.000796) - test_idcode: .: (0.000285) + test_comment: .: (0.000615) + test_idcode: .: (0.000324) Bio::TestPDBRecord::TestCISPEP: - test_chainID1: .: (0.000668) - test_chainID2: .: (0.000351) - test_icode1: .: (0.000389) - test_icode2: .: (0.000344) - test_measure: .: (0.000345) - test_modNum: .: (0.000336) - test_pep1: .: (0.000360) - test_pep2: .: (0.000339) - test_seqNum1: .: (0.000331) - test_seqNum2: .: (0.000330) - test_serNum: .: (0.000833) + test_chainID1: .: (0.000726) + test_chainID2: .: (0.000415) + test_icode1: .: (0.000448) + test_icode2: .: (0.000413) + test_measure: .: (0.000420) + test_modNum: .: (0.000424) + test_pep1: .: (0.000394) + test_pep2: .: (0.000399) + test_seqNum1: .: (0.000442) + test_seqNum2: .: (0.000379) + test_serNum: .: (0.000374) Bio::TestPDBRecord::TestCOMPND: - test_compound: .: (0.000820) + test_compound: .: (0.000715) Bio::TestPDBRecord::TestCONECT: - test_serial: .: (0.000571) + test_serial: .: (0.000647) Bio::TestPDBRecord::TestCRYST1: - test_a: .: (0.000597) - test_alpha: .: (0.000344) - test_b: .: (0.000293) - test_beta: .: (0.000281) - test_c: .: (0.000298) - test_gamma: .: (0.000543) - test_sGroup: .: (0.000314) - test_z: .: (0.000285) + test_a: .: (0.000665) + test_alpha: .: (0.000357) + test_b: .: (0.000345) + test_beta: .: (0.000368) + test_c: .: (0.000987) + test_gamma: .: (0.000356) + test_sGroup: .: (0.000358) + test_z: .: (0.000339) Bio::TestPDBRecord::TestDBREF: - test_chainID: .: (0.001442) - test_database: .: (0.000406) - test_dbAccession: .: (0.000387) - test_dbIdCode: .: (0.000403) - test_dbseqBegin: .: (0.000434) - test_dbseqEnd: .: (0.000381) - test_idCode: .: (0.000376) - test_idbnsBeg: .: (0.000402) - test_insertBegin: .: (0.000378) - test_insertEnd: .: (0.000376) - test_seqBegin: .: (0.000657) - test_seqEnd: .: (0.000430) + test_chainID: .: (0.000755) + test_database: .: (0.000453) + test_dbAccession: .: (0.000462) + test_dbIdCode: .: (0.000477) + test_dbseqBegin: .: (0.000482) + test_dbseqEnd: .: (0.000436) + test_idCode: .: (0.000432) + test_idbnsBeg: .: (0.000470) + test_insertBegin: .: (0.001157) + test_insertEnd: .: (0.000477) + test_seqBegin: .: (0.000451) + test_seqEnd: .: (0.000487) Bio::TestPDBRecord::TestDefault: - test_text: .: (0.000922) + test_text: .: (0.000776) Bio::TestPDBRecord::TestENDMDL: - test_serial: .: (0.000795) + test_serial: .: (0.000650) Bio::TestPDBRecord::TestEXPDTA: - test_technique: .: (0.000547) + test_technique: .: (0.000618) Bio::TestPDBRecord::TestEnd: - test_serial: .: (0.000521) + test_serial: .: (0.000646) Bio::TestPDBRecord::TestHEADER: - test_classification: .: (0.000546) - test_depDate: .: (0.000310) - test_idCode: .: (0.000283) + test_classification: .: (0.000641) + test_depDate: .: (0.000407) + test_idCode: .: (0.000374) Bio::TestPDBRecord::TestHET: - test_ChainID: .: (0.000621) - test_hetID: .: (0.000330) - test_iCode: .: (0.000316) - test_numHetAtoms: .: (0.000346) - test_seqNum: .: (0.000667) - test_text: .: (0.000327) + test_ChainID: .: (0.000741) + test_hetID: .: (0.000377) + test_iCode: .: (0.000393) + test_numHetAtoms: .: (0.000435) + test_seqNum: .: (0.000420) + test_text: .: (0.000383) Bio::TestPDBRecord::TestHETATM: - test_altLoc: .: (0.000550) - test_anisou: .: (0.000267) - test_chainID: .: (0.000264) - test_charge: .: (0.000255) - test_comparable: .: (0.000379) - test_do_parse: .: (0.000273) - test_element: .: (0.000254) - test_iCode: .: (0.000263) - test_name: .: (0.000248) - test_occupancy: .: (0.000399) - test_original_data: .: (0.000265) - test_record_name: .: (0.000254) - test_resName: .: (0.000829) - test_resSeq: .: (0.000317) - test_residue: .: (0.000256) - test_segID: .: (0.000244) - test_serial: .: (0.000262) - test_sigatm: .: (0.000244) - test_tempFactor: .: (0.000372) - test_ter: .: (0.000259) - test_to_a: .: (0.000274) - test_to_s: .: (0.000348) - test_x: .: (0.000380) - test_xyz: .: (0.000331) - test_y: .: (0.000339) - test_z: .: (0.001102) + test_altLoc: .: (0.000619) + test_anisou: .: (0.000336) + test_chainID: .: (0.000321) + test_charge: .: (0.000326) + test_comparable: .: (0.000442) + test_do_parse: .: (0.000351) + test_element: .: (0.000343) + test_iCode: .: (0.000308) + test_name: .: (0.000985) + test_occupancy: .: (0.000498) + test_original_data: .: (0.000335) + test_record_name: .: (0.000335) + test_resName: .: (0.000319) + test_resSeq: .: (0.000301) + test_residue: .: (0.000310) + test_segID: .: (0.000340) + test_serial: .: (0.000317) + test_sigatm: .: (0.000298) + test_tempFactor: .: (0.000408) + test_ter: .: (0.000351) + test_to_a: .: (0.000325) + test_to_s: .: (0.000860) + test_x: .: (0.000419) + test_xyz: .: (0.000390) + test_y: .: (0.000433) + test_z: .: (0.000422) Bio::TestPDBRecord::TestHYDBND: - test_Chain1: .: (0.000765) - test_ChainH: .: (0.000473) - test_ICode1: .: (0.000423) - test_altLoc1: .: (0.000426) - test_altLoc2: .: (0.000675) - test_altLocH: .: (0.000436) - test_chainID2: .: (0.000420) - test_iCode2: .: (0.000418) - test_iCodeH: .: (0.000456) - test_name1: .: (0.000440) - test_name2: .: (0.000834) - test_nameH: .: (0.000461) - test_resName1: .: (0.000416) - test_resName2: .: (0.000408) - test_resSeq1: .: (0.000466) - test_resSeq2: .: (0.000510) - test_resSeqH: .: (0.000425) - test_sym1: .: (0.000688) - test_sym2: .: (0.000439) + test_Chain1: .: (0.000815) + test_ChainH: .: (0.000487) + test_ICode1: .: (0.000493) + test_altLoc1: .: (0.000493) + test_altLoc2: .: (0.000512) + test_altLocH: .: (0.000989) + test_chainID2: .: (0.000516) + test_iCode2: .: (0.000522) + test_iCodeH: .: (0.000478) + test_name1: .: (0.000486) + test_name2: .: (0.000523) + test_nameH: .: (0.000469) + test_resName1: .: (0.000513) + test_resName2: .: (0.000501) + test_resSeq1: .: (0.000489) + test_resSeq2: .: (0.000656) + test_resSeqH: .: (0.000605) + test_sym1: .: (0.001245) + test_sym2: .: (0.000620) Bio::TestPDBRecord::TestKEYWDS: - test_keywds: .: (0.000575) + test_keywds: .: (0.000733) Bio::TestPDBRecord::TestLINK: - test_altLoc1: .: (0.000870) - test_altLoc2: .: (0.000598) - test_chainID1: .: (0.000412) - test_chainID2: .: (0.000377) - test_iCode1: .: (0.000376) - test_iCode2: .: (0.000376) - test_name1: .: (0.000391) - test_name2: .: (0.000372) - test_resName1: .: (0.000369) - test_resName2: .: (0.000593) - test_resSeq1: .: (0.000378) - test_resSeq2: .: (0.000906) - test_sym1: .: (0.000406) - test_sym2: .: (0.000382) + test_altLoc1: .: (0.000754) + test_altLoc2: .: (0.000455) + test_chainID1: .: (0.000488) + test_chainID2: .: (0.000445) + test_iCode1: .: (0.000485) + test_iCode2: .: (0.000481) + test_name1: .: (0.000443) + test_name2: .: (0.000491) + test_resName1: .: (0.001085) + test_resName2: .: (0.000456) + test_resSeq1: .: (0.000440) + test_resSeq2: .: (0.000459) + test_sym1: .: (0.000445) + test_sym2: .: (0.000436) Bio::TestPDBRecord::TestMASTER: - test_numConect: .: (0.000763) - test_numCoord: .: (0.000302) - test_numHelix: .: (0.000283) - test_numHet: .: (0.000279) - test_numRemark: .: (0.000288) - test_numSeq: .: (0.000279) - test_numSheet: .: (0.000337) - test_numSite: .: (0.000283) - test_numTer: .: (0.000270) - test_numTurn: .: (0.000290) - test_numXform: .: (0.000501) + test_numConect: .: (0.000669) + test_numCoord: .: (0.000352) + test_numHelix: .: (0.000374) + test_numHet: .: (0.000344) + test_numRemark: .: (0.000348) + test_numSeq: .: (0.000344) + test_numSheet: .: (0.000344) + test_numSite: .: (0.000361) + test_numTer: .: (0.000322) + test_numTurn: .: (0.000391) + test_numXform: .: (0.000325) Bio::TestPDBRecord::TestMODEL: - test_serial: .: (0.000712) + test_serial: .: (0.000587) Bio::TestPDBRecord::TestMODRES: - test_chainID: .: (0.000646) - test_comment: .: (0.000330) - test_iCode: .: (0.000329) - test_idCode: .: (0.000531) - test_resName: .: (0.000344) - test_seqNum: .: (0.000327) - test_stdRes: .: (0.000344) + test_chainID: .: (0.000742) + test_comment: .: (0.000398) + test_iCode: .: (0.000386) + test_idCode: .: (0.000356) + test_resName: .: (0.000347) + test_seqNum: .: (0.000364) + test_stdRes: .: (0.000387) Bio::TestPDBRecord::TestMTRIX1: - test_Mn1: .: (0.000627) - test_Mn2: .: (0.000286) - test_Mn3: .: (0.000264) - test_Vn: .: (0.000266) - test_iGiven: .: (0.000989) - test_serial: .: (0.000324) + test_Mn1: .: (0.000672) + test_Mn2: .: (0.000362) + test_Mn3: .: (0.000382) + test_Vn: .: (0.000334) + test_iGiven: .: (0.000708) + test_serial: .: (0.000346) Bio::TestPDBRecord::TestMTRIX2: - test_Mn1: .: (0.000561) - test_Mn2: .: (0.000288) - test_Mn3: .: (0.000263) - test_Vn: .: (0.000263) - test_iGiven: .: (0.000268) - test_serial: .: (0.000513) + test_Mn1: .: (0.000628) + test_Mn2: .: (0.000343) + test_Mn3: .: (0.000380) + test_Vn: .: (0.000300) + test_iGiven: .: (0.000328) + test_serial: .: (0.000318) Bio::TestPDBRecord::TestMTRIX3: - test_Mn1: .: (0.000559) - test_Mn2: .: (0.000276) - test_Mn3: .: (0.000260) - test_Vn: .: (0.000306) - test_iGiven: .: (0.000285) - test_serial: .: (0.000263) + test_Mn1: .: (0.000674) + test_Mn2: .: (0.000340) + test_Mn3: .: (0.000387) + test_Vn: .: (0.000328) + test_iGiven: .: (0.000348) + test_serial: .: (0.000320) Bio::TestPDBRecord::TestOBSLTE: - test_idCode: .: (0.000774) - test_rIdCode: .: (0.000592) - test_repDate: .: (0.000316) + test_idCode: .: (0.001180) + test_rIdCode: .: (0.000360) + test_repDate: .: (0.000359) Bio::TestPDBRecord::TestORIGX1: - test_On1: .: (0.000593) - test_On2: .: (0.000272) - test_On3: .: (0.000246) - test_Tn: .: (0.000246) + test_On1: .: (0.000668) + test_On2: .: (0.000339) + test_On3: .: (0.000319) + test_Tn: .: (0.000315) Bio::TestPDBRecord::TestREVDAT: - test_modDate: .: (0.000848) - test_modId: .: (0.000312) - test_modNum: .: (0.000289) - test_modType: .: (0.000292) - test_record: .: (0.000295) + test_modDate: .: (0.000685) + test_modId: .: (0.000377) + test_modNum: .: (0.000407) + test_modType: .: (0.000356) + test_record: .: (0.000352) Bio::TestPDBRecord::TestRemarkN: - test_remarkNum: .: (0.000531) - test_text: .: (0.000261) + test_remarkNum: .: (0.000722) + test_text: .: (0.000325) Bio::TestPDBRecord::TestSCALE1: - test_Sn1: .: (0.001265) - test_Sn2: .: (0.000270) - test_Sn3: .: (0.000251) - test_Un: .: (0.000250) + test_Sn1: .: (0.000710) + test_Sn2: .: (0.000312) + test_Sn3: .: (0.000344) + test_Un: .: (0.000313) Bio::TestPDBRecord::TestSCALE2: - test_Sn1: .: (0.000559) - test_Sn2: .: (0.000268) - test_Sn3: .: (0.000250) - test_Un: .: (0.000461) + test_Sn1: .: (0.000655) + test_Sn2: .: (0.000375) + test_Sn3: .: (0.000332) + test_Un: .: (0.000354) Bio::TestPDBRecord::TestSCALE3: - test_Sn1: .: (0.000550) - test_Sn2: .: (0.000275) - test_Sn3: .: (0.000257) - test_Un: .: (0.000250) + test_Sn1: .: (0.000658) + test_Sn2: .: (0.000334) + test_Sn3: .: (0.000647) + test_Un: .: (0.000352) Bio::TestPDBRecord::TestSEQADV: - test_chainID: .: (0.000635) - test_conflict: .: (0.000352) - test_database: .: (0.000611) - test_dbIdCode: .: (0.000700) - test_dbRes: .: (0.000347) - test_dbSeq: .: (0.000331) - test_iCode: .: (0.000392) - test_idCode: .: (0.000345) - test_resName: .: (0.000339) - test_seqNum: .: (0.000330) + test_chainID: .: (0.000838) + test_conflict: .: (0.000415) + test_database: .: (0.000405) + test_dbIdCode: .: (0.000413) + test_dbRes: .: (0.000441) + test_dbSeq: .: (0.000389) + test_iCode: .: (0.000406) + test_idCode: .: (0.000497) + test_resName: .: (0.000528) + test_seqNum: .: (0.000453) Bio::TestPDBRecord::TestSEQRES: - test_chainID: .: (0.000651) - test_numRes: .: (0.000370) - test_resName: .: (0.000349) + test_chainID: .: (0.000753) + test_numRes: .: (0.000414) + test_resName: .: (0.000424) Bio::TestPDBRecord::TestSHEET: - test_curAtom: .: (0.012800) - test_curChainId: .: (0.000796) - test_curICode: .: (0.000480) - test_curResName: .: (0.000469) - test_curResSeq: .: (0.000451) - test_endChainID: .: (0.000502) - test_endICode: .: (0.000449) - test_endResName: .: (0.000451) - test_endSeqNum: .: (0.000702) - test_initChainID: .: (0.000990) - test_initICode: .: (0.000449) - test_initResName: .: (0.000455) - test_initSeqNum: .: (0.000441) - test_numStrands: .: (0.000436) - test_prevAtom: .: (0.000465) - test_prevChainId: .: (0.000434) - test_prevICode: .: (0.000439) - test_prevResName: .: (0.000472) - test_prevResSeq: .: (0.000455) - test_sense: .: (0.000848) - test_sheetID: .: (0.000665) - test_strand: .: (0.000442) + test_curAtom: .: (0.000808) + test_curChainId: .: (0.000529) + test_curICode: .: (0.000621) + test_curResName: .: (0.000999) + test_curResSeq: .: (0.000567) + test_endChainID: .: (0.000506) + test_endICode: .: (0.000497) + test_endResName: .: (0.000538) + test_endSeqNum: .: (0.000510) + test_initChainID: .: (0.000542) + test_initICode: .: (0.000510) + test_initResName: .: (0.000539) + test_initSeqNum: .: (0.000539) + test_numStrands: .: (0.000986) + test_prevAtom: .: (0.000530) + test_prevChainId: .: (0.000556) + test_prevICode: .: (0.000560) + test_prevResName: .: (0.000508) + test_prevResSeq: .: (0.000544) + test_sense: .: (0.000503) + test_sheetID: .: (0.000508) + test_strand: .: (0.000508) Bio::TestPDBRecord::TestSIGATM: - test_altLoc: .: (0.000741) - test_chainID: .: (0.000384) - test_charge: .: (0.000364) - test_element: .: (0.000360) - test_iCode: .: (0.000596) - test_name: .: (0.000376) - test_resName: .: (0.000365) - test_resSeq: .: (0.000359) - test_segID: .: (0.000803) - test_serial: .: (0.000379) - test_sigOcc: .: (0.000356) - test_sigTemp: .: (0.000587) - test_sigX: .: (0.000376) - test_sigY: .: (0.000465) - test_sigZ: .: (0.000366) + test_altLoc: .: (0.000866) + test_chainID: .: (0.000912) + test_charge: .: (0.000471) + test_element: .: (0.000470) + test_iCode: .: (0.000425) + test_name: .: (0.000424) + test_resName: .: (0.000414) + test_resSeq: .: (0.000501) + test_segID: .: (0.000429) + test_serial: .: (0.000415) + test_sigOcc: .: (0.000442) + test_sigTemp: .: (0.000410) + test_sigX: .: (0.000404) + test_sigY: .: (0.000429) + test_sigZ: .: (0.000939) Bio::TestPDBRecord::TestSIGUIJ: - test_SigmaU11: .: (0.000725) - test_SigmaU12: .: (0.000376) - test_SigmaU13: .: (0.000373) - test_SigmaU22: .: (0.000384) - test_SigmaU23: .: (0.000357) - test_SigmaU33: .: (0.000371) - test_altLoc: .: (0.000434) - test_chainID: .: (0.000364) - test_charge: .: (0.000354) - test_element: .: (0.000352) - test_iCode: .: (0.000387) - test_name: .: (0.000359) - test_resName: .: (0.000355) - test_resSeq: .: (0.000397) - test_segID: .: (0.000408) - test_serial: .: (0.000357) + test_SigmaU11: .: (0.000825) + test_SigmaU12: .: (0.000426) + test_SigmaU13: .: (0.000420) + test_SigmaU22: .: (0.000409) + test_SigmaU23: .: (0.000427) + test_SigmaU33: .: (0.000474) + test_altLoc: .: (0.000430) + test_chainID: .: (0.000421) + test_charge: .: (0.000443) + test_element: .: (0.000410) + test_iCode: .: (0.000405) + test_name: .: (0.000804) + test_resName: .: (0.000437) + test_resSeq: .: (0.000532) + test_segID: .: (0.000419) + test_serial: .: (0.000411) Bio::TestPDBRecord::TestSITE: - test_chainID1: .: (0.000915) - test_chainID2: .: (0.000826) - test_chainID3: .: (0.000409) - test_chainID4: .: (0.000381) - test_iCode1: .: (0.000411) - test_iCode2: .: (0.000383) - test_iCode3: .: (0.000381) - test_iCode4: .: (0.000672) - test_numRes: .: (0.000398) - test_resName1: .: (0.000384) - test_resName2: .: (0.000385) - test_resName3: .: (0.000478) - test_resName4: .: (0.000433) - test_seq1: .: (0.000395) - test_seq2: .: (0.000422) + test_chainID1: .: (0.000814) + test_chainID2: .: (0.000518) + test_chainID3: .: (0.000488) + test_chainID4: .: (0.000448) + test_iCode1: .: (0.000451) + test_iCode2: .: (0.000438) + test_iCode3: .: (0.000986) + test_iCode4: .: (0.000556) + test_numRes: .: (0.000453) + test_resName1: .: (0.000645) + test_resName2: .: (0.000635) + test_resName3: .: (0.000460) + test_resName4: .: (0.000468) + test_seq1: .: (0.000480) + test_seq2: .: (0.000465) test_seq3: .: (0.000521) - test_seq4: .: (0.000389) - test_seqNum: .: (0.000414) - test_siteID: .: (0.000402) + test_seq4: .: (0.000432) + test_seqNum: .: (0.000511) + test_siteID: .: (0.000441) Bio::TestPDBRecord::TestSLTBRG: - test_altLoc1: .: (0.000644) - test_altLoc2: .: (0.000550) - test_atom1: .: (0.000334) - test_atom2: .: (0.000320) - test_chainID1: .: (0.000323) - test_chainID2: .: (0.000318) - test_iCode1: .: (0.000345) - test_iCode2: .: (0.000379) - test_resName1: .: (0.000534) - test_resName2: .: (0.000347) - test_resSeq1: .: (0.000320) - test_resSeq2: .: (0.000331) - test_sym1: .: (0.000328) - test_sym2: .: (0.000362) + test_altLoc1: .: (0.000877) + test_altLoc2: .: (0.000430) + test_atom1: .: (0.000393) + test_atom2: .: (0.000421) + test_chainID1: .: (0.000385) + test_chainID2: .: (0.000444) + test_iCode1: .: (0.000448) + test_iCode2: .: (0.000382) + test_resName1: .: (0.000387) + test_resName2: .: (0.000386) + test_resSeq1: .: (0.000398) + test_resSeq2: .: (0.000403) + test_sym1: .: (0.000446) + test_sym2: .: (0.000894) Bio::TestPDBRecord::TestSOURCE: - test_srcName: .: (0.000605) + test_srcName: .: (0.000674) Bio::TestPDBRecord::TestSPRSDE: - test_idCode: .: (0.000796) - test_sIdCode: .: (0.000303) - test_sprsdeDate: .: (0.000290) + test_idCode: .: (0.000667) + test_sIdCode: .: (0.000349) + test_sprsdeDate: .: (0.000388) Bio::TestPDBRecord::TestTER: - test_chainID: .: (0.001000) - test_iCode: .: (0.000306) - test_resName: .: (0.000302) - test_resSeq: .: (0.000287) - test_serial: .: (0.000315) + test_chainID: .: (0.000680) + test_iCode: .: (0.000351) + test_resName: .: (0.000348) + test_resSeq: .: (0.000344) + test_serial: .: (0.000355) Bio::TestPDBRecord::TestTITLE: - test_title: .: (0.000553) + test_title: .: (0.000611) Bio::TestPDBRecord::TestTVECT: - test_serial: .: (0.000637) - test_t1: .: (0.000306) - test_t2: .: (0.000285) - test_t3: .: (0.000285) - test_text: .: (0.000530) + test_serial: .: (0.001157) + test_t1: .: (0.000387) + test_t2: .: (0.000349) + test_t3: .: (0.000359) + test_text: .: (0.000352) Bio::TestPROSITE: - test_ac: .: (0.004745) - test_cc: .: (0.004562) - test_de: .: (0.004505) - test_division: .: (0.004664) - test_dr: .: (0.039549) - test_dt: .: (0.020945) - test_false_neg: .: (0.024569) - test_false_pos: .: (0.036413) - test_false_positive_sequences: .: (0.049540) - test_list_falsenegative: .: (0.044461) - test_list_falsepositive: .: (0.040878) - test_list_potentialhit: .: (0.043448) - test_list_truepositive: .: (0.045791) - test_list_unknown: .: (0.050145) - test_list_xref: .: (0.045134) - test_ma: .: (0.005592) - test_max_repeat: .: (0.004831) - test_name: .: (0.005243) - test_nr: .: (0.003936) - test_pa: .: (0.004856) - test_pa2re: .: (0.005614) - test_partial: .: (0.005867) - test_pdb_xref: .: (0.005886) - test_pdoc_xref: .: (0.005279) - test_positive: .: (0.005536) - test_positive_hits: .: (0.004804) - test_positive_sequences: .: (0.009321) - test_release: .: (0.004752) - test_ru: .: (0.005941) - test_self_pa2re: .: (0.006070) - test_site: .: (0.005970) - test_skip_flag: .: (0.005700) - test_swissprot_release_number: .: (0.005492) - test_swissprot_release_sequences: .: (0.005288) - test_taxon_range: .: (0.005250) - test_total: .: (0.005964) - test_total_hits: .: (0.005398) - test_total_sequences: .: (0.005862) - test_unknown: .: (0.005677) - test_unknown_hits: .: (0.004994) - test_unknown_sequences: .: (0.005247) + test_ac: .: (0.004439) + test_cc: .: (0.004368) + test_de: .: (0.003831) + test_division: .: (0.004404) + test_dr: .: (0.041796) + test_dt: .: (0.020528) + test_false_neg: .: (0.040709) + test_false_pos: .: (0.035228) + test_false_positive_sequences: .: (0.034318) + test_list_falsenegative: .: (0.041336) + test_list_falsepositive: .: (0.041276) + test_list_potentialhit: .: (0.043827) + test_list_truepositive: .: (0.050278) + test_list_unknown: .: (0.043758) + test_list_xref: .: (0.045728) + test_ma: .: (0.004157) + test_max_repeat: .: (0.005569) + test_name: .: (0.004560) + test_nr: .: (0.004615) + test_pa: .: (0.004938) + test_pa2re: .: (0.005078) + test_partial: .: (0.005517) + test_pdb_xref: .: (0.004273) + test_pdoc_xref: .: (0.005574) + test_positive: .: (0.010629) + test_positive_hits: .: (0.005155) + test_positive_sequences: .: (0.004572) + test_release: .: (0.004289) + test_ru: .: (0.005434) + test_self_pa2re: .: (0.005283) + test_site: .: (0.005385) + test_skip_flag: .: (0.004967) + test_swissprot_release_number: .: (0.004680) + test_swissprot_release_sequences: .: (0.005576) + test_taxon_range: .: (0.005564) + test_total: .: (0.005149) + test_total_hits: .: (0.005629) + test_total_sequences: .: (0.004390) + test_unknown: .: (0.004695) + test_unknown_hits: .: (0.004597) + test_unknown_sequences: .: (0.004210) Bio::TestPROSITEConst: - test_delimiter: .: (0.001376) - test_tagsize: .: (0.000219) + test_delimiter: .: (0.000635) + test_tagsize: .: (0.000270) Bio::TestPTS1: - test_function_set: .: (0.000558) - test_function_set_number_1: .: (0.000275) - test_function_set_number_2: .: (0.000250) - test_function_set_number_3: .: (0.000249) - test_function_show: .: (0.000224) + test_function_set: .: (0.001131) + test_function_set_number_1: .: (0.000342) + test_function_set_number_2: .: (0.000305) + test_function_set_number_3: .: (0.000356) + test_function_show: .: (0.000278) Bio::TestPTS1Constant: - test_FUNCTION: .: (0.000480) + test_FUNCTION: .: (0.000528) Bio::TestPTS1New: - test_fungi: .: (0.000488) - test_general: .: (0.000558) - test_metazoa: .: (0.000261) + test_fungi: .: (0.000579) + test_general: .: (0.000309) + test_metazoa: .: (0.000298) Bio::TestQualifier: - test_qualifier: .: (0.000989) - test_value: .: (0.000240) + test_qualifier: .: (0.000551) + test_value: .: (0.000266) Bio::TestREBASE: - test_methods: .: (0.002422) + test_methods: .: (0.002888) Bio::TestRPSBlast::TestRPSBlastHSP: - test_align_len: .: (0.002022) - test_bit_score: .: (0.002125) - test_evalue: .: (0.001461) - test_gaps: .: (0.001678) - test_hit_from: .: (0.001544) - test_hit_to: .: (0.001749) - test_hseq: .: (0.002121) - test_identity: .: (0.001686) - test_midline: .: (0.001533) - test_percent_identity: .: (0.001641) - test_positive: .: (0.001402) - test_qseq: .: (0.002420) - test_query_from: .: (0.001565) - test_query_to: .: (0.001564) - test_score: .: (0.001694) + test_align_len: .: (0.002127) + test_bit_score: .: (0.001625) + test_evalue: .: (0.001616) + test_gaps: .: (0.001970) + test_hit_from: .: (0.001571) + test_hit_to: .: (0.001558) + test_hseq: .: (0.001623) + test_identity: .: (0.001533) + test_midline: .: (0.002110) + test_percent_identity: .: (0.001580) + test_positive: .: (0.001533) + test_qseq: .: (0.001784) + test_query_from: .: (0.001635) + test_query_to: .: (0.001723) + test_score: .: (0.001616) Bio::TestRPSBlast::TestRPSBlastReport: - test_db: .: (0.001604) - test_hits_size: .: (0.003933) - test_iterations_size: .: (0.003298) - test_program: .: (0.001509) - test_query_def: .: (0.003705) - test_query_len: .: (0.002983) - test_version: .: (0.001512) - test_version_date: .: (0.001258) - test_version_number: .: (0.002004) + test_db: .: (0.001775) + test_hits_size: .: (0.003418) + test_iterations_size: .: (0.003706) + test_program: .: (0.001311) + test_query_def: .: (0.003172) + test_query_len: .: (0.003668) + test_version: .: (0.001309) + test_version_date: .: (0.001294) + test_version_number: .: (0.001318) Bio::TestRPSBlast::TestRPSBlastReportHit: - test_bit_score: .: (0.001861) - test_definition: .: (0.001785) - test_evalue: .: (0.001515) - test_hsps_size: .: (0.001357) - test_identity: .: (0.001574) - test_lap_at: .: (0.001701) - test_len: .: (0.001506) - test_midline: .: (0.001649) - test_overlap: .: (0.002408) - test_query_end: .: (0.001672) - test_query_seq: .: (0.001649) - test_query_start: .: (0.001653) - test_target_def: .: (0.002278) - test_target_end: .: (0.001660) - test_target_len: .: (0.001769) - test_target_seq: .: (0.001665) - test_target_start: .: (0.001924) + test_bit_score: .: (0.002069) + test_definition: .: (0.002189) + test_evalue: .: (0.001698) + test_hsps_size: .: (0.001497) + test_identity: .: (0.001611) + test_lap_at: .: (0.002143) + test_len: .: (0.001740) + test_midline: .: (0.001758) + test_overlap: .: (0.001609) + test_query_end: .: (0.001893) + test_query_seq: .: (0.001738) + test_query_start: .: (0.001809) + test_target_def: .: (0.001667) + test_target_end: .: (0.001845) + test_target_len: .: (0.001648) + test_target_seq: .: (0.001769) + test_target_start: .: (0.002008) Bio::TestRPSBlast::TestRPSBlastSplitter: - test_entry_pos: .: (0.001329) - test_get_entry: .: (0.001313) - test_rewind: .: (0.000295) - test_skip_leader: .: (0.000537) + test_entry_pos: .: (0.001494) + test_get_entry: .: (0.001344) + test_rewind: .: (0.000352) + test_skip_leader: .: (0.000607) Bio::TestReference: - test_abstract: .: (0.000549) - test_affiliations: .: (0.000243) - test_authors: .: (0.000229) - test_format_bibitem: .: (0.000390) - test_format_bibtex: .: (0.000688) - test_format_bibtex_with_arguments: .: (0.000569) - test_format_cell: .: (0.000308) - test_format_current: .: (0.000411) - test_format_endnote: .: (0.000373) - test_format_general: .: (0.000364) - test_format_genome_biol: .: (0.000326) - test_format_genome_res: .: (0.000581) - test_format_nar: .: (0.000343) - test_format_nature: .: (0.000366) - test_format_rd: .: (0.000342) - test_format_science: .: (0.000567) - test_format_trends: .: (0.000278) - test_issue: .: (0.000223) - test_journal: .: (0.000227) - test_mesh: .: (0.000226) - test_pages: .: (0.000474) - test_pubmed: .: (0.000245) - test_pubmed_url: .: (0.000240) - test_url: .: (0.000223) - test_volume: .: (0.000224) - test_year: .: (0.000219) + test_abstract: .: (0.000607) + test_affiliations: .: (0.000343) + test_authors: .: (0.000294) + test_format_bibitem: .: (0.000446) + test_format_bibtex: .: (0.000734) + test_format_bibtex_with_arguments: .: (0.000647) + test_format_cell: .: (0.000404) + test_format_current: .: (0.000496) + test_format_endnote: .: (0.000428) + test_format_general: .: (0.000420) + test_format_genome_biol: .: (0.000433) + test_format_genome_res: .: (0.000457) + test_format_nar: .: (0.000376) + test_format_nature: .: (0.000462) + test_format_rd: .: (0.000378) + test_format_science: .: (0.000610) + test_format_trends: .: (0.000325) + test_issue: .: (0.000292) + test_journal: .: (0.000290) + test_mesh: .: (0.000311) + test_pages: .: (0.000355) + test_pubmed: .: (0.000313) + test_pubmed_url: .: (0.000283) + test_url: .: (0.000264) + test_volume: .: (0.000257) + test_year: .: (0.000259) Bio::TestReference_noURL: - test_format_endnote: .: (0.000632) - test_url: .: (0.000234) + test_format_endnote: .: (0.000686) + test_url: .: (0.000286) Bio::TestReferences: - test_append: .: (0.000850) - test_each: .: (0.000311) + test_append: .: (0.000801) + test_each: .: (0.000410) Bio::TestRelation: - test_comparison_operator: .: (0.000621) - test_uniq: .: (0.000383) + test_comparison_operator: .: (0.000708) + test_uniq: .: (0.000395) Bio::TestResidue: - test_addAtom: .: (0.000901) - test_each: .: (0.000794) - test_each_atom: .: (0.000527) - test_get_residue_id_from_atom: .: (0.000465) - test_het_atom: .: (0.000514) - test_iCode: .: (0.000419) - test_inspect: .: (0.000447) - test_resSeq: .: (0.000580) - test_sort: .: (0.000510) - test_square_bracket: .: (0.000538) - test_to_s: .: (0.000636) - test_update_resudue_id: .: (0.000433) + test_addAtom: .: (0.001023) + test_each: .: (0.000730) + test_each_atom: .: (0.000581) + test_get_residue_id_from_atom: .: (0.000597) + test_het_atom: .: (0.000467) + test_iCode: .: (0.000487) + test_inspect: .: (0.000572) + test_resSeq: .: (0.000469) + test_sort: .: (0.000551) + test_square_bracket: .: (0.000612) + test_to_s: .: (0.000709) + test_update_resudue_id: .: (0.000526) Bio::TestResidueFinder: - test_each_residue: .: (0.000703) - test_find_residue: .: (0.000503) - test_residues: .: (0.000382) + test_each_residue: .: (0.000754) + test_find_residue: .: (0.000392) + test_residues: .: (0.000437) Bio::TestRestrictionEnzyme::TestAnalysis: - test_cut: .: (0.326972) - test_cut_from_bio_sequence_na: .: (0.091123) - test_cut_without_permutations: .: (0.065292) - test_view_ranges: .: (0.059822) + test_cut: .: (0.328293) + test_cut_from_bio_sequence_na: .: (0.095227) + test_cut_without_permutations: .: (0.074760) + test_view_ranges: .: (0.067494) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: - test_cuts: .: (0.003466) - test_cuts_after_remove_incomplete_cuts: .: (0.001879) - test_strands_for_display: .: (0.007547) - test_strands_for_display_current: .: (0.002173) + test_cuts: .: (0.004163) + test_cuts_after_remove_incomplete_cuts: .: (0.002568) + test_strands_for_display: .: (0.009149) + test_strands_for_display_current: .: (0.002218) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: - test_fragments: .: (0.001514) - test_fragments_for_display_1: .: (0.002338) - test_fragments_for_display_10: .: (0.003086) - test_fragments_for_display_2: .: (0.002307) - test_fragments_for_display_3: .: (0.003790) - test_fragments_for_display_4: .: (0.002694) - test_fragments_for_display_5: .: (0.002119) - test_fragments_for_display_6: .: (0.001820) - test_fragments_for_display_7: .: (0.001839) - test_fragments_for_display_8: .: (0.002092) - test_fragments_for_display_9: .: (0.001790) + test_fragments: .: (0.002123) + test_fragments_for_display_1: .: (0.002745) + test_fragments_for_display_10: .: (0.003542) + test_fragments_for_display_2: .: (0.002717) + test_fragments_for_display_3: .: (0.004304) + test_fragments_for_display_4: .: (0.003203) + test_fragments_for_display_5: .: (0.002069) + test_fragments_for_display_6: .: (0.002444) + test_fragments_for_display_7: .: (0.002238) + test_fragments_for_display_8: .: (0.001876) + test_fragments_for_display_9: .: (0.002291) Bio::TestRestrictionEnzyme::TestCutRanges: - test_obj_2: .: (0.001041) - test_obj_3: .: (0.000779) - test_obj_7: .: (0.000715) - test_obj_z: .: (0.000873) + test_obj_2: .: (0.001200) + test_obj_3: .: (0.000944) + test_obj_7: .: (0.000801) + test_obj_z: .: (0.000802) Bio::TestRestrictionEnzyme::TestCutSymbol: - test_methods: .: (0.000939) + test_methods: .: (0.001355) Bio::TestRestrictionEnzyme::TestDenseIntArray: - test_bracket: .: (0.000703) - test_bracket_eq: .: (0.000443) - test_concat: .: (0.000340) - test_delete: .: (0.000331) - test_dup: .: (0.000495) - test_each: .: (0.000456) - test_eqeq: .: (0.000302) - test_eqeq_false: .: (0.000439) - test_eqeq_other: .: (0.000255) - test_eqeq_self: .: (0.000231) - test_include?: .: (0.000293) - test_internal_data: .: (0.000267) - test_internal_data_eq: .: (0.000306) - test_length: .: (0.000255) - test_ltlt: .: (0.000347) - test_ltlt_larger: .: (0.000300) - test_ltlt_middle: .: (0.000290) - test_plus: .: (0.000341) - test_plus_error: .: (0.000366) - test_push: .: (0.000361) - test_reverse_each: .: (0.000451) - test_self_bracket: .: (0.000253) - test_self_new: .: (0.000295) - test_size: .: (0.000304) - test_sort!: .: (0.000265) - test_to_a: .: (0.000290) - test_uniq!: .: (0.000249) - test_unshift: .: (0.000333) + test_bracket: .: (0.000867) + test_bracket_eq: .: (0.000514) + test_concat: .: (0.000447) + test_delete: .: (0.000440) + test_dup: .: (0.000536) + test_each: .: (0.000605) + test_eqeq: .: (0.000411) + test_eqeq_false: .: (0.000374) + test_eqeq_other: .: (0.000336) + test_eqeq_self: .: (0.000371) + test_include?: .: (0.000375) + test_internal_data: .: (0.000364) + test_internal_data_eq: .: (0.000435) + test_length: .: (0.000566) + test_ltlt: .: (0.000393) + test_ltlt_larger: .: (0.000389) + test_ltlt_middle: .: (0.000420) + test_plus: .: (0.000450) + test_plus_error: .: (0.000476) + test_push: .: (0.000443) + test_reverse_each: .: (0.000532) + test_self_bracket: .: (0.000341) + test_self_new: .: (0.000383) + test_size: .: (0.000342) + test_sort!: .: (0.000325) + test_to_a: .: (0.000352) + test_uniq!: .: (0.000379) + test_unshift: .: (0.000429) Bio::TestRestrictionEnzyme::TestDoubleStranded: - test_argument_error: .: (0.012718) - test_complement: .: (0.011190) - test_complement_with_cut_symbols: .: (0.011836) - test_cut_locations: .: (0.011212) - test_cut_locations_in_enzyme_notation: .: (0.017389) - test_primary: .: (0.011520) - test_primary_with_cut_symbols: .: (0.012334) - test_to_re: .: (0.011661) + test_argument_error: .: (0.013289) + test_complement: .: (0.011759) + test_complement_with_cut_symbols: .: (0.018144) + test_cut_locations: .: (0.012211) + test_cut_locations_in_enzyme_notation: .: (0.011526) + test_primary: .: (0.011864) + test_primary_with_cut_symbols: .: (0.012234) + test_to_re: .: (0.011689) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: - test_align: .: (0.002960) - test_align_with_cuts: .: (0.002178) - test_argument_error: .: (0.003132) - test_ds: .: (0.002319) + test_align: .: (0.003179) + test_align_with_cuts: .: (0.002505) + test_argument_error: .: (0.003013) + test_ds: .: (0.002724) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: - test_argument_error: .: (0.001475) - test_complement: .: (0.000561) - test_contents: .: (0.000532) - test_primary: .: (0.000531) + test_argument_error: .: (0.001371) + test_complement: .: (0.000681) + test_contents: .: (0.000603) + test_primary: .: (0.000585) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: - test_argument_error: .: (0.000947) - test_complement: .: (0.000558) - test_contents: .: (0.000514) - test_primary: .: (0.000786) + test_argument_error: .: (0.001168) + test_complement: .: (0.000685) + test_contents: .: (0.000728) + test_primary: .: (0.000608) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: - test_complement: .: (0.000703) - test_contents: .: (0.000417) - test_primary: .: (0.000376) + test_complement: .: (0.000815) + test_contents: .: (0.000977) + test_primary: .: (0.000486) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: - test_complement: .: (0.000752) - test_complement_to_array_index: .: (0.000637) - test_complement_to_array_index_class: .: (0.000581) - test_contents: .: (0.000496) - test_primary: .: (0.000739) - test_primary_to_array_index: .: (0.000738) - test_primary_to_array_index_class: .: (0.000584) - test_to_array_index: .: (0.001266) - test_to_array_index_class: .: (0.001117) + test_complement: .: (0.000810) + test_complement_to_array_index: .: (0.000714) + test_complement_to_array_index_class: .: (0.000698) + test_contents: .: (0.000518) + test_primary: .: (0.000516) + test_primary_to_array_index: .: (0.000719) + test_primary_to_array_index_class: .: (0.000644) + test_to_array_index: .: (0.001636) + test_to_array_index_class: .: (0.001219) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: - test_enzyme_name: .: (0.001336) - test_rebase: .: (0.000382) + test_enzyme_name: .: (0.001384) + test_rebase: .: (0.000436) Bio::TestRestrictionEnzyme::TestSingleStrand: - test_argument_error: .: (0.002829) - test_creation_with_no_cuts: .: (0.001298) - test_cut_locations: .: (0.001698) - test_cut_locations_in_enzyme_notation: .: (0.001280) - test_orientation: .: (0.001236) - test_pattern: .: (0.001333) - test_pattern_palindromic?: .: (0.001803) - test_stripped: .: (0.001199) - test_to_re: .: (0.001115) - test_with_cut_symbols: .: (0.001627) - test_with_spaces: .: (0.001482) + test_argument_error: .: (0.002699) + test_creation_with_no_cuts: .: (0.001362) + test_cut_locations: .: (0.001481) + test_cut_locations_in_enzyme_notation: .: (0.001719) + test_orientation: .: (0.001277) + test_pattern: .: (0.001639) + test_pattern_palindromic?: .: (0.001626) + test_stripped: .: (0.001573) + test_to_re: .: (0.001241) + test_with_cut_symbols: .: (0.001421) + test_with_spaces: .: (0.002002) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: - test_argument_error: .: (0.002715) - test_creation_with_no_cuts: .: (0.001354) - test_cut_locations: .: (0.001264) - test_cut_locations_in_enzyme_notation: .: (0.001304) - test_orientation: .: (0.001545) - test_pattern: .: (0.001340) - test_pattern_palindromic?: .: (0.001519) - test_stripped: .: (0.001505) - test_to_re: .: (0.001110) - test_with_cut_symbols: .: (0.001327) - test_with_spaces: .: (0.001809) + test_argument_error: .: (0.002331) + test_creation_with_no_cuts: .: (0.001379) + test_cut_locations: .: (0.001752) + test_cut_locations_in_enzyme_notation: .: (0.001461) + test_orientation: .: (0.001237) + test_pattern: .: (0.001811) + test_pattern_palindromic?: .: (0.001563) + test_stripped: .: (0.001322) + test_to_re: .: (0.001185) + test_with_cut_symbols: .: (0.001665) + test_with_spaces: .: (0.001512) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: - test_argument_error: .: (0.001315) - test_initialize_with_pattern: .: (0.000931) - test_max: .: (0.000382) - test_min: .: (0.000364) - test_to_array_index: .: (0.000504) + test_argument_error: .: (0.001297) + test_initialize_with_pattern: .: (0.001239) + test_max: .: (0.000408) + test_min: .: (0.000595) + test_to_array_index: .: (0.000482) Bio::TestRestrictionEnzyme::TestSortedNumArray: - test_bracket: .: (0.001046) - test_bracket_eq: .: (0.000429) - test_concat: .: (0.000286) - test_delete: .: (0.000251) - test_dup: .: (0.000348) - test_each: .: (0.000479) - test_eqeq: .: (0.000272) - test_eqeq_false: .: (0.000231) - test_eqeq_other: .: (0.000218) - test_eqeq_self: .: (0.000215) - test_include?: .: (0.000292) - test_internal_data_hash: .: (0.000246) - test_internal_data_hash_eq: .: (0.000283) - test_length: .: (0.000225) - test_ltlt: .: (0.000262) - test_ltlt_noeffect: .: (0.000261) - test_plus: .: (0.000252) - test_plus_error: .: (0.000341) - test_private_push_element: .: (0.000280) - test_private_push_element_intermediate: .: (0.000270) - test_private_push_element_last: .: (0.000306) - test_private_push_element_noeffect: .: (0.000315) - test_private_sorted_keys: .: (0.000237) - test_private_unshift_element: .: (0.000253) - test_private_unshift_element_first: .: (0.000271) - test_private_unshift_element_intermediate: .: (0.000264) - test_private_unshift_element_noeffect: .: (0.000251) - test_push: .: (0.000285) - test_reverse_each: .: (0.000439) - test_self_bracket: .: (0.000236) - test_self_new: .: (0.000269) - test_size: .: (0.000240) - test_sort!: .: (0.000242) - test_to_a: .: (0.000231) - test_uniq!: .: (0.000217) - test_unshift: .: (0.000261) + test_bracket: .: (0.000661) + test_bracket_eq: .: (0.000370) + test_concat: .: (0.000295) + test_delete: .: (0.000255) + test_dup: .: (0.000351) + test_each: .: (0.000688) + test_eqeq: .: (0.000565) + test_eqeq_false: .: (0.000294) + test_eqeq_other: .: (0.000269) + test_eqeq_self: .: (0.000275) + test_include?: .: (0.000290) + test_internal_data_hash: .: (0.000304) + test_internal_data_hash_eq: .: (0.000323) + test_length: .: (0.000285) + test_ltlt: .: (0.000310) + test_ltlt_noeffect: .: (0.000300) + test_plus: .: (0.000289) + test_plus_error: .: (0.000399) + test_private_push_element: .: (0.000318) + test_private_push_element_intermediate: .: (0.000306) + test_private_push_element_last: .: (0.000311) + test_private_push_element_noeffect: .: (0.000619) + test_private_sorted_keys: .: (0.000282) + test_private_unshift_element: .: (0.000298) + test_private_unshift_element_first: .: (0.000310) + test_private_unshift_element_intermediate: .: (0.000311) + test_private_unshift_element_noeffect: .: (0.000335) + test_push: .: (0.000313) + test_reverse_each: .: (0.000504) + test_self_bracket: .: (0.000277) + test_self_new: .: (0.000326) + test_size: .: (0.000262) + test_sort!: .: (0.000252) + test_to_a: .: (0.000266) + test_uniq!: .: (0.000254) + test_unshift: .: (0.000340) Bio::TestRestrictionEnzyme::TestStringFormatting: - test_add_spacing: .: (0.000623) - test_left_padding: .: (0.000335) - test_right_padding: .: (0.000318) - test_strip_padding: .: (0.000385) + test_add_spacing: .: (0.000707) + test_left_padding: .: (0.000444) + test_right_padding: .: (0.000378) + test_strip_padding: .: (0.000392) Bio::TestSOFT: - test_dataset: .: (0.019489) - test_series: .: (0.019100) + test_dataset: .: (0.020553) + test_series: .: (0.020036) Bio::TestSOSUIReport: - test_entry_id: .: (0.000747) - test_prediction: .: (0.000397) - test_tmh: .: (0.000372) - test_tmhs: .: (0.000429) + test_entry_id: .: (0.000799) + test_prediction: .: (0.000463) + test_tmh: .: (0.000430) + test_tmhs: .: (0.000490) Bio::TestSOSUIReportConst: - test_delimiter: .: (0.000766) - test_rs: .: (0.000223) + test_delimiter: .: (0.000526) + test_rs: .: (0.000250) Bio::TestSOSUITMH: - test_grade: .: (0.000724) - test_range: .: (0.000394) - test_sequence: .: (0.000380) + test_grade: .: (0.000680) + test_range: .: (0.000436) + test_sequence: .: (0.000706) Bio::TestSampleGraph: - test_bellman_ford: .: (0.001226) - test_bfs_shortest_path: .: (0.000494) - test_breadth_first_search: .: (0.000552) - test_depth_first_search: .: (0.000819) - test_dijkstra: .: (0.000869) - test_dump_list: .: (0.000682) - test_dump_matrix: .: (0.000855) - test_extract_subgraph_by_label: .: (0.000614) - test_extract_subgraph_by_list: .: (0.000594) - test_extract_subgraph_retains_disconnected_nodes: .: (0.000434) - test_small_world_aka_node_degree_histogram: .: (0.000402) - test_to_matrix: .: (0.000979) - test_to_matrix_fixed_index: .: (0.000737) - test_undirected_cliquishness: .: (0.001076) + test_bellman_ford: .: (0.001302) + test_bfs_shortest_path: .: (0.000553) + test_breadth_first_search: .: (0.000553) + test_depth_first_search: .: (0.000856) + test_dijkstra: .: (0.000742) + test_dump_list: .: (0.000687) + test_dump_matrix: .: (0.000979) + test_extract_subgraph_by_label: .: (0.000853) + test_extract_subgraph_by_list: .: (0.000650) + test_extract_subgraph_retains_disconnected_nodes: .: (0.000495) + test_small_world_aka_node_degree_histogram: .: (0.000494) + test_to_matrix: .: (0.001101) + test_to_matrix_fixed_index: .: (0.000751) + test_undirected_cliquishness: .: (0.000953) Bio::TestScf_version_2: - test_complement: .: (0.029921) - test_seq: .: (0.028337) - test_to_biosequence: .: (0.029073) + test_complement: .: (0.030595) + test_seq: .: (0.029104) + test_to_biosequence: .: (0.029119) Bio::TestScf_version_3: - test_complement: .: (0.093293) - test_seq: .: (0.091625) - test_to_biosequence: .: (0.091635) + test_complement: .: (0.094506) + test_seq: .: (0.094036) + test_to_biosequence: .: (0.094547) Bio::TestSequence: - test_AA_new_blank_sequence: .: (0.000771) - test_AA_new_sequence_all_legal_symbols: .: (0.000284) - test_AA_new_sequence_removes_whitespace: .: (0.000244) - test_AA_new_sequence_upcases_symbols: .: (0.000229) - test_DNA_new_blank_sequence: .: (0.000225) - test_DNA_new_sequence_downcases_symbols: .: (0.000229) - test_DNA_new_sequence_removes_whitespace: .: (0.000226) - test_NA_randomize_with_counts: .: (0.002310) - test_NA_randomize_with_counts_and_block: .: (0.002502) - test_RNA_new_sequence: .: (0.000247) - test_ambiguous_dna_sequence_complement: .: (0.000516) - test_ambiguous_rna_sequence_complement: .: (0.000302) - test_amino_acid_codes: .: (0.000318) - test_amino_acid_molecular_weight: .: (0.000498) - test_amino_acid_names: .: (0.000325) - test_amino_acid_randomize_can_be_chained: .: (0.003433) - test_amino_acid_randomize_has_same_composition: .: (0.001638) - test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.002025) - test_dna_composition: .: (0.000325) - test_dna_gc_percent: .: (0.000339) - test_dna_molecular_weight: .: (0.000481) - test_dna_pikachu: .: (0.000267) - test_dna_sequence_complement: .: (0.000236) - test_dna_sequence_translate: .: (0.001183) - test_dna_to_re: .: (0.000466) - test_element_reference_operator_with_one_argument: .: (0.000247) - test_element_reference_operator_with_two_arguments: .: (0.000230) - test_invalid_nucleic_acid_illegal_bases: .: (0.000322) - test_invalid_nucleic_acid_illegal_bases_more: .: (0.000424) - test_nucleic_acid_names: .: (0.000291) - test_randomize_dna_can_be_chained: .: (0.000944) - test_randomize_dna_retains_composition: .: (0.000928) - test_randomize_dna_with_block: .: (0.000808) - test_rna_composition: .: (0.000348) - test_rna_gc_percent: .: (0.000356) - test_rna_molecular_weight: .: (0.000430) - test_rna_pikachu: .: (0.000257) - test_rna_sequence_complement: .: (0.000379) - test_rna_sequence_translate: .: (0.000723) - test_rna_to_re: .: (0.000405) - test_total: .: (0.000272) - test_two_consecutive_dna_randomizations_not_equal: .: (0.001012) - test_valid_dna_sequence_illegal_bases: .: (0.000236) + test_AA_new_blank_sequence: .: (0.000730) + test_AA_new_sequence_all_legal_symbols: .: (0.000510) + test_AA_new_sequence_removes_whitespace: .: (0.000651) + test_AA_new_sequence_upcases_symbols: .: (0.000553) + test_DNA_new_blank_sequence: .: (0.000588) + test_DNA_new_sequence_downcases_symbols: .: (0.000536) + test_DNA_new_sequence_removes_whitespace: .: (0.000287) + test_NA_randomize_with_counts: .: (0.002677) + test_NA_randomize_with_counts_and_block: .: (0.003428) + test_RNA_new_sequence: .: (0.000359) + test_ambiguous_dna_sequence_complement: .: (0.000390) + test_ambiguous_rna_sequence_complement: .: (0.000352) + test_amino_acid_codes: .: (0.000494) + test_amino_acid_molecular_weight: .: (0.000681) + test_amino_acid_names: .: (0.000401) + test_amino_acid_randomize_can_be_chained: .: (0.003827) + test_amino_acid_randomize_has_same_composition: .: (0.002156) + test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.002231) + test_dna_composition: .: (0.000480) + test_dna_gc_percent: .: (0.000549) + test_dna_molecular_weight: .: (0.000708) + test_dna_pikachu: .: (0.000600) + test_dna_sequence_complement: .: (0.000467) + test_dna_sequence_translate: .: (0.001594) + test_dna_to_re: .: (0.000512) + test_element_reference_operator_with_one_argument: .: (0.000314) + test_element_reference_operator_with_two_arguments: .: (0.000294) + test_invalid_nucleic_acid_illegal_bases: .: (0.000715) + test_invalid_nucleic_acid_illegal_bases_more: .: (0.000469) + test_nucleic_acid_names: .: (0.000479) + test_randomize_dna_can_be_chained: .: (0.001285) + test_randomize_dna_retains_composition: .: (0.000745) + test_randomize_dna_with_block: .: (0.001004) + test_rna_composition: .: (0.000730) + test_rna_gc_percent: .: (0.000407) + test_rna_molecular_weight: .: (0.000696) + test_rna_pikachu: .: (0.000317) + test_rna_sequence_complement: .: (0.000345) + test_rna_sequence_translate: .: (0.000955) + test_rna_to_re: .: (0.000473) + test_total: .: (0.000341) + test_two_consecutive_dna_randomizations_not_equal: .: (0.000850) + test_valid_dna_sequence_illegal_bases: .: (0.000297) Bio::TestSequenceAA: - test_codes: .: (0.000574) - test_molecular_weight: .: (0.000415) - test_names: .: (0.000292) - test_to_re: .: (0.000361) - test_to_s: .: (0.000218) + test_codes: .: (0.001001) + test_molecular_weight: .: (0.000491) + test_names: .: (0.001201) + test_to_re: .: (0.000642) + test_to_s: .: (0.000809) Bio::TestSequenceAACompat: - test_aa_self_randomize: .: (0.000684) + test_aa_self_randomize: .: (0.001431) Bio::TestSequenceAANew: - test_new: .: (0.000658) - test_new_n: .: (0.000249) - test_new_r: .: (0.000214) - test_new_t: .: (0.000209) + test_new: .: (0.001820) + test_new_n: .: (0.000543) + test_new_r: .: (0.000280) + test_new_t: .: (0.000268) Bio::TestSequenceCommon::TestSequenceCommon: - test_composition: .: (0.000583) - test_concat: .: (0.000233) - test_push: .: (0.000264) - test_seq: .: (0.000204) - test_splicing: .: (0.000418) - test_sum: .: (0.000217) - test_to_s: .: (0.000196) - test_to_str: .: (0.000215) - test_total: .: (0.000243) - test_window_search: .: (0.000989) + test_composition: .: (0.001477) + test_concat: .: (0.000299) + test_push: .: (0.000434) + test_seq: .: (0.000274) + test_splicing: .: (0.000544) + test_sum: .: (0.000276) + test_to_s: .: (0.000294) + test_to_str: .: (0.000236) + test_total: .: (0.000299) + test_window_search: .: (0.001342) Bio::TestSequenceCommon::TestSequenceCommonNormalize: - test_no_normalize: .: (0.000488) - test_normalize_A: .: (0.000251) - test_normalize_a: .: (0.000229) + test_no_normalize: .: (0.000579) + test_normalize_A: .: (0.000448) + test_normalize_a: .: (0.000351) Bio::TestSequenceCommon::TestSequenceCommonRandomize: - test_randomize: .: (0.003049) - test_randomize_with_block: .: (0.021702) - test_randomize_with_hash: .: (0.003746) - test_randomize_with_hash_block: .: (0.014458) + test_randomize: .: (0.020424) + test_randomize_with_block: .: (0.016979) + test_randomize_with_hash: .: (0.004108) + test_randomize_with_hash_block: .: (0.026360) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/ruby-bio-2.0.4/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== -: (0.002322) +: (0.005280) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/ruby-bio-2.0.4/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== -: (0.002181) +: (0.002520) Bio::TestSequenceCommon::TestSequenceCommonSubseq: - test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000652) - test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000298) - test_subseq_returns_subsequence: .: (0.000230) - test_to_s_returns_self_as_string: .: (0.000272) + test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.000937) + test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000366) + test_subseq_returns_subsequence: .: (0.000294) + test_to_s_returns_self_as_string: .: (0.000454) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: - test_window_search_with_width_3_default_step_no_residual: .: (0.000526) - test_window_search_with_width_3_step_two_with_residual: .: (0.000270) + test_window_search_with_width_3_default_step_no_residual: .: (0.000784) + test_window_search_with_width_3_step_two_with_residual: .: (0.000338) Bio::TestSequenceCompat::TestSequenceCommonCompat: - test_to_fasta: .: (0.000969) + test_to_fasta: .: (0.000659) Bio::TestSequenceCompat::TestSequenceCompat: - test_to_s: .: (0.000454) + test_to_s: .: (0.000526) Bio::TestSequenceCompat::TestSequenceNACompat: - test_aa_self_randomize: .: (0.000699) - test_na_self_randomize: .: (0.000443) + test_aa_self_randomize: .: (0.001144) + test_na_self_randomize: .: (0.000542) Bio::TestSequenceDBLink: - test_database: .: (0.000463) - test_id: .: (0.000258) - test_secondary_ids: .: (0.000223) + test_database: .: (0.000574) + test_id: .: (0.000256) + test_secondary_ids: .: (0.000250) Bio::TestSequenceDBLinkClassMethods: - test_parse_embl_DR_line: .: (0.000559) - test_parse_uniprot_DR_line: .: (0.000339) + test_parse_embl_DR_line: .: (0.000640) + test_parse_uniprot_DR_line: .: (0.000392) Bio::TestSequenceFormatFormatterFasta_numeric: - test_output: .: (0.002509) - test_output_width_35: .: (0.001263) - test_output_width_nil: .: (0.000876) + test_output: .: (0.002960) + test_output_width_35: .: (0.000958) + test_output_width_nil: .: (0.001318) Bio::TestSequenceFormatFormatterQual: - test_output: .: (0.001330) - test_output_after_adding_sequence: .: (0.000824) - test_output_after_truncating_sequence: .: (0.000602) - test_output_from_error_probabilities: .: (0.010295) - test_output_width45: .: (0.000733) - test_output_with_converting_score_phred2solexa: .: (0.002356) - test_output_with_converting_score_solexa2phred: .: (0.001078) - test_output_with_default_score: .: (0.000675) + test_output: .: (0.001394) + test_output_after_adding_sequence: .: (0.000911) + test_output_after_truncating_sequence: .: (0.000665) + test_output_from_error_probabilities: .: (0.010478) + test_output_width45: .: (0.000839) + test_output_with_converting_score_phred2solexa: .: (0.002656) + test_output_with_converting_score_solexa2phred: .: (0.001116) + test_output_with_default_score: .: (0.000724) Bio::TestSequenceMasker: - test_mask: .: (0.000689) - test_mask_with_enumerator: .: (0.000898) - test_mask_with_enumerator_empty_mask_char: .: (0.000432) - test_mask_with_enumerator_excess: .: (0.001542) - test_mask_with_enumerator_longer_mask_char: .: (0.000430) - test_mask_with_enumerator_shorter: .: (0.000566) - test_mask_with_error_probability: .: (0.000451) - test_mask_with_quality_score: .: (0.000395) + test_mask: .: (0.001193) + test_mask_with_enumerator: .: (0.000560) + test_mask_with_enumerator_empty_mask_char: .: (0.000609) + test_mask_with_enumerator_excess: .: (0.001678) + test_mask_with_enumerator_longer_mask_char: .: (0.000520) + test_mask_with_enumerator_shorter: .: (0.001030) + test_mask_with_error_probability: .: (0.001228) + test_mask_with_quality_score: .: (0.000651) Bio::TestSequenceNA: - test_at_content: .: (0.000991) - test_at_skew: .: (0.000716) - test_codon_usage: .: (0.000331) - test_complement: .: (0.000325) - test_dna: .: (0.000263) - test_dna!: .: (0.000238) - test_forward_complement: .: (0.000383) - test_gc_content: .: (0.000715) - test_gc_percent: .: (0.000498) - test_gc_skew: .: (0.000987) - test_iliegal_bases: .: (0.000271) - test_molecular_weight: .: (0.000995) - test_names: .: (0.000359) - test_reverse_complement: .: (0.000444) - test_rna: .: (0.000263) - test_rna!: .: (0.000239) - test_splicing: .: (0.000396) - test_to_re: .: (0.000460) - test_to_s: .: (0.000225) + test_at_content: .: (0.001438) + test_at_skew: .: (0.000779) + test_codon_usage: .: (0.000577) + test_complement: .: (0.000378) + test_dna: .: (0.000396) + test_dna!: .: (0.000408) + test_forward_complement: .: (0.000441) + test_gc_content: .: (0.001434) + test_gc_percent: .: (0.000635) + test_gc_skew: .: (0.001337) + test_iliegal_bases: .: (0.000386) + test_molecular_weight: .: (0.000854) + test_names: .: (0.000973) + test_reverse_complement: .: (0.000817) + test_rna: .: (0.000392) + test_rna!: .: (0.000303) + test_splicing: .: (0.001008) + test_to_re: .: (0.001070) + test_to_s: .: (0.000289) Bio::TestSequenceNACommon: - test_composition: .: (0.000586) - test_concat: .: (0.000235) - test_push: .: (0.000215) - test_seq: .: (0.000237) - test_splicing: .: (0.000385) - test_sum: .: (0.000232) - test_to_s: .: (0.000643) - test_to_str: .: (0.000233) - test_total: .: (0.000249) - test_window_search: .: (0.000746) + test_composition: .: (0.000726) + test_concat: .: (0.000291) + test_push: .: (0.000275) + test_seq: .: (0.000562) + test_splicing: .: (0.000686) + test_sum: .: (0.000567) + test_to_s: .: (0.000278) + test_to_str: .: (0.000300) + test_total: .: (0.000311) + test_window_search: .: (0.002054) Bio::TestSequenceNANew: - test_new: .: (0.000489) - test_new_n: .: (0.000240) - test_new_r: .: (0.000212) - test_new_t: .: (0.000210) + test_new: .: (0.000646) + test_new_n: .: (0.000330) + test_new_r: .: (0.000320) + test_new_t: .: (0.000301) Bio::TestSequenceNATranslation: - test_translate: .: (0.000975) - test_translate_0: .: (0.002711) - test_translate_1: .: (0.000698) - test_translate_2: .: (0.000574) - test_translate_3: .: (0.000573) - test_translate_4: .: (0.000692) - test_translate_5: .: (0.000580) - test_translate_6: .: (0.000611) - test_translate_7: .: (0.001725) - test_translate_given_codon_table: .: (0.129044) - test_translate_n1: .: (0.001477) - test_translate_n2: .: (0.001406) - test_translate_n3: .: (0.001261) - test_translate_unknown_o: .: (0.007721) - test_translate_unknown_x: .: (0.000720) + test_translate: .: (0.001282) + test_translate_0: .: (0.006012) + test_translate_1: .: (0.002297) + test_translate_2: .: (0.000705) + test_translate_3: .: (0.001226) + test_translate_4: .: (0.000869) + test_translate_5: .: (0.001570) + test_translate_6: .: (0.001645) + test_translate_7: .: (0.001610) + test_translate_given_codon_table: .: (0.188360) + test_translate_n1: .: (0.001923) + test_translate_n2: .: (0.007645) + test_translate_n3: .: (0.001600) + test_translate_unknown_o: .: (0.000811) + test_translate_unknown_x: .: (0.000832) Bio::TestSequenceQualityScore::TestConverter: - test_convert_nothing: .: (0.000492) - test_convert_scores_from_phred_to_solexa: .: (0.007399) - test_convert_scores_from_solexa_to_phred: .: (0.000578) + test_convert_nothing: .: (0.008332) + test_convert_scores_from_phred_to_solexa: .: (0.009656) + test_convert_scores_from_solexa_to_phred: .: (0.008197) Bio::TestSequenceQualityScore::TestPhred: - test_convert_nothing: .: (0.009457) - test_convert_scores_from_phred: .: (0.000261) - test_convert_scores_from_phred_to_solexa: .: (0.001316) - test_convert_scores_from_solexa: .: (0.008858) - test_convert_scores_from_solexa_to_phred: .: (0.007770) - test_convert_scores_to_phred: .: (0.000231) - test_convert_scores_to_solexa: .: (0.005640) - test_p2q: .: (0.000548) - test_phred_p2q: .: (0.006885) - test_phred_q2p: .: (0.079597) - test_q2p: .: (0.014565) - test_quality_score_type: .: (0.000230) - test_self_convert_scores_to_solexa: .: (0.001293) - test_self_p2q: .: (0.000782) - test_self_q2p: .: (0.015031) + test_convert_nothing: .: (0.000694) + test_convert_scores_from_phred: .: (0.000361) + test_convert_scores_from_phred_to_solexa: .: (0.006960) + test_convert_scores_from_solexa: .: (0.008054) + test_convert_scores_from_solexa_to_phred: .: (0.008154) + test_convert_scores_to_phred: .: (0.000385) + test_convert_scores_to_solexa: .: (0.009040) + test_p2q: .: (0.000643) + test_phred_p2q: .: (0.007864) + test_phred_q2p: .: (0.040970) + test_q2p: .: (0.017327) + test_quality_score_type: .: (0.000362) + test_self_convert_scores_to_solexa: .: (0.001812) + test_self_p2q: .: (0.000562) + test_self_q2p: .: (0.017248) Bio::TestSequenceQualityScore::TestSolexa: - test_convert_nothing: .: (0.000548) - test_convert_scores_from_phred: .: (0.001762) - test_convert_scores_from_phred_to_solexa: .: (0.001235) - test_convert_scores_from_solexa: .: (0.000217) - test_convert_scores_from_solexa_to_phred: .: (0.000568) - test_convert_scores_to_phred: .: (0.000869) - test_convert_scores_to_solexa: .: (0.000210) - test_p2q: .: (0.000764) - test_q2p: .: (0.016556) - test_quality_score_type: .: (0.000235) - test_self_convert_scores_to_phred: .: (0.000613) - test_self_p2q: .: (0.000644) - test_self_q2p: .: (0.016243) - test_solexa_p2q: .: (0.000686) - test_solexa_q2p: .: (0.015788) + test_convert_nothing: .: (0.000645) + test_convert_scores_from_phred: .: (0.001529) + test_convert_scores_from_phred_to_solexa: .: (0.001719) + test_convert_scores_from_solexa: .: (0.000334) + test_convert_scores_from_solexa_to_phred: .: (0.001805) + test_convert_scores_to_phred: .: (0.000652) + test_convert_scores_to_solexa: .: (0.000303) + test_p2q: .: (0.000983) + test_q2p: .: (0.019404) + test_quality_score_type: .: (0.000352) + test_self_convert_scores_to_phred: .: (0.000764) + test_self_p2q: .: (0.000797) + test_self_q2p: .: (0.019814) + test_solexa_p2q: .: (0.000788) + test_solexa_q2p: .: (0.018340) Bio::TestSequenceRuby3::TestSequenceCommon: - test_capitalize: .: (0.000571) - test_center: .: (0.000290) - test_chomp: .: (0.000389) - test_chop: .: (0.000341) - test_delete: .: (0.000262) - test_delete_prefix: .: (0.000257) - test_delete_suffix: .: (0.000261) - test_downcase: .: (0.000260) - test_each_char: .: (0.000515) - test_each_char_enum: .: (0.000407) - test_each_grapheme_cluster: .: (0.000979) - test_each_grapheme_cluster_enum: .: (0.000795) - test_each_line: .: (0.000425) - test_each_line_enum: .: (0.000353) - test_gsub: .: (0.000364) - test_gsub_with_block: .: (0.001128) - test_ljust: .: (0.000338) - test_lstrip: .: (0.000271) - test_multiply: .: (0.000264) - test_next: .: (0.000261) - test_reverse: .: (0.000258) - test_rjust: .: (0.000271) - test_rstrip: .: (0.000279) - test_slice: .: (0.000340) - test_slice2: .: (0.000263) - test_split: .: (0.000391) - test_squeeze: .: (0.000273) - test_strip: .: (0.000256) - test_sub: .: (0.000288) - test_sub_with_block: .: (0.000587) - test_succ: .: (0.000272) - test_swapcase: .: (0.000283) - test_tr: .: (0.000270) - test_tr_s: .: (0.000256) - test_upcase: .: (0.000260) + test_capitalize: .: (0.001236) + test_center: .: (0.000448) + test_chomp: .: (0.000504) + test_chop: .: (0.000493) + test_delete: .: (0.000414) + test_delete_prefix: .: (0.000405) + test_delete_suffix: .: (0.000423) + test_downcase: .: (0.000383) + test_each_char: .: (0.000696) + test_each_char_enum: .: (0.000566) + test_each_grapheme_cluster: .: (0.001057) + test_each_grapheme_cluster_enum: .: (0.000974) + test_each_line: .: (0.000618) + test_each_line_enum: .: (0.000523) + test_gsub: .: (0.000448) + test_gsub_with_block: .: (0.001532) + test_ljust: .: (0.000407) + test_lstrip: .: (0.000441) + test_multiply: .: (0.000368) + test_next: .: (0.000385) + test_reverse: .: (0.000376) + test_rjust: .: (0.000469) + test_rstrip: .: (0.000424) + test_slice: .: (0.000381) + test_slice2: .: (0.000383) + test_split: .: (0.000478) + test_squeeze: .: (0.000369) + test_strip: .: (0.000369) + test_sub: .: (0.000410) + test_sub_with_block: .: (0.000824) + test_succ: .: (0.000428) + test_swapcase: .: (0.000385) + test_tr: .: (0.000383) + test_tr_s: .: (0.000327) + test_upcase: .: (0.000369) Bio::TestSequenceRuby3::TestSequenceCommonPartition: - test_partition: .: (0.000623) - test_partition_nomatch: .: (0.000773) - test_partition_sep_TSeq: .: (0.000371) - test_partition_sep_regexp: .: (0.000424) + test_partition: .: (0.000804) + test_partition_nomatch: .: (0.000523) + test_partition_sep_TSeq: .: (0.000480) + test_partition_sep_regexp: .: (0.000524) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: - test_rpartition: .: (0.000620) - test_rpartition_nomatch: .: (0.000405) - test_rpartition_sep_TSeq: .: (0.000355) - test_rpartition_sep_regexp: .: (0.000356) + test_rpartition: .: (0.000745) + test_rpartition_nomatch: .: (0.000478) + test_rpartition_sep_TSeq: .: (0.000440) + test_rpartition_sep_regexp: .: (0.000500) Bio::TestShRNA: - test_blocK_it: .: (0.069253) - test_blocK_it_: .: (0.066810) - test_blocK_it_BLOCK_IT: .: (0.070836) - test_blocK_it_BLOCK_iT: .: (0.067332) - test_blocK_it_piGene: .: (0.067309) - test_bottom_strand: .: (0.066381) - test_bottom_strand_class: .: (0.069065) - test_bottom_strand_nil: .: (0.066296) - test_design: .: (0.067505) - test_design_BLOCK_IT: .: (0.067217) - test_report: .: (0.068534) - test_report_before_design: .: (0.066358) - test_top_strand: .: (0.067553) - test_top_strand_class: .: (0.066567) - test_top_strand_nil: .: (0.068218) + test_blocK_it: .: (0.082125) + test_blocK_it_: .: (0.083252) + test_blocK_it_BLOCK_IT: .: (0.082614) + test_blocK_it_BLOCK_iT: .: (0.082143) + test_blocK_it_piGene: .: (0.083064) + test_bottom_strand: .: (0.080077) + test_bottom_strand_class: .: (0.081510) + test_bottom_strand_nil: .: (0.080434) + test_design: .: (0.080685) + test_design_BLOCK_IT: .: (0.081565) + test_report: .: (0.083416) + test_report_before_design: .: (0.079288) + test_top_strand: .: (0.082125) + test_top_strand_class: .: (0.079818) + test_top_strand_nil: .: (0.082727) Bio::TestShRNANew: - test_new: .: (0.000942) + test_new: .: (0.001262) Bio::TestSiRNA: - test_antisense_size: .: (0.000527) - test_design: .: (0.066481) - test_design_reynolds: .: (0.083760) - test_design_uitei: .: (0.066175) - test_max_gc_percent: .: (0.000246) - test_min_gc_percent: .: (0.000216) - test_reynolds: .: (0.085736) - test_reynolds?: .: (0.000394) - test_uitei: .: (0.066135) - test_uitei?: .: (0.000317) + test_antisense_size: .: (0.000634) + test_design: .: (0.079335) + test_design_reynolds: .: (0.099814) + test_design_uitei: .: (0.078091) + test_max_gc_percent: .: (0.000400) + test_min_gc_percent: .: (0.000363) + test_reynolds: .: (0.100314) + test_reynolds?: .: (0.000464) + test_uitei: .: (0.079467) + test_uitei?: .: (0.000469) Bio::TestSiRNANew: - test_new: .: (0.000910) + test_new: .: (0.001953) Bio::TestSiRNAPair: - test_antisense: .: (0.067510) - test_gc_percent: .: (0.066239) - test_report: .: (0.069400) - test_rule: .: (0.066348) - test_sense: .: (0.067303) - test_start: .: (0.066626) - test_stop: .: (0.068599) - test_target: .: (0.066719) + test_antisense: .: (0.081463) + test_gc_percent: .: (0.082511) + test_report: .: (0.082397) + test_rule: .: (0.076393) + test_sense: .: (0.070247) + test_start: .: (0.070406) + test_stop: .: (0.069526) + test_target: .: (0.078271) Bio::TestSiRNAPairNew: - test_new: .: (0.001426) + test_new: .: (0.001977) Bio::TestSim4Report: - test_all_hits: .: (0.000947) - test_each: .: (0.000628) - test_each_hit: .: (0.000499) - test_hits: .: (0.000525) - test_num_hits: .: (0.000433) - test_query_def: .: (0.000482) - test_query_id: .: (0.000437) - test_query_len: .: (0.000439) - test_seq1: .: (0.000740) + test_all_hits: .: (0.001118) + test_each: .: (0.000694) + test_each_hit: .: (0.000755) + test_hits: .: (0.000882) + test_num_hits: .: (0.000622) + test_query_def: .: (0.000592) + test_query_id: .: (0.000571) + test_query_len: .: (0.000631) + test_seq1: .: (0.001355) Bio::TestSim4Report2: - test_all_hits: .: (0.000777) - test_each: .: (0.000566) - test_each_hit: .: (0.000508) - test_hits: .: (0.000521) - test_num_hits: .: (0.000440) - test_query_def: .: (0.000446) - test_query_id: .: (0.000437) - test_query_len: .: (0.000445) - test_seq1: .: (0.000574) + test_all_hits: .: (0.000994) + test_each: .: (0.000674) + test_each_hit: .: (0.000650) + test_hits: .: (0.000701) + test_num_hits: .: (0.000598) + test_query_def: .: (0.000624) + test_query_id: .: (0.000562) + test_query_len: .: (0.000625) + test_seq1: .: (0.001360) Bio::TestSim4Report4: - test_all_hits: .: (0.000966) - test_each: .: (0.000539) - test_each_hit: .: (0.000520) - test_hits: .: (0.000577) - test_num_hits: .: (0.000457) - test_query_def: .: (0.000464) - test_query_id: .: (0.000526) - test_query_len: .: (0.000462) - test_seq1: .: (0.000609) + test_all_hits: .: (0.001364) + test_each: .: (0.000688) + test_each_hit: .: (0.000661) + test_hits: .: (0.000679) + test_num_hits: .: (0.000590) + test_query_def: .: (0.000589) + test_query_id: .: (0.000604) + test_query_len: .: (0.000590) + test_seq1: .: (0.001449) Bio::TestSim4ReportHit: - test_align: .: (0.001128) - test_complement?: .: (0.000500) - test_definition: .: (0.000448) - test_each: .: (0.000862) - test_exons: .: (0.000853) - test_hit_id: .: (0.000445) - test_hsps: .: (0.000846) - test_introns: .: (0.001351) - test_len: .: (0.000795) - test_query_def: .: (0.000447) - test_query_id: .: (0.000437) - test_query_len: .: (0.000526) - test_segmentpairs: .: (0.000828) - test_seq1: .: (0.000574) - test_seq2: .: (0.000609) - test_target_def: .: (0.000441) - test_target_id: .: (0.000433) - test_target_len: .: (0.000511) + test_align: .: (0.001406) + test_complement?: .: (0.000601) + test_definition: .: (0.000623) + test_each: .: (0.001121) + test_exons: .: (0.001054) + test_hit_id: .: (0.000581) + test_hsps: .: (0.001575) + test_introns: .: (0.001130) + test_len: .: (0.000593) + test_query_def: .: (0.000594) + test_query_id: .: (0.000548) + test_query_len: .: (0.000553) + test_segmentpairs: .: (0.001052) + test_seq1: .: (0.000726) + test_seq2: .: (0.000701) + test_target_def: .: (0.000550) + test_target_id: .: (0.001241) + test_target_len: .: (0.000541) Bio::TestSim4ReportHit2: - test_align: .: (0.001497) - test_complement?: .: (0.000486) - test_definition: .: (0.000434) - test_each: .: (0.000832) - test_exons: .: (0.000779) - test_hit_id: .: (0.000439) - test_hsps: .: (0.000800) - test_introns: .: (0.001180) - test_len: .: (0.000682) - test_query_def: .: (0.000444) - test_query_id: .: (0.000428) - test_query_len: .: (0.000430) - test_segmentpairs: .: (0.000854) - test_seq1: .: (0.000577) - test_seq2: .: (0.000611) - test_target_def: .: (0.000437) - test_target_id: .: (0.001019) - test_target_len: .: (0.000486) + test_align: .: (0.001024) + test_complement?: .: (0.000522) + test_definition: .: (0.000536) + test_each: .: (0.000907) + test_exons: .: (0.000984) + test_hit_id: .: (0.000563) + test_hsps: .: (0.001676) + test_introns: .: (0.001219) + test_len: .: (0.000560) + test_query_def: .: (0.000595) + test_query_id: .: (0.000550) + test_query_len: .: (0.000548) + test_segmentpairs: .: (0.001003) + test_seq1: .: (0.000706) + test_seq2: .: (0.000725) + test_target_def: .: (0.001249) + test_target_id: .: (0.000753) + test_target_len: .: (0.000512) Bio::TestSim4ReportHit4: - test_align: .: (0.001124) - test_complement?: .: (0.000472) - test_definition: .: (0.000465) - test_each: .: (0.001083) - test_exons: .: (0.001496) - test_hit_id: .: (0.000604) - test_hsps: .: (0.000991) - test_introns: .: (0.001034) - test_len: .: (0.000464) - test_query_def: .: (0.000546) - test_query_id: .: (0.000463) - test_query_len: .: (0.000454) - test_segmentpairs: .: (0.001564) - test_seq1: .: (0.000754) - test_seq2: .: (0.000609) - test_target_def: .: (0.000460) - test_target_id: .: (0.000457) - test_target_len: .: (0.000494) + test_align: .: (0.001307) + test_complement?: .: (0.000759) + test_definition: .: (0.000595) + test_each: .: (0.001350) + test_exons: .: (0.001438) + test_hit_id: .: (0.000788) + test_hsps: .: (0.001293) + test_introns: .: (0.001255) + test_len: .: (0.000552) + test_query_def: .: (0.000584) + test_query_id: .: (0.000538) + test_query_len: .: (0.000531) + test_segmentpairs: .: (0.001897) + test_seq1: .: (0.000931) + test_seq2: .: (0.000769) + test_target_def: .: (0.000629) + test_target_id: .: (0.000577) + test_target_len: .: (0.000561) Bio::TestSim4ReportSegment: - test_from: .: (0.000467) - test_self_new: .: (0.000302) - test_seq: .: (0.000213) - test_to: .: (0.000226) + test_from: .: (0.000603) + test_self_new: .: (0.000465) + test_seq: .: (0.000376) + test_to: .: (0.000302) Bio::TestSim4ReportSegmentPair2_exon: - test_align_len: .: (0.001528) - test_direction: .: (0.000685) - test_hit_from: .: (0.000653) - test_hit_to: .: (0.000707) - test_hseq: .: (0.000664) - test_midline: .: (0.000655) - test_percent_identity: .: (0.000695) - test_qseq: .: (0.001192) - test_query_from: .: (0.000820) - test_query_to: .: (0.000649) - test_seq1: .: (0.000818) - test_seq2: .: (0.000773) + test_align_len: .: (0.001902) + test_direction: .: (0.000889) + test_hit_from: .: (0.000921) + test_hit_to: .: (0.000856) + test_hseq: .: (0.000811) + test_midline: .: (0.000863) + test_percent_identity: .: (0.000812) + test_qseq: .: (0.001390) + test_query_from: .: (0.000930) + test_query_to: .: (0.000857) + test_seq1: .: (0.001002) + test_seq2: .: (0.000984) Bio::TestSim4ReportSegmentPair2_intron: - test_align_len: .: (0.000910) - test_direction: .: (0.000657) - test_hit_from: .: (0.001179) - test_hit_to: .: (0.000787) - test_hseq: .: (0.000669) - test_midline: .: (0.000659) - test_percent_identity: .: (0.000650) - test_qseq: .: (0.000663) - test_query_from: .: (0.000653) - test_query_to: .: (0.000699) - test_seq1: .: (0.001259) - test_seq2: .: (0.000800) + test_align_len: .: (0.001202) + test_direction: .: (0.001467) + test_hit_from: .: (0.001070) + test_hit_to: .: (0.000853) + test_hseq: .: (0.000874) + test_midline: .: (0.000782) + test_percent_identity: .: (0.000855) + test_qseq: .: (0.000819) + test_query_from: .: (0.000867) + test_query_to: .: (0.001292) + test_seq1: .: (0.001217) + test_seq2: .: (0.000986) Bio::TestSim4ReportSegmentPair4_exon: - test_align_len: .: (0.001170) - test_direction: .: (0.000852) - test_hit_from: .: (0.001280) - test_hit_to: .: (0.000938) - test_hseq: .: (0.000901) - test_midline: .: (0.000836) - test_percent_identity: .: (0.000880) - test_qseq: .: (0.001340) - test_query_from: .: (0.000965) - test_query_to: .: (0.000841) - test_seq1: .: (0.001002) - test_seq2: .: (0.001004) + test_align_len: .: (0.001414) + test_direction: .: (0.001038) + test_hit_from: .: (0.001668) + test_hit_to: .: (0.001394) + test_hseq: .: (0.000999) + test_midline: .: (0.001069) + test_percent_identity: .: (0.001101) + test_qseq: .: (0.001727) + test_query_from: .: (0.001048) + test_query_to: .: (0.001089) + test_seq1: .: (0.001170) + test_seq2: .: (0.001661) Bio::TestSim4ReportSegmentPair4_intron: - test_align_len: .: (0.001538) - test_direction: .: (0.000852) - test_hit_from: .: (0.000911) - test_hit_to: .: (0.000835) - test_hseq: .: (0.000832) - test_midline: .: (0.001244) - test_percent_identity: .: (0.000969) - test_qseq: .: (0.000834) - test_query_from: .: (0.000867) - test_query_to: .: (0.000832) - test_seq1: .: (0.001449) - test_seq2: .: (0.001150) + test_align_len: .: (0.001339) + test_direction: .: (0.001058) + test_hit_from: .: (0.001102) + test_hit_to: .: (0.001494) + test_hseq: .: (0.001208) + test_midline: .: (0.001100) + test_percent_identity: .: (0.001054) + test_qseq: .: (0.001055) + test_query_from: .: (0.001606) + test_query_to: .: (0.001185) + test_seq1: .: (0.001246) + test_seq2: .: (0.001171) Bio::TestSim4ReportSegmentPair4_intron1: - test_align_len: .: (0.001102) - test_direction: .: (0.000903) - test_hit_from: .: (0.001361) - test_hit_to: .: (0.001084) - test_hseq: .: (0.000925) - test_midline: .: (0.000852) - test_percent_identity: .: (0.000839) - test_qseq: .: (0.000858) - test_query_from: .: (0.001369) - test_query_to: .: (0.000839) - test_seq1: .: (0.001003) - test_seq2: .: (0.000960) -Bio::TestSim4ReportSegmentPair_exon: test_align_len: .: (0.001340) - test_direction: .: (0.000659) - test_hit_from: .: (0.000664) - test_hit_to: .: (0.000649) - test_hseq: .: (0.000703) - test_midline: .: (0.000649) - test_percent_identity: .: (0.001104) - test_qseq: .: (0.000777) - test_query_from: .: (0.000736) - test_query_to: .: (0.000654) - test_seq1: .: (0.000764) - test_seq2: .: (0.000788) + test_direction: .: (0.001805) + test_hit_from: .: (0.001085) + test_hit_to: .: (0.001043) + test_hseq: .: (0.001096) + test_midline: .: (0.001041) + test_percent_identity: .: (0.001610) + test_qseq: .: (0.001179) + test_query_from: .: (0.001104) + test_query_to: .: (0.001196) + test_seq1: .: (0.001284) + test_seq2: .: (0.001714) +Bio::TestSim4ReportSegmentPair_exon: + test_align_len: .: (0.001113) + test_direction: .: (0.000918) + test_hit_from: .: (0.000903) + test_hit_to: .: (0.000915) + test_hseq: .: (0.000895) + test_midline: .: (0.001375) + test_percent_identity: .: (0.001047) + test_qseq: .: (0.000913) + test_query_from: .: (0.000917) + test_query_to: .: (0.000909) + test_seq1: .: (0.001015) + test_seq2: .: (0.001490) Bio::TestSim4ReportSegmentPair_intron: - test_align_len: .: (0.001541) - test_direction: .: (0.000659) - test_hit_from: .: (0.000653) - test_hit_to: .: (0.000657) - test_hseq: .: (0.000651) - test_midline: .: (0.000717) - test_percent_identity: .: (0.000647) - test_qseq: .: (0.000645) - test_query_from: .: (0.001063) - test_query_to: .: (0.000804) - test_seq1: .: (0.000769) - test_seq2: .: (0.000747) + test_align_len: .: (0.001213) + test_direction: .: (0.000882) + test_hit_from: .: (0.000846) + test_hit_to: .: (0.000869) + test_hseq: .: (0.000822) + test_midline: .: (0.000837) + test_percent_identity: .: (0.000856) + test_qseq: .: (0.001283) + test_query_from: .: (0.000921) + test_query_to: .: (0.000825) + test_seq1: .: (0.001006) + test_seq2: .: (0.000935) Bio::TestSim4ReportSeqDesc: - test_definition: .: (0.000547) - test_entry_id: .: (0.000250) - test_filename: .: (0.000237) - test_len: .: (0.000230) - test_self_new: .: (0.000361) - test_self_parse: .: (0.000362) + test_definition: .: (0.000734) + test_entry_id: .: (0.000373) + test_filename: .: (0.000340) + test_len: .: (0.000345) + test_self_new: .: (0.000372) + test_self_parse: .: (0.000450) Bio::TestTMHMMReport: - test_entry_id: .: (0.001185) - test_exp_aas_in_tmhs: .: (0.000789) - test_exp_first_60aa: .: (0.000835) - test_helix: .: (0.001226) - test_predicted_tmhs: .: (0.000809) - test_query_len: .: (0.000757) - test_tmhs: .: (0.000890) - test_to_s: .: (0.001450) - test_total_prob_of_N_in: .: (0.000822) + test_entry_id: .: (0.001365) + test_exp_aas_in_tmhs: .: (0.000960) + test_exp_first_60aa: .: (0.000955) + test_helix: .: (0.001478) + test_predicted_tmhs: .: (0.000917) + test_query_len: .: (0.000909) + test_tmhs: .: (0.000946) + test_to_s: .: (0.001241) + test_total_prob_of_N_in: .: (0.001334) Bio::TestTMHMMReport_reports: - test_reports: .: (0.000502) + test_reports: .: (0.000644) Bio::TestTMHMMTMH: - test_entry_id: .: (0.001038) - test_pos: .: (0.000775) - test_range: .: (0.000777) - test_status: .: (0.001266) - test_version: .: (0.000765) + test_entry_id: .: (0.001258) + test_pos: .: (0.000917) + test_range: .: (0.000890) + test_status: .: (0.001493) + test_version: .: (0.000923) Bio::TestTargetPReport: - test_cleavage_site_prediction: .: (0.000866) - test_cutoff: .: (0.000556) - test_entry_id: .: (0.000521) - test_length: .: (0.000526) - test_loc: .: (0.000522) - test_name: .: (0.000508) - test_networks: .: (0.000931) - test_prediction: .: (0.000578) - test_query_len: .: (0.000591) - test_query_sequences: .: (0.000513) - test_rc: .: (0.000505) - test_version: .: (0.000508) + test_cleavage_site_prediction: .: (0.001011) + test_cutoff: .: (0.000737) + test_entry_id: .: (0.000608) + test_length: .: (0.000630) + test_loc: .: (0.000615) + test_name: .: (0.000661) + test_networks: .: (0.000644) + test_prediction: .: (0.000719) + test_query_len: .: (0.000761) + test_query_sequences: .: (0.000653) + test_rc: .: (0.000698) + test_version: .: (0.000641) Bio::TestTargetPReportConst: - test_delimiter: .: (0.000441) - test_rs: .: (0.000211) + test_delimiter: .: (0.000594) + test_rs: .: (0.000301) Bio::TestTogoWSAccessWait: - test_reset_togows_access_wait: .: (0.000491) - test_togows_access_wait: .: (2.008327) + test_reset_togows_access_wait: .: (0.000912) + test_togows_access_wait: .: (2.005831) Bio::TestTogoWSREST: - test_debug: .: (0.001329) - test_debug_default: .: (0.000448) - test_internal_http: .: (0.000483) + test_debug: .: (0.001321) + test_debug_default: .: (0.000533) + test_internal_http: .: (0.000539) Bio::TestTogoWSRESTclassMethod: - test_convert: .: (0.000478) - test_entry: .: (0.000218) - test_entry_database_list: .: (0.000207) - test_new: .: (0.000495) - test_new_with_uri_object: .: (0.000583) - test_new_with_uri_string: .: (0.000547) - test_retrieve: .: (0.000225) - test_search: .: (0.000286) - test_search_database_list: .: (0.000664) + test_convert: .: (0.007765) + test_entry: .: (0.000349) + test_entry_database_list: .: (0.000273) + test_new: .: (0.000820) + test_new_with_uri_object: .: (0.000703) + test_new_with_uri_string: .: (0.000660) + test_retrieve: .: (0.000308) + test_search: .: (0.000310) + test_search_database_list: .: (0.000300) Bio::TestTogoWSRESTprivate: - test_make_path: .: (0.000972) - test_prepare_return_value: .: (0.000574) + test_make_path: .: (0.001118) + test_prepare_return_value: .: (0.000692) Bio::TestTopologicalSort: - test_dfs_topological_sort: .: (0.005246) + test_dfs_topological_sort: .: (0.001341) Bio::TestTree: - test_get_edge_distance: .: (0.000637) - test_get_edge_distance_string: .: (0.000427) - test_get_node_name: .: (0.000282) - test_initialize: .: (0.000279) - test_options: .: (0.004432) - test_root: .: (0.000270) - test_root=: .: (0.000266) + test_get_edge_distance: .: (0.000726) + test_get_edge_distance_string: .: (0.000463) + test_get_node_name: .: (0.000364) + test_initialize: .: (0.000391) + test_options: .: (0.000331) + test_root: .: (0.000279) + test_root=: .: (0.000363) Bio::TestTree2: - test_add_edge: .: (0.000918) - test_add_node: .: (0.000615) - test_adjacency_matrix: .: (0.000599) - test_adjacency_matrix_with_block: .: (0.000948) - test_adjacent_nodes: .: (0.000636) - test_adjacent_nodes_nonexistent: .: (0.000408) - test_ancestors: .: (0.000539) - test_children: .: (0.000873) - test_clear: .: (0.004693) - test_clear_node: .: (0.000610) - test_clear_node_nonexistent: .: (0.000668) - test_collect_edge!: .: (0.000805) - test_collect_node!: .: (0.000802) - test_concat: .: (0.000875) - test_descendents: .: (0.000537) - test_distance_matrix: .: (0.001849) - test_each_edge: .: (0.004805) - test_each_node: .: (0.000604) - test_each_out_edge: .: (0.000547) + test_add_edge: .: (0.001506) + test_add_node: .: (0.000824) + test_adjacency_matrix: .: (0.000673) + test_adjacency_matrix_with_block: .: (0.000899) + test_adjacent_nodes: .: (0.000766) + test_adjacent_nodes_nonexistent: .: (0.000524) + test_ancestors: .: (0.000614) + test_children: .: (0.000596) + test_clear: .: (0.000660) + test_clear_node: .: (0.000717) + test_clear_node_nonexistent: .: (0.001786) + test_collect_edge!: .: (0.000979) + test_collect_node!: .: (0.000944) + test_concat: .: (0.000908) + test_descendents: .: (0.000654) + test_distance_matrix: .: (0.001706) + test_each_edge: .: (0.000691) + test_each_node: .: (0.001517) + test_each_out_edge: .: (0.000585) test_each_out_edge_chimpanzee: .: (0.000563) - test_each_out_edge_human: .: (0.000515) - test_each_out_edge_mammals: .: (0.000580) - test_each_out_edge_nonexistent: .: (0.004681) - test_each_out_edge_primates: .: (0.001705) - test_each_out_edge_rat: .: (0.000522) - test_each_out_edge_rodents: .: (0.000651) - test_edges: .: (0.000785) - test_get_edge: .: (0.001071) - test_get_edge_indirect: .: (0.000470) - test_get_edge_merged: .: (0.000448) - test_get_edge_nonexistent: .: (0.000396) - test_get_node_bootstrap: .: (0.004621) - test_get_node_bootstrap_string=: .: (0.000905) - test_get_node_by_name: .: (0.000646) - test_get_node_by_name_noexistent: .: (0.000439) - test_include?: .: (0.000575) - test_include_nonexistent: .: (0.000475) - test_insert_node: .: (0.000972) - test_leaves: .: (0.000571) - test_leaves_noargs: .: (0.000579) - test_lowest_common_ancestor: .: (0.000499) - test_nodes: .: (0.000446) - test_number_of_edges: .: (0.000448) - test_number_of_nodes: .: (0.000404) - test_out_degree: .: (0.000577) - test_out_degree_nonexistent: .: (0.000558) - test_out_edges: .: (0.000564) - test_out_edges_mammals: .: (0.000717) - test_out_edges_nonexistent: .: (0.001092) - test_out_edges_primates: .: (0.004893) - test_out_edges_rodents: .: (0.000761) - test_parent: .: (0.000535) - test_path: .: (0.000541) - test_remove_edge: .: (0.000521) - test_remove_edge_if: .: (0.000548) - test_remove_edge_if_nothing_removed: .: (0.004783) - test_remove_edge_nonexistent: .: (0.000668) - test_remove_node: .: (0.001218) - test_remove_node_if: .: (0.000473) - test_remove_node_if_false: .: (0.004643) - test_remove_node_nonexistent: .: (0.000727) - test_remove_nonsense_nodes: .: (0.000547) - test_subtree: .: (0.000764) - test_subtree_with_all_paths: .: (0.000964) - test_total_distance: .: (0.004625) + test_each_out_edge_human: .: (0.000558) + test_each_out_edge_mammals: .: (0.000667) + test_each_out_edge_nonexistent: .: (0.000497) + test_each_out_edge_primates: .: (0.000963) + test_each_out_edge_rat: .: (0.000566) + test_each_out_edge_rodents: .: (0.000709) + test_edges: .: (0.000560) + test_get_edge: .: (0.001254) + test_get_edge_indirect: .: (0.000510) + test_get_edge_merged: .: (0.000529) + test_get_edge_nonexistent: .: (0.000489) + test_get_node_bootstrap: .: (0.000506) + test_get_node_bootstrap_string=: .: (0.000556) + test_get_node_by_name: .: (0.000741) + test_get_node_by_name_noexistent: .: (0.000483) + test_include?: .: (0.000666) + test_include_nonexistent: .: (0.000534) + test_insert_node: .: (0.001027) + test_leaves: .: (0.000645) + test_leaves_noargs: .: (0.000553) + test_lowest_common_ancestor: .: (0.000581) + test_nodes: .: (0.000546) + test_number_of_edges: .: (0.000483) + test_number_of_nodes: .: (0.000478) + test_out_degree: .: (0.000661) + test_out_degree_nonexistent: .: (0.000510) + test_out_edges: .: (0.000702) + test_out_edges_mammals: .: (0.000897) + test_out_edges_nonexistent: .: (0.000502) + test_out_edges_primates: .: (0.000781) + test_out_edges_rodents: .: (0.000835) + test_parent: .: (0.000600) + test_path: .: (0.000590) + test_remove_edge: .: (0.000616) + test_remove_edge_if: .: (0.000637) + test_remove_edge_if_nothing_removed: .: (0.001318) + test_remove_edge_nonexistent: .: (0.000768) + test_remove_node: .: (0.000737) + test_remove_node_if: .: (0.000565) + test_remove_node_if_false: .: (0.000618) + test_remove_node_nonexistent: .: (0.000544) + test_remove_nonsense_nodes: .: (0.000567) + test_subtree: .: (0.000731) + test_subtree_with_all_paths: .: (0.001124) + test_total_distance: .: (0.000529) Bio::TestTreeEdge: - test_distance: .: (0.000542) - test_distance=: .: (0.000966) - test_distance_string: .: (0.000264) - test_distance_string=: .: (0.000341) - test_initialize: .: (0.000315) - test_inspect: .: (0.000493) - test_to_s: .: (0.000253) + test_distance: .: (0.001255) + test_distance=: .: (0.000394) + test_distance_string: .: (0.000276) + test_distance_string=: .: (0.000417) + test_initialize: .: (0.000417) + test_inspect: .: (0.000280) + test_to_s: .: (0.000261) Bio::TestTreeNode: - test_bootstrap: .: (0.000473) - test_bootstrap=: .: (0.000331) - test_bootstrap_string: .: (0.000258) - test_bootstrap_string=: .: (0.000417) - test_initialize: .: (0.000294) - test_inspect: .: (0.000295) - test_name: .: (0.000517) - test_to_s: .: (0.000802) + test_bootstrap: .: (0.000514) + test_bootstrap=: .: (0.000355) + test_bootstrap_string: .: (0.000230) + test_bootstrap_string=: .: (0.000468) + test_initialize: .: (0.000368) + test_inspect: .: (0.000327) + test_name: .: (0.000915) + test_to_s: .: (0.000274) Bio::TestUniProt: - test_gene_name: .: (0.013635) + test_gene_name: .: (0.013604) Bio::TestUniProtKB: - test_ac: .: (0.013858) - test_accession: .: (0.013819) - test_cc: .: (0.017612) - test_cc_alternative_products: .: (0.017289) - test_cc_database: .: (0.017682) - test_cc_mass_spectrometry: .: (0.018090) - test_de: .: (0.016923) - test_dr: .: (0.036142) - test_dr_with_key: .: (0.035842) - test_dr_with_key_empty: .: (0.031075) - test_dt: .: (0.032807) - test_dt_annotation: .: (0.062188) - test_dt_created: .: (0.044189) - test_dt_sequence: .: (0.040580) - test_entry: .: (0.042587) - test_ft: .: (0.032900) - test_gene_name: .: (0.012994) - test_gene_names: .: (0.012668) - test_gn: .: (0.013556) - test_gn_old_parser: .: (0.013151) - test_gn_uniprot_parser: .: (0.012955) - test_id_line: .: (0.013053) - test_id_line_data_class: .: (0.014133) - test_id_line_entry_name: .: (0.013222) - test_id_line_molecule_type: .: (0.012673) - test_id_line_sequence_length: .: (0.013162) - test_kw: .: (0.013112) - test_molecule: .: (0.012677) - test_oc: .: (0.012930) - test_og_1: .: (0.012901) - test_og_2: .: (0.013090) - test_og_3: .: (0.015925) - test_og_4: .: (0.012838) - test_og_5: .: (0.013820) - test_og_6: .: (0.012877) - test_os: .: (0.012914) - test_os_access: .: (0.012586) - test_os_access2: .: (0.012757) - test_ox: .: (0.012428) - test_protein_name: .: (0.012975) - test_ref: .: (0.029785) - test_seq: .: (0.013939) - test_sequence_length: .: (0.012410) - test_sq: .: (0.012583) - test_sq_crc64: .: (0.012571) - test_sq_len: .: (0.012915) - test_sq_mw: .: (0.012964) - test_synonyms: .: (0.012904) + test_ac: .: (0.013583) + test_accession: .: (0.013063) + test_cc: .: (0.016798) + test_cc_alternative_products: .: (0.017018) + test_cc_database: .: (0.017806) + test_cc_mass_spectrometry: .: (0.016834) + test_de: .: (0.012582) + test_dr: .: (0.017695) + test_dr_with_key: .: (0.017802) + test_dr_with_key_empty: .: (0.032760) + test_dt: .: (0.039675) + test_dt_annotation: .: (0.038709) + test_dt_created: .: (0.062838) + test_dt_sequence: .: (0.012123) + test_entry: .: (0.012067) + test_ft: .: (0.031866) + test_gene_name: .: (0.012416) + test_gene_names: .: (0.012128) + test_gn: .: (0.011868) + test_gn_old_parser: .: (0.012529) + test_gn_uniprot_parser: .: (0.012075) + test_id_line: .: (0.012926) + test_id_line_data_class: .: (0.013003) + test_id_line_entry_name: .: (0.012482) + test_id_line_molecule_type: .: (0.012889) + test_id_line_sequence_length: .: (0.011807) + test_kw: .: (0.013065) + test_molecule: .: (0.012276) + test_oc: .: (0.012947) + test_og_1: .: (0.015559) + test_og_2: .: (0.012252) + test_og_3: .: (0.012266) + test_og_4: .: (0.012384) + test_og_5: .: (0.013359) + test_og_6: .: (0.012402) + test_os: .: (0.012526) + test_os_access: .: (0.012632) + test_os_access2: .: (0.011935) + test_ox: .: (0.012186) + test_protein_name: .: (0.012409) + test_ref: .: (0.029867) + test_seq: .: (0.012582) + test_sequence_length: .: (0.012135) + test_sq: .: (0.013180) + test_sq_crc64: .: (0.012034) + test_sq_len: .: (0.012619) + test_sq_mw: .: (0.015231) + test_synonyms: .: (0.012977) Bio::TestUniProtKB_CC: - test_allergen: .: (0.001094) - test_alternative_products_access_as_hash: .: (0.000592) - test_alternative_products_ai: .: (0.000795) - test_alternative_products_apu: .: (0.001894) - test_alternative_products_as: .: (0.000797) - test_alternative_products_rf: .: (0.000245) - test_biophysicochemical_properties: .: (0.001204) - test_biotechnology: .: (0.000769) - test_catalytic_activity: .: (0.000539) - test_caution: .: (0.000872) - test_cofactor: .: (0.000554) - test_developmental_stage: .: (0.000575) - test_disease: .: (0.000856) - test_domain: .: (0.001184) - test_enzyme_regulation: .: (0.001103) - test_function: .: (0.000717) - test_induction: .: (0.000496) - test_interaction: .: (0.000667) - test_mass_spectrometry: .: (0.001013) - test_miscellaneous: .: (0.000490) - test_pathway: .: (0.000576) - test_pharmaceutical: .: (0.000574) - test_polymorphism: .: (0.001601) - test_ptm: .: (0.000554) - test_rna_editing: .: (0.000663) - test_similarity: .: (0.000531) - test_subcellular_location: .: (0.000598) - test_subunit: .: (0.000463) - test_tissue_specificity: .: (0.000588) - test_toxic_dose: .: (0.000450) - test_web_resource: .: (0.000758) + test_allergen: .: (0.000906) + test_alternative_products_access_as_hash: .: (0.000744) + test_alternative_products_ai: .: (0.000857) + test_alternative_products_apu: .: (0.001785) + test_alternative_products_as: .: (0.001023) + test_alternative_products_rf: .: (0.000344) + test_biophysicochemical_properties: .: (0.001328) + test_biotechnology: .: (0.000714) + test_catalytic_activity: .: (0.000658) + test_caution: .: (0.000672) + test_cofactor: .: (0.000625) + test_developmental_stage: .: (0.000728) + test_disease: .: (0.001018) + test_domain: .: (0.000952) + test_enzyme_regulation: .: (0.000624) + test_function: .: (0.000691) + test_induction: .: (0.000578) + test_interaction: .: (0.000791) + test_mass_spectrometry: .: (0.000857) + test_miscellaneous: .: (0.001190) + test_pathway: .: (0.000782) + test_pharmaceutical: .: (0.000624) + test_polymorphism: .: (0.000892) + test_ptm: .: (0.000583) + test_rna_editing: .: (0.000727) + test_similarity: .: (0.000622) + test_subcellular_location: .: (0.000665) + test_subunit: .: (0.000550) + test_tissue_specificity: .: (0.000628) + test_toxic_dose: .: (0.000598) + test_web_resource: .: (0.000829) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: - test_cc_web_resource: .: (0.001883) + test_cc_web_resource: .: (0.001126) Bio::TestUniProtKB_DE_since_rel14_0: - test_private_parse_DE_line_rel14: .: (0.001300) - test_protein_name: .: (0.000957) - test_synonyms: .: (0.001889) + test_private_parse_DE_line_rel14: .: (0.001440) + test_protein_name: .: (0.001582) + test_synonyms: .: (0.001277) Bio::TestUniProtKB_ID_since_rel9_0: - test_aalen: .: (0.000571) - test_entry: .: (0.000353) - test_entry_id: .: (0.000292) - test_entry_name: .: (0.000285) - test_id_line: .: (0.000331) - test_molecule: .: (0.000583) - test_sequence_length: .: (0.000322) + test_aalen: .: (0.000642) + test_entry: .: (0.000384) + test_entry_id: .: (0.000376) + test_entry_name: .: (0.000365) + test_id_line: .: (0.000426) + test_molecule: .: (0.000406) + test_sequence_length: .: (0.000351) Bio::TestUniProtKB_P28907: - test_ac: .: (0.005194) - test_accession: .: (0.005493) - test_cc: .: (0.006507) - test_cc_alternative_products: .: (0.006535) - test_cc_database: .: (0.006967) - test_cc_mass_spectrometry: .: (0.006207) - test_de: .: (0.005558) - test_dr: .: (0.012055) - test_dr_with_key: .: (0.012018) - test_dr_with_key_empty: .: (0.011714) - test_dt: .: (0.004827) - test_dt_annotation: .: (0.004720) - test_dt_created: .: (0.004642) - test_dt_sequence: .: (0.004728) - test_entry: .: (0.004951) - test_ft: .: (0.009286) - test_gene_name: .: (0.005402) - test_gene_names: .: (0.005037) - test_gn: .: (0.005111) - test_gn_old_parser: .: (0.005276) - test_gn_uniprot_parser: .: (0.005113) - test_id_line: .: (0.005431) - test_id_line_data_class: .: (0.005056) - test_id_line_entry_name: .: (0.004992) - test_id_line_sequence_length: .: (0.004871) - test_kw: .: (0.005150) - test_oc: .: (0.004984) - test_os: .: (0.005436) - test_os_access: .: (0.004981) - test_os_access2: .: (0.005062) - test_ox: .: (0.004968) - test_protein_name: .: (0.004969) - test_protein_name_after_calling_de: .: (0.005160) - test_ref: .: (0.007906) - test_seq: .: (0.005466) - test_sequence_length: .: (0.004873) - test_sq: .: (0.004822) - test_sq_crc64: .: (0.004887) - test_sq_len: .: (0.004865) - test_sq_mw: .: (0.005536) - test_synonyms: .: (0.005151) - test_synonyms_after_calling_de: .: (0.005220) + test_ac: .: (0.005674) + test_accession: .: (0.004793) + test_cc: .: (0.005805) + test_cc_alternative_products: .: (0.007054) + test_cc_database: .: (0.005936) + test_cc_mass_spectrometry: .: (0.006180) + test_de: .: (0.004928) + test_dr: .: (0.012295) + test_dr_with_key: .: (0.012642) + test_dr_with_key_empty: .: (0.011496) + test_dt: .: (0.004646) + test_dt_annotation: .: (0.004382) + test_dt_created: .: (0.004402) + test_dt_sequence: .: (0.004526) + test_entry: .: (0.004701) + test_ft: .: (0.009186) + test_gene_name: .: (0.004734) + test_gene_names: .: (0.004791) + test_gn: .: (0.005726) + test_gn_old_parser: .: (0.004988) + test_gn_uniprot_parser: .: (0.004828) + test_id_line: .: (0.004859) + test_id_line_data_class: .: (0.005360) + test_id_line_entry_name: .: (0.004604) + test_id_line_sequence_length: .: (0.004762) + test_kw: .: (0.004794) + test_oc: .: (0.004885) + test_os: .: (0.004672) + test_os_access: .: (0.004944) + test_os_access2: .: (0.005309) + test_ox: .: (0.004885) + test_protein_name: .: (0.005483) + test_protein_name_after_calling_de: .: (0.005699) + test_ref: .: (0.008361) + test_seq: .: (0.005262) + test_sequence_length: .: (0.004951) + test_sq: .: (0.004818) + test_sq_crc64: .: (0.004557) + test_sq_len: .: (0.010648) + test_sq_mw: .: (0.004995) + test_synonyms: .: (0.005232) + test_synonyms_after_calling_de: .: (0.005931) Bio::TestUniProtKB_Ref: - test_RA: .: (0.001460) - test_RC: .: (0.001124) - test_RG: .: (0.000721) - test_RL: .: (0.006101) - test_RN: .: (0.001133) - test_RP: .: (0.000751) - test_RT: .: (0.000779) - test_RX: .: (0.000768) - test_ref: .: (0.001651) + test_RA: .: (0.001206) + test_RC: .: (0.000883) + test_RG: .: (0.000846) + test_RL: .: (0.001386) + test_RN: .: (0.000964) + test_RP: .: (0.000882) + test_RT: .: (0.000792) + test_RX: .: (0.000893) + test_ref: .: (0.001424) Bio::TestUniProtKB_SwissProtRel41_0: - test_multiple_RP_lines: .: (0.000692) + test_multiple_RP_lines: .: (0.000757) Bio::TestUniProtKB_SwissProtRel41_1: - test_alternative_products: .: (0.001206) - test_alternative_products_with_ft: .: (0.002714) + test_alternative_products: .: (0.001393) + test_alternative_products_with_ft: .: (0.002023) Bio::TestUniProtKB_SwissProtRel41_10: - test_RC_lines: .: (0.000873) + test_RC_lines: .: (0.001022) Bio::TestUniProtKB_SwissProtRel41_20: - test_CC_allergen: .: (0.000768) - test_RL_lines: .: (0.000359) + test_CC_allergen: .: (0.000879) + test_RL_lines: .: (0.000422) Bio::TestUniProtKB_SwissProtRel42_6: - test_CC_rna_editing: .: (0.002299) + test_CC_rna_editing: .: (0.001644) Bio::TestUniProtKB_UniProtRel1_12: - test_DOI_in_RX_line: .: (0.000639) - test_RG_line: .: (0.000403) + test_DOI_in_RX_line: .: (0.000693) + test_RG_line: .: (0.000474) Bio::TestUniProtKB_UniProtRel2_0: - test_GN_line: .: (0.001355) + test_GN_line: .: (0.001368) Bio::TestUniProtKB_UniProtRel2_1: - test_CC_mass_spectrometry: .: (0.001043) + test_CC_mass_spectrometry: .: (0.000829) Bio::TestUniProtKB_UniProtRel2_3: - test_DR_PDB: .: (0.001019) - test_RL_line: .: (0.000415) + test_DR_PDB: .: (0.000608) + test_RL_line: .: (0.000444) Bio::TestUniProtKB_UniProtRel3_4: - test_CC_biophysiochemical_properties: .: (0.002109) - test_RP_line: .: (0.000649) + test_CC_biophysiochemical_properties: .: (0.002405) + test_RP_line: .: (0.000842) Bio::TestUniProtKB_UniProtRel3_5: - test_entry_name_format: .: (0.000428) + test_entry_name_format: .: (0.000482) Bio::TestUniProtKB_UniProtRel4_0: - test_CC_interaction: .: (0.000745) - test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000843) - test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000537) - test_CC_interaction_isoform: .: (0.000525) - test_CC_interaction_no_gene_name: .: (0.000498) - test_CC_interaction_self_association: .: (0.000552) + test_CC_interaction: .: (0.000829) + test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000618) + test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000576) + test_CC_interaction_isoform: .: (0.000547) + test_CC_interaction_no_gene_name: .: (0.001187) + test_CC_interaction_self_association: .: (0.000646) Bio::TestUniProtKB_UniProtRel5_0: - test_DR_line: .: (0.000703) + test_DR_line: .: (0.000769) Bio::TestUniProtKB_UniProtRel5_4: - test_multiple_cofactors: .: (0.000785) + test_multiple_cofactors: .: (0.000884) Bio::TestUniProtKB_UniProtRel6_0: - test_OG_line: .: (0.001539) + test_OG_line: .: (0.001130) Bio::TestUniProtKB_UniProtRel6_1: - test_FT_metal: .: (0.000841) + test_FT_metal: .: (0.001600) Bio::TestUniProtKB_UniProtRel6_5: - test_HI_line: .: (0.000790) + test_HI_line: .: (0.000858) Bio::TestUniProtKB_UniProtRel7_0: - test_CC_copyright_statement: .: (0.000661) - test_DT_line: .: (0.000695) + test_CC_copyright_statement: .: (0.000700) + test_DT_line: .: (0.000532) Bio::TestUniProtKB_UniProtRel7_6: - test_10000aa: .: (0.010926) + test_10000aa: .: (0.010813) Bio::TestUniProtKB_UniProtRel8_0: - test_CC_alternative_products: .: (0.002045) - test_CC_web_resource: .: (0.000263) - test_FT_VER_SEQ: .: (0.000509) - test_OH_line_exception: .: (0.001113) - test_OH_lines: .: (0.000884) + test_CC_alternative_products: .: (0.001730) + test_CC_web_resource: .: (0.000308) + test_FT_VER_SEQ: .: (0.000551) + test_OH_line_exception: .: (0.000606) + test_OH_lines: .: (0.001002) Bio::TestUtils: - test_centreOfGravity: .: (0.001414) - test_dihedral_angle: .: (0.001948) - test_distance: .: (0.000958) - test_geometricCentre: .: (0.000908) - test_rad2deg: .: (0.000523) + test_centreOfGravity: .: (0.002157) + test_dihedral_angle: .: (0.001197) + test_distance: .: (0.000998) + test_geometricCentre: .: (0.001680) + test_rad2deg: .: (0.000616) Bio::TestWeightedGraph: - test_bellman_ford_on_negative_weighted_graph: .: (0.001509) - test_dijkstra_on_weighted_graph: .: (0.000441) + test_bellman_ford_on_negative_weighted_graph: .: (0.000826) + test_dijkstra_on_weighted_graph: .: (0.000420) -Finished in 48.353134777 seconds. +Finished in 45.13335762 seconds. ------------------------------------------------------------------------------- 3857 tests, 21486 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- -79.77 tests/s, 444.36 assertions/s +85.46 tests/s, 476.06 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ @@ -5500,12 +5543,14 @@ 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/28272/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28272/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/13379 and its subdirectories -I: Current time: Wed May 31 18:51:58 -12 2023 -I: pbuilder-time-stamp: 1685602318 +I: removing directory /srv/workspace/pbuilder/28272 and its subdirectories +I: Current time: Thu Jun 1 20:56:18 +14 2023 +I: pbuilder-time-stamp: 1685602578