Diff of the two buildlogs: -- --- b1/build.log 2024-12-05 13:20:13.885229415 +0000 +++ b2/build.log 2024-12-05 13:25:54.969790502 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 5 01:17:34 -12 2024 -I: pbuilder-time-stamp: 1733404654 +I: Current time: Fri Dec 6 03:20:27 +14 2024 +I: pbuilder-time-stamp: 1733404827 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying fix_definition_CutSymbol_in_test_cut_symbol.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28256/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27617/tmp/hooks/D01_modify_environment starting +debug: Running on ff64a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 5 13:21 /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/27617/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27617/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - 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]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='d0b6f6d2c10a4018a96311980803ac28' - 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='28256' - PS1='# ' - PS2='> ' + INVOCATION_ID=a62bbc3c650f48cd9b0b95c474c5ae43 + 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=27617 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.nRzEcwY4/pbuilderrc_NsnB --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nRzEcwY4/b1 --logfile b1/build.log ruby-bio_2.0.5-1.dsc' - SUDO_GID='110' - SUDO_UID='103' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+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.nRzEcwY4/pbuilderrc_aWbj --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nRzEcwY4/b2 --logfile b2/build.log ruby-bio_2.0.5-1.dsc' + SUDO_GID=114 + SUDO_UID=109 + 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 virt32z 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28256/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/27617/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -258,7 +290,7 @@ Get: 137 http://deb.debian.org/debian trixie/main armhf ruby-rd all 0.6.38-4.1 [64.0 kB] Get: 138 http://deb.debian.org/debian trixie/main armhf rdtool all 0.6.38-4.1 [44.5 kB] Get: 139 http://deb.debian.org/debian trixie/main armhf ruby-libxml armhf 5.0.3-1+b1 [72.1 kB] -Fetched 43.4 MB in 1s (33.7 MB/s) +Fetched 43.4 MB in 2s (17.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19684 files and directories currently installed.) @@ -726,8 +758,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Dec 5 13:18:41 UTC 2024. -Universal Time is now: Thu Dec 5 13:18:41 UTC 2024. +Local time is now: Thu Dec 5 13:22:30 UTC 2024. +Universal Time is now: Thu Dec 5 13:22:30 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -853,7 +885,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes +I: user script /srv/workspace/pbuilder/27617/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/27617/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ruby-bio-2.0.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ruby-bio_2.0.5-1_source.changes dpkg-buildpackage: info: source package ruby-bio dpkg-buildpackage: info: source version 2.0.5-1 dpkg-buildpackage: info: source distribution unstable @@ -1110,4392 +1146,4392 @@ Loaded suite /usr/share/rubygems-integration/all/gems/rake-13.2.1/lib/rake/rake_test_loader Started Bio::External2go: - test_db_ids: .: (0.002060) - test_dbs: .: (0.000791) - test_go_ids: .: (0.000534) - test_go_terms: .: (0.000512) - test_parser: .: (0.000952) - test_set_date: .: (0.000547) - test_set_desc: .: (0.000587) - test_to_str: .: (0.000595) + test_db_ids: .: (0.003690) + test_dbs: .: (0.001486) + test_go_ids: .: (0.001216) + test_go_terms: .: (0.001051) + test_parser: .: (0.002223) + test_set_date: .: (0.001140) + test_set_desc: .: (0.001165) + test_to_str: .: (0.001200) Bio::FuncTestCommandBackports: - test_mktmpdir_with_block: .: (0.002033) - test_mktmpdir_without_block: .: (0.001704) - test_remove_entry_secure: .: (0.000996) + test_mktmpdir_with_block: .: (0.003577) + test_mktmpdir_without_block: .: (0.003427) + test_remove_entry_secure: .: (0.001911) Bio::FuncTestCommandCallMisc1: - test_call_command: .: (0.023518) - test_call_command_fork: .: (0.000442) - test_call_command_open3: .: (0.013218) - test_call_command_popen: .: (0.006824) + test_call_command: .: (0.015722) + test_call_command_fork: .: (0.000720) + test_call_command_open3: .: (0.015057) + test_call_command_popen: .: (0.014106) Bio::FuncTestCommandCallSimple: - test_call_command: .: (0.006959) - test_call_command_fork: .: (0.000543) - test_call_command_open3: .: (0.010109) - test_call_command_popen: .: (0.004876) + test_call_command: .: (0.014866) + test_call_command_fork: .: (0.000747) + test_call_command_open3: .: (0.014592) + test_call_command_popen: .: (0.015257) Bio::FuncTestCommandCallWithSpace: - test_call_command: .: (0.004657) - test_call_command_fork: .: (0.000416) - test_call_command_open3: .: (0.004543) - test_call_command_popen: .: (0.004423) + test_call_command: .: (0.015299) + test_call_command_fork: .: (0.000665) + test_call_command_open3: .: (0.014606) + test_call_command_popen: .: (0.014384) Bio::FuncTestCommandChdir: - test_call_command_chdir: .: (0.005630) - test_call_command_fork_chdir: .: (0.000815) - test_call_command_popen_chdir: .: (0.003569) - test_query_command_chdir: .: (0.003963) - test_query_command_fork_chdir: .: (0.000796) - test_query_command_popen_chdir: .: (0.003848) + test_call_command_chdir: .: (0.009082) + test_call_command_fork_chdir: .: (0.001507) + test_call_command_popen_chdir: .: (0.008156) + test_query_command_chdir: .: (0.008499) + test_query_command_fork_chdir: .: (0.001378) + test_query_command_popen_chdir: .: (0.008029) Bio::FuncTestCommandQuery: - test_query_command: .: (0.015036) - test_query_command_fork: .: (0.005302) - test_query_command_open3: .: (0.014912) - test_query_command_popen: .: (0.015174) + test_query_command: .: (0.022532) + test_query_command_fork: .: (0.011570) + test_query_command_open3: .: (0.022996) + test_query_command_popen: .: (0.021583) Bio::FuncTestCommandTmpdir: - test_close!: .: (0.001982) - test_initialize: .: (0.001359) - test_path: .: (0.000910) - test_path_after_close: .: (0.001321) + test_close!: .: (0.003783) + test_initialize: .: (0.001839) + test_path: .: (0.001734) + test_path_after_close: .: (0.002429) Bio::FuncTestSequenceOutputEMBL: - test_output_embl: .: (0.035995) - test_output_fasta: .: (0.021211) + test_output_embl: .: (0.073924) + test_output_fasta: .: (0.059992) Bio::NCBIDB::TestCommon: - test_acc_version: .: (0.000976) - test_accession: .: (0.000488) - test_accessions: .: (0.000448) - test_comment: .: (0.000436) - test_common_name: .: (0.000669) - test_definition: .: (0.000651) - test_features: .: (0.000832) - test_gi: .: (0.000456) - test_keywords: .: (0.000699) - test_locus: .: (0.000370) - test_nid: .: (0.000594) - test_organism: .: (0.000605) - test_origin: .: (0.000571) - test_references: .: (0.002446) - test_segment: .: (0.000644) - test_source: .: (0.000728) - test_taxonomy: .: (0.000485) - test_version: .: (0.000530) - test_versions: .: (0.000484) + test_acc_version: .: (0.001758) + test_accession: .: (0.001018) + test_accessions: .: (0.000885) + test_comment: .: (0.000861) + test_common_name: .: (0.001110) + test_definition: .: (0.001214) + test_features: .: (0.001747) + test_gi: .: (0.000918) + test_keywords: .: (0.001157) + test_locus: .: (0.000624) + test_nid: .: (0.000851) + test_organism: .: (0.000968) + test_origin: .: (0.000994) + test_references: .: (0.003095) + test_segment: .: (0.001105) + test_source: .: (0.001651) + test_taxonomy: .: (0.001091) + test_version: .: (0.001135) + test_versions: .: (0.000894) Bio::TestAA: - test_13: .: (0.000558) - test_1n: .: (0.000285) - test_name2one: .: (0.000357) - test_name2three: .: (0.000412) - test_one2name: .: (0.000322) - test_one2three: .: (0.000352) - test_three2name: .: (0.000317) - test_three2one: .: (0.000350) - test_to_1_1: .: (0.000318) - test_to_1_3: .: (0.000452) - test_to_1_name: .: (0.000236) - test_to_3_1: .: (0.000163) - test_to_3_3: .: (0.000145) - test_to_3_name: .: (0.000191) - test_to_re: .: (0.000243) + test_13: .: (0.001130) + test_1n: .: (0.000481) + test_name2one: .: (0.000684) + test_name2three: .: (0.000699) + test_one2name: .: (0.000519) + test_one2three: .: (0.000461) + test_three2name: .: (0.000455) + test_three2one: .: (0.000611) + test_to_1_1: .: (0.000449) + test_to_1_3: .: (0.000597) + test_to_1_name: .: (0.000639) + test_to_3_1: .: (0.000463) + test_to_3_3: .: (0.000471) + test_to_3_name: .: (0.000631) + test_to_re: .: (0.000680) Bio::TestAAConstants: - test_bio_aminoacid: .: (0.000468) + test_bio_aminoacid: .: (0.001306) Bio::TestAAindex: - test_api: .: (0.000288) - test_auto_aax1: .: (0.001541) - test_auto_aax2: .: (0.002991) + test_api: .: (0.000991) + test_auto_aax1: .: (0.002459) + test_auto_aax2: .: (0.002806) Bio::TestAAindex1: - test_author: .: (0.002064) - test_comment: .: (0.000866) - test_correlation_coefficient: .: (0.001210) - test_dblinks: .: (0.000685) - test_definition: .: (0.000877) - test_entry_id: .: (0.000693) - test_index: .: (0.001067) - test_journal: .: (0.000718) - test_title: .: (0.000644) + test_author: .: (0.003042) + test_comment: .: (0.002122) + test_correlation_coefficient: .: (0.004722) + test_dblinks: .: (0.002115) + test_definition: .: (0.002045) + test_entry_id: .: (0.001983) + test_index: .: (0.003158) + test_journal: .: (0.002448) + test_title: .: (0.002182) Bio::TestAAindex2: - test_access_A_R: .: (0.002397) - test_access_R_A: .: (0.001944) - test_author: .: (0.000719) - test_cols: .: (0.000671) - test_comment: .: (0.000657) - test_dblinks: .: (0.000994) - test_definition: .: (0.000720) - test_entry_id: .: (0.000729) - test_journal: .: (0.000844) - test_matrix: .: (0.001897) - test_matrix_1_2: .: (0.001893) - test_matrix_2_2: .: (0.001756) - test_matrix_A_R: .: (0.001943) - test_matrix_R_A: .: (0.001694) - test_matrix_determinant: .: (0.010289) - test_matrix_rank: .: (0.010421) - test_matrix_transpose: .: (0.002206) - test_rows: .: (0.000794) - test_title: .: (0.018603) + test_access_A_R: .: (0.009845) + test_access_R_A: .: (0.008045) + test_author: .: (0.002209) + test_cols: .: (0.002122) + test_comment: .: (0.002087) + test_dblinks: .: (0.002103) + test_definition: .: (0.002122) + test_entry_id: .: (0.002321) + test_journal: .: (0.002387) + test_matrix: .: (0.007855) + test_matrix_1_2: .: (0.004584) + test_matrix_2_2: .: (0.004283) + test_matrix_A_R: .: (0.004546) + test_matrix_R_A: .: (0.004291) + test_matrix_determinant: .: (0.025963) + test_matrix_rank: .: (0.025609) + test_matrix_transpose: .: (0.004989) + test_rows: .: (0.001159) + test_title: .: (0.035667) Bio::TestAAindexConstant: - test_delimiter: .: (0.001633) - test_tagsize: .: (0.000391) + test_delimiter: .: (0.001182) + test_tagsize: .: (0.000495) Bio::TestAbif: - test_complement: .: (0.070688) - test_seq: .: (0.021957) - test_to_biosequence: .: (0.018822) + test_complement: .: (0.059452) + test_seq: .: (0.045488) + test_to_biosequence: .: (0.048256) Bio::TestActsLikeMap: - test_mixin: .: (0.000981) + test_mixin: .: (0.002010) Bio::TestActsLikeMapAndMarker: - test_mixin: .: (0.000971) + test_mixin: .: (0.001971) Bio::TestActsLikeMarker: - test_mixin: .: (0.000704) + test_mixin: .: (0.001406) Bio::TestAlignment: - test_add_seq_no_key: .: (0.000864) - test_add_seq_using_seq_with_aaseq_method: .: (0.000501) - test_add_seq_using_seq_with_definition_method: .: (0.000399) - test_add_seq_using_seq_with_entry_id_method: .: (0.000508) - test_add_seq_using_seq_with_naseq_method: .: (0.001015) - test_add_seq_using_seq_with_seq_method: .: (0.000453) - test_consensus_iupac_gap_modes: .: (0.001091) - test_consensus_iupac_missing_char: .: (0.000509) - test_consensus_iupac_missing_char_option: .: (0.000772) - test_consensus_iupac_no_gaps: .: (0.000713) - test_consensus_iupac_of_ambiguous_bases: .: (0.000983) - test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.016084) - test_consensus_opt_gap_mode: .: (0.001855) - test_consensus_opt_missing_char: .: (0.000704) - test_consensus_string_no_gaps: .: (0.000721) - test_consensus_threshold_four_sequences: .: (0.001425) - test_consensus_threshold_two_sequences: .: (0.001048) - test_convert_match: .: (0.000972) - test_convert_unmatch: .: (0.000538) - test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000532) - test_convert_unmatch_different_match_char: .: (0.000464) - test_convert_unmatch_multiple_sequences: .: (0.001112) - test_default_gap_char: .: (0.000375) - test_default_gap_regexp_matches_default_gap_char: .: (0.000366) - test_default_missing_char: .: (0.000363) - test_each_site_equal_length: .: (0.000550) - test_each_site_unequal_length: .: (0.000525) - test_equals: .: (0.000618) - test_match_line_protein: .: (0.001169) - test_normalizebang_extends_sequences_with_gaps: .: (0.000608) - test_seq_length_is_max_seq_length: .: (0.002118) - test_seq_length_when_one_sequence: .: (0.000398) - test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000433) - test_seqclass_when_seqclass_set: .: (0.000383) - test_seqclass_when_sequence_used: .: (0.000386) - test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000366) - test_set_and_get_gap_char: .: (0.000335) - test_store_cannot_override_key: .: (0.000444) - test_store_with_default_keys_and_user_defined_keys: .: (0.000529) - test_store_with_nil_key_uses_next_number_for_key: .: (0.000426) + test_add_seq_no_key: .: (0.001624) + test_add_seq_using_seq_with_aaseq_method: .: (0.000816) + test_add_seq_using_seq_with_definition_method: .: (0.000618) + test_add_seq_using_seq_with_entry_id_method: .: (0.000662) + test_add_seq_using_seq_with_naseq_method: .: (0.001833) + test_add_seq_using_seq_with_seq_method: .: (0.000831) + test_consensus_iupac_gap_modes: .: (0.002428) + test_consensus_iupac_missing_char: .: (0.001122) + test_consensus_iupac_missing_char_option: .: (0.001250) + test_consensus_iupac_no_gaps: .: (0.001635) + test_consensus_iupac_of_ambiguous_bases: .: (0.002467) + test_consensus_iupac_yields_correct_ambiguous_bases: .: (0.032939) + test_consensus_opt_gap_mode: .: (0.003834) + test_consensus_opt_missing_char: .: (0.001559) + test_consensus_string_no_gaps: .: (0.001487) + test_consensus_threshold_four_sequences: .: (0.003153) + test_consensus_threshold_two_sequences: .: (0.002316) + test_convert_match: .: (0.001847) + test_convert_unmatch: .: (0.001010) + test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched:.: (0.000995) + test_convert_unmatch_different_match_char: .: (0.000855) + test_convert_unmatch_multiple_sequences: .: (0.002034) + test_default_gap_char: .: (0.000553) + test_default_gap_regexp_matches_default_gap_char: .: (0.000553) + test_default_missing_char: .: (0.000494) + test_each_site_equal_length: .: (0.000983) + test_each_site_unequal_length: .: (0.001096) + test_equals: .: (0.001187) + test_match_line_protein: .: (0.002752) + test_normalizebang_extends_sequences_with_gaps: .: (0.000921) + test_seq_length_is_max_seq_length: .: (0.004560) + test_seq_length_when_one_sequence: .: (0.000644) + test_seqclass_String_seq_not_present_no_seqclass_set: .: (0.000580) + test_seqclass_when_seqclass_set: .: (0.000570) + test_seqclass_when_sequence_used: .: (0.000547) + test_seqclass_when_sequence_used_no_seqclass_set: .: (0.000566) + test_set_and_get_gap_char: .: (0.000591) + test_store_cannot_override_key: .: (0.000602) + test_store_with_default_keys_and_user_defined_keys: .: (0.000631) + test_store_with_nil_key_uses_next_number_for_key: .: (0.000593) Bio::TestAlignmentEnumerableExtension: - test_alignment_collect: .: (0.000677) - test_alignment_concat: .: (0.000566) - test_alignment_length: .: (0.000319) - test_alignment_lstrip!: .: (0.000563) - test_alignment_lstrip_nil: .: (0.000416) - test_alignment_normalize!: .: (0.000344) - test_alignment_rstrip!: .: (0.000607) - test_alignment_rstrip_nil: .: (0.000464) - test_alignment_site: .: (0.000484) - test_alignment_slice: .: (0.000375) - test_alignment_strip!: .: (0.000729) - test_alignment_strip_nil: .: (0.000419) - test_alignment_subseq: .: (0.000481) - test_alignment_window: .: (0.000343) - test_collect_each_site: .: (0.000472) - test_consensus_each_site_default: .: (0.000545) - test_consensus_each_site_gap_mode_1: .: (0.000495) - test_consensus_each_site_gap_mode_minus1: .: (0.000520) - test_consensus_iupac: .: (0.001464) - test_consensus_string_default: .: (0.000576) - test_consensus_string_half: .: (0.000485) - test_convert_match: .: (0.000471) - test_convert_unmatch: .: (0.000366) - test_each_seq: .: (0.000487) - test_each_site: .: (0.000563) - test_each_site_step: .: (0.000433) - test_each_window: .: (0.000532) - test_match_line: .: (0.002582) - test_match_line_amino: .: (0.003063) - test_match_line_nuc: .: (0.000681) - test_private_alignment_site: .: (0.000372) - test_remove_all_gaps!: .: (0.001924) - test_seqclass: .: (0.000331) - test_seqclass=: .: (0.000321) - test_seqclass_default: .: (0.000182) + test_alignment_collect: .: (0.001395) + test_alignment_concat: .: (0.000827) + test_alignment_length: .: (0.000488) + test_alignment_lstrip!: .: (0.000982) + test_alignment_lstrip_nil: .: (0.000715) + test_alignment_normalize!: .: (0.000564) + test_alignment_rstrip!: .: (0.001023) + test_alignment_rstrip_nil: .: (0.000768) + test_alignment_site: .: (0.000950) + test_alignment_slice: .: (0.000566) + test_alignment_strip!: .: (0.001282) + test_alignment_strip_nil: .: (0.000755) + test_alignment_subseq: .: (0.000776) + test_alignment_window: .: (0.000582) + test_collect_each_site: .: (0.000829) + test_consensus_each_site_default: .: (0.001023) + test_consensus_each_site_gap_mode_1: .: (0.000916) + test_consensus_each_site_gap_mode_minus1: .: (0.001016) + test_consensus_iupac: .: (0.003417) + test_consensus_string_default: .: (0.000977) + test_consensus_string_half: .: (0.000825) + test_convert_match: .: (0.000678) + test_convert_unmatch: .: (0.000681) + test_each_seq: .: (0.000761) + test_each_site: .: (0.001092) + test_each_site_step: .: (0.000810) + test_each_window: .: (0.001060) + test_match_line: .: (0.006382) + test_match_line_amino: .: (0.007867) + test_match_line_nuc: .: (0.001124) + test_private_alignment_site: .: (0.000613) + test_remove_all_gaps!: .: (0.001691) + test_seqclass: .: (0.000627) + test_seqclass=: .: (0.000727) + test_seqclass_default: .: (0.000457) Bio::TestAlignmentMultiFastaFormat: - test_alignment: .: (0.012014) - test_determine_seq_method: .: (0.004696) - test_entries: .: (0.000939) + test_alignment: .: (0.019836) + test_determine_seq_method: .: (0.012425) + test_entries: .: (0.002392) Bio::TestAlignmentOutput: - test_avoid_same_name: .: (0.000942) - test_avoid_same_name_numbering: .: (0.000548) - test_clustal_have_same_name_true: .: (0.000381) - test_have_same_name_false: .: (0.000361) + test_avoid_same_name: .: (0.001582) + test_avoid_same_name_numbering: .: (0.000835) + test_clustal_have_same_name_true: .: (0.000621) + test_have_same_name_false: .: (0.000629) Bio::TestAlignmentPropertyMethods: - test_gap_char=: .: (0.001328) - test_gap_char_default: .: (0.000369) - test_gap_char_never_nil: .: (0.000361) - test_gap_regexp: .: (0.000291) - test_gap_regexp=: .: (0.000315) - test_gap_regexp_never_nil: .: (0.000252) - test_get_all_property_default: .: (0.000285) - test_get_all_property_nodefault: .: (0.000357) - test_is_gap_default_false: .: (0.000487) - test_is_gap_default_true: .: (0.000356) - test_is_gap_nodefault_false: .: (0.000338) - test_is_gap_nodefault_true: .: (0.000368) - test_missing_char=: .: (0.000277) - test_missing_char_default: .: (0.000330) - test_missing_char_never_nil: .: (0.000323) - test_seqclass=: .: (0.000668) - test_seqclass_default: .: (0.000434) - test_seqclass_never_nil: .: (0.000309) - test_set_all_property: .: (0.000342) + test_gap_char=: .: (0.002806) + test_gap_char_default: .: (0.000688) + test_gap_char_never_nil: .: (0.000551) + test_gap_regexp: .: (0.000592) + test_gap_regexp=: .: (0.000605) + test_gap_regexp_never_nil: .: (0.000536) + test_get_all_property_default: .: (0.000600) + test_get_all_property_nodefault: .: (0.000640) + test_is_gap_default_false: .: (0.000612) + test_is_gap_default_true: .: (0.000594) + test_is_gap_nodefault_false: .: (0.000679) + test_is_gap_nodefault_true: .: (0.000682) + test_missing_char=: .: (0.000579) + test_missing_char_default: .: (0.000559) + test_missing_char_never_nil: .: (0.000750) + test_seqclass=: .: (0.001867) + test_seqclass_default: .: (0.000669) + test_seqclass_never_nil: .: (0.000631) + test_set_all_property: .: (0.000674) Bio::TestAlignmentSite: - test_consensus_iupac: .: (0.001858) - test_consensus_string_50percent: .: (0.000396) - test_consensus_string_50percent_nil: .: (0.000344) - test_consensus_string_default: .: (0.000321) - test_consensus_string_default_nil: .: (0.000337) - test_has_gap_false: .: (0.000323) - test_has_gap_true: .: (0.000300) - test_match_line_amino_100percent: .: (0.000459) - test_match_line_amino_missing: .: (0.001059) - test_match_line_amino_strong: .: (0.000476) - test_match_line_amino_weak: .: (0.000493) - test_match_line_nuc_100percent: .: (0.000467) - test_match_line_nuc_missing: .: (0.000457) - test_remove_gaps!: .: (0.000357) - test_remove_gaps_bang_not_removed: .: (0.000532) + test_consensus_iupac: .: (0.003672) + test_consensus_string_50percent: .: (0.000655) + test_consensus_string_50percent_nil: .: (0.000611) + test_consensus_string_default: .: (0.000530) + test_consensus_string_default_nil: .: (0.000537) + test_has_gap_false: .: (0.000554) + test_has_gap_true: .: (0.000499) + test_match_line_amino_100percent: .: (0.000690) + test_match_line_amino_missing: .: (0.002072) + test_match_line_amino_strong: .: (0.000820) + test_match_line_amino_weak: .: (0.001029) + test_match_line_nuc_100percent: .: (0.000711) + test_match_line_nuc_missing: .: (0.000722) + test_remove_gaps!: .: (0.000555) + test_remove_gaps_bang_not_removed: .: (0.000467) Bio::TestAtomFinder: - test_atoms: .: (0.047131) - test_each_atom: .: (0.000720) - test_find_atom: .: (0.000544) + test_atoms: .: (0.105132) + test_each_atom: .: (0.001369) + test_find_atom: .: (0.001175) Bio::TestBioFastaDefline: - test_acc_version: .: (0.001326) - test_accession: .: (0.001330) - test_accessions: .: (0.000992) - test_description: .: (0.000976) - test_descriptions: .: (0.001008) - test_entry_id: .: (0.000925) - test_get: .: (0.001040) - test_get_all_by_type: .: (0.000787) - test_get_by_type: .: (0.000964) - test_gi: .: (0.000849) - test_id_strings: .: (0.001686) - test_locus: .: (0.000947) - test_method_missing: .: (0.000999) - test_to_s: .: (0.001059) - test_words: .: (0.002340) + test_acc_version: .: (0.002678) + test_accession: .: (0.002560) + test_accessions: .: (0.002479) + test_description: .: (0.001968) + test_descriptions: .: (0.001896) + test_entry_id: .: (0.001869) + test_get: .: (0.002223) + test_get_all_by_type: .: (0.001954) + test_get_by_type: .: (0.001813) + test_gi: .: (0.001704) + test_id_strings: .: (0.003617) + test_locus: .: (0.001556) + test_method_missing: .: (0.002055) + test_to_s: .: (0.001839) + test_words: .: (0.004110) Bio::TestBioGOOntology: - test_dag_edit_format_parser: .: (0.002982) - test_goid2term: .: (0.001050) - test_parse_goids: .: (0.001050) + test_dag_edit_format_parser: .: (0.005632) + test_goid2term: .: (0.001973) + test_parse_goids: .: (0.001928) Bio::TestBioGenBank: - test_basecount: .: (0.001666) - test_circular: .: (0.000673) - test_classification: .: (0.001007) - test_date: .: (0.000729) - test_date_modified: .: (0.001735) - test_division: .: (0.000714) - test_each_cds_feature: .: (0.002265) - test_each_cds_qualifiers: .: (0.002065) - test_each_gene: .: (0.002306) - test_entry_id: .: (0.000727) - test_length: .: (0.000757) - test_locus_circular: .: (0.001048) - test_locus_class: .: (0.001119) - test_locus_date: .: (0.000881) - test_locus_division: .: (0.000937) - test_locus_entry_id: .: (0.001040) - test_locus_length: .: (0.000929) - test_locus_natype: .: (0.000969) - test_locus_strand: .: (0.000996) - test_natype: .: (0.000899) - test_seq: .: (0.000959) - test_seq_len: .: (0.000990) - test_strand: .: (0.000992) - test_strandedness: .: (0.000793) - test_to_biosequence: .: (0.005334) + test_basecount: .: (0.002447) + test_circular: .: (0.001280) + test_classification: .: (0.001847) + test_date: .: (0.001185) + test_date_modified: .: (0.003531) + test_division: .: (0.001234) + test_each_cds_feature: .: (0.004319) + test_each_cds_qualifiers: .: (0.004472) + test_each_gene: .: (0.004535) + test_entry_id: .: (0.001533) + test_length: .: (0.001485) + test_locus_circular: .: (0.001760) + test_locus_class: .: (0.001951) + test_locus_date: .: (0.001637) + test_locus_division: .: (0.001679) + test_locus_entry_id: .: (0.001612) + test_locus_length: .: (0.001704) + test_locus_natype: .: (0.001718) + test_locus_strand: .: (0.001717) + test_natype: .: (0.001642) + test_seq: .: (0.001924) + test_seq_len: .: (0.001759) + test_strand: .: (0.001713) + test_strandedness: .: (0.001426) + test_to_biosequence: .: (0.011946) Bio::TestBioGenPept: - test_circular: .: (0.001594) - test_date: .: (0.000585) - test_dbsource: .: (0.012699) - test_division: .: (0.000642) - test_entry_id: .: (0.000538) - test_length: .: (0.000601) - test_locus: .: (0.000529) - test_seq: .: (0.000578) - test_seq_len: .: (0.000474) + test_circular: .: (0.002441) + test_date: .: (0.001154) + test_dbsource: .: (0.027619) + test_division: .: (0.001429) + test_entry_id: .: (0.001151) + test_length: .: (0.001089) + test_locus: .: (0.001275) + test_seq: .: (0.001337) + test_seq_len: .: (0.001355) Bio::TestBioKEGGGENES_b0529: - test_aalen: .: (0.001594) - test_aaseq: .: (0.000736) - test_chromosome: .: (0.001097) - test_codon_usage: .: (0.001009) - test_cu_list: .: (0.000604) - test_dblinks_as_hash: .: (0.000684) - test_dblinks_as_strings: .: (0.000495) - test_definition: .: (0.000523) - test_division: .: (0.000461) - test_eclinks: .: (0.000558) - test_entry: .: (0.000887) - test_entry_id: .: (0.000528) - test_gbposition: .: (0.000540) - test_gene: .: (0.000471) - test_genes: .: (0.000527) - test_keggclass: .: (0.000585) - test_keggclasses: .: (0.000704) - test_locations: .: (0.000808) - test_motifs_as_hash: .: (0.000580) - test_motifs_as_strings: .: (0.000867) - test_name: .: (0.000493) - test_names_as_array: .: (0.000879) - test_new: .: (0.000601) - test_ntlen: .: (0.000777) - test_ntseq: .: (0.000787) - test_organism: .: (0.000465) - test_orthologs_as_hash: .: (0.000661) - test_orthologs_as_strings: .: (0.000508) - test_pathway: .: (0.000821) - test_pathway_after_pathways_as_strings: .: (0.000691) - test_pathway_before_pathways_as_strings: .: (0.000652) - test_pathways_as_hash: .: (0.000579) - test_pathways_as_strings: .: (0.000544) - test_position: .: (0.000511) - test_structure: .: (0.000488) + test_aalen: .: (0.002674) + test_aaseq: .: (0.001606) + test_chromosome: .: (0.002280) + test_codon_usage: .: (0.002020) + test_cu_list: .: (0.001153) + test_dblinks_as_hash: .: (0.001500) + test_dblinks_as_strings: .: (0.001213) + test_definition: .: (0.001324) + test_division: .: (0.001152) + test_eclinks: .: (0.001317) + test_entry: .: (0.002032) + test_entry_id: .: (0.001230) + test_gbposition: .: (0.001397) + test_gene: .: (0.001280) + test_genes: .: (0.001316) + test_keggclass: .: (0.001392) + test_keggclasses: .: (0.001429) + test_locations: .: (0.001847) + test_motifs_as_hash: .: (0.001596) + test_motifs_as_strings: .: (0.002238) + test_name: .: (0.001276) + test_names_as_array: .: (0.001440) + test_new: .: (0.001217) + test_ntlen: .: (0.001821) + test_ntseq: .: (0.001971) + test_organism: .: (0.001220) + test_orthologs_as_hash: .: (0.001275) + test_orthologs_as_strings: .: (0.001205) + test_pathway: .: (0.002347) + test_pathway_after_pathways_as_strings: .: (0.002088) + test_pathway_before_pathways_as_strings: .: (0.001859) + test_pathways_as_hash: .: (0.001379) + test_pathways_as_strings: .: (0.001307) + test_position: .: (0.001299) + test_structure: .: (0.001401) Bio::TestBioKEGGGENOME_T00005: - test_chromosomes: .: (0.004366) - test_comment: .: (0.001149) - test_data_source: .: (0.001069) - test_definition: .: (0.001022) - test_disease: .: (0.000881) - test_entry_id: .: (0.001264) - test_lineage: .: (0.001365) - test_nalen: .: (0.001047) - test_name: .: (0.001123) - test_new: .: (0.000994) - test_num_gene: .: (0.001072) - test_num_rna: .: (0.000916) - test_original_databases: .: (0.001066) - test_original_db: .: (0.000974) - test_plasmids: .: (0.000959) - test_references: .: (0.007519) - test_statistics: .: (0.001502) - test_taxid: .: (0.001134) - test_taxonomy: .: (0.001127) + test_chromosomes: .: (0.008891) + test_comment: .: (0.002728) + test_data_source: .: (0.002201) + test_definition: .: (0.002114) + test_disease: .: (0.002213) + test_entry_id: .: (0.002089) + test_lineage: .: (0.002852) + test_nalen: .: (0.002264) + test_name: .: (0.002139) + test_new: .: (0.002148) + test_num_gene: .: (0.002645) + test_num_rna: .: (0.002442) + test_original_databases: .: (0.002262) + test_original_db: .: (0.002357) + test_plasmids: .: (0.002129) + test_references: .: (0.016891) + test_statistics: .: (0.003054) + test_taxid: .: (0.002726) + test_taxonomy: .: (0.002640) Bio::TestBioKEGGGENOME_T00070: - test_chromosomes: .: (0.005113) - test_comment: .: (0.000811) - test_data_source: .: (0.000997) - test_definition: .: (0.000753) - test_disease: .: (0.000785) - test_entry_id: .: (0.000693) - test_lineage: .: (0.000640) - test_nalen: .: (0.000618) - test_name: .: (0.000659) - test_new: .: (0.001165) - test_num_gene: .: (0.000977) - test_num_rna: .: (0.000704) - test_original_databases: .: (0.000696) - test_original_db: .: (0.000738) - test_plasmids: .: (0.000992) - test_references: .: (0.001031) - test_statistics: .: (0.000611) - test_taxid: .: (0.001173) - test_taxonomy: .: (0.000697) + test_chromosomes: .: (0.003297) + test_comment: .: (0.001611) + test_data_source: .: (0.002231) + test_definition: .: (0.001570) + test_disease: .: (0.001497) + test_entry_id: .: (0.001487) + test_lineage: .: (0.001572) + test_nalen: .: (0.001287) + test_name: .: (0.001278) + test_new: .: (0.001313) + test_num_gene: .: (0.002012) + test_num_rna: .: (0.001527) + test_original_databases: .: (0.001255) + test_original_db: .: (0.001340) + test_plasmids: .: (0.001895) + test_references: .: (0.002114) + test_statistics: .: (0.001420) + test_taxid: .: (0.002347) + test_taxonomy: .: (0.001568) Bio::TestBioKEGGPATHWAY_ec00072: - test_compounds_as_hash: .: (0.003288) - test_compounds_as_strings: .: (0.000616) - test_dblinks_as_hash: .: (0.000513) - test_dblinks_as_strings: .: (0.000468) - test_description: .: (0.000529) - test_diseases_as_hash: .: (0.000544) - test_diseases_as_strings: .: (0.000532) - test_entry_id: .: (0.001204) - test_enzymes_as_strings: .: (0.000725) - test_genes_as_hash: .: (0.000438) - test_genes_as_strings: .: (0.000429) - test_keggclass: .: (0.000586) - test_ko_pathway: .: (0.000544) - test_modules_as_hash: .: (0.000517) - test_modules_as_strings: .: (0.000494) - test_name: .: (0.000499) - test_new: .: (0.000507) - test_organism: .: (0.000635) - test_orthologs_as_hash: .: (0.001140) - test_orthologs_as_strings: .: (0.000726) - test_pathways_as_hash: .: (0.000599) - test_pathways_as_strings: .: (0.000640) - test_reactions_as_hash: .: (0.000571) - test_reactions_as_strings: .: (0.000488) - test_references: .: (0.000505) - test_rel_pathways_as_hash: .: (0.000655) - test_rel_pathways_as_strings: .: (0.000558) + test_compounds_as_hash: .: (0.002618) + test_compounds_as_strings: .: (0.001212) + test_dblinks_as_hash: .: (0.001131) + test_dblinks_as_strings: .: (0.001063) + test_description: .: (0.001243) + test_diseases_as_hash: .: (0.001023) + test_diseases_as_strings: .: (0.000960) + test_entry_id: .: (0.002516) + test_enzymes_as_strings: .: (0.001789) + test_genes_as_hash: .: (0.001205) + test_genes_as_strings: .: (0.001084) + test_keggclass: .: (0.001259) + test_ko_pathway: .: (0.001189) + test_modules_as_hash: .: (0.001091) + test_modules_as_strings: .: (0.001147) + test_name: .: (0.001237) + test_new: .: (0.001181) + test_organism: .: (0.001112) + test_orthologs_as_hash: .: (0.002459) + test_orthologs_as_strings: .: (0.001723) + test_pathways_as_hash: .: (0.001258) + test_pathways_as_strings: .: (0.001058) + test_reactions_as_hash: .: (0.001156) + test_reactions_as_strings: .: (0.001109) + test_references: .: (0.001103) + test_rel_pathways_as_hash: .: (0.001334) + test_rel_pathways_as_strings: .: (0.001106) Bio::TestBioKEGGPATHWAY_hsa00790: - test_compounds_as_hash: .: (0.005537) - test_compounds_as_strings: .: (0.001367) - test_dblinks_as_hash: .: (0.000605) - test_dblinks_as_strings: .: (0.000698) - test_description: .: (0.000629) - test_diseases_as_hash: .: (0.000663) - test_diseases_as_strings: .: (0.000620) - test_entry_id: .: (0.000689) - test_enzymes_as_strings: .: (0.000844) - test_genes_as_hash: .: (0.001086) - test_genes_as_strings: .: (0.000727) - test_keggclass: .: (0.000685) - test_ko_pathway: .: (0.000562) - test_modules_as_hash: .: (0.000698) - test_modules_as_strings: .: (0.000556) - test_name: .: (0.000579) - test_new: .: (0.000579) - test_organism: .: (0.000675) - test_orthologs_as_hash: .: (0.000965) - test_orthologs_as_strings: .: (0.000688) - test_pathways_as_hash: .: (0.000604) - test_pathways_as_strings: .: (0.000529) - test_reactions_as_hash: .: (0.000574) - test_reactions_as_strings: .: (0.000576) - test_references: .: (0.000561) - test_rel_pathways_as_hash: .: (0.000656) - test_rel_pathways_as_strings: .: (0.000612) + test_compounds_as_hash: .: (0.003607) + test_compounds_as_strings: .: (0.003092) + test_dblinks_as_hash: .: (0.001359) + test_dblinks_as_strings: .: (0.001346) + test_description: .: (0.001263) + test_diseases_as_hash: .: (0.001346) + test_diseases_as_strings: .: (0.001319) + test_entry_id: .: (0.001334) + test_enzymes_as_strings: .: (0.001152) + test_genes_as_hash: .: (0.002417) + test_genes_as_strings: .: (0.001800) + test_keggclass: .: (0.001322) + test_ko_pathway: .: (0.001370) + test_modules_as_hash: .: (0.001399) + test_modules_as_strings: .: (0.001277) + test_name: .: (0.001343) + test_new: .: (0.001271) + test_organism: .: (0.001528) + test_orthologs_as_hash: .: (0.001925) + test_orthologs_as_strings: .: (0.001359) + test_pathways_as_hash: .: (0.001356) + test_pathways_as_strings: .: (0.001243) + test_reactions_as_hash: .: (0.001101) + test_reactions_as_strings: .: (0.001064) + test_references: .: (0.001170) + test_rel_pathways_as_hash: .: (0.001408) + test_rel_pathways_as_strings: .: (0.001420) Bio::TestBioKEGGPATHWAY_ko00312: - test_compounds_as_hash: .: (0.002077) - test_compounds_as_strings: .: (0.000647) - test_dblinks_as_hash: .: (0.000468) - test_dblinks_as_strings: .: (0.000493) - test_description: .: (0.000528) - test_diseases_as_hash: .: (0.001456) - test_diseases_as_strings: .: (0.000472) - test_entry_id: .: (0.000483) - test_enzymes_as_strings: .: (0.000438) - test_genes_as_hash: .: (0.000445) - test_genes_as_strings: .: (0.000625) - test_keggclass: .: (0.000566) - test_ko_pathway: .: (0.000553) - test_modules_as_hash: .: (0.000533) - test_modules_as_strings: .: (0.001061) - test_name: .: (0.000830) - test_new: .: (0.000522) - test_organism: .: (0.000575) - test_orthologs_as_hash: .: (0.000732) - test_orthologs_as_strings: .: (0.000600) - test_pathways_as_hash: .: (0.000601) - test_pathways_as_strings: .: (0.000520) - test_reactions_as_hash: .: (0.000453) - test_reactions_as_strings: .: (0.000464) - test_references: .: (0.000421) - test_rel_pathways_as_hash: .: (0.001053) - test_rel_pathways_as_strings: .: (0.000538) + test_compounds_as_hash: .: (0.002375) + test_compounds_as_strings: .: (0.001524) + test_dblinks_as_hash: .: (0.000984) + test_dblinks_as_strings: .: (0.000950) + test_description: .: (0.001273) + test_diseases_as_hash: .: (0.001071) + test_diseases_as_strings: .: (0.001001) + test_entry_id: .: (0.001136) + test_enzymes_as_strings: .: (0.001091) + test_genes_as_hash: .: (0.000955) + test_genes_as_strings: .: (0.000931) + test_keggclass: .: (0.001066) + test_ko_pathway: .: (0.000973) + test_modules_as_hash: .: (0.000977) + test_modules_as_strings: .: (0.002142) + test_name: .: (0.001495) + test_new: .: (0.001001) + test_organism: .: (0.001044) + test_orthologs_as_hash: .: (0.001539) + test_orthologs_as_strings: .: (0.001191) + test_pathways_as_hash: .: (0.001047) + test_pathways_as_strings: .: (0.001030) + test_reactions_as_hash: .: (0.000953) + test_reactions_as_strings: .: (0.001019) + test_references: .: (0.001163) + test_rel_pathways_as_hash: .: (0.002601) + test_rel_pathways_as_strings: .: (0.001169) Bio::TestBioKEGGPATHWAY_map00030: - test_compounds_as_hash: .: (0.001822) - test_compounds_as_strings: .: (0.000646) - test_dblinks_as_hash: .: (0.000987) - test_dblinks_as_strings: .: (0.000614) - test_description: .: (0.001119) - test_diseases_as_hash: .: (0.000856) - test_diseases_as_strings: .: (0.001213) - test_entry_id: .: (0.000837) - test_enzymes_as_strings: .: (0.000796) - test_genes_as_hash: .: (0.000588) - test_genes_as_strings: .: (0.000612) - test_keggclass: .: (0.000690) - test_ko_pathway: .: (0.000720) - test_modules_as_hash: .: (0.000978) - test_modules_as_strings: .: (0.001064) - test_name: .: (0.000755) - test_new: .: (0.000630) - test_organism: .: (0.000783) - test_orthologs_as_hash: .: (0.000658) - test_orthologs_as_strings: .: (0.000706) - test_pathways_as_hash: .: (0.000728) - test_pathways_as_strings: .: (0.000754) - test_reactions_as_hash: .: (0.000816) - test_reactions_as_strings: .: (0.000889) - test_references: .: (0.001944) - test_rel_pathways_as_hash: .: (0.001148) - test_rel_pathways_as_strings: .: (0.000716) + test_compounds_as_hash: .: (0.002456) + test_compounds_as_strings: .: (0.001220) + test_dblinks_as_hash: .: (0.001284) + test_dblinks_as_strings: .: (0.001370) + test_description: .: (0.002029) + test_diseases_as_hash: .: (0.001275) + test_diseases_as_strings: .: (0.002027) + test_entry_id: .: (0.001566) + test_enzymes_as_strings: .: (0.001121) + test_genes_as_hash: .: (0.001079) + test_genes_as_strings: .: (0.001191) + test_keggclass: .: (0.001289) + test_ko_pathway: .: (0.001476) + test_modules_as_hash: .: (0.001785) + test_modules_as_strings: .: (0.002120) + test_name: .: (0.001438) + test_new: .: (0.001189) + test_organism: .: (0.001432) + test_orthologs_as_hash: .: (0.001218) + test_orthologs_as_strings: .: (0.001341) + test_pathways_as_hash: .: (0.001221) + test_pathways_as_strings: .: (0.001134) + test_reactions_as_hash: .: (0.001149) + test_reactions_as_strings: .: (0.001675) + test_references: .: (0.004359) + test_rel_pathways_as_hash: .: (0.001613) + test_rel_pathways_as_strings: .: (0.001232) Bio::TestBioKeggDRUG: - test_activity: .: (0.002641) - test_comment: .: (0.000843) - test_dblinks_as_hash: .: (0.000812) - test_dblinks_as_strings: .: (0.000705) - test_entry_id: .: (0.000825) - test_formula: .: (0.000610) - test_kcf: .: (0.000580) - test_mass: .: (0.000634) - test_name: .: (0.000673) - test_names: .: (0.001035) - test_pathways_as_hash: .: (0.000638) - test_pathways_as_strings: .: (0.000590) - test_products: .: (0.000716) - test_remark: .: (0.000755) + test_activity: .: (0.002562) + test_comment: .: (0.002137) + test_dblinks_as_hash: .: (0.001760) + test_dblinks_as_strings: .: (0.001375) + test_entry_id: .: (0.001310) + test_formula: .: (0.001324) + test_kcf: .: (0.001289) + test_mass: .: (0.001345) + test_name: .: (0.001512) + test_names: .: (0.002271) + test_pathways_as_hash: .: (0.001524) + test_pathways_as_strings: .: (0.001279) + test_products: .: (0.001501) + test_remark: .: (0.001501) Bio::TestBioKeggGLYCAN: - test_comment: .: (0.003440) - test_composition: .: (0.000790) - test_compounds: .: (0.000646) - test_dblinks_as_hash: .: (0.001230) - test_dblinks_as_strings: .: (0.000676) - test_entry_id: .: (0.000835) - test_enzymes: .: (0.000575) - test_kcf: .: (0.000497) - test_keggclass: .: (0.000571) - test_mass: .: (0.000529) - test_name: .: (0.000580) - test_orthologs_as_hash: .: (0.001335) - test_orthologs_as_strings: .: (0.000721) - test_pathways_as_hash: .: (0.000686) - test_pathways_as_strings: .: (0.000664) - test_reactions: .: (0.001411) - test_references: .: (0.000636) - test_remark: .: (0.000437) + test_comment: .: (0.002674) + test_composition: .: (0.001489) + test_compounds: .: (0.001315) + test_dblinks_as_hash: .: (0.002864) + test_dblinks_as_strings: .: (0.001850) + test_entry_id: .: (0.001359) + test_enzymes: .: (0.001403) + test_kcf: .: (0.001124) + test_keggclass: .: (0.001367) + test_mass: .: (0.001415) + test_name: .: (0.001430) + test_orthologs_as_hash: .: (0.002514) + test_orthologs_as_strings: .: (0.001535) + test_pathways_as_hash: .: (0.001452) + test_pathways_as_strings: .: (0.001176) + test_reactions: .: (0.001236) + test_references: .: (0.001592) + test_remark: .: (0.001301) Bio::TestBioKeggGLYCAN_G01366: - test_comment: .: (0.002223) - test_composition: .: (0.000886) - test_compounds: .: (0.000437) - test_dblinks_as_hash: .: (0.000518) - test_dblinks_as_strings: .: (0.000368) - test_entry_id: .: (0.000364) - test_enzymes: .: (0.000626) - test_kcf: .: (0.000495) - test_keggclass: .: (0.000549) - test_mass: .: (0.000606) - test_name: .: (0.000639) - test_orthologs_as_hash: .: (0.000584) - test_orthologs_as_strings: .: (0.001088) - test_pathways_as_hash: .: (0.000618) - test_pathways_as_strings: .: (0.000581) - test_reactions: .: (0.000608) - test_references: .: (0.000712) - test_remark: .: (0.000571) + test_comment: .: (0.002278) + test_composition: .: (0.002279) + test_compounds: .: (0.001232) + test_dblinks_as_hash: .: (0.001287) + test_dblinks_as_strings: .: (0.001088) + test_entry_id: .: (0.001220) + test_enzymes: .: (0.001261) + test_kcf: .: (0.001059) + test_keggclass: .: (0.001056) + test_mass: .: (0.001152) + test_name: .: (0.001034) + test_orthologs_as_hash: .: (0.000983) + test_orthologs_as_strings: .: (0.002037) + test_pathways_as_hash: .: (0.001005) + test_pathways_as_strings: .: (0.000893) + test_reactions: .: (0.001065) + test_references: .: (0.000928) + test_remark: .: (0.001095) Bio::TestBioKeggPathway_rn00250: - test_compounds_as_hash: .: (0.004194) - test_compounds_as_strings: .: (0.000834) - test_dblinks_as_hash: .: (0.000990) - test_dblinks_as_strings: .: (0.002384) - test_description: .: (0.000715) - test_diseases_as_hash: .: (0.000747) - test_diseases_as_strings: .: (0.000854) - test_entry_id: .: (0.000737) - test_enzymes_as_strings: .: (0.000665) - test_genes_as_hash: .: (0.000682) - test_genes_as_strings: .: (0.000713) - test_keggclass: .: (0.000738) - test_ko_pathway: .: (0.001132) - test_modules_as_hash: .: (0.000926) - test_modules_as_strings: .: (0.000957) - test_name: .: (0.000738) - test_new: .: (0.000611) - test_organism: .: (0.000671) - test_orthologs_as_hash: .: (0.000619) - test_orthologs_as_strings: .: (0.000641) - test_pathways_as_hash: .: (0.000696) - test_pathways_as_strings: .: (0.000973) - test_reactions_as_hash: .: (0.001338) - test_reactions_as_strings: .: (0.001207) - test_references: .: (0.007529) - test_rel_pathways_as_hash: .: (0.001133) - test_rel_pathways_as_strings: .: (0.000820) + test_compounds_as_hash: .: (0.003497) + test_compounds_as_strings: .: (0.001860) + test_dblinks_as_hash: .: (0.002336) + test_dblinks_as_strings: .: (0.001426) + test_description: .: (0.001322) + test_diseases_as_hash: .: (0.001468) + test_diseases_as_strings: .: (0.001345) + test_entry_id: .: (0.001497) + test_enzymes_as_strings: .: (0.001191) + test_genes_as_hash: .: (0.001194) + test_genes_as_strings: .: (0.001483) + test_keggclass: .: (0.001325) + test_ko_pathway: .: (0.002397) + test_modules_as_hash: .: (0.001682) + test_modules_as_strings: .: (0.001490) + test_name: .: (0.001295) + test_new: .: (0.001183) + test_organism: .: (0.001325) + test_orthologs_as_hash: .: (0.001140) + test_orthologs_as_strings: .: (0.001095) + test_pathways_as_hash: .: (0.001223) + test_pathways_as_strings: .: (0.002003) + test_reactions_as_hash: .: (0.002908) + test_reactions_as_strings: .: (0.002101) + test_references: .: (0.016069) + test_rel_pathways_as_hash: .: (0.002366) + test_rel_pathways_as_strings: .: (0.001706) Bio::TestBioLITDB: - test_author: .: (0.001719) - test_entry_id: .: (0.000570) - test_field: .: (0.000588) - test_journal: .: (0.000563) - test_keyword: .: (0.001308) - test_reference: .: (0.001061) - test_title: .: (0.000644) - test_volume: .: (0.000543) + test_author: .: (0.002526) + test_entry_id: .: (0.001119) + test_field: .: (0.001150) + test_journal: .: (0.001187) + test_keyword: .: (0.002589) + test_reference: .: (0.002223) + test_title: .: (0.001325) + test_volume: .: (0.001041) Bio::TestBioNBRF: - test_aalen: .: (0.002356) - test_aaseq: .: (0.000468) - test_entry: .: (0.000405) - test_length: .: (0.000407) - test_nalen: .: (0.000712) - test_naseq: .: (0.000565) - test_seq: .: (0.001108) - test_seq_class: .: (0.000404) - test_to_nbrf: .: (0.000457) + test_aalen: .: (0.002138) + test_aaseq: .: (0.000867) + test_entry: .: (0.000732) + test_length: .: (0.000776) + test_nalen: .: (0.001117) + test_naseq: .: (0.000932) + test_seq: .: (0.002361) + test_seq_class: .: (0.000825) + test_to_nbrf: .: (0.000903) Bio::TestBioTreeOutputPrivate: - test_to_newick_format_label: .: (0.001034) - test_to_newick_format_leaf: .: (0.000768) - test_to_newick_format_leaf_NHX: .: (0.000501) + test_to_newick_format_label: .: (0.001862) + test_to_newick_format_leaf: .: (0.001610) + test_to_newick_format_leaf_NHX: .: (0.001037) Bio::TestBl2seqReport: - test_db_len: .: (0.002912) - test_db_num: .: (0.001777) - test_new: .: (0.002445) - test_undefed_methods: .: (0.002405) - test_undefed_methods_for_iteration: .: (0.002380) + test_db_len: .: (0.004822) + test_db_num: .: (0.003865) + test_new: .: (0.002132) + test_undefed_methods: .: (0.006076) + test_undefed_methods_for_iteration: .: (0.006074) Bio::TestBl2seqReportConstants: - test_rs: .: (0.000677) + test_rs: .: (0.001131) Bio::TestBl2seqReportHit: - test_empty_hits: .: (0.001632) - test_hits: .: (0.000973) + test_empty_hits: .: (0.003399) + test_hits: .: (0.002278) Bio::TestBlast: - test_blast_reports_format0: .: (0.016228) - test_blast_reports_format0_with_block: .: (0.002090) - test_blast_reports_format7: .: (0.040317) - test_blast_reports_format7_with_block: .: (0.039862) - test_blast_reports_format7_with_parser: .: (0.034539) - test_blast_reports_format7_with_parser_with_block: .: (0.045356) - test_blast_reports_format8: .: (0.003532) - test_blast_reports_format8_with_block: .: (0.001431) - test_blast_reports_format8_with_parser: .: (0.000921) - test_blast_reports_format8_with_parser_with_block: .: (0.000669) - test_blast_reports_xml: .: (0.035728) - test_blast_reports_xml_with_block: .: (0.035975) - test_blastll: .: (0.000509) - test_db: .: (0.000440) - test_exec_genomenet: .: (0.000380) - test_exec_local: .: (0.000361) - test_exec_ncbi: .: (0.000847) - test_filter: .: (0.000397) - test_format: .: (0.000381) - test_make_command_line: .: (0.001358) - test_make_command_line_2: .: (0.001017) - test_matrix: .: (0.000502) - test_new: .: (0.000942) - test_new_opt_string: .: (0.000779) - test_option: .: (0.000393) - test_option_set: .: (0.000603) - test_option_set_m0: .: (0.000656) - test_options: .: (0.000386) - test_output: .: (0.000350) - test_parse_result: .: (0.068798) - test_parser: .: (0.000504) - test_program: .: (0.000437) - test_query: .: (0.000397) - test_self_local: .: (0.000540) - test_self_remote: .: (0.011553) - test_server: .: (0.000528) + test_blast_reports_format0: .: (0.031689) + test_blast_reports_format0_with_block: .: (0.004338) + test_blast_reports_format7: .: (0.092918) + test_blast_reports_format7_with_block: .: (0.087356) + test_blast_reports_format7_with_parser: .: (0.087887) + test_blast_reports_format7_with_parser_with_block: .: (0.101388) + test_blast_reports_format8: .: (0.005282) + test_blast_reports_format8_with_block: .: (0.003174) + test_blast_reports_format8_with_parser: .: (0.001602) + test_blast_reports_format8_with_parser_with_block: .: (0.001294) + test_blast_reports_xml: .: (0.084933) + test_blast_reports_xml_with_block: .: (0.085548) + test_blastll: .: (0.000981) + test_db: .: (0.000804) + test_exec_genomenet: .: (0.000729) + test_exec_local: .: (0.000697) + test_exec_ncbi: .: (0.001440) + test_filter: .: (0.000801) + test_format: .: (0.000809) + test_make_command_line: .: (0.002876) + test_make_command_line_2: .: (0.002233) + test_matrix: .: (0.000795) + test_new: .: (0.001960) + test_new_opt_string: .: (0.001511) + test_option: .: (0.000940) + test_option_set: .: (0.001365) + test_option_set_m0: .: (0.001417) + test_options: .: (0.000904) + test_output: .: (0.000806) + test_parse_result: .: (0.152798) + test_parser: .: (0.001081) + test_program: .: (0.001066) + test_query: .: (0.000894) + test_self_local: .: (0.001617) + test_self_remote: .: (0.027103) + test_server: .: (0.001089) Bio::TestBlastNCBIOptions: - test_add_options: .: (0.001094) - test_delete: .: (0.009302) - test_equal_equal: .: (0.000998) - test_get: .: (0.000985) - test_make_command_line_options: .: (0.008026) - test_normalize!: .: (0.000595) - test_parse: .: (0.008448) - test_set: .: (0.001394) + test_add_options: .: (0.002328) + test_delete: .: (0.002318) + test_equal_equal: .: (0.002412) + test_get: .: (0.002404) + test_make_command_line_options: .: (0.018218) + test_normalize!: .: (0.001303) + test_parse: .: (0.001343) + test_set: .: (0.019891) Bio::TestBlastReport: - test_db: .: (0.056053) - test_db_len: .: (0.037960) - test_db_num: .: (0.035992) - test_each_hit: .: (0.037892) - test_each_iteration: .: (0.039607) - test_eff_space: .: (0.036610) - test_entrez_query: .: (0.038446) - test_entropy: .: (0.037874) - test_expect: .: (0.038033) - test_filter: .: (0.040028) - test_gap_extend: .: (0.036685) - test_gap_open: .: (0.037537) - test_hits: .: (0.031768) - test_hsp_len: .: (0.032189) - test_inclusion: .: (0.037013) - test_iterations: .: (0.040252) - test_kappa: .: (0.034752) - test_lambda: .: (0.034899) - test_matrix: .: (0.032005) - test_message: .: (0.034668) - test_parameters: .: (0.034318) - test_pattern: .: (0.034142) - test_program: .: (0.034283) - test_query_def: .: (0.033709) - test_query_id: .: (0.035577) - test_query_len: .: (0.032841) - test_reference: .: (0.033067) - test_sc_match: .: (0.032515) - test_sc_mismatch: .: (0.033355) - test_statistics: .: (0.035598) - test_version: .: (0.031697) + test_db: .: (0.129621) + test_db_len: .: (0.089750) + test_db_num: .: (0.088414) + test_each_hit: .: (0.087135) + test_each_iteration: .: (0.089025) + test_eff_space: .: (0.087144) + test_entrez_query: .: (0.085870) + test_entropy: .: (0.084019) + test_expect: .: (0.086201) + test_filter: .: (0.086358) + test_gap_extend: .: (0.081707) + test_gap_open: .: (0.084716) + test_hits: .: (0.085153) + test_hsp_len: .: (0.085512) + test_inclusion: .: (0.088476) + test_iterations: .: (0.086615) + test_kappa: .: (0.085514) + test_lambda: .: (0.085258) + test_matrix: .: (0.081960) + test_message: .: (0.089998) + test_parameters: .: (0.083476) + test_pattern: .: (0.084015) + test_program: .: (0.084029) + test_query_def: .: (0.083421) + test_query_id: .: (0.087618) + test_query_len: .: (0.084698) + test_reference: .: (0.082914) + test_sc_match: .: (0.084223) + test_sc_mismatch: .: (0.082777) + test_statistics: .: (0.088481) + test_version: .: (0.083928) Bio::TestBlastReportDefault: - test_db: .: (0.001704) - test_db_len: .: (0.001140) - test_db_num: .: (0.001196) - test_each_hit: .: (0.001005) - test_each_iteration: .: (0.000855) - test_eff_space: .: (0.001659) - test_entropy: .: (0.001095) - test_expect: .: (0.001223) - test_gap_extend: .: (0.001287) - test_gap_open: .: (0.001238) - test_gapped_entropy: .: (0.001126) - test_gapped_kappa: .: (0.001106) - test_gapped_lambda: .: (0.001177) - test_hits: .: (0.001016) - test_iterations: .: (0.000889) - test_kappa: .: (0.001080) - test_lambda: .: (0.000971) - test_matrix: .: (0.001279) - test_message: .: (0.001132) - test_pattern: .: (0.001036) - test_program: .: (0.001172) - test_query_def: .: (0.001220) - test_query_len: .: (0.001037) - test_reference: .: (0.019287) - test_sc_match: .: (0.001133) - test_sc_mismatch: .: (0.001065) - test_version: .: (0.001115) + test_db: .: (0.003623) + test_db_len: .: (0.002641) + test_db_num: .: (0.002788) + test_each_hit: .: (0.002697) + test_each_iteration: .: (0.002345) + test_eff_space: .: (0.003707) + test_entropy: .: (0.002918) + test_expect: .: (0.003141) + test_gap_extend: .: (0.002984) + test_gap_open: .: (0.002887) + test_gapped_entropy: .: (0.002487) + test_gapped_kappa: .: (0.002499) + test_gapped_lambda: .: (0.002879) + test_hits: .: (0.002436) + test_iterations: .: (0.002321) + test_kappa: .: (0.002500) + test_lambda: .: (0.002486) + test_matrix: .: (0.003035) + test_message: .: (0.002458) + test_pattern: .: (0.002352) + test_program: .: (0.002497) + test_query_def: .: (0.002554) + test_query_len: .: (0.002477) + test_reference: .: (0.002655) + test_sc_match: .: (0.003002) + test_sc_mismatch: .: (0.003014) + test_version: .: (0.002434) Bio::TestBlastReportHit: - test_Hit_accession: .: (0.034099) - test_Hit_bit_score: .: (0.030549) - test_Hit_definition: .: (0.034635) - test_Hit_evalue: .: (0.036074) - test_Hit_hit_id: .: (0.035408) - test_Hit_hsps: .: (0.033825) - test_Hit_identity: .: (0.033093) - test_Hit_lap_at: .: (0.035281) - test_Hit_len: .: (0.030101) - test_Hit_midline: .: (0.032121) - test_Hit_num: .: (0.033002) - test_Hit_overlap: .: (0.035684) - test_Hit_query_def: .: (0.034748) - test_Hit_query_end: .: (0.033915) - test_Hit_query_id: .: (0.035507) - test_Hit_query_len: .: (0.037052) - test_Hit_query_seq: .: (0.035263) - test_Hit_query_start: .: (0.033201) - test_Hit_taeget_def: .: (0.032247) - test_Hit_target_end: .: (0.034841) - test_Hit_target_id: .: (0.033978) - test_Hit_target_len: .: (0.036182) - test_Hit_target_seq: .: (0.033856) - test_Hit_target_start: .: (0.033579) + test_Hit_accession: .: (0.082911) + test_Hit_bit_score: .: (0.083030) + test_Hit_definition: .: (0.090913) + test_Hit_evalue: .: (0.083238) + test_Hit_hit_id: .: (0.086412) + test_Hit_hsps: .: (0.085555) + test_Hit_identity: .: (0.083843) + test_Hit_lap_at: .: (0.088985) + test_Hit_len: .: (0.084681) + test_Hit_midline: .: (0.084085) + test_Hit_num: .: (0.083749) + test_Hit_overlap: .: (0.086902) + test_Hit_query_def: .: (0.086313) + test_Hit_query_end: .: (0.083994) + test_Hit_query_id: .: (0.084631) + test_Hit_query_len: .: (0.084619) + test_Hit_query_seq: .: (0.089626) + test_Hit_query_start: .: (0.086623) + test_Hit_taeget_def: .: (0.086537) + test_Hit_target_end: .: (0.082863) + test_Hit_target_id: .: (0.085096) + test_Hit_target_len: .: (0.090359) + test_Hit_target_seq: .: (0.085868) + test_Hit_target_start: .: (0.081575) Bio::TestBlastReportHitDefault: - test_Hit_bit_score: .: (0.001899) - test_Hit_definition: .: (0.001165) - test_Hit_evalue: .: (0.001087) - test_Hit_hsps: .: (0.001081) - test_Hit_identity: .: (0.001077) - test_Hit_lap_at: .: (0.001550) - test_Hit_len: .: (0.001289) - test_Hit_midline: .: (0.001427) - test_Hit_overlap: .: (0.001107) - test_Hit_query_end: .: (0.001420) - test_Hit_query_seq: .: (0.001467) - test_Hit_query_start: .: (0.001883) - test_Hit_taeget_def: .: (0.001033) - test_Hit_target_end: .: (0.001419) - test_Hit_target_id: .: (0.001218) - test_Hit_target_len: .: (0.000937) - test_Hit_target_seq: .: (0.001272) - test_Hit_target_start: .: (0.001710) + test_Hit_bit_score: .: (0.003912) + test_Hit_definition: .: (0.002823) + test_Hit_evalue: .: (0.002713) + test_Hit_hsps: .: (0.002580) + test_Hit_identity: .: (0.003128) + test_Hit_lap_at: .: (0.003734) + test_Hit_len: .: (0.002680) + test_Hit_midline: .: (0.003647) + test_Hit_overlap: .: (0.002698) + test_Hit_query_end: .: (0.003592) + test_Hit_query_seq: .: (0.004348) + test_Hit_query_start: .: (0.003567) + test_Hit_taeget_def: .: (0.002651) + test_Hit_target_end: .: (0.003576) + test_Hit_target_id: .: (0.002708) + test_Hit_target_len: .: (0.002747) + test_Hit_target_seq: .: (0.004353) + test_Hit_target_start: .: (0.003589) Bio::TestBlastReportHitMulti: - test_Hit_accession: .: (0.105039) - test_Hit_bit_score: .: (0.097024) - test_Hit_definition: .: (0.099472) - test_Hit_evalue: .: (0.105223) - test_Hit_hit_id: .: (0.095988) - test_Hit_hsps: .: (0.088372) - test_Hit_identity: .: (0.094896) - test_Hit_lap_at: .: (0.094458) - test_Hit_len: .: (0.088124) - test_Hit_midline: .: (0.154507) - test_Hit_num: .: (0.096155) - test_Hit_overlap: .: (0.085296) - test_Hit_query_def: .: (0.083376) - test_Hit_query_end: .: (0.087604) - test_Hit_query_id: .: (0.085747) - test_Hit_query_len: .: (0.085819) - test_Hit_query_seq: .: (0.088213) - test_Hit_query_start: .: (0.086801) - test_Hit_taeget_def: .: (0.084008) - test_Hit_target_end: .: (0.086016) - test_Hit_target_id: .: (0.086130) - test_Hit_target_len: .: (0.080886) - test_Hit_target_seq: .: (0.085888) - test_Hit_target_start: .: (0.086411) + test_Hit_accession: .: (0.268685) + test_Hit_bit_score: .: (0.256387) + test_Hit_definition: .: (0.251607) + test_Hit_evalue: .: (0.257746) + test_Hit_hit_id: .: (0.247718) + test_Hit_hsps: .: (0.259020) + test_Hit_identity: .: (0.260998) + test_Hit_lap_at: .: (0.264340) + test_Hit_len: .: (0.257830) + test_Hit_midline: .: (0.262147) + test_Hit_num: .: (0.254621) + test_Hit_overlap: .: (0.245692) + test_Hit_query_def: .: (0.255506) + test_Hit_query_end: .: (0.266359) + test_Hit_query_id: .: (0.244921) + test_Hit_query_len: .: (0.244182) + test_Hit_query_seq: .: (0.266885) + test_Hit_query_start: .: (0.267463) + test_Hit_taeget_def: .: (0.246439) + test_Hit_target_end: .: (0.259663) + test_Hit_target_id: .: (0.260561) + test_Hit_target_len: .: (0.241890) + test_Hit_target_seq: .: (0.248266) + test_Hit_target_start: .: (0.250823) Bio::TestBlastReportHitMultiREXML: - test_Hit_accession: .: (0.133242) - test_Hit_bit_score: .: (0.127565) - test_Hit_definition: .: (0.105682) - test_Hit_evalue: .: (0.137447) - test_Hit_hit_id: .: (0.097108) - test_Hit_hsps: .: (0.098205) - test_Hit_identity: .: (0.094006) - test_Hit_lap_at: .: (0.112284) - test_Hit_len: .: (0.099687) - test_Hit_midline: .: (0.140362) - test_Hit_num: .: (0.103811) - test_Hit_overlap: .: (0.100330) - test_Hit_query_def: .: (0.100870) - test_Hit_query_end: .: (0.100513) - test_Hit_query_id: .: (0.096318) - test_Hit_query_len: .: (0.092107) - test_Hit_query_seq: .: (0.089285) - test_Hit_query_start: .: (0.090540) - test_Hit_taeget_def: .: (0.093337) - test_Hit_target_end: .: (0.106235) - test_Hit_target_id: .: (0.090866) - test_Hit_target_len: .: (0.097154) - test_Hit_target_seq: .: (0.099551) - test_Hit_target_start: .: (0.098647) + test_Hit_accession: .: (0.246892) + test_Hit_bit_score: .: (0.256814) + test_Hit_definition: .: (0.248448) + test_Hit_evalue: .: (0.247232) + test_Hit_hit_id: .: (0.248340) + test_Hit_hsps: .: (0.255824) + test_Hit_identity: .: (0.257158) + test_Hit_lap_at: .: (0.248416) + test_Hit_len: .: (0.254169) + test_Hit_midline: .: (0.258190) + test_Hit_num: .: (0.253171) + test_Hit_overlap: .: (0.250421) + test_Hit_query_def: .: (0.255054) + test_Hit_query_end: .: (0.254379) + test_Hit_query_id: .: (0.248659) + test_Hit_query_len: .: (0.252770) + test_Hit_query_seq: .: (0.257101) + test_Hit_query_start: .: (0.247097) + test_Hit_taeget_def: .: (0.254296) + test_Hit_target_end: .: (0.258533) + test_Hit_target_id: .: (0.252386) + test_Hit_target_len: .: (0.254805) + test_Hit_target_seq: .: (0.254307) + test_Hit_target_start: .: (0.258710) Bio::TestBlastReportHitREXML: - test_Hit_accession: .: (0.031530) - test_Hit_bit_score: .: (0.031860) - test_Hit_definition: .: (0.032859) - test_Hit_evalue: .: (0.034163) - test_Hit_hit_id: .: (0.032763) - test_Hit_hsps: .: (0.032941) - test_Hit_identity: .: (0.033336) - test_Hit_lap_at: .: (0.032671) - test_Hit_len: .: (0.035176) - test_Hit_midline: .: (0.032278) - test_Hit_num: .: (0.032082) - test_Hit_overlap: .: (0.031860) - test_Hit_query_def: .: (0.035003) - test_Hit_query_end: .: (0.031699) - test_Hit_query_id: .: (0.033040) - test_Hit_query_len: .: (0.032936) - test_Hit_query_seq: .: (0.034386) - test_Hit_query_start: .: (0.035482) - test_Hit_taeget_def: .: (0.035431) - test_Hit_target_end: .: (0.035820) - test_Hit_target_id: .: (0.028796) - test_Hit_target_len: .: (0.034762) - test_Hit_target_seq: .: (0.033418) - test_Hit_target_start: .: (0.034151) + test_Hit_accession: .: (0.085921) + test_Hit_bit_score: .: (0.086180) + test_Hit_definition: .: (0.085965) + test_Hit_evalue: .: (0.089778) + test_Hit_hit_id: .: (0.086267) + test_Hit_hsps: .: (0.085502) + test_Hit_identity: .: (0.087059) + test_Hit_lap_at: .: (0.084123) + test_Hit_len: .: (0.088632) + test_Hit_midline: .: (0.084794) + test_Hit_num: .: (0.084174) + test_Hit_overlap: .: (0.084137) + test_Hit_query_def: .: (0.090176) + test_Hit_query_end: .: (0.088709) + test_Hit_query_id: .: (0.088969) + test_Hit_query_len: .: (0.088097) + test_Hit_query_seq: .: (0.086336) + test_Hit_query_start: .: (0.085727) + test_Hit_taeget_def: .: (0.083744) + test_Hit_target_end: .: (0.084383) + test_Hit_target_id: .: (0.082354) + test_Hit_target_len: .: (0.088464) + test_Hit_target_seq: .: (0.084830) + test_Hit_target_start: .: (0.084118) Bio::TestBlastReportHitTabular: - test_Hit_accession: .: (0.001168) - test_Hit_bit_score: .: (0.000597) - test_Hit_definition: .: (0.000554) - test_Hit_evalue: .: (0.000544) - test_Hit_hit_id: .: (0.000609) - test_Hit_hsps: .: (0.000564) - test_Hit_identity: .: (0.000543) - test_Hit_lap_at: .: (0.000584) - test_Hit_len: .: (0.000549) - test_Hit_midline: .: (0.000592) - test_Hit_num: .: (0.000520) - test_Hit_overlap: .: (0.000908) - test_Hit_query_def: .: (0.000571) - test_Hit_query_end: .: (0.000578) - test_Hit_query_id: .: (0.000533) - test_Hit_query_len: .: (0.000522) - test_Hit_query_seq: .: (0.000546) - test_Hit_query_start: .: (0.000601) - test_Hit_taeget_def: .: (0.000572) - test_Hit_target_end: .: (0.000553) - test_Hit_target_id: .: (0.000530) - test_Hit_target_len: .: (0.000602) - test_Hit_target_seq: .: (0.000565) - test_Hit_target_start: .: (0.000539) + test_Hit_accession: .: (0.002125) + test_Hit_bit_score: .: (0.000874) + test_Hit_definition: .: (0.000715) + test_Hit_evalue: .: (0.000707) + test_Hit_hit_id: .: (0.000873) + test_Hit_hsps: .: (0.000751) + test_Hit_identity: .: (0.000683) + test_Hit_lap_at: .: (0.000732) + test_Hit_len: .: (0.000788) + test_Hit_midline: .: (0.000893) + test_Hit_num: .: (0.001336) + test_Hit_overlap: .: (0.000946) + test_Hit_query_def: .: (0.000787) + test_Hit_query_end: .: (0.000693) + test_Hit_query_id: .: (0.000702) + test_Hit_query_len: .: (0.000689) + test_Hit_query_seq: .: (0.000838) + test_Hit_query_start: .: (0.000894) + test_Hit_taeget_def: .: (0.000719) + test_Hit_target_end: .: (0.000703) + test_Hit_target_id: .: (0.000727) + test_Hit_target_len: .: (0.000689) + test_Hit_target_seq: .: (0.000675) + test_Hit_target_start: .: (0.000686) Bio::TestBlastReportHsp: - test_Hsp_align_len: .: (0.033573) - test_Hsp_bit_score: .: (0.035312) - test_Hsp_density: .: (0.034244) - test_Hsp_evalue: .: (0.033062) - test_Hsp_gaps: .: (0.033208) - test_Hsp_hit_frame: .: (0.034084) - test_Hsp_hit_from: .: (0.034078) - test_Hsp_hit_to: .: (0.034046) - test_Hsp_hseq: .: (0.033269) - test_Hsp_identity: .: (0.036131) - test_Hsp_midline: .: (0.038849) - test_Hsp_mismatch_count: .: (0.034639) - test_Hsp_num: .: (0.032981) - test_Hsp_pattern_from: .: (0.032246) - test_Hsp_pattern_to: .: (0.034828) - test_Hsp_percent_identity: .: (0.032785) - test_Hsp_positive: .: (0.028320) - test_Hsp_qseq: .: (0.030355) - test_Hsp_query_frame: .: (0.028554) - test_Hsp_query_from: .: (0.030295) - test_Hsp_query_to: .: (0.029353) - test_Hsp_score: .: (0.032082) + test_Hsp_align_len: .: (0.083746) + test_Hsp_bit_score: .: (0.089459) + test_Hsp_density: .: (0.085111) + test_Hsp_evalue: .: (0.084168) + test_Hsp_gaps: .: (0.085370) + test_Hsp_hit_frame: .: (0.087509) + test_Hsp_hit_from: .: (0.086510) + test_Hsp_hit_to: .: (0.082984) + test_Hsp_hseq: .: (0.083922) + test_Hsp_identity: .: (0.083588) + test_Hsp_midline: .: (0.088418) + test_Hsp_mismatch_count: .: (0.083142) + test_Hsp_num: .: (0.083702) + test_Hsp_pattern_from: .: (0.083930) + test_Hsp_pattern_to: .: (0.088475) + test_Hsp_percent_identity: .: (0.083751) + test_Hsp_positive: .: (0.084036) + test_Hsp_qseq: .: (0.084059) + test_Hsp_query_frame: .: (0.084104) + test_Hsp_query_from: .: (0.088144) + test_Hsp_query_to: .: (0.085157) + test_Hsp_score: .: (0.084286) Bio::TestBlastReportHspDefault: - test_Hsp_align_len: .: (0.001710) - test_Hsp_bit_score: .: (0.001264) - test_Hsp_evalue: .: (0.001422) - test_Hsp_gaps: .: (0.001312) - test_Hsp_hit_frame: .: (0.001200) - test_Hsp_hit_from: .: (0.001291) - test_Hsp_hit_to: .: (0.001466) - test_Hsp_hseq: .: (0.001443) - test_Hsp_identity: .: (0.001236) - test_Hsp_midline: .: (0.001722) - test_Hsp_percent_identity: .: (0.001164) - test_Hsp_positive: .: (0.000993) - test_Hsp_qseq: .: (0.001279) - test_Hsp_query_frame: .: (0.001039) - test_Hsp_query_from: .: (0.001212) - test_Hsp_query_to: .: (0.001265) - test_Hsp_score: .: (0.001191) + test_Hsp_align_len: .: (0.003655) + test_Hsp_bit_score: .: (0.002727) + test_Hsp_evalue: .: (0.003263) + test_Hsp_gaps: .: (0.002876) + test_Hsp_hit_frame: .: (0.002671) + test_Hsp_hit_from: .: (0.003497) + test_Hsp_hit_to: .: (0.003500) + test_Hsp_hseq: .: (0.003552) + test_Hsp_identity: .: (0.002583) + test_Hsp_midline: .: (0.004378) + test_Hsp_percent_identity: .: (0.002752) + test_Hsp_positive: .: (0.002741) + test_Hsp_qseq: .: (0.003579) + test_Hsp_query_frame: .: (0.002690) + test_Hsp_query_from: .: (0.003503) + test_Hsp_query_to: .: (0.003407) + test_Hsp_score: .: (0.003622) Bio::TestBlastReportHspMulti: - test_Hsp_align_len: .: (0.097891) - test_Hsp_bit_score: .: (0.094354) - test_Hsp_density: .: (0.086640) - test_Hsp_evalue: .: (0.090805) - test_Hsp_gaps: .: (0.093568) - test_Hsp_hit_frame: .: (0.087059) - test_Hsp_hit_from: .: (0.082106) - test_Hsp_hit_to: .: (0.082030) - test_Hsp_hseq: .: (0.082509) - test_Hsp_identity: .: (0.081532) - test_Hsp_midline: .: (0.079706) - test_Hsp_mismatch_count: .: (0.083444) - test_Hsp_num: .: (0.085757) - test_Hsp_pattern_from: .: (0.085164) - test_Hsp_pattern_to: .: (0.118902) - test_Hsp_percent_identity: .: (0.117153) - test_Hsp_positive: .: (0.092654) - test_Hsp_qseq: .: (0.090234) - test_Hsp_query_frame: .: (0.091661) - test_Hsp_query_from: .: (0.096447) - test_Hsp_query_to: .: (0.087308) - test_Hsp_score: .: (0.082750) + test_Hsp_align_len: .: (0.256202) + test_Hsp_bit_score: .: (0.258454) + test_Hsp_density: .: (0.250290) + test_Hsp_evalue: .: (0.259401) + test_Hsp_gaps: .: (0.256685) + test_Hsp_hit_frame: .: (0.258295) + test_Hsp_hit_from: .: (0.252566) + test_Hsp_hit_to: .: (0.257233) + test_Hsp_hseq: .: (0.260066) + test_Hsp_identity: .: (0.252417) + test_Hsp_midline: .: (0.258441) + test_Hsp_mismatch_count: .: (0.259156) + test_Hsp_num: .: (0.255770) + test_Hsp_pattern_from: .: (0.249645) + test_Hsp_pattern_to: .: (0.256817) + test_Hsp_percent_identity: .: (0.256951) + test_Hsp_positive: .: (0.254742) + test_Hsp_qseq: .: (0.252255) + test_Hsp_query_frame: .: (0.252559) + test_Hsp_query_from: .: (0.260570) + test_Hsp_query_to: .: (0.259200) + test_Hsp_score: .: (0.251451) Bio::TestBlastReportHspMultiREXML: - test_Hsp_align_len: .: (0.087834) - test_Hsp_bit_score: .: (0.088180) - test_Hsp_density: .: (0.083570) - test_Hsp_evalue: .: (0.084617) - test_Hsp_gaps: .: (0.085062) - test_Hsp_hit_frame: .: (0.088689) - test_Hsp_hit_from: .: (0.091360) - test_Hsp_hit_to: .: (0.112734) - test_Hsp_hseq: .: (0.093489) - test_Hsp_identity: .: (0.094070) - test_Hsp_midline: .: (0.089654) - test_Hsp_mismatch_count: .: (0.092311) - test_Hsp_num: .: (0.092945) - test_Hsp_pattern_from: .: (0.094248) - test_Hsp_pattern_to: .: (0.091163) - test_Hsp_percent_identity: .: (0.093947) - test_Hsp_positive: .: (0.094015) - test_Hsp_qseq: .: (0.093958) - test_Hsp_query_frame: .: (0.089895) - test_Hsp_query_from: .: (0.093956) - test_Hsp_query_to: .: (0.173678) - test_Hsp_score: .: (0.092998) + test_Hsp_align_len: .: (0.258553) + test_Hsp_bit_score: .: (0.258381) + test_Hsp_density: .: (0.262577) + test_Hsp_evalue: .: (0.254753) + test_Hsp_gaps: .: (0.255167) + test_Hsp_hit_frame: .: (0.257599) + test_Hsp_hit_from: .: (0.252549) + test_Hsp_hit_to: .: (0.253022) + test_Hsp_hseq: .: (0.257725) + test_Hsp_identity: .: (0.258766) + test_Hsp_midline: .: (0.250158) + test_Hsp_mismatch_count: .: (0.257054) + test_Hsp_num: .: (0.258917) + test_Hsp_pattern_from: .: (0.259378) + test_Hsp_pattern_to: .: (0.251348) + test_Hsp_percent_identity: .: (0.256486) + test_Hsp_positive: .: (0.260366) + test_Hsp_qseq: .: (0.258856) + test_Hsp_query_frame: .: (0.249771) + test_Hsp_query_from: .: (0.259671) + test_Hsp_query_to: .: (0.448298) + test_Hsp_score: .: (0.265674) Bio::TestBlastReportHspREXML: - test_Hsp_align_len: .: (0.034617) - test_Hsp_bit_score: .: (0.032130) - test_Hsp_density: .: (0.032703) - test_Hsp_evalue: .: (0.030902) - test_Hsp_gaps: .: (0.031275) - test_Hsp_hit_frame: .: (0.033530) - test_Hsp_hit_from: .: (0.030679) - test_Hsp_hit_to: .: (0.030344) - test_Hsp_hseq: .: (0.031397) - test_Hsp_identity: .: (0.031090) - test_Hsp_midline: .: (0.033073) - test_Hsp_mismatch_count: .: (0.032054) - test_Hsp_num: .: (0.031041) - test_Hsp_pattern_from: .: (0.031336) - test_Hsp_pattern_to: .: (0.031311) - test_Hsp_percent_identity: .: (0.033717) - test_Hsp_positive: .: (0.031757) - test_Hsp_qseq: .: (0.031154) - test_Hsp_query_frame: .: (0.031623) - test_Hsp_query_from: .: (0.030087) - test_Hsp_query_to: .: (0.032749) - test_Hsp_score: .: (0.032377) + test_Hsp_align_len: .: (0.094226) + test_Hsp_bit_score: .: (0.089234) + test_Hsp_density: .: (0.088455) + test_Hsp_evalue: .: (0.083517) + test_Hsp_gaps: .: (0.083668) + test_Hsp_hit_frame: .: (0.088268) + test_Hsp_hit_from: .: (0.084863) + test_Hsp_hit_to: .: (0.082895) + test_Hsp_hseq: .: (0.083968) + test_Hsp_identity: .: (0.082448) + test_Hsp_midline: .: (0.087749) + test_Hsp_mismatch_count: .: (0.084062) + test_Hsp_num: .: (0.083718) + test_Hsp_pattern_from: .: (0.083667) + test_Hsp_pattern_to: .: (0.086311) + test_Hsp_percent_identity: .: (0.086441) + test_Hsp_positive: .: (0.084727) + test_Hsp_qseq: .: (0.082598) + test_Hsp_query_frame: .: (0.083773) + test_Hsp_query_from: .: (0.087614) + test_Hsp_query_to: .: (0.085730) + test_Hsp_score: .: (0.085396) Bio::TestBlastReportHspTabular: - test_Hsp_align_len: .: (0.001064) - test_Hsp_bit_score: .: (0.000656) - test_Hsp_density: .: (0.000539) - test_Hsp_evalue: .: (0.000501) - test_Hsp_gaps: .: (0.000515) - test_Hsp_hit_frame: .: (0.000556) - test_Hsp_hit_from: .: (0.000546) - test_Hsp_hit_to: .: (0.000536) - test_Hsp_hseq: .: (0.000598) - test_Hsp_identity: .: (0.000560) - test_Hsp_midline: .: (0.000456) - test_Hsp_mismatch_count: .: (0.000448) - test_Hsp_num: .: (0.000564) - test_Hsp_pattern_from: .: (0.000525) - test_Hsp_pattern_to: .: (0.000439) - test_Hsp_percent_identity: .: (0.000420) - test_Hsp_positive: .: (0.000489) - test_Hsp_qseq: .: (0.000433) - test_Hsp_query_frame: .: (0.000499) - test_Hsp_query_from: .: (0.000518) - test_Hsp_query_to: .: (0.000464) - test_Hsp_score: .: (0.000457) + test_Hsp_align_len: .: (0.002029) + test_Hsp_bit_score: .: (0.000907) + test_Hsp_density: .: (0.000917) + test_Hsp_evalue: .: (0.000943) + test_Hsp_gaps: .: (0.000883) + test_Hsp_hit_frame: .: (0.000792) + test_Hsp_hit_from: .: (0.000977) + test_Hsp_hit_to: .: (0.000896) + test_Hsp_hseq: .: (0.000865) + test_Hsp_identity: .: (0.001677) + test_Hsp_midline: .: (0.001221) + test_Hsp_mismatch_count: .: (0.000897) + test_Hsp_num: .: (0.000896) + test_Hsp_pattern_from: .: (0.000858) + test_Hsp_pattern_to: .: (0.000853) + test_Hsp_percent_identity: .: (0.000838) + test_Hsp_positive: .: (0.000929) + test_Hsp_qseq: .: (0.000855) + test_Hsp_query_frame: .: (0.000845) + test_Hsp_query_from: .: (0.000866) + test_Hsp_query_to: .: (0.000907) + test_Hsp_score: .: (0.000884) Bio::TestBlastReportIteration: - test_hits: .: (0.031306) - test_message: .: (0.031976) - test_num: .: (0.031832) - test_statistics: .: (0.031426) + test_hits: .: (0.085923) + test_message: .: (0.084916) + test_num: .: (0.088530) + test_statistics: .: (0.085575) Bio::TestBlastReportIterationDefault: - test_hits: .: (0.001820) - test_message: .: (0.001118) - test_num: .: (0.000948) + test_hits: .: (0.003639) + test_message: .: (0.002483) + test_num: .: (0.002545) Bio::TestBlastReportIterationMulti: - test_each: .: (0.091015) - test_hits: .: (0.093360) - test_message: .: (0.094906) - test_num: .: (0.090355) - test_query_def: .: (0.093274) - test_query_id: .: (0.093539) - test_query_len: .: (0.086061) - test_statistics: .: (0.083783) + test_each: .: (0.253665) + test_hits: .: (0.251301) + test_message: .: (0.259859) + test_num: .: (0.250060) + test_query_def: .: (0.254379) + test_query_id: .: (0.259228) + test_query_len: .: (0.247641) + test_statistics: .: (0.252758) Bio::TestBlastReportIterationMultiREXML: - test_each: .: (0.090853) - test_hits: .: (0.082976) - test_message: .: (0.083366) - test_num: .: (0.083609) - test_query_def: .: (0.080896) - test_query_id: .: (0.086514) - test_query_len: .: (0.085187) - test_statistics: .: (0.081369) + test_each: .: (0.260714) + test_hits: .: (0.248523) + test_message: .: (0.266702) + test_num: .: (0.260003) + test_query_def: .: (0.247991) + test_query_id: .: (0.252745) + test_query_len: .: (0.256587) + test_statistics: .: (0.247155) Bio::TestBlastReportIterationREXML: - test_hits: .: (0.028060) - test_message: .: (0.029463) - test_num: .: (0.028655) - test_statistics: .: (0.027300) + test_hits: .: (0.090955) + test_message: .: (0.086739) + test_num: .: (0.085685) + test_statistics: .: (0.083788) Bio::TestBlastReportIterationTabular: - test_hits: .: (0.001026) - test_message: .: (0.000518) - test_num: .: (0.000537) - test_statistics: .: (0.000505) + test_hits: .: (0.001929) + test_message: .: (0.000880) + test_num: .: (0.000807) + test_statistics: .: (0.000852) Bio::TestBlastReportMulti: - test_db: .: (0.081684) - test_db_len: .: (0.080214) - test_db_num: .: (0.082107) - test_each_hit: .: (0.084144) - test_each_iteration: .: (0.079613) - test_eff_space: .: (0.081316) - test_entropy: .: (0.082140) - test_expect: .: (0.082846) - test_filter: .: (0.081609) - test_gap_extend: .: (0.082550) - test_gap_open: .: (0.078222) - test_hits: .: (0.081177) - test_hsp_len: .: (0.083848) - test_iterations: .: (0.079023) - test_kappa: .: (0.084830) - test_lambda: .: (0.082756) - test_matrix: .: (0.077807) - test_message: .: (0.080948) - test_parameters: .: (0.082727) - test_pattern: .: (0.079962) - test_program: .: (0.080607) - test_query_def: .: (0.085869) - test_query_id: .: (0.090266) - test_query_len: .: (0.092258) - test_reference: .: (0.096040) - test_reports: .: (0.092030) - test_statistics: .: (0.085302) - test_version: .: (0.089189) + test_db: .: (0.252812) + test_db_len: .: (0.250153) + test_db_num: .: (0.255916) + test_each_hit: .: (0.253992) + test_each_iteration: .: (0.251315) + test_eff_space: .: (0.248061) + test_entropy: .: (0.254868) + test_expect: .: (0.255203) + test_filter: .: (0.247497) + test_gap_extend: .: (0.251527) + test_gap_open: .: (0.250499) + test_hits: .: (0.245765) + test_hsp_len: .: (0.250156) + test_iterations: .: (0.255610) + test_kappa: .: (0.243150) + test_lambda: .: (0.253868) + test_matrix: .: (0.255968) + test_message: .: (0.245736) + test_parameters: .: (0.255001) + test_pattern: .: (0.257008) + test_program: .: (0.255175) + test_query_def: .: (0.247993) + test_query_id: .: (0.253588) + test_query_len: .: (0.252673) + test_reference: .: (0.244630) + test_reports: .: (0.252435) + test_statistics: .: (0.257753) + test_version: .: (0.248541) Bio::TestBlastReportMultiREXML: - test_db: .: (0.092046) - test_db_len: .: (0.086566) - test_db_num: .: (0.086643) - test_each_hit: .: (0.089335) - test_each_iteration: .: (0.090139) - test_eff_space: .: (0.085314) - test_entropy: .: (0.090793) - test_expect: .: (0.089998) - test_filter: .: (0.089281) - test_gap_extend: .: (0.082651) - test_gap_open: .: (0.085181) - test_hits: .: (0.085353) - test_hsp_len: .: (0.082030) - test_iterations: .: (0.084074) - test_kappa: .: (0.084244) - test_lambda: .: (0.083438) - test_matrix: .: (0.082529) - test_message: .: (0.085589) - test_parameters: .: (0.084216) - test_pattern: .: (0.080962) - test_program: .: (0.084715) - test_query_def: .: (0.085982) - test_query_id: .: (0.083644) - test_query_len: .: (0.084618) - test_reference: .: (0.085664) - test_reports: .: (0.086513) - test_statistics: .: (0.084080) - test_version: .: (0.082788) + test_db: .: (0.252673) + test_db_len: .: (0.248380) + test_db_num: .: (0.251165) + test_each_hit: .: (0.250330) + test_each_iteration: .: (0.256420) + test_eff_space: .: (0.257445) + test_entropy: .: (0.252896) + test_expect: .: (0.252248) + test_filter: .: (0.256984) + test_gap_extend: .: (0.257663) + test_gap_open: .: (0.249672) + test_hits: .: (0.255906) + test_hsp_len: .: (0.249225) + test_iterations: .: (0.246201) + test_kappa: .: (0.248173) + test_lambda: .: (0.256225) + test_matrix: .: (0.255241) + test_message: .: (0.252214) + test_parameters: .: (0.253672) + test_pattern: .: (0.255013) + test_program: .: (0.255506) + test_query_def: .: (0.247764) + test_query_id: .: (0.254865) + test_query_len: .: (0.253615) + test_reference: .: (0.255127) + test_reports: .: (0.248119) + test_statistics: .: (0.255170) + test_version: .: (0.255078) Bio::TestBlastReportREXML: - test_db: .: (0.030814) - test_db_len: .: (0.028414) - test_db_num: .: (0.026713) - test_each_hit: .: (0.027155) - test_each_iteration: .: (0.029516) - test_eff_space: .: (0.029470) - test_entrez_query: .: (0.028907) - test_entropy: .: (0.030313) - test_expect: .: (0.028602) - test_filter: .: (0.028255) - test_gap_extend: .: (0.028325) - test_gap_open: .: (0.028888) - test_hits: .: (0.027856) - test_hsp_len: .: (0.030024) - test_inclusion: .: (0.028529) - test_iterations: .: (0.028720) - test_kappa: .: (0.028601) - test_lambda: .: (0.029346) - test_matrix: .: (0.028575) - test_message: .: (0.029226) - test_parameters: .: (0.029090) - test_pattern: .: (0.030866) - test_program: .: (0.028526) - test_query_def: .: (0.028996) - test_query_id: .: (0.030947) - test_query_len: .: (0.030247) - test_reference: .: (0.028256) - test_sc_match: .: (0.028408) - test_sc_mismatch: .: (0.028287) - test_statistics: .: (0.030781) - test_version: .: (0.027880) + test_db: .: (0.083767) + test_db_len: .: (0.085698) + test_db_num: .: (0.088578) + test_each_hit: .: (0.083503) + test_each_iteration: .: (0.084366) + test_eff_space: .: (0.084738) + test_entrez_query: .: (0.088950) + test_entropy: .: (0.084108) + test_expect: .: (0.084211) + test_filter: .: (0.084818) + test_gap_extend: .: (0.087739) + test_gap_open: .: (0.084273) + test_hits: .: (0.083106) + test_hsp_len: .: (0.082612) + test_inclusion: .: (0.087411) + test_iterations: .: (0.084530) + test_kappa: .: (0.084354) + test_lambda: .: (0.084851) + test_matrix: .: (0.087877) + test_message: .: (0.086341) + test_parameters: .: (0.080922) + test_pattern: .: (0.079721) + test_program: .: (0.079909) + test_query_def: .: (0.083959) + test_query_id: .: (0.080172) + test_query_len: .: (0.079633) + test_reference: .: (0.080123) + test_sc_match: .: (0.084356) + test_sc_mismatch: .: (0.082080) + test_statistics: .: (0.079384) + test_version: .: (0.080746) Bio::TestBlastReportTabular: - test_db: .: (0.000947) - test_db_len: .: (0.000504) - test_db_num: .: (0.000435) - test_each_hit: .: (0.000437) - test_each_iteration: .: (0.000527) - test_eff_space: .: (0.000434) - test_entrez_query: .: (0.000423) - test_entropy: .: (0.000415) - test_expect: .: (0.000417) - test_filter: .: (0.000515) - test_gap_extend: .: (0.000426) - test_gap_open: .: (0.000423) - test_hits: .: (0.000860) - test_hsp_len: .: (0.000742) - test_inclusion: .: (0.000441) - test_iterations: .: (0.000419) - test_kappa: .: (0.000418) - test_lambda: .: (0.000417) - test_matrix: .: (0.000515) - test_message: .: (0.000412) - test_parameters: .: (0.000383) - test_pattern: .: (0.000376) - test_program: .: (0.000371) - test_query_def: .: (0.000537) - test_query_id: .: (0.000417) - test_query_len: .: (0.000522) - test_reference: .: (0.000381) - test_sc_match: .: (0.000373) - test_sc_mismatch: .: (0.000552) - test_statistics: .: (0.000414) - test_version: .: (0.000380) + test_db: .: (0.001623) + test_db_len: .: (0.000751) + test_db_num: .: (0.000753) + test_each_hit: .: (0.000703) + test_each_iteration: .: (0.000673) + test_eff_space: .: (0.000674) + test_entrez_query: .: (0.000857) + test_entropy: .: (0.000778) + test_expect: .: (0.000692) + test_filter: .: (0.000670) + test_gap_extend: .: (0.000843) + test_gap_open: .: (0.000728) + test_hits: .: (0.000715) + test_hsp_len: .: (0.000671) + test_inclusion: .: (0.000781) + test_iterations: .: (0.001061) + test_kappa: .: (0.000703) + test_lambda: .: (0.000788) + test_matrix: .: (0.000703) + test_message: .: (0.000703) + test_parameters: .: (0.000688) + test_pattern: .: (0.000848) + test_program: .: (0.000836) + test_query_def: .: (0.000751) + test_query_id: .: (0.000700) + test_query_len: .: (0.000730) + test_reference: .: (0.000824) + test_sc_match: .: (0.000755) + test_sc_mismatch: .: (0.001418) + test_statistics: .: (0.001090) + test_version: .: (0.000692) Bio::TestChain: - test_aaseq: .: (0.000765) - test_addLigand: .: (0.000324) - test_addResidue: .: (0.000366) - test_atom_seq: .: (0.000365) - test_comp: .: (0.000386) - test_each: .: (0.000412) - test_each_heterogen: .: (0.000396) - test_each_residue: .: (0.000392) - test_get_heterogen_by_id: .: (0.000356) - test_get_residue_by_id: .: (0.000326) - test_inspect: .: (0.000377) - test_rehash: .: (0.000314) - test_rehash_heterogens: .: (0.000292) - test_rehash_residues: .: (0.000368) - test_square_brace: .: (0.000356) - test_to_s: .: (0.000549) + test_aaseq: .: (0.001632) + test_addLigand: .: (0.000581) + test_addResidue: .: (0.000547) + test_atom_seq: .: (0.000598) + test_comp: .: (0.000686) + test_each: .: (0.000633) + test_each_heterogen: .: (0.000581) + test_each_residue: .: (0.000599) + test_get_heterogen_by_id: .: (0.000725) + test_get_residue_by_id: .: (0.000589) + test_inspect: .: (0.000708) + test_rehash: .: (0.000573) + test_rehash_heterogens: .: (0.000516) + test_rehash_residues: .: (0.000539) + test_square_brace: .: (0.000585) + test_to_s: .: (0.000626) Bio::TestChainFinder: - test_chains: .: (0.000671) - test_each_chain: .: (0.000439) - test_find_chain: .: (0.000398) + test_chains: .: (0.001279) + test_each_chain: .: (0.000740) + test_find_chain: .: (0.000586) Bio::TestClustalWReport::TestClustalWReport: - test_alignment: .: (0.019855) - test_header: .: (0.001807) - test_match_line: .: (0.001504) - test_sequence0: .: (0.001480) - test_sequence1: .: (0.001200) + test_alignment: .: (0.056895) + test_header: .: (0.004796) + test_match_line: .: (0.003327) + test_sequence0: .: (0.003278) + test_sequence1: .: (0.004070) Bio::TestClustalWReport::TestClustalWReportSeqnos: - test_alignment: .: (0.018961) - test_header: .: (0.002383) - test_match_line: .: (0.001895) - test_sequence0: .: (0.001997) - test_sequence1: .: (0.002171) + test_alignment: .: (0.057298) + test_header: .: (0.005917) + test_match_line: .: (0.004839) + test_sequence0: .: (0.004582) + test_sequence1: .: (0.005413) Bio::TestClustalWReport::TestClustalWReportWith2ndArgument: - test_alignment: .: (0.029357) - test_header: .: (0.001835) - test_match_line: .: (0.001462) - test_sequence0: .: (0.001266) - test_sequence1: .: (0.001672) + test_alignment: .: (0.066650) + test_header: .: (0.005052) + test_match_line: .: (0.003273) + test_sequence0: .: (0.003242) + test_sequence1: .: (0.003310) Bio::TestCodonTable: - test_Tables: .: (0.000556) - test_accessor: .: (0.000364) - test_definition: .: (0.000273) - test_each: .: (0.000361) - test_revtrans: .: (0.000443) - test_self_accessor: .: (0.000292) - test_self_copy: .: (0.001483) - test_set_accessor: .: (0.180680) - test_start: .: (0.000401) - test_start_codon?: .: (0.000361) - test_stop: .: (0.000324) - test_stop_codon?: .: (0.000339) - test_table: .: (0.000346) + test_Tables: .: (0.001223) + test_accessor: .: (0.000692) + test_definition: .: (0.000443) + test_each: .: (0.000533) + test_revtrans: .: (0.000940) + test_self_accessor: .: (0.000480) + test_self_copy: .: (0.004061) + test_set_accessor: .: (0.547823) + test_start: .: (0.000517) + test_start_codon?: .: (0.000546) + test_stop: .: (0.000447) + test_stop_codon?: .: (0.000526) + test_table: .: (0.000431) Bio::TestCodonTableConstants: - test_Definitions: .: (0.000636) - test_Starts: .: (0.000401) - test_Tables: .: (0.000310) - test_stops: .: (0.000325) + test_Definitions: .: (0.001050) + test_Starts: .: (0.000526) + test_Tables: .: (0.000424) + test_stops: .: (0.000496) Bio::TestColorScheme: - test_buried: .: (0.002674) + test_buried: .: (0.005213) Bio::TestCommand: - test_command_constants: .: (0.000558) - test_escape_shell: .: (0.000518) - test_escape_shell_unix: .: (0.000388) - test_escape_shell_windows: .: (0.000370) - test_make_cgi_params_by_array_of_array: .: (0.000720) - test_make_cgi_params_by_array_of_hash: .: (0.000707) - test_make_cgi_params_by_array_of_string: .: (0.000522) - test_make_cgi_params_by_hash_in_string: .: (0.001142) - test_make_cgi_params_by_hash_in_symbol: .: (0.000952) - test_make_cgi_params_by_string: .: (0.000514) - test_make_command_line: .: (0.000385) - test_make_command_line_unix: .: (0.000348) - test_make_command_line_windows: .: (0.000367) - test_safe_command_line_array: .: (0.000386) - test_safe_command_line_array_passthrough: .: (0.000490) + test_command_constants: .: (0.001175) + test_escape_shell: .: (0.000705) + test_escape_shell_unix: .: (0.000588) + test_escape_shell_windows: .: (0.000594) + test_make_cgi_params_by_array_of_array: .: (0.001644) + test_make_cgi_params_by_array_of_hash: .: (0.002110) + test_make_cgi_params_by_array_of_string: .: (0.000885) + test_make_cgi_params_by_hash_in_string: .: (0.002362) + test_make_cgi_params_by_hash_in_symbol: .: (0.002366) + test_make_cgi_params_by_string: .: (0.000691) + test_make_command_line: .: (0.000600) + test_make_command_line_unix: .: (0.000587) + test_make_command_line_windows: .: (0.000568) + test_safe_command_line_array: .: (0.000608) + test_safe_command_line_array_passthrough: .: (0.000645) Bio::TestContingencyTable: - test_lite_example: .: (0.351284) + test_lite_example: .: (1.122563) Bio::TestDB: - test_entry_id: .: (0.000729) - test_exists: .: (0.000336) - test_fetch: .: (0.000579) - test_get: .: (0.000452) - test_open: .: (0.000324) - test_tags: .: (0.000311) + test_entry_id: .: (0.001286) + test_exists: .: (0.000461) + test_fetch: .: (0.000714) + test_get: .: (0.000441) + test_open: .: (0.000432) + test_tags: .: (0.000433) Bio::TestDataType: - test_const_like_method: .: (0.001132) - test_pdb_achar: .: (0.000733) - test_pdb_atom: .: (0.000528) - test_pdb_character: .: (0.000515) - test_pdb_date: .: (0.002237) - test_pdb_idcode: .: (0.000776) - test_pdb_integer: .: (0.000349) - test_pdb_list: .: (0.000493) - test_pdb_lstring: .: (0.000550) - test_pdb_real: .: (0.000453) - test_pdb_resudue_name: .: (0.000789) - test_pdb_slist: .: (0.000396) - test_pdb_string: .: (0.000568) - test_pdb_stringrj: .: (0.000338) - test_pdb_symop: .: (0.000525) - test_specification_list: .: (0.000382) + test_const_like_method: .: (0.002455) + test_pdb_achar: .: (0.001017) + test_pdb_atom: .: (0.000884) + test_pdb_character: .: (0.000873) + test_pdb_date: .: (0.000858) + test_pdb_idcode: .: (0.000901) + test_pdb_integer: .: (0.000443) + test_pdb_list: .: (0.000477) + test_pdb_lstring: .: (0.000794) + test_pdb_real: .: (0.000659) + test_pdb_resudue_name: .: (0.000911) + test_pdb_slist: .: (0.000484) + test_pdb_string: .: (0.000871) + test_pdb_stringrj: .: (0.000467) + test_pdb_symop: .: (0.001283) + test_specification_list: .: (0.000545) Bio::TestEMBL: - test_ac: .: (0.002039) - test_accession: .: (0.001086) - test_cc: .: (0.001018) - test_de: .: (0.001109) - test_division: .: (0.001017) - test_dr: .: (0.000808) - test_dt: .: (0.000838) - test_dt_created: .: (0.001230) - test_dt_iterator: .: (0.000840) - test_dt_updated: .: (0.000810) - test_each_cds: .: (0.001419) - test_each_gene: .: (0.001096) - test_entry: .: (0.001216) - test_fh: .: (0.000837) - test_ft: .: (0.001123) - test_ft_accessor: .: (0.001252) - test_ft_iterator: .: (0.001370) - test_id_line: .: (0.001030) - test_id_line_data_class: .: (0.000993) - test_id_line_division: .: (0.000879) - test_id_line_entry_name: .: (0.000969) - test_id_line_iterator: .: (0.000940) - test_id_line_molecule_type: .: (0.000921) - test_id_line_sequence_length: .: (0.000996) - test_kw: .: (0.004517) - test_molecule: .: (0.000977) - test_oc: .: (0.001055) - test_og: .: (0.000907) - test_os: .: (0.001349) - test_ref: .: (0.001174) - test_references: .: (0.001367) - test_seq: .: (0.001682) - test_sequence_length: .: (0.000901) - test_sq: .: (0.000831) - test_sq_get: .: (0.000856) - test_sv: .: (0.001001) - test_version: .: (0.000755) + test_ac: .: (0.003276) + test_accession: .: (0.001861) + test_cc: .: (0.001702) + test_de: .: (0.002263) + test_division: .: (0.001994) + test_dr: .: (0.001786) + test_dt: .: (0.001768) + test_dt_created: .: (0.001800) + test_dt_iterator: .: (0.001746) + test_dt_updated: .: (0.002152) + test_each_cds: .: (0.002715) + test_each_gene: .: (0.002602) + test_entry: .: (0.002148) + test_fh: .: (0.002106) + test_ft: .: (0.002715) + test_ft_accessor: .: (0.002834) + test_ft_iterator: .: (0.002871) + test_id_line: .: (0.001958) + test_id_line_data_class: .: (0.002029) + test_id_line_division: .: (0.001885) + test_id_line_entry_name: .: (0.001982) + test_id_line_iterator: .: (0.002309) + test_id_line_molecule_type: .: (0.001938) + test_id_line_sequence_length: .: (0.001964) + test_kw: .: (0.001901) + test_molecule: .: (0.002533) + test_oc: .: (0.002189) + test_og: .: (0.001806) + test_os: .: (0.001937) + test_ref: .: (0.002790) + test_references: .: (0.003289) + test_seq: .: (0.003296) + test_sequence_length: .: (0.002412) + test_sq: .: (0.001900) + test_sq_get: .: (0.001884) + test_sv: .: (0.001749) + test_version: .: (0.001833) Bio::TestEMBL89: - test_ac: .: (0.008441) - test_accession: .: (0.000860) - test_cc: .: (0.000922) - test_de: .: (0.001013) - test_division: .: (0.000980) - test_dr: .: (0.000796) - test_dt: .: (0.001170) - test_dt_created: .: (0.000859) - test_dt_iterator: .: (0.000787) - test_dt_updated: .: (0.000946) - test_each_cds: .: (0.001432) - test_each_gene: .: (0.001011) - test_entry: .: (0.000863) - test_fh: .: (0.000799) - test_ft: .: (0.001189) - test_ft_accessor: .: (0.001141) - test_ft_iterator: .: (0.001112) - test_id_line: .: (0.000963) - test_id_line_data_class: .: (0.001015) - test_id_line_division: .: (0.000949) - test_id_line_entry_name: .: (0.000853) - test_id_line_iterator: .: (0.001378) - test_id_line_molecule_type: .: (0.000859) - test_id_line_sequence_length: .: (0.000749) - test_id_line_sequence_version: .: (0.000748) - test_kw: .: (0.000867) - test_molecule: .: (0.000929) - test_oc: .: (0.000958) - test_og: .: (0.000766) - test_os: .: (0.000773) - test_ref: .: (0.001244) - test_references: .: (0.001498) - test_seq: .: (0.001199) - test_sequence_length: .: (0.001061) - test_sq: .: (0.000892) - test_sq_get: .: (0.000736) - test_sv: .: (0.000795) - test_version: .: (0.001026) + test_ac: .: (0.003534) + test_accession: .: (0.001875) + test_cc: .: (0.001703) + test_de: .: (0.001814) + test_division: .: (0.001921) + test_dr: .: (0.001635) + test_dt: .: (0.001753) + test_dt_created: .: (0.001665) + test_dt_iterator: .: (0.001686) + test_dt_updated: .: (0.001635) + test_each_cds: .: (0.002964) + test_each_gene: .: (0.002489) + test_entry: .: (0.002049) + test_fh: .: (0.001761) + test_ft: .: (0.002941) + test_ft_accessor: .: (0.002533) + test_ft_iterator: .: (0.002713) + test_id_line: .: (0.002013) + test_id_line_data_class: .: (0.002237) + test_id_line_division: .: (0.001934) + test_id_line_entry_name: .: (0.001846) + test_id_line_iterator: .: (0.001903) + test_id_line_molecule_type: .: (0.002217) + test_id_line_sequence_length: .: (0.001930) + test_id_line_sequence_version: .: (0.001833) + test_kw: .: (0.010752) + test_molecule: .: (0.002252) + test_oc: .: (0.002168) + test_og: .: (0.001743) + test_os: .: (0.001961) + test_ref: .: (0.002935) + test_references: .: (0.003154) + test_seq: .: (0.004109) + test_sequence_length: .: (0.002252) + test_sq: .: (0.001862) + test_sq_get: .: (0.001871) + test_sv: .: (0.002884) + test_version: .: (0.002264) Bio::TestEMBLAPI: - test_ac: .: (0.000745) - test_accessions: .: (0.000413) + test_ac: .: (0.001510) + test_accessions: .: (0.000812) Bio::TestEMBLCommon: - test_ac: .: (0.000595) - test_accession: .: (0.000321) - test_accessions: .: (0.000291) - test_de: .: (0.000277) - test_definition: .: (0.000278) - test_description: .: (0.000280) - test_dr: .: (0.000331) - test_keywords: .: (0.000401) - test_kw: .: (0.000286) - test_oc: .: (0.000285) - test_og: .: (0.000278) - test_os: .: (0.000272) - test_ref: .: (0.000471) - test_references: .: (0.000399) + test_ac: .: (0.000996) + test_accession: .: (0.000509) + test_accessions: .: (0.000480) + test_de: .: (0.000455) + test_definition: .: (0.000465) + test_description: .: (0.001089) + test_dr: .: (0.000507) + test_keywords: .: (0.000439) + test_kw: .: (0.000435) + test_oc: .: (0.000460) + test_og: .: (0.000452) + test_os: .: (0.000434) + test_ref: .: (0.000456) + test_references: .: (0.000440) Bio::TestEMBLDB: - test_fetch: .: (0.000674) - test_p_entry2hash: .: (0.000271) + test_fetch: .: (0.001391) + test_p_entry2hash: .: (0.000444) Bio::TestEMBLToBioSequence: - test_classification: .: (0.006467) - test_date_created: .: (0.001120) - test_date_modified: .: (0.001136) - test_definition: .: (0.000884) - test_division: .: (0.000871) - test_entry_id: .: (0.001037) - test_entry_version: .: (0.001071) - test_features: .: (0.001372) - test_keywords: .: (0.000871) - test_molecule_type: .: (0.000880) - test_primary_accession: .: (0.001218) - test_references: .: (0.001556) - test_release_created: .: (0.000904) - test_release_modified: .: (0.001654) - test_secondary_accessions: .: (0.000997) - test_sequence_version: .: (0.001118) - test_species: .: (0.000854) - test_topology: .: (0.001346) + test_classification: .: (0.017866) + test_date_created: .: (0.003290) + test_date_modified: .: (0.002537) + test_definition: .: (0.002109) + test_division: .: (0.002264) + test_entry_id: .: (0.002618) + test_entry_version: .: (0.002034) + test_features: .: (0.002999) + test_keywords: .: (0.002499) + test_molecule_type: .: (0.002183) + test_primary_accession: .: (0.002125) + test_references: .: (0.004071) + test_release_created: .: (0.002262) + test_release_modified: .: (0.002072) + test_secondary_accessions: .: (0.002055) + test_sequence_version: .: (0.003123) + test_species: .: (0.002249) + test_topology: .: (0.002235) Bio::TestEMBLToBioSequenceRoundTrip: - test_classification: .: (0.006803) - test_date_created: .: (0.009536) - test_date_modified: .: (0.031850) - test_definition: .: (0.038303) - test_division: .: (0.026553) - test_entry_id: .: (0.006638) - test_entry_version: .: (0.006261) - test_features: .: (0.006424) - test_keywords: .: (0.005720) - test_molecule_type: .: (0.006020) - test_primary_accession: .: (0.006143) - test_references: .: (0.006531) - test_release_created: .: (0.005910) - test_release_modified: .: (0.005676) - test_secondary_accessions: .: (0.006067) - test_sequence_version: .: (0.006983) - test_species: .: (0.007083) - test_topology: .: (0.006369) + test_classification: .: (0.018241) + test_date_created: .: (0.018344) + test_date_modified: .: (0.018451) + test_definition: .: (0.017315) + test_division: .: (0.016859) + test_entry_id: .: (0.015740) + test_entry_version: .: (0.016202) + test_features: .: (0.095056) + test_keywords: .: (0.074678) + test_molecule_type: .: (0.070516) + test_primary_accession: .: (0.016272) + test_references: .: (0.018325) + test_release_created: .: (0.016690) + test_release_modified: .: (0.017125) + test_secondary_accessions: .: (0.015730) + test_sequence_version: .: (0.016663) + test_species: .: (0.016944) + test_topology: .: (0.016104) Bio::TestFasta: - test_db: .: (0.000613) - test_format: .: (0.000347) - test_format_arg_integer: .: (0.000363) - test_format_arg_str: .: (0.000425) - test_ktup: .: (0.000336) - test_matrix: .: (0.000323) - test_option: .: (0.000457) - test_options: .: (0.000356) - test_output: .: (0.000302) - test_program: .: (0.000401) - test_server: .: (0.000827) + test_db: .: (0.001218) + test_format: .: (0.000468) + test_format_arg_integer: .: (0.000558) + test_format_arg_str: .: (0.001684) + test_ktup: .: (0.000587) + test_matrix: .: (0.000511) + test_option: .: (0.000672) + test_options: .: (0.000535) + test_output: .: (0.000428) + test_program: .: (0.000538) + test_server: .: (0.000503) Bio::TestFastaDeflineEmb: - test_acc_version: .: (0.000625) - test_accession: .: (0.000365) - test_accessions: .: (0.000474) - test_description: .: (0.000349) - test_descriptions: .: (0.000409) - test_entry_id: .: (0.000356) - test_get_all_by_type: .: (0.000346) - test_gi: .: (0.000350) - test_id_strings: .: (0.000495) - test_list_ids: .: (0.000349) - test_locus: .: (0.000429) - test_words: .: (0.000435) + test_acc_version: .: (0.001166) + test_accession: .: (0.000620) + test_accessions: .: (0.000599) + test_description: .: (0.000544) + test_descriptions: .: (0.000541) + test_entry_id: .: (0.000534) + test_get_all_by_type: .: (0.000542) + test_gi: .: (0.000561) + test_id_strings: .: (0.001999) + test_list_ids: .: (0.000604) + test_locus: .: (0.000564) + test_words: .: (0.000742) Bio::TestFastaDeflineGI1: - test_acc_version: .: (0.000729) - test_accession: .: (0.000428) - test_accessions: .: (0.000393) - test_description: .: (0.000358) - test_descriptions: .: (0.000430) - test_emb: .: (0.000397) - test_entry_id: .: (0.000359) - test_get_all_by_type: .: (0.000369) - test_get_emb: .: (0.000375) - test_gi: .: (0.000629) - test_id_strings: .: (0.000483) - test_list_ids: .: (0.000384) - test_locus: .: (0.000368) - test_words: .: (0.000466) + test_acc_version: .: (0.001243) + test_accession: .: (0.000733) + test_accessions: .: (0.000731) + test_description: .: (0.000639) + test_descriptions: .: (0.000603) + test_emb: .: (0.000811) + test_entry_id: .: (0.000678) + test_get_all_by_type: .: (0.000659) + test_get_emb: .: (0.000691) + test_gi: .: (0.000701) + test_id_strings: .: (0.000918) + test_list_ids: .: (0.000663) + test_locus: .: (0.001960) + test_words: .: (0.000926) Bio::TestFastaDeflineGI2: - test_acc_version: .: (0.000644) - test_accession: .: (0.000380) - test_accessions: .: (0.000915) - test_description: .: (0.000424) - test_descriptions: .: (0.000346) - test_entry_id: .: (0.000342) - test_get_all_by_type: .: (0.000342) - test_gi: .: (0.000345) - test_id_strings: .: (0.000537) - test_list_ids: .: (0.000390) - test_locus: .: (0.000353) - test_sp: .: (0.000370) - test_words: .: (0.000422) + test_acc_version: .: (0.001219) + test_accession: .: (0.000687) + test_accessions: .: (0.000620) + test_description: .: (0.000554) + test_descriptions: .: (0.000550) + test_entry_id: .: (0.000546) + test_get_all_by_type: .: (0.000600) + test_gi: .: (0.000590) + test_id_strings: .: (0.000784) + test_list_ids: .: (0.000603) + test_locus: .: (0.000629) + test_sp: .: (0.000645) + test_words: .: (0.000760) Bio::TestFastaDeflineGIMultiple: - test_acc_version: .: (0.000785) - test_accession: .: (0.000440) - test_accessions: .: (0.000472) - test_description: .: (0.000418) - test_descriptions: .: (0.001218) - test_entry_id: .: (0.000421) - test_get_all_by_type: .: (0.000414) - test_gi: .: (0.000448) - test_id_strings: .: (0.000755) - test_list_ids: .: (0.000446) - test_locus: .: (0.000429) - test_words: .: (0.000650) + test_acc_version: .: (0.002648) + test_accession: .: (0.000921) + test_accessions: .: (0.000894) + test_description: .: (0.000840) + test_descriptions: .: (0.000783) + test_entry_id: .: (0.000767) + test_get_all_by_type: .: (0.000792) + test_gi: .: (0.000830) + test_id_strings: .: (0.001451) + test_list_ids: .: (0.001914) + test_locus: .: (0.000952) + test_words: .: (0.001532) Bio::TestFastaDeflineSce: - test_acc_version: .: (0.000746) - test_accession: .: (0.000404) - test_accessions: .: (0.000990) - test_description: .: (0.000364) - test_descriptions: .: (0.000482) - test_entry_id: .: (0.000361) - test_get_all_by_type: .: (0.000345) - test_gi: .: (0.000341) - test_id_strings: .: (0.000497) - test_list_ids: .: (0.000551) - test_locus: .: (0.000379) - test_words: .: (0.000507) + test_acc_version: .: (0.001353) + test_accession: .: (0.000753) + test_accessions: .: (0.000713) + test_description: .: (0.000711) + test_descriptions: .: (0.000696) + test_entry_id: .: (0.000672) + test_get_all_by_type: .: (0.000686) + test_gi: .: (0.000738) + test_id_strings: .: (0.002215) + test_list_ids: .: (0.000777) + test_locus: .: (0.000737) + test_words: .: (0.001190) Bio::TestFastaDeflineSimple: - test_acc_version: .: (0.000514) - test_accession: .: (0.000307) - test_accessions: .: (0.000334) - test_description: .: (0.000329) - test_descriptions: .: (0.000810) - test_entry_id: .: (0.000312) - test_get_all_by_type: .: (0.000437) - test_gi: .: (0.000401) - test_id_strings: .: (0.000404) - test_list_ids: .: (0.000294) - test_locus: .: (0.000326) - test_words: .: (0.000337) + test_acc_version: .: (0.001184) + test_accession: .: (0.000566) + test_accessions: .: (0.000542) + test_description: .: (0.000511) + test_descriptions: .: (0.000509) + test_entry_id: .: (0.000539) + test_get_all_by_type: .: (0.000518) + test_gi: .: (0.000515) + test_id_strings: .: (0.001714) + test_list_ids: .: (0.000663) + test_locus: .: (0.000542) + test_words: .: (0.000646) Bio::TestFastaDeflineSwissProt: - test_acc_version: .: (0.000701) - test_accession: .: (0.000347) - test_accessions: .: (0.000321) - test_description: .: (0.000305) - test_descriptions: .: (0.000313) - test_entry_id: .: (0.000370) - test_get: .: (0.000943) - test_get_all_by_type: .: (0.000315) - test_id_strings: .: (0.000463) - test_list_ids: .: (0.000311) - test_locus: .: (0.000536) - test_sp: .: (0.000356) - test_words: .: (0.000446) + test_acc_version: .: (0.001251) + test_accession: .: (0.000651) + test_accessions: .: (0.000612) + test_description: .: (0.000559) + test_descriptions: .: (0.000560) + test_entry_id: .: (0.000602) + test_get: .: (0.000613) + test_get_all_by_type: .: (0.000558) + test_id_strings: .: (0.000983) + test_list_ids: .: (0.001621) + test_locus: .: (0.000661) + test_sp: .: (0.000636) + test_words: .: (0.000974) Bio::TestFastaDeflineTrembl: - test_acc_version: .: (0.000559) - test_accession: .: (0.000510) - test_accessions: .: (0.000333) - test_description: .: (0.000305) - test_descriptions: .: (0.000301) - test_entry_id: .: (0.000299) - test_get: .: (0.000322) - test_get_all_by_type: .: (0.000430) - test_id_strings: .: (0.000871) - test_list_ids: .: (0.000316) - test_locus: .: (0.000319) - test_tr: .: (0.000325) - test_words: .: (0.000675) + test_acc_version: .: (0.001196) + test_accession: .: (0.000637) + test_accessions: .: (0.000601) + test_description: .: (0.000587) + test_descriptions: .: (0.000576) + test_entry_id: .: (0.000563) + test_get: .: (0.000601) + test_get_all_by_type: .: (0.000546) + test_id_strings: .: (0.002277) + test_list_ids: .: (0.000629) + test_locus: .: (0.000613) + test_tr: .: (0.000634) + test_words: .: (0.001164) Bio::TestFastaFirstName: - test_first_name1: .: (0.000542) - test_first_name_multi_identifier: .: (0.000312) - test_first_name_single_worded_defintion: .: (0.005090) - test_no_definition: .: (0.000455) - test_space_before_first_name: .: (0.000452) - test_tabbed_defintion: .: (0.000310) + test_first_name1: .: (0.001215) + test_first_name_multi_identifier: .: (0.000571) + test_first_name_single_worded_defintion: .: (0.000531) + test_no_definition: .: (0.000512) + test_space_before_first_name: .: (0.000530) + test_tabbed_defintion: .: (0.000549) Bio::TestFastaFormat: - test_aalen: .: (0.000593) - test_aaseq: .: (0.000376) - test_acc_version: .: (0.000437) - test_accession: .: (0.000422) - test_accessions: .: (0.000416) - test_data: .: (0.000310) - test_definition: .: (0.000310) - test_entry: .: (0.000371) - test_entry_id: .: (0.000521) - test_entry_overrun: .: (0.000772) - test_first_name: .: (0.000444) - test_gi: .: (0.000399) - test_identifiers: .: (0.000478) - test_length: .: (0.000364) - test_query: .: (0.000364) - test_seq: .: (0.000327) + test_aalen: .: (0.001225) + test_aaseq: .: (0.000634) + test_acc_version: .: (0.000888) + test_accession: .: (0.000816) + test_accessions: .: (0.001811) + test_data: .: (0.001012) + test_definition: .: (0.000566) + test_entry: .: (0.000556) + test_entry_id: .: (0.000766) + test_entry_overrun: .: (0.000599) + test_first_name: .: (0.000603) + test_gi: .: (0.000781) + test_identifiers: .: (0.000792) + test_length: .: (0.000596) + test_query: .: (0.000725) + test_seq: .: (0.000596) Bio::TestFastaFormatConst: - test_delimiter: .: (0.000517) + test_delimiter: .: (0.001092) Bio::TestFastaFormatKeggGenesAA: - test_acc_version: .: (0.000663) - test_data: .: (0.000325) - test_definition: .: (0.000313) - test_entry: .: (0.000309) - test_entry_id: .: (0.001165) - test_first_name: .: (0.000346) + test_acc_version: .: (0.001466) + test_data: .: (0.000603) + test_definition: .: (0.000551) + test_entry: .: (0.002090) + test_entry_id: .: (0.000937) + test_first_name: .: (0.000633) Bio::TestFastaFormatKeggGenesNT: - test_nalen: .: (0.000540) - test_naseq: .: (0.000311) - test_naseq_class: .: (0.000347) + test_nalen: .: (0.001171) + test_naseq: .: (0.000532) + test_naseq_class: .: (0.000531) Bio::TestFastaFormatSwissProt: - test_locus: .: (0.000566) + test_locus: .: (0.001231) Bio::TestFastaInitialize: - test_new_1: .: (0.001115) - test_option: .: (0.000348) - test_option_backward_compatibility: .: (0.000372) + test_new_1: .: (0.002438) + test_option: .: (0.000540) + test_option_backward_compatibility: .: (0.000609) Bio::TestFastaNumericFormat: - test_arg: .: (0.001139) - test_data: .: (0.000370) - test_definition: .: (0.000329) - test_each: .: (0.000363) - test_entry: .: (0.000294) - test_entry_id: .: (0.000358) - test_length: .: (0.000382) - test_to_biosequence: .: (0.001797) + test_arg: .: (0.001288) + test_data: .: (0.000730) + test_definition: .: (0.000488) + test_each: .: (0.000659) + test_entry: .: (0.000480) + test_entry_id: .: (0.000545) + test_length: .: (0.000662) + test_to_biosequence: .: (0.003582) Bio::TestFastaQuery: - test_query: .: (0.000437) - test_self_local: .: (0.000236) - test_self_parser: .: (0.000226) - test_self_remote: .: (0.000665) + test_query: .: (0.000861) + test_self_local: .: (0.000342) + test_self_parser: .: (0.000337) + test_self_remote: .: (0.000333) Bio::TestFastacmd: - test_database: .: (0.000639) - test_fastacmd: .: (0.000285) - test_methods: .: (0.000337) + test_database: .: (0.001944) + test_fastacmd: .: (0.000429) + test_methods: .: (0.000623) Bio::TestFastq::TestFastq_error_diff_ids: - test_validate_format: .: (0.003335) + test_validate_format: .: (0.003453) Bio::TestFastq::TestFastq_error_double_qual: - test_validate_format: .: (0.001789) + test_validate_format: .: (0.003087) Bio::TestFastq::TestFastq_error_double_seq: - test_validate_format: .: (0.006159) + test_validate_format: .: (0.004006) Bio::TestFastq::TestFastq_error_long_qual: - test_validate_format: .: (0.002866) + test_validate_format: .: (0.003086) Bio::TestFastq::TestFastq_error_no_qual: - test_validate_format: .: (0.001587) + test_validate_format: .: (0.003298) Bio::TestFastq::TestFastq_error_qual_del: - test_validate_format: .: (0.001583) + test_validate_format: .: (0.004316) Bio::TestFastq::TestFastq_error_qual_escape: - test_validate_format: .: (0.001622) + test_validate_format: .: (0.003430) Bio::TestFastq::TestFastq_error_qual_null: - test_validate_format: .: (0.001555) + test_validate_format: .: (0.003123) Bio::TestFastq::TestFastq_error_qual_space: - test_validate_format: .: (0.001538) + test_validate_format: .: (0.003090) Bio::TestFastq::TestFastq_error_qual_tab: - test_validate_format: .: (0.001923) + test_validate_format: .: (0.003027) Bio::TestFastq::TestFastq_error_qual_unit_sep: - test_validate_format: .: (0.001548) + test_validate_format: .: (0.003238) Bio::TestFastq::TestFastq_error_qual_vtab: - test_validate_format: .: (0.001532) + test_validate_format: .: (0.016956) Bio::TestFastq::TestFastq_error_short_qual: - test_validate_format: .: (0.001507) + test_validate_format: .: (0.003497) Bio::TestFastq::TestFastq_error_spaces: - test_validate_format: .: (0.003255) + test_validate_format: .: (0.008054) Bio::TestFastq::TestFastq_error_tabs: - test_validate_format: .: (0.003403) + test_validate_format: .: (0.007082) Bio::TestFastq::TestFastq_error_trunc_at_plus: - test_validate_format: .: (0.001585) + test_validate_format: .: (0.004135) Bio::TestFastq::TestFastq_error_trunc_at_qual: - test_validate_format: .: (0.001497) + test_validate_format: .: (0.003314) Bio::TestFastq::TestFastq_error_trunc_at_seq: - test_validate_format: .: (0.001533) + test_validate_format: .: (0.002993) Bio::TestFastq::TestFastq_illumina_full_range: - test_error_probabilities_as_illumina: .: (0.012951) - test_error_probabilities_as_sanger: .: (0.013518) - test_error_probabilities_as_solexa: .: (0.014719) - test_quality_scores_as_illumina: .: (0.001287) - test_quality_scores_as_sanger: .: (0.000679) - test_quality_scores_as_solexa: .: (0.000897) - test_validate_format: .: (0.001703) + test_error_probabilities_as_illumina: .: (0.034724) + test_error_probabilities_as_sanger: .: (0.034370) + test_error_probabilities_as_solexa: .: (0.034497) + test_quality_scores_as_illumina: .: (0.002731) + test_quality_scores_as_sanger: .: (0.001673) + test_quality_scores_as_solexa: .: (0.003263) + test_validate_format: .: (0.003081) Bio::TestFastq::TestFastq_longreads_original_sanger: - test_definition: .: (0.002837) - test_entry_id: .: (0.002452) - test_error_probabilities: .: (0.309756) - test_nalen: .: (0.002284) - test_naseq: .: (0.002484) - test_quality_scores: .: (0.004646) - test_quality_string: .: (0.001976) - test_roundtrip: .: (0.325671) - test_seq: .: (0.002082) - test_sequence_string: .: (0.001976) - test_to_biosequence: .: (0.306969) - test_to_biosequence_and_output: .: (0.010625) - test_to_s: .: (0.002471) - test_validate_format: .: (0.001970) - test_validate_format_with_array: .: (0.002845) + test_definition: .: (0.006141) + test_entry_id: .: (0.006614) + test_error_probabilities: .: (0.860735) + test_nalen: .: (0.006558) + test_naseq: .: (0.005571) + test_quality_scores: .: (0.011983) + test_quality_string: .: (0.004822) + test_roundtrip: .: (0.930716) + test_seq: .: (0.005874) + test_sequence_string: .: (0.004746) + test_to_biosequence: .: (0.872674) + test_to_biosequence_and_output: .: (0.030588) + test_to_s: .: (0.005648) + test_validate_format: .: (0.009173) + test_validate_format_with_array: .: (0.006894) Bio::TestFastq::TestFastq_mask: - test_mask_20: .: (0.001738) - test_mask_20_with_empty_string: .: (0.000887) - test_mask_20_with_longer_string: .: (0.000982) - test_mask_20_with_x: .: (0.000732) - test_mask_60: .: (0.000819) + test_mask_20: .: (0.003343) + test_mask_20_with_empty_string: .: (0.002083) + test_mask_20_with_longer_string: .: (0.002015) + test_mask_20_with_x: .: (0.001995) + test_mask_60: .: (0.002424) Bio::TestFastq::TestFastq_sanger_full_range: - test_error_probabilities_as_illumina: .: (0.015964) - test_error_probabilities_as_sanger: .: (0.015861) - test_error_probabilities_as_solexa: .: (0.019542) - test_quality_scores_as_illumina: .: (0.001195) - test_quality_scores_as_sanger: .: (0.000662) - test_quality_scores_as_solexa: .: (0.001335) - test_validate_format: .: (0.001152) + test_error_probabilities_as_illumina: .: (0.047798) + test_error_probabilities_as_sanger: .: (0.045760) + test_error_probabilities_as_solexa: .: (0.052334) + test_quality_scores_as_illumina: .: (0.002153) + test_quality_scores_as_sanger: .: (0.001783) + test_quality_scores_as_solexa: .: (0.002631) + test_validate_format: .: (0.004781) Bio::TestFastq::TestFastq_solexa_full_range: - test_error_probabilities_as_illumina: .: (0.013158) - test_error_probabilities_as_sanger: .: (0.012480) - test_error_probabilities_as_solexa: .: (0.011800) - test_quality_scores_as_illumina: .: (0.000911) - test_quality_scores_as_sanger: .: (0.000772) - test_quality_scores_as_solexa: .: (0.000710) - test_validate_format: .: (0.002841) + test_error_probabilities_as_illumina: .: (0.035488) + test_error_probabilities_as_sanger: .: (0.034238) + test_error_probabilities_as_solexa: .: (0.034446) + test_quality_scores_as_illumina: .: (0.002402) + test_quality_scores_as_sanger: .: (0.002233) + test_quality_scores_as_solexa: .: (0.002256) + test_validate_format: .: (0.003391) Bio::TestFeature: - test_append: .: (0.000622) - test_append_nil: .: (0.000230) - test_assoc: .: (0.000235) - test_each: .: (0.000209) - test_feature: .: (0.000180) - test_locations: .: (0.000410) - test_new: .: (0.000195) - test_position: .: (0.000191) - test_qualifiers: .: (0.000188) + test_append: .: (0.001217) + test_append_nil: .: (0.000568) + test_assoc: .: (0.000549) + test_each: .: (0.000458) + test_feature: .: (0.000517) + test_locations: .: (0.000806) + test_new: .: (0.000475) + test_position: .: (0.000461) + test_qualifiers: .: (0.000462) Bio::TestFeatures: - test_append: .: (0.001000) - test_arg: .: (0.000228) - test_each: .: (0.000186) - test_features: .: (0.000223) + test_append: .: (0.001992) + test_arg: .: (0.000582) + test_each: .: (0.000530) + test_features: .: (0.000606) Bio::TestFlatFile::TestDefaultAutoDetect: - test_aaindex1: .: (0.001873) - test_aaindex2: .: (0.000554) - test_blast: .: (0.000461) - test_blastxml: .: (0.002142) - test_embl: .: (0.000563) - test_embl_oldrelease: .: (0.000828) - test_fastaformat: .: (0.001842) - test_fastanumericformat: .: (0.000324) - test_fastq: .: (0.000377) - test_genbank: .: (0.000413) - test_genpept: .: (0.000650) - test_hmmer: .: (0.001439) - test_maxml_cluster: .: (0.006300) - test_maxml_sequence: .: (0.000300) - test_medline: .: (0.000363) - test_prosite: .: (0.007413) + test_aaindex1: .: (0.005090) + test_aaindex2: .: (0.001353) + test_blast: .: (0.001044) + test_blastxml: .: (0.004741) + test_embl: .: (0.001566) + test_embl_oldrelease: .: (0.001404) + test_fastaformat: .: (0.003315) + test_fastanumericformat: .: (0.001483) + test_fastq: .: (0.001088) + test_genbank: .: (0.001251) + test_genpept: .: (0.001295) + test_hmmer: .: (0.002300) + test_maxml_cluster: .: (0.015194) + test_maxml_sequence: .: (0.000721) + test_medline: .: (0.000870) + test_prosite: .: (0.020909) test_sptr: Bio::SPTR is changed to an alias of Bio::UniProtKB. Please use Bio::UniProtKB. Bio::SPTR may be deprecated in the future. -.: (0.006440) - test_transfac: .: (0.003416) +.: (0.018148) + test_transfac: .: (0.008086) Bio::TestFlatFile::TestFlatFileClassMethod: - test_auto_0arg: .: (0.000569) - test_auto_1arg_filename: .: (0.000938) - test_auto_1arg_io: .: (0.000668) - test_auto_1arg_io_with_block: .: (0.001714) - test_auto_1arg_with_block: .: (0.001372) - test_auto_2arg_filename_mode: .: (0.000629) - test_auto_2arg_filename_mode_with_block: .: (0.001111) - test_auto_3arg: .: (0.000576) - test_auto_3arg_with_block: .: (0.001848) - test_foreach: .: (0.001198) - test_new_2arg_class: .: (0.000498) - test_new_2arg_nil: .: (0.000720) - test_open_0arg: .: (0.000310) - test_open_1arg_class: .: (0.000271) - test_open_1arg_filename: .: (0.000664) - test_open_1arg_io: .: (0.000962) - test_open_1arg_io_with_block: .: (0.001406) - test_open_1arg_nil: .: (0.000276) - test_open_1arg_with_block: .: (0.001129) - test_open_2arg_autodetect: .: (0.000701) - test_open_2arg_autodetect_io: .: (0.000909) - test_open_2arg_autodetect_io_with_block: .: (0.001655) - test_open_2arg_autodetect_with_block: .: (0.001418) - test_open_2arg_class: .: (0.000427) - test_open_2arg_class_io: .: (0.000486) - test_open_2arg_class_io_with_block: .: (0.001516) - test_open_2arg_class_with_block: .: (0.001243) - test_open_2arg_filename_mode: .: (0.000966) - test_open_2arg_filename_mode_with_block: .: (0.001483) - test_open_3arg: .: (0.001419) - test_open_3arg_with_block: .: (0.003481) - test_open_4arg: .: (0.003034) - test_to_a: .: (0.001123) + test_auto_0arg: .: (0.001422) + test_auto_1arg_filename: .: (0.002057) + test_auto_1arg_io: .: (0.001852) + test_auto_1arg_io_with_block: .: (0.003823) + test_auto_1arg_with_block: .: (0.003947) + test_auto_2arg_filename_mode: .: (0.009951) + test_auto_2arg_filename_mode_with_block: .: (0.003527) + test_auto_3arg: .: (0.001792) + test_auto_3arg_with_block: .: (0.003389) + test_foreach: .: (0.003732) + test_new_2arg_class: .: (0.000956) + test_new_2arg_nil: .: (0.001759) + test_open_0arg: .: (0.000617) + test_open_1arg_class: .: (0.000575) + test_open_1arg_filename: .: (0.001779) + test_open_1arg_io: .: (0.001658) + test_open_1arg_io_with_block: .: (0.004281) + test_open_1arg_nil: .: (0.000712) + test_open_1arg_with_block: .: (0.003359) + test_open_2arg_autodetect: .: (0.001709) + test_open_2arg_autodetect_io: .: (0.001617) + test_open_2arg_autodetect_io_with_block: .: (0.004425) + test_open_2arg_autodetect_with_block: .: (0.003642) + test_open_2arg_class: .: (0.001037) + test_open_2arg_class_io: .: (0.000993) + test_open_2arg_class_io_with_block: .: (0.002801) + test_open_2arg_class_with_block: .: (0.003440) + test_open_2arg_filename_mode: .: (0.002286) + test_open_2arg_filename_mode_with_block: .: (0.003763) + test_open_3arg: .: (0.004003) + test_open_3arg_with_block: .: (0.009472) + test_open_4arg: .: (0.008422) + test_to_a: .: (0.002990) Bio::TestFlatFile::TestFlatFileFastaFormat: - test_autodetect: .: (0.001042) - test_close: .: (0.000316) - test_dbclass: .: (0.000268) - test_dbclass_eq: .: (0.000332) - test_dbclass_nil: .: (0.000428) - test_each: .: (0.000901) - test_each_entry: .: (0.000956) - test_ended_pos: .: (0.000598) - test_entry_pos_flag: .: (0.000353) - test_entry_raw: .: (0.000651) - test_eof?: .: (0.000566) - test_next_entry: .: (0.000745) - test_path: .: (0.000656) - test_pos: .: (0.000550) - test_raw: .: (0.000651) - test_rewind: .: (0.000450) - test_start_pos: .: (0.000482) - test_start_pos_ended_pos_not_recorded: .: (0.000535) - test_to_io: .: (0.000344) + test_autodetect: .: (0.002476) + test_close: .: (0.000847) + test_dbclass: .: (0.000771) + test_dbclass_eq: .: (0.001004) + test_dbclass_nil: .: (0.001173) + test_each: .: (0.002587) + test_each_entry: .: (0.002278) + test_ended_pos: .: (0.001504) + test_entry_pos_flag: .: (0.000982) + test_entry_raw: .: (0.001890) + test_eof?: .: (0.001610) + test_next_entry: .: (0.002135) + test_path: .: (0.000838) + test_pos: .: (0.001975) + test_raw: .: (0.001873) + test_rewind: .: (0.001266) + test_start_pos: .: (0.001430) + test_start_pos_ended_pos_not_recorded: .: (0.001517) + test_to_io: .: (0.000919) Bio::TestFlatFile::TestFlatFileWithCustomClass: - test_simpleformat: .: (0.000655) - test_simpleformat2: .: (0.000382) + test_simpleformat: .: (0.001553) + test_simpleformat2: .: (0.001009) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStream: - test_close: .: (0.000447) - test_eof_false_after_prefetch: .: (0.000704) - test_eof_false_first: .: (0.000231) - test_eof_true: .: (0.000442) - test_getc: .: (0.000294) - test_getc_after_prefetch: .: (0.000287) - test_gets: .: (0.000246) - test_gets_equal_prefetch_gets: .: (0.000284) - test_gets_paragraph_mode: .: (0.000378) - test_gets_paragraph_mode_equal_prefetch_gets: .: (0.000660) - test_gets_paragraph_mode_within_buffer: .: (0.000783) - test_gets_rs: .: (0.000374) - test_gets_rs_equal_prefetch_gets: .: (0.000495) - test_gets_rs_within_buffer: .: (0.001092) - test_pos: .: (0.000310) - test_pos=: .: (0.000335) - test_prefetch_buffer: .: (0.000274) - test_prefetch_gets: .: (0.000297) - test_prefetch_gets_with_arg: .: (0.000359) - test_rewind: .: (0.000322) - test_skip_spaces: .: (0.000342) - test_to_io: .: (0.000279) - test_ungetc: .: (0.000300) - test_ungetc_after_prefetch: .: (0.000342) - test_ungets: .: (0.000345) + test_close: .: (0.001189) + test_eof_false_after_prefetch: .: (0.001836) + test_eof_false_first: .: (0.000820) + test_eof_true: .: (0.001032) + test_getc: .: (0.000597) + test_getc_after_prefetch: .: (0.000586) + test_gets: .: (0.000636) + test_gets_equal_prefetch_gets: .: (0.000690) + test_gets_paragraph_mode: .: (0.000852) + test_gets_paragraph_mode_equal_prefetch_gets: .: (0.002025) + test_gets_paragraph_mode_within_buffer: .: (0.002120) + test_gets_rs: .: (0.000825) + test_gets_rs_equal_prefetch_gets: .: (0.000897) + test_gets_rs_within_buffer: .: (0.002367) + test_pos: .: (0.000882) + test_pos=: .: (0.000705) + test_prefetch_buffer: .: (0.000622) + test_prefetch_gets: .: (0.000711) + test_prefetch_gets_with_arg: .: (0.000911) + test_rewind: .: (0.000652) + test_skip_spaces: .: (0.000685) + test_to_io: .: (0.000636) + test_ungetc: .: (0.000710) + test_ungetc_after_prefetch: .: (0.000809) + test_ungets: .: (0.000945) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamClassMethod: - test_self_for_io: .: (0.000830) - test_self_open_file: .: (0.000307) - test_self_open_file_with_block: .: (0.000429) + test_self_for_io: .: (0.001358) + test_self_open_file: .: (0.000739) + test_self_open_file_with_block: .: (0.000847) Bio::TestFlatFileBufferedInputStream::TestBufferedInputStreamParseFileOpenArg: - test_parse_file_open_arg_int_opt: .: (0.000510) - test_parse_file_open_arg_int_perm: .: (0.000202) - test_parse_file_open_arg_int_perm_opt: .: (0.000242) - test_parse_file_open_arg_integer: .: (0.000228) - test_parse_file_open_arg_nil: .: (0.000242) - test_parse_file_open_arg_opt: .: (0.000286) - test_parse_file_open_arg_opt_with_integer_mode: .: (0.000236) - test_parse_file_open_arg_str: .: (0.000247) - test_parse_file_open_arg_str_opt: .: (0.000285) - test_parse_file_open_arg_str_perm: .: (0.000299) - test_parse_file_open_arg_str_perm_opt: .: (0.000252) - test_parse_file_open_arg_str_with_enc: .: (0.000267) - test_parse_file_open_arg_str_with_ext_enc: .: (0.000556) - test_parse_file_open_mode_integer: .: (0.000219) - test_parse_file_open_mode_nil: .: (0.000246) - test_parse_file_open_mode_str: .: (0.000207) - test_parse_file_open_mode_str_with_enc: .: (0.000244) - test_parse_file_open_mode_str_with_ext_enc: .: (0.000222) + test_parse_file_open_arg_int_opt: .: (0.002017) + test_parse_file_open_arg_int_perm: .: (0.000503) + test_parse_file_open_arg_int_perm_opt: .: (0.000511) + test_parse_file_open_arg_integer: .: (0.000533) + test_parse_file_open_arg_nil: .: (0.000561) + test_parse_file_open_arg_opt: .: (0.000657) + test_parse_file_open_arg_opt_with_integer_mode: .: (0.000533) + test_parse_file_open_arg_str: .: (0.000533) + test_parse_file_open_arg_str_opt: .: (0.000567) + test_parse_file_open_arg_str_perm: .: (0.000560) + test_parse_file_open_arg_str_perm_opt: .: (0.000564) + test_parse_file_open_arg_str_with_enc: .: (0.000658) + test_parse_file_open_arg_str_with_ext_enc: .: (0.000620) + test_parse_file_open_mode_integer: .: (0.000477) + test_parse_file_open_mode_nil: .: (0.000620) + test_parse_file_open_mode_str: .: (0.000562) + test_parse_file_open_mode_str_with_enc: .: (0.000607) + test_parse_file_open_mode_str_with_ext_enc: .: (0.001299) Bio::TestFlatFileSplitter::TestTemplate: - test_dbclass: .: (0.000585) - test_entry: .: (0.000268) - test_entry_ended_pos: .: (0.000199) - test_entry_pos_flag: .: (0.000220) - test_entry_start_pos: .: (0.000186) - test_get_entry: .: (0.000310) - test_rewind: .: (0.000216) - test_skip_leader: .: (0.000231) - test_stream: .: (0.000187) - test_stream_pos: .: (0.000561) + test_dbclass: .: (0.001107) + test_entry: .: (0.000534) + test_entry_ended_pos: .: (0.000555) + test_entry_pos_flag: .: (0.000608) + test_entry_start_pos: .: (0.000521) + test_get_entry: .: (0.000649) + test_rewind: .: (0.000644) + test_skip_leader: .: (0.000747) + test_stream: .: (0.000549) + test_stream_pos: .: (0.000641) Bio::TestFlatFileSplitter::TestDefault: - test_delimiter: .: (0.000491) - test_delimiter_overrun: .: (0.000235) - test_entry: .: (0.000270) - test_entry_ended_pos: .: (0.000230) - test_entry_ended_pos_default_nil: .: (0.000247) - test_entry_start_pos: .: (0.000262) - test_entry_start_pos_default_nil: .: (0.000243) - test_get_entry: .: (0.000486) - test_get_parsed_entry: .: (0.000467) - test_header: .: (0.000187) - test_skip_leader: .: (0.000277) - test_skip_leader_without_header: .: (0.000340) + test_delimiter: .: (0.001186) + test_delimiter_overrun: .: (0.000583) + test_entry: .: (0.000833) + test_entry_ended_pos: .: (0.000620) + test_entry_ended_pos_default_nil: .: (0.001306) + test_entry_start_pos: .: (0.000620) + test_entry_start_pos_default_nil: .: (0.000601) + test_get_entry: .: (0.001197) + test_get_parsed_entry: .: (0.001231) + test_header: .: (0.000487) + test_skip_leader: .: (0.000705) + test_skip_leader_without_header: .: (0.000701) Bio::TestFlatFileSplitter::TestLineOriented: - test_dbclass: .: (0.000617) - test_entry_ended_pos: .: (0.000455) - test_entry_start_pos: .: (0.000419) - test_flag_to_fetch_header: .: (0.000391) - test_get_entry: .: (0.000570) - test_get_parsed_entry: .: (0.000977) - test_rewind: .: (0.000442) - test_skip_leader: .: (0.000260) + test_dbclass: .: (0.001580) + test_entry_ended_pos: .: (0.001961) + test_entry_start_pos: .: (0.001204) + test_flag_to_fetch_header: .: (0.001072) + test_get_entry: .: (0.001584) + test_get_parsed_entry: .: (0.001651) + test_rewind: .: (0.001858) + test_skip_leader: .: (0.000773) Bio::TestGCGMsf: - test_alignment: .: (0.002147) - test_checksum: .: (0.000813) - test_compcheck: .: (0.000484) - test_date: .: (0.000457) - test_description: .: (0.000431) - test_entry_id: .: (0.000454) - test_gap_length_weight: .: (0.000508) - test_gap_weight: .: (0.000506) - test_heading: .: (0.000700) - test_length: .: (0.000430) - test_seq_type: .: (0.000409) - test_symbol_comparison_table: .: (0.000422) - test_validate_checksum: .: (0.003267) + test_alignment: .: (0.005396) + test_checksum: .: (0.001210) + test_compcheck: .: (0.001291) + test_date: .: (0.002211) + test_description: .: (0.001245) + test_entry_id: .: (0.001214) + test_gap_length_weight: .: (0.001261) + test_gap_weight: .: (0.001232) + test_heading: .: (0.001194) + test_length: .: (0.001226) + test_seq_type: .: (0.002394) + test_symbol_comparison_table: .: (0.001781) + test_validate_checksum: .: (0.009827) Bio::TestGFF: - test_record_class: .: (0.001051) - test_records: .: (0.006565) + test_record_class: .: (0.002629) + test_records: .: (0.003210) Bio::TestGFF2: - test_const_version: .: (0.001160) - test_gff_version: .: (0.000917) - test_metadata: .: (0.001577) - test_metadata_size: .: (0.000775) - test_records_size: .: (0.000887) - test_to_s: .: (0.001844) + test_const_version: .: (0.003070) + test_gff_version: .: (0.002367) + test_metadata: .: (0.003231) + test_metadata_size: .: (0.002267) + test_records_size: .: (0.002278) + test_to_s: .: (0.077610) Bio::TestGFF2ComplexAttributes: - test_attributes_case1: .: (0.000522) - test_attributes_case2: .: (0.000337) - test_attributes_incompatible_backslash_semicolon: .: (0.000458) + test_attributes_case1: .: (0.001508) + test_attributes_case2: .: (0.000985) + test_attributes_incompatible_backslash_semicolon: .: (0.029170) Bio::TestGFF2MetaData: - test_data: .: (0.000400) - test_directive: .: (0.000177) - test_parse: .: (0.000691) + test_data: .: (0.001110) + test_directive: .: (0.000489) + test_parse: .: (0.000564) Bio::TestGFF2Record: - test_attribute: .: (0.000922) - test_attribute_nonexistent: .: (0.000485) - test_attributes: .: (0.000637) - test_attributes_to_hash: .: (0.000553) - test_comment_only?: .: (0.000856) - test_delete_attribute: .: (0.000597) - test_delete_attribute_multiple: .: (0.000565) - test_delete_attribute_multiple2: .: (0.000673) - test_delete_attribute_multiple_nil: .: (0.000567) - test_delete_attribute_nil: .: (0.000548) - test_delete_attribute_nonexistent: .: (0.000961) - test_delete_attributes: .: (0.000689) - test_delete_attributes_multiple: .: (0.000600) - test_delete_attributes_nonexistent: .: (0.000592) - test_end: .: (0.000477) - test_eqeq: .: (0.001579) - test_eqeq_false: .: (0.001106) - test_feature: .: (0.000506) - test_frame: .: (0.000459) - test_get_attribute: .: (0.001114) - test_get_attribute_nonexistent: .: (0.000485) - test_get_attributes: .: (0.000786) - test_get_attributes_nonexistent: .: (0.000544) - test_replace_attributes: .: (0.000616) - test_replace_attributes_multiple_multiple_over: .: (0.001060) - test_replace_attributes_multiple_multiple_same: .: (0.000906) - test_replace_attributes_multiple_multiple_two: .: (0.000678) - test_replace_attributes_multiple_single: .: (0.000594) - test_replace_attributes_nonexistent: .: (0.000539) - test_replace_attributes_nonexistent_multiple: .: (0.000541) - test_replace_attributes_single_multiple: .: (0.001125) - test_score: .: (0.000543) - test_self_parse: .: (0.001182) - test_seqname: .: (0.000526) - test_set_attribute: .: (0.000583) - test_set_attribute_multiple: .: (0.001357) - test_set_attribute_nonexistent: .: (0.000612) - test_sort_attributes_by_tag!: .: (0.000740) - test_sort_attributes_by_tag_bang_test2: .: (0.000698) - test_sort_attributes_by_tag_bang_with_block: .: (0.000664) - test_source: .: (0.000552) - test_start: .: (0.000561) - test_strand: .: (0.000485) - test_to_s: .: (0.000938) + test_attribute: .: (0.034266) + test_attribute_nonexistent: .: (0.001525) + test_attributes: .: (0.001558) + test_attributes_to_hash: .: (0.028101) + test_comment_only?: .: (0.001420) + test_delete_attribute: .: (0.031387) + test_delete_attribute_multiple: .: (0.001789) + test_delete_attribute_multiple2: .: (0.010875) + test_delete_attribute_multiple_nil: .: (0.001701) + test_delete_attribute_nil: .: (0.001639) + test_delete_attribute_nonexistent: .: (0.001585) + test_delete_attributes: .: (0.001846) + test_delete_attributes_multiple: .: (0.001666) + test_delete_attributes_nonexistent: .: (0.002854) + test_end: .: (0.001658) + test_eqeq: .: (0.003444) + test_eqeq_false: .: (0.004203) + test_feature: .: (0.001481) + test_frame: .: (0.001328) + test_get_attribute: .: (0.001930) + test_get_attribute_nonexistent: .: (0.001346) + test_get_attributes: .: (0.002073) + test_get_attributes_nonexistent: .: (0.002370) + test_replace_attributes: .: (0.001673) + test_replace_attributes_multiple_multiple_over: .: (0.001627) + test_replace_attributes_multiple_multiple_same: .: (0.001986) + test_replace_attributes_multiple_multiple_two: .: (0.001619) + test_replace_attributes_multiple_single: .: (0.001786) + test_replace_attributes_nonexistent: .: (0.002579) + test_replace_attributes_nonexistent_multiple: .: (0.001671) + test_replace_attributes_single_multiple: .: (0.001621) + test_score: .: (0.001421) + test_self_parse: .: (0.004180) + test_seqname: .: (0.001367) + test_set_attribute: .: (0.001584) + test_set_attribute_multiple: .: (0.001969) + test_set_attribute_nonexistent: .: (0.001637) + test_sort_attributes_by_tag!: .: (0.002888) + test_sort_attributes_by_tag_bang_test2: .: (0.002017) + test_sort_attributes_by_tag_bang_with_block: .: (0.001874) + test_source: .: (0.001328) + test_start: .: (0.001368) + test_strand: .: (0.001352) + test_to_s: .: (0.003156) Bio::TestGFF2RecordEmpty: - test_comment: .: (0.000549) - test_comment_eq: .: (0.000287) - test_comment_only?: .: (0.000261) - test_comment_only_false: .: (0.000213) - test_to_s: .: (0.000230) - test_to_s_not_empty: .: (0.000432) + test_comment: .: (0.001199) + test_comment_eq: .: (0.000550) + test_comment_only?: .: (0.000553) + test_comment_only_false: .: (0.000514) + test_to_s: .: (0.000568) + test_to_s_not_empty: .: (0.000969) Bio::TestGFF3: - test_const_version: .: (0.001659) - test_gff_version: .: (0.001683) - test_records: .: (0.001669) - test_sequence_regions: .: (0.001662) - test_sequences: .: (0.001673) - test_to_s: .: (0.003165) + test_const_version: .: (0.004981) + test_gff_version: .: (0.003305) + test_records: .: (0.004929) + test_sequence_regions: .: (0.003543) + test_sequences: .: (0.004831) + test_to_s: .: (0.005812) Bio::TestGFF3MetaData: - test_data: .: (0.000493) - test_directive: .: (0.000197) - test_parse: .: (0.000287) + test_data: .: (0.001590) + test_directive: .: (0.000497) + test_parse: .: (0.000559) Bio::TestGFF3Record: - test_attributes: .: (0.000873) - test_end: .: (0.001022) - test_feature: .: (0.000512) - test_frame: .: (0.000470) - test_id: .: (0.000521) - test_score: .: (0.000518) - test_seqname: .: (0.000456) - test_source: .: (0.000982) - test_start: .: (0.000582) - test_strand: .: (0.000467) - test_to_s: .: (0.000927) - test_to_s_attr_order_changed: .: (0.000906) + test_attributes: .: (0.002169) + test_end: .: (0.001366) + test_feature: .: (0.001384) + test_frame: .: (0.002316) + test_id: .: (0.001457) + test_score: .: (0.001242) + test_seqname: .: (0.001229) + test_source: .: (0.001270) + test_start: .: (0.001238) + test_strand: .: (0.001525) + test_to_s: .: (0.002121) + test_to_s_attr_order_changed: .: (0.002574) Bio::TestGFF3RecordEscape: - test_escape: .: (0.000997) - test_escape_attribute: .: (0.000322) - test_escape_seqid: .: (0.000379) - test_unescape: .: (0.000341) + test_escape: .: (0.001398) + test_escape_attribute: .: (0.000851) + test_escape_seqid: .: (0.000829) + test_unescape: .: (0.001794) Bio::TestGFF3RecordGap: - test___scan_gap: .: (0.000860) - test_eqeq: .: (0.000622) - test_new_from_sequences_na: .: (0.000507) - test_new_from_sequences_na_aa: .: (0.000701) - test_new_from_sequences_na_aa_boundary_gap: .: (0.014761) - test_new_from_sequences_na_aa_example: .: (0.000731) - test_new_from_sequences_na_aa_reverse_frameshift: .: (0.000718) - test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.014368) - test_process_sequences_na: .: (0.000491) - test_process_sequences_na_aa: .: (0.000517) - test_process_sequences_na_aa_reverse_frameshift: .: (0.014415) - test_process_sequences_na_aa_reverse_frameshift_more: .: (0.000483) - test_process_sequences_na_aa_tooshort: .: (0.012871) - test_process_sequences_na_tooshort: .: (0.000663) - test_to_s: .: (0.000450) + test___scan_gap: .: (0.001942) + test_eqeq: .: (0.001182) + test_new_from_sequences_na: .: (0.001162) + test_new_from_sequences_na_aa: .: (0.001815) + test_new_from_sequences_na_aa_boundary_gap: .: (0.002509) + test_new_from_sequences_na_aa_example: .: (0.002922) + test_new_from_sequences_na_aa_reverse_frameshift: .: (0.001789) + test_new_from_sequences_na_aa_reverse_frameshift_more:.: (0.001555) + test_process_sequences_na: .: (0.001243) + test_process_sequences_na_aa: .: (0.001183) + test_process_sequences_na_aa_reverse_frameshift: .: (0.001131) + test_process_sequences_na_aa_reverse_frameshift_more: .: (0.001232) + test_process_sequences_na_aa_tooshort: .: (0.001774) + test_process_sequences_na_tooshort: .: (0.002836) + test_to_s: .: (0.001196) Bio::TestGFF3RecordMisc: - test_attributes_none: .: (0.015747) - test_attributes_one: .: (0.000303) - test_attributes_with_escaping: .: (0.000311) - test_id_multiple: .: (0.000553) - test_id_multiple2: .: (0.000494) - test_id_replace: .: (0.000418) - test_id_set: .: (0.000417) - test_initialize_9: .: (0.000213) - test_phase: .: (0.000919) - test_score: .: (0.000331) - test_to_s_void: .: (0.000279) + test_attributes_none: .: (0.001502) + test_attributes_one: .: (0.000711) + test_attributes_with_escaping: .: (0.000793) + test_id_multiple: .: (0.001439) + test_id_multiple2: .: (0.001361) + test_id_replace: .: (0.000838) + test_id_set: .: (0.001065) + test_initialize_9: .: (0.000520) + test_phase: .: (0.001642) + test_score: .: (0.000729) + test_to_s_void: .: (0.000663) Bio::TestGFF3RecordTarget: - test_end: .: (0.000587) - test_parse: .: (0.000463) - test_start: .: (0.000231) - test_strand: .: (0.000223) - test_target_id: .: (0.000233) - test_to_s: .: (0.000401) + test_end: .: (0.001226) + test_parse: .: (0.001048) + test_start: .: (0.000612) + test_strand: .: (0.000585) + test_target_id: .: (0.000598) + test_to_s: .: (0.000976) Bio::TestGFF3SequenceRegion: - test_end: .: (0.000535) - test_parse: .: (0.000983) - test_seqid: .: (0.000292) - test_start: .: (0.000234) - test_to_s: .: (0.000390) + test_end: .: (0.001240) + test_parse: .: (0.001039) + test_seqid: .: (0.000655) + test_start: .: (0.001309) + test_to_s: .: (0.000960) Bio::TestGFFRecord: - test_attributes: .: (0.000568) - test_comment: .: (0.000258) - test_end: .: (0.000253) - test_feature: .: (0.000269) - test_frame: .: (0.000257) - test_score: .: (0.000289) - test_seqname: .: (0.000293) - test_source: .: (0.000253) - test_start: .: (0.000246) - test_strand: .: (0.000757) + test_attributes: .: (0.001367) + test_comment: .: (0.000694) + test_end: .: (0.000662) + test_feature: .: (0.000650) + test_frame: .: (0.000643) + test_score: .: (0.000613) + test_seqname: .: (0.000612) + test_source: .: (0.000606) + test_start: .: (0.000630) + test_strand: .: (0.001528) Bio::TestGFFRecordConstruct: - test_add_seqname: .: (0.000510) + test_add_seqname: .: (0.001120) Bio::TestGeneAssociation: - test_aspect: .: (0.000462) - test_assigned_by: .: (0.000280) - test_date: .: (0.000272) - test_db: .: (0.000257) - test_db_object_id: .: (0.000240) - test_db_object_name: .: (0.000237) - test_db_object_symbol: .: (0.000224) - test_db_object_synonym: .: (0.000222) - test_db_object_type: .: (0.000219) - test_db_reference: .: (0.000215) - test_evidence: .: (0.000292) - test_goid: .: (0.000244) - test_parser: .: (0.029439) - test_qualifier: .: (0.000263) - test_taxon: .: (0.000254) - test_to_str: .: (0.000273) - test_with: .: (0.000229) + test_aspect: .: (0.001273) + test_assigned_by: .: (0.000648) + test_date: .: (0.000607) + test_db: .: (0.000672) + test_db_object_id: .: (0.000670) + test_db_object_name: .: (0.000613) + test_db_object_symbol: .: (0.000596) + test_db_object_synonym: .: (0.000614) + test_db_object_type: .: (0.000638) + test_db_reference: .: (0.000617) + test_evidence: .: (0.001606) + test_goid: .: (0.000788) + test_parser: .: (0.003482) + test_qualifier: .: (0.000674) + test_taxon: .: (0.000613) + test_to_str: .: (0.000654) + test_with: .: (0.000614) Bio::TestGenscanReport: - test_date_run: .: (0.012498) - test_gccontent: .: (0.001543) - test_genscan_version: .: (0.001851) - test_isochore: .: (0.001455) - test_length: .: (0.001383) - test_matrix: .: (0.001780) - test_predictions_size: .: (0.001319) - test_query_name: .: (0.001562) - test_time: .: (0.001289) + test_date_run: .: (0.006392) + test_gccontent: .: (0.003947) + test_genscan_version: .: (0.005444) + test_isochore: .: (0.003898) + test_length: .: (0.003883) + test_matrix: .: (0.004842) + test_predictions_size: .: (0.003898) + test_query_name: .: (0.005083) + test_time: .: (0.003927) Bio::TestGenscanReportExon: - test_acceptor_score: .: (0.001860) - test_donor_score: .: (0.001185) - test_exon_type: .: (0.001848) - test_exon_type_long: .: (0.001440) - test_first: .: (0.001477) - test_initiation_score: .: (0.001872) - test_last: .: (0.001428) - test_number: .: (0.001705) - test_p_value: .: (0.001314) - test_phase: .: (0.001735) - test_range: .: (0.001400) - test_score: .: (0.001361) - test_strand: .: (0.001807) - test_t_score: .: (0.001269) - test_termination_score: .: (0.001763) + test_acceptor_score: .: (0.005478) + test_donor_score: .: (0.004199) + test_exon_type: .: (0.003872) + test_exon_type_long: .: (0.005285) + test_first: .: (0.003948) + test_initiation_score: .: (0.004953) + test_last: .: (0.003898) + test_number: .: (0.003811) + test_p_value: .: (0.005011) + test_phase: .: (0.003931) + test_range: .: (0.004453) + test_score: .: (0.003844) + test_strand: .: (0.015914) + test_t_score: .: (0.004004) + test_termination_score: .: (0.004826) Bio::TestGenscanReportGene: - test_aaseq: .: (0.001667) - test_naseq: .: (0.001465) - test_number: .: (0.001895) - test_polyA: .: (0.001424) - test_promoter: .: (0.001694) + test_aaseq: .: (0.004782) + test_naseq: .: (0.004874) + test_number: .: (0.003882) + test_polyA: .: (0.004717) + test_promoter: .: (0.004026) Bio::TestHMMERReportClassMethods: - test_reports_ary: .: (0.001799) - test_reports_ary_contents: .: (0.001408) + test_reports_ary: .: (0.004767) + test_reports_ary_contents: .: (0.004563) Bio::TestHMMERReportConstants: - test_rs: .: (0.000434) + test_rs: .: (0.001152) Bio::TestHMMERReportHit: - test_accession: .: (0.002184) - test_append_hsp: .: (0.001359) - test_bit_score: .: (0.001386) - test_definition: .: (0.001354) - test_description: .: (0.001713) - test_each: .: (0.001555) - test_each_hsp: .: (0.001258) - test_entry_id: .: (0.001173) - test_evalue: .: (0.001697) - test_hit: .: (0.001360) - test_hit_id: .: (0.001459) - test_hsps: .: (0.001697) - test_num: .: (0.001368) - test_score: .: (0.001391) - test_target_def: .: (0.001324) - test_target_id: .: (0.001702) + test_accession: .: (0.004428) + test_append_hsp: .: (0.004443) + test_bit_score: .: (0.003973) + test_definition: .: (0.003869) + test_description: .: (0.003819) + test_each: .: (0.004707) + test_each_hsp: .: (0.004170) + test_entry_id: .: (0.003920) + test_evalue: .: (0.004565) + test_hit: .: (0.004051) + test_hit_id: .: (0.003879) + test_hsps: .: (0.003893) + test_num: .: (0.004432) + test_score: .: (0.003937) + test_target_def: .: (0.003854) + test_target_id: .: (0.003838) Bio::TestHMMERReportHmmpfam: - test_domain_top_hits: .: (0.001539) - test_each: .: (0.001479) - test_each_hit: .: (0.001847) - test_histogram: .: (0.001508) - test_hits: .: (0.001744) - test_hsps: .: (0.001540) - test_parameter: .: (0.001965) - test_program: .: (0.001615) - test_query_info: .: (0.001450) - test_statistical_detail: .: (0.001308) - test_total_seq_searched: .: (0.001747) - test_whole_seq_top_hits: .: (0.001519) + test_domain_top_hits: .: (0.004571) + test_each: .: (0.003888) + test_each_hit: .: (0.003849) + test_histogram: .: (0.004521) + test_hits: .: (0.004040) + test_hsps: .: (0.003857) + test_parameter: .: (0.004026) + test_program: .: (0.004921) + test_query_info: .: (0.004113) + test_statistical_detail: .: (0.003853) + test_total_seq_searched: .: (0.004475) + test_whole_seq_top_hits: .: (0.004049) Bio::TestHMMERReportHmmsearch: - test_domain_top_hits: .: (0.001875) - test_histogram: .: (0.001638) - test_statistical_detail: .: (0.001979) - test_total_seq_searched: .: (0.001623) - test_whole_seq_top_hit: .: (0.001594) + test_domain_top_hits: .: (0.005368) + test_histogram: .: (0.005468) + test_statistical_detail: .: (0.004751) + test_total_seq_searched: .: (0.004415) + test_whole_seq_top_hit: .: (0.005373) Bio::TestHMMERReportHsp: - test_accession: .: (0.001670) - test_bit_score: .: (0.001644) - test_csline: .: (0.001270) - test_domain: .: (0.001384) - test_evalue: .: (0.001802) - test_flatseq: .: (0.001589) - test_hmm_f: .: (0.001321) - test_hmm_t: .: (0.001267) - test_hmmseq: .: (0.001595) - test_hsp: .: (0.001367) - test_midline: .: (0.005567) - test_query_frame: .: (0.001444) - test_query_from: .: (0.001323) - test_query_seq: .: (0.001448) - test_query_to: .: (0.001691) - test_rfline: .: (0.001412) - test_score: .: (0.001361) - test_seq_f: .: (0.001690) - test_seq_ft: .: (0.001505) - test_seq_t: .: (0.001295) - test_set_alignment: .: (0.001271) - test_targat_to: .: (0.001994) - test_target_frame: .: (0.001314) - test_target_from: .: (0.001395) - test_target_seq: .: (0.001803) + test_accession: .: (0.004446) + test_bit_score: .: (0.003855) + test_csline: .: (0.003834) + test_domain: .: (0.004451) + test_evalue: .: (0.003989) + test_flatseq: .: (0.003812) + test_hmm_f: .: (0.003803) + test_hmm_t: .: (0.004468) + test_hmmseq: .: (0.003975) + test_hsp: .: (0.003819) + test_midline: .: (0.003816) + test_query_frame: .: (0.004851) + test_query_from: .: (0.003852) + test_query_seq: .: (0.003845) + test_query_to: .: (0.004750) + test_rfline: .: (0.004262) + test_score: .: (0.003840) + test_seq_f: .: (0.003841) + test_seq_ft: .: (0.004967) + test_seq_t: .: (0.004261) + test_set_alignment: .: (0.003811) + test_targat_to: .: (0.003865) + test_target_frame: .: (0.004930) + test_target_from: .: (0.004274) + test_target_seq: .: (0.003857) Bio::TestHetatmFinder: - test_each_hetatm: .: (0.000947) - test_find_hetatm: .: (0.000537) - test_hetatms: .: (0.000612) + test_each_hetatm: .: (0.003629) + test_find_hetatm: .: (0.001483) + test_hetatms: .: (0.001685) Bio::TestHeterogen: - test_addAtom: .: (0.001312) - test_each: .: (0.000437) - test_each_hetatm: .: (0.000428) - test_get_residue_id_from_atom: .: (0.000431) - test_het_atom: .: (0.000306) - test_iCode: .: (0.000283) - test_inspect: .: (0.001011) - test_resSeq: .: (0.000317) - test_sort: .: (0.000385) - test_square_bracket: .: (0.000322) - test_to_s: .: (0.000545) - test_update_resudue_id: .: (0.000339) + test_addAtom: .: (0.001938) + test_each: .: (0.001140) + test_each_hetatm: .: (0.001128) + test_get_residue_id_from_atom: .: (0.001044) + test_het_atom: .: (0.000899) + test_iCode: .: (0.000817) + test_inspect: .: (0.001323) + test_resSeq: .: (0.000951) + test_sort: .: (0.001041) + test_square_bracket: .: (0.000951) + test_to_s: .: (0.001412) + test_update_resudue_id: .: (0.000988) Bio::TestHeterogenFinder: - test_each_heterogen: .: (0.000536) - test_find_heterogen: .: (0.000753) - test_heterogens: .: (0.000321) + test_each_heterogen: .: (0.001477) + test_find_heterogen: .: (0.000691) + test_heterogens: .: (0.000763) Bio::TestIprscanPTxtReport: - test_match_accession: .: (0.000606) - test_match_description: .: (0.000368) - test_match_evalue: .: (0.000359) - test_match_ipr_description: .: (0.000360) - test_match_ipr_id: .: (0.000342) - test_match_match_end: .: (0.000353) - test_match_match_start: .: (0.000331) - test_match_method: .: (0.000870) - test_matches_size: .: (0.000382) - test_query_id: .: (0.000384) - test_query_length: .: (0.000329) + test_match_accession: .: (0.001575) + test_match_description: .: (0.000889) + test_match_evalue: .: (0.000852) + test_match_ipr_description: .: (0.000908) + test_match_ipr_id: .: (0.000871) + test_match_match_end: .: (0.002091) + test_match_match_start: .: (0.000870) + test_match_method: .: (0.000834) + test_matches_size: .: (0.000810) + test_query_id: .: (0.000878) + test_query_length: .: (0.000820) Bio::TestIprscanRawReport: - test_entry_id: .: (0.026376) - test_match_accession: .: (0.004532) - test_match_crc64: .: (0.004446) - test_match_date: .: (0.005041) - test_match_description: .: (0.004679) - test_match_evalue: .: (0.004553) - test_match_go_terms: .: (0.004656) - test_match_ipr_description: .: (0.004898) - test_match_ipr_id: .: (0.007583) - test_match_match_end: .: (0.005244) - test_match_match_start: .: (0.004262) - test_match_method: .: (0.004250) - test_match_query_id: .: (0.005293) - test_match_query_length: .: (0.005223) - test_match_status: .: (0.004583) - test_obj: .: (0.004448) - test_query_id: .: (0.004631) - test_query_length: .: (0.005302) - test_self_reports_in_raw: .: (0.011696) + test_entry_id: .: (0.023218) + test_match_accession: .: (0.013009) + test_match_crc64: .: (0.012498) + test_match_date: .: (0.013906) + test_match_description: .: (0.013029) + test_match_evalue: .: (0.012774) + test_match_go_terms: .: (0.012710) + test_match_ipr_description: .: (0.012482) + test_match_ipr_id: .: (0.013839) + test_match_match_end: .: (0.011670) + test_match_match_start: .: (0.012070) + test_match_method: .: (0.017554) + test_match_query_id: .: (0.012411) + test_match_query_length: .: (0.012268) + test_match_status: .: (0.013040) + test_obj: .: (0.012399) + test_query_id: .: (0.012361) + test_query_length: .: (0.012040) + test_self_reports_in_raw: .: (0.060709) Bio::TestIprscanReport: - test_output_raw: .: (0.007995) - test_to_raw: .: (0.001636) + test_output_raw: .: (0.036410) + test_to_raw: .: (0.034603) Bio::TestIprscanTxtEntry: - test_iprscan_report_class: .: (0.001437) - test_match_accession: .: (0.001002) - test_match_date: .: (0.001049) - test_match_description: .: (0.001700) - test_match_evalue: .: (0.001089) - test_match_go_terms: .: (0.001066) - test_match_ipr_description: .: (0.001179) - test_match_ipr_id: .: (0.001432) - test_match_match_end: .: (0.001013) - test_match_match_start: .: (0.000992) - test_match_method: .: (0.000925) - test_match_status: .: (0.001408) - test_matches_size: .: (0.001157) - test_query_id: .: (0.000960) - test_query_length: .: (0.001013) + test_iprscan_report_class: .: (0.003445) + test_match_accession: .: (0.035233) + test_match_date: .: (0.002816) + test_match_description: .: (0.031975) + test_match_evalue: .: (0.002839) + test_match_go_terms: .: (0.027077) + test_match_ipr_description: .: (0.024134) + test_match_ipr_id: .: (0.002963) + test_match_match_end: .: (0.002728) + test_match_match_start: .: (0.002727) + test_match_method: .: (0.003672) + test_match_status: .: (0.002905) + test_matches_size: .: (0.002690) + test_query_id: .: (0.002644) + test_query_length: .: (0.003605) Bio::TestIprscanTxtEntryList: - test_to_hash: .: (0.002297) - test_to_hash_match?: .: (0.001389) + test_to_hash: .: (0.003766) + test_to_hash_match?: .: (0.003812) Bio::TestIprscanTxtReport: - test_parse_txt: .: (0.003081) + test_parse_txt: .: (0.008379) Bio::TestKeggCompound: - test_comment: .: (0.019244) - test_dblinks_as_hash: .: (0.000748) - test_dblinks_as_strings: .: (0.000561) - test_entry_id: .: (0.000550) - test_enzymes: .: (0.001701) - test_formula: .: (0.000568) - test_kcf: .: (0.000495) - test_mass: .: (0.000529) - test_name: .: (0.000572) - test_names: .: (0.000673) - test_pathways_as_hash: .: (0.001571) - test_pathways_as_strings: .: (0.000697) - test_reactions: .: (0.001262) - test_remark: .: (0.000566) - test_rpairs: .: (0.000516) + test_comment: .: (0.002987) + test_dblinks_as_hash: .: (0.001984) + test_dblinks_as_strings: .: (0.002715) + test_entry_id: .: (0.001602) + test_enzymes: .: (0.003370) + test_formula: .: (0.001624) + test_kcf: .: (0.001405) + test_mass: .: (0.001559) + test_name: .: (0.002480) + test_names: .: (0.001967) + test_pathways_as_hash: .: (0.002776) + test_pathways_as_strings: .: (0.001940) + test_reactions: .: (0.004509) + test_remark: .: (0.001653) + test_rpairs: .: (0.001530) Bio::TestKeggEnzyme: - test_all_reac: .: (0.023718) - test_classes: .: (0.001043) - test_cofactors: .: (0.000870) - test_comment: .: (0.001021) - test_dblinks_as_hash: .: (0.000988) - test_dblinks_as_strings: .: (0.000853) - test_diseases: .: (0.001759) - test_entry: .: (0.001335) - test_entry_id: .: (0.001311) - test_genes: .: (0.119842) - test_genes_as_hash: .: (0.029941) - test_genes_as_strings: .: (0.009624) - test_inhibitors: .: (0.001093) - test_iubmb_reactions: .: (0.000959) - test_kegg_reactions: .: (0.001486) - test_motifs: .: (0.000914) - test_name: .: (0.001069) - test_names: .: (0.001232) - test_obsolete?: .: (0.001375) - test_orthologs_as_hash: .: (0.001341) - test_orthologs_as_strings: .: (0.001778) - test_pathways_as_hash: .: (0.001183) - test_pathways_as_strings: .: (0.001003) - test_products: .: (0.001444) - test_reaction: .: (0.001527) - test_structures: .: (0.002433) - test_substrates: .: (0.001614) - test_sysname: .: (0.001339) + test_all_reac: .: (0.004346) + test_classes: .: (0.002543) + test_cofactors: .: (0.002661) + test_comment: .: (0.003629) + test_dblinks_as_hash: .: (0.003132) + test_dblinks_as_strings: .: (0.002547) + test_diseases: .: (0.002661) + test_entry: .: (0.003018) + test_entry_id: .: (0.003028) + test_genes: .: (0.080085) + test_genes_as_hash: .: (0.089476) + test_genes_as_strings: .: (0.024637) + test_inhibitors: .: (0.002591) + test_iubmb_reactions: .: (0.002825) + test_kegg_reactions: .: (0.002750) + test_motifs: .: (0.003744) + test_name: .: (0.003050) + test_names: .: (0.002947) + test_obsolete?: .: (0.002539) + test_orthologs_as_hash: .: (0.003095) + test_orthologs_as_strings: .: (0.003009) + test_pathways_as_hash: .: (0.004540) + test_pathways_as_strings: .: (0.003624) + test_products: .: (0.003167) + test_reaction: .: (0.003240) + test_structures: .: (0.004256) + test_substrates: .: (0.004110) + test_sysname: .: (0.003515) Bio::TestKeggGenesDblinks: - test_data: .: (0.000583) - test_dblinks_0: .: (0.000320) - test_dblinks_1: .: (0.000272) - test_dblinks_2: .: (0.000235) + test_data: .: (0.001329) + test_dblinks_0: .: (0.000820) + test_dblinks_1: .: (0.000737) + test_dblinks_2: .: (0.000694) Bio::TestKeggGenesStructure: - test_data: .: (0.000403) - test_ids: .: (0.000307) - test_ids_in_array: .: (0.000824) + test_data: .: (0.001350) + test_ids: .: (0.001053) + test_ids_in_array: .: (0.000853) Bio::TestKeggKGML::TestKGMLEntry1: - test_components: .: (0.018585) - test_graphics__size: .: (0.018050) - test_id: .: (0.024047) - test_link: .: (0.018049) - test_name: .: (0.019382) - test_reaction: .: (0.018581) - test_type: .: (0.018190) + test_components: .: (0.051187) + test_graphics__size: .: (0.046144) + test_id: .: (0.045284) + test_link: .: (0.044193) + test_name: .: (0.044220) + test_reaction: .: (0.043911) + test_type: .: (0.043609) Bio::TestKeggKGML::TestKGMLEntry1234: - test_components: .: (0.019670) - test_graphics__size: .: (0.018231) - test_id: .: (0.017576) - test_link: .: (0.017875) - test_name: .: (0.019022) - test_reaction: .: (0.017466) - test_type: .: (0.017295) + test_components: .: (0.044240) + test_graphics__size: .: (0.043642) + test_id: .: (0.043448) + test_link: .: (0.046059) + test_name: .: (0.051055) + test_reaction: .: (0.062863) + test_type: .: (0.059361) Bio::TestKeggKGML::TestKGMLEntry1Deprecated: - test_bgcolor=: .: (0.016647) - test_category: .: (0.015742) - test_entry_id: .: (0.016715) - test_fgcolor=: .: (0.015553) - test_height=: .: (0.016085) - test_label=: .: (0.017501) - test_shape=: .: (0.017783) - test_width=: .: (0.018295) - test_x=: .: (0.019562) - test_y=: .: (0.017647) + test_bgcolor=: .: (0.054714) + test_category: .: (0.052326) + test_entry_id: .: (0.050990) + test_fgcolor=: .: (0.052132) + test_height=: .: (0.052413) + test_label=: .: (0.050819) + test_shape=: .: (0.050646) + test_width=: .: (0.050127) + test_x=: .: (0.050503) + test_y=: .: (0.050466) Bio::TestKeggKGML::TestKGMLEntry567: - test_components: .: (0.016365) - test_graphics__size: .: (0.016664) - test_id: .: (0.017449) - test_link: .: (0.016902) - test_name: .: (0.015547) - test_reaction: .: (0.015711) - test_type: .: (0.015122) + test_components: .: (0.050613) + test_graphics__size: .: (0.050691) + test_id: .: (0.053586) + test_link: .: (0.052391) + test_name: .: (0.051279) + test_reaction: .: (0.050630) + test_type: .: (0.050551) Bio::TestKeggKGML::TestKGMLEntrySetter: - test_components=: .: (0.000612) - test_graphics=: .: (0.000249) - test_id=: .: (0.000254) - test_link=: .: (0.000245) - test_name=: .: (0.000230) - test_reaction=: .: (0.000221) - test_type=: .: (0.000217) + test_components=: .: (0.001428) + test_graphics=: .: (0.000705) + test_id=: .: (0.001392) + test_link=: .: (0.000769) + test_name=: .: (0.000751) + test_reaction=: .: (0.000722) + test_type=: .: (0.000689) Bio::TestKeggKGML::TestKGMLEntrySetterDeprecated: - test_bgcolor=: .: (0.000488) - test_category=: .: (0.000287) - test_entry_id=: .: (0.000331) - test_fgcolor=: .: (0.000548) - test_height=: .: (0.000299) - test_label=: .: (0.000354) - test_pathway=: .: (0.000259) - test_shape=: .: (0.000329) - test_width=: .: (0.000275) - test_x=: .: (0.000270) - test_y=: .: (0.000261) + test_bgcolor=: .: (0.001558) + test_category=: .: (0.000951) + test_entry_id=: .: (0.000946) + test_fgcolor=: .: (0.000903) + test_height=: .: (0.000879) + test_label=: .: (0.001018) + test_pathway=: .: (0.000755) + test_shape=: .: (0.000939) + test_width=: .: (0.001036) + test_x=: .: (0.000861) + test_y=: .: (0.000847) Bio::TestKeggKGML::TestKGMLGraphics1234: - test_bgcolor: .: (0.016349) - test_coords: .: (0.016775) - test_fgcolor: .: (0.015288) - test_height: .: (0.015149) - test_name: .: (0.015676) - test_type: .: (0.018800) - test_width: .: (0.018654) - test_x: .: (0.017009) - test_y: .: (0.016628) + test_bgcolor: .: (0.050667) + test_coords: .: (0.049669) + test_fgcolor: .: (0.049077) + test_height: .: (0.049938) + test_name: .: (0.049397) + test_type: .: (0.049338) + test_width: .: (0.049088) + test_x: .: (0.048182) + test_y: .: (0.049264) Bio::TestKeggKGML::TestKGMLGraphics1_0: - test_bgcolor: .: (0.015735) - test_coords: .: (0.015685) - test_fgcolor: .: (0.015668) - test_height: .: (0.016167) - test_name: .: (0.015696) - test_type: .: (0.017263) - test_width: .: (0.017661) - test_x: .: (0.017156) - test_y: .: (0.018732) + test_bgcolor: .: (0.055874) + test_coords: .: (0.050995) + test_fgcolor: .: (0.050732) + test_height: .: (0.051332) + test_name: .: (0.050624) + test_type: .: (0.050045) + test_width: .: (0.050207) + test_x: .: (0.049644) + test_y: .: (0.049427) Bio::TestKeggKGML::TestKGMLGraphicsSetter: - test_bgcolor=: .: (0.000606) - test_coords=: .: (0.000298) - test_fgcolor=: .: (0.000286) - test_height=: .: (0.000497) - test_name=: .: (0.000262) - test_type=: .: (0.000259) - test_width=: .: (0.000255) - test_x=: .: (0.000265) - test_y=: .: (0.000285) + test_bgcolor=: .: (0.001441) + test_coords=: .: (0.001179) + test_fgcolor=: .: (0.000733) + test_height=: .: (0.000660) + test_name=: .: (0.000669) + test_type=: .: (0.000723) + test_width=: .: (0.000673) + test_x=: .: (0.000742) + test_y=: .: (0.000798) Bio::TestKeggKGML::TestKGMLPathway: - test_entries=: .: (0.017014) - test_entries__size: .: (0.019078) - test_image: .: (0.018225) - test_link: .: (0.017822) - test_name: .: (0.016179) - test_number: .: (0.017589) - test_org: .: (0.016063) - test_reactions=: .: (0.016207) - test_reactions__size: .: (0.015958) - test_relations=: .: (0.015874) - test_relations__size: .: (0.016556) - test_title: .: (0.016819) + test_entries=: .: (0.049864) + test_entries__size: .: (0.048797) + test_image: .: (0.048999) + test_link: .: (0.048659) + test_name: .: (0.048925) + test_number: .: (0.049134) + test_org: .: (0.055140) + test_reactions=: .: (0.050929) + test_reactions__size: .: (0.051247) + test_relations=: .: (0.051524) + test_relations__size: .: (0.046662) + test_title: .: (0.044193) Bio::TestKeggKGML::TestKGMLProduct: - test_id: .: (0.033008) - test_name: .: (0.033923) + test_id: .: (0.088376) + test_name: .: (0.087339) Bio::TestKeggKGML::TestKGMLProductSetter: - test_id=: .: (0.000607) - test_initialize_0: .: (0.000230) - test_initialize_1: .: (0.000243) - test_initialize_2: .: (0.000215) - test_name=: .: (0.000266) + test_id=: .: (0.001252) + test_initialize_0: .: (0.000476) + test_initialize_1: .: (0.000514) + test_initialize_2: .: (0.000860) + test_name=: .: (0.000667) Bio::TestKeggKGML::TestKGMLReaction: - test_id: .: (0.020946) - test_name: .: (0.017550) - test_products: .: (0.017189) - test_substrates: .: (0.016428) - test_type: .: (0.016757) + test_id: .: (0.044247) + test_name: .: (0.043532) + test_products: .: (0.043737) + test_substrates: .: (0.043756) + test_type: .: (0.048930) Bio::TestKeggKGML::TestKGMLReactionSetter: - test_id=: .: (0.000556) - test_name=: .: (0.000544) - test_products=: .: (0.000297) - test_substraces=: .: (0.000295) - test_type=: .: (0.000270) + test_id=: .: (0.001243) + test_name=: .: (0.000727) + test_products=: .: (0.000671) + test_substraces=: .: (0.000657) + test_type=: .: (0.000676) Bio::TestKeggKGML::TestKGMLReactionSetterDeprecated: - test_direction=: .: (0.000617) - test_entry_id=: .: (0.000318) + test_direction=: .: (0.002111) + test_entry_id=: .: (0.000823) Bio::TestKeggKGML::TestKGMLRelation: - test_entry1: .: (0.016188) - test_entry2: .: (0.016076) - test_name: .: (0.015692) - test_type: .: (0.015397) - test_value: .: (0.015550) + test_entry1: .: (0.045434) + test_entry2: .: (0.044432) + test_name: .: (0.045559) + test_type: .: (0.044328) + test_value: .: (0.044223) Bio::TestKeggKGML::TestKGMLRelationDeprecated: - test_edge: .: (0.000449) - test_node1=: .: (0.000317) - test_node2=: .: (0.000379) - test_rel=: .: (0.000368) + test_edge: .: (0.001007) + test_node1=: .: (0.000801) + test_node2=: .: (0.000830) + test_rel=: .: (0.000797) Bio::TestKeggKGML::TestKGMLRelationSetter: - test_entry1=: .: (0.000491) - test_entry2=: .: (0.000267) - test_name=: .: (0.000596) - test_type=: .: (0.000281) - test_value=: .: (0.000288) + test_entry1=: .: (0.001159) + test_entry2=: .: (0.000655) + test_name=: .: (0.000665) + test_type=: .: (0.000653) + test_value=: .: (0.001197) Bio::TestKeggKGML::TestKGMLSubstrate: - test_id: .: (0.031797) - test_name: .: (0.029467) + test_id: .: (0.088188) + test_name: .: (0.087030) Bio::TestKeggKGML::TestKGMLSubstrateProductSetter: - test_id=: .: (0.000505) - test_initialize_0: .: (0.000170) - test_initialize_1: .: (0.000167) - test_initialize_2: .: (0.000185) - test_name=: .: (0.000230) + test_id=: .: (0.001269) + test_initialize_0: .: (0.000461) + test_initialize_1: .: (0.000464) + test_initialize_2: .: (0.000485) + test_name=: .: (0.000711) Bio::TestKeggKGML::TestKGMLSubstrateSetter: - test_id=: .: (0.000422) - test_initialize_0: .: (0.000198) - test_initialize_1: .: (0.000173) - test_initialize_2: .: (0.000181) - test_name=: .: (0.000231) + test_id=: .: (0.001789) + test_initialize_0: .: (0.000458) + test_initialize_1: .: (0.000503) + test_initialize_2: .: (0.000476) + test_name=: .: (0.000662) Bio::TestKeggModule: - test_compounds: .: (0.001568) - test_compounds_as_hash: .: (0.000526) - test_compounds_as_strings: .: (0.000443) - test_definition: .: (0.000435) - test_entry_id: .: (0.000381) - test_keggclass: .: (0.000382) - test_name: .: (0.000380) - test_new: .: (0.000815) - test_orthologs: .: (0.000609) - test_orthologs_as_array: .: (0.000569) - test_orthologs_as_hash: .: (0.000501) - test_orthologs_as_strings: .: (0.000429) - test_pathways: .: (0.000364) - test_pathways_as_hash: .: (0.000360) - test_pathways_as_strings: .: (0.000396) - test_reactions: .: (0.000744) - test_reactions_as_hash: .: (0.000515) - test_reactions_as_strings: .: (0.000411) + test_compounds: .: (0.002670) + test_compounds_as_hash: .: (0.001404) + test_compounds_as_strings: .: (0.001174) + test_definition: .: (0.001121) + test_entry_id: .: (0.000992) + test_keggclass: .: (0.001159) + test_name: .: (0.001002) + test_new: .: (0.000941) + test_orthologs: .: (0.001469) + test_orthologs_as_array: .: (0.001525) + test_orthologs_as_hash: .: (0.001387) + test_orthologs_as_strings: .: (0.001172) + test_pathways: .: (0.000969) + test_pathways_as_hash: .: (0.001324) + test_pathways_as_strings: .: (0.000977) + test_reactions: .: (0.001372) + test_reactions_as_hash: .: (0.001417) + test_reactions_as_strings: .: (0.001122) Bio::TestKeggOrthology: - test_dblinks: .: (0.001758) - test_dblinks_as_hash: .: (0.000841) - test_dblinks_as_strings: .: (0.000717) - test_definition: .: (0.001135) - test_entry_id: .: (0.000867) - test_genes_as_hash: .: (0.023911) - test_genes_as_strings: .: (0.007986) - test_keggclass: .: (0.001048) - test_keggclasses: .: (0.000957) - test_modules: .: (0.000741) - test_modules_as_hash: .: (0.000769) - test_modules_as_strings: .: (0.000718) - test_name: .: (0.000717) - test_names: .: (0.000714) - test_pathways_as_strings: .: (0.000706) - test_pathways_in_keggclass: .: (0.001235) - test_references: .: (0.000979) + test_dblinks: .: (0.003578) + test_dblinks_as_hash: .: (0.002207) + test_dblinks_as_strings: .: (0.001959) + test_definition: .: (0.002960) + test_entry_id: .: (0.002045) + test_genes_as_hash: .: (0.063595) + test_genes_as_strings: .: (0.021136) + test_keggclass: .: (0.002711) + test_keggclasses: .: (0.002623) + test_modules: .: (0.002298) + test_modules_as_hash: .: (0.001985) + test_modules_as_strings: .: (0.001989) + test_name: .: (0.002021) + test_names: .: (0.002006) + test_pathways_as_strings: .: (0.002063) + test_pathways_in_keggclass: .: (0.002627) + test_references: .: (0.003547) Bio::TestKeggPathway_map00052: - test_compounds_as_hash: .: (0.001168) - test_compounds_as_strings: .: (0.000377) - test_dblinks_as_hash: .: (0.000442) - test_dblinks_as_strings: .: (0.000370) - test_description: .: (0.000389) - test_diseases_as_hash: .: (0.000355) - test_diseases_as_strings: .: (0.000348) - test_entry_id: .: (0.000759) - test_enzymes_as_strings: .: (0.000502) - test_genes_as_hash: .: (0.000465) - test_genes_as_strings: .: (0.000459) - test_keggclass: .: (0.000473) - test_ko_pathway: .: (0.000450) - test_modules_as_hash: .: (0.000565) - test_modules_as_strings: .: (0.000444) - test_name: .: (0.000428) - test_organism: .: (0.000434) - test_orthologs_as_hash: .: (0.000774) - test_orthologs_as_strings: .: (0.000503) - test_pathways_as_hash: .: (0.000457) - test_pathways_as_strings: .: (0.000426) - test_reactions_as_hash: .: (0.000406) - test_reactions_as_strings: .: (0.000401) - test_references: .: (0.000439) - test_rel_pathways_as_hash: .: (0.000550) - test_rel_pathways_as_strings: .: (0.000457) + test_compounds_as_hash: .: (0.002279) + test_compounds_as_strings: .: (0.001061) + test_dblinks_as_hash: .: (0.001061) + test_dblinks_as_strings: .: (0.000984) + test_description: .: (0.001089) + test_diseases_as_hash: .: (0.001060) + test_diseases_as_strings: .: (0.000982) + test_entry_id: .: (0.002022) + test_enzymes_as_strings: .: (0.001034) + test_genes_as_hash: .: (0.000977) + test_genes_as_strings: .: (0.000980) + test_keggclass: .: (0.001124) + test_ko_pathway: .: (0.001052) + test_modules_as_hash: .: (0.001464) + test_modules_as_strings: .: (0.001118) + test_name: .: (0.001912) + test_organism: .: (0.001322) + test_orthologs_as_hash: .: (0.000997) + test_orthologs_as_strings: .: (0.000972) + test_pathways_as_hash: .: (0.001116) + test_pathways_as_strings: .: (0.001017) + test_reactions_as_hash: .: (0.000971) + test_reactions_as_strings: .: (0.001058) + test_references: .: (0.000993) + test_rel_pathways_as_hash: .: (0.002039) + test_rel_pathways_as_strings: .: (0.001347) Bio::TestKeggReaction: - test_definition: .: (0.001744) - test_entry_id: .: (0.000516) - test_enzymes: .: (0.000607) - test_equation: .: (0.000485) - test_name: .: (0.000488) - test_orthologs_as_hash: .: (0.000560) - test_orthologs_as_strings: .: (0.000462) - test_pathways_as_hash: .: (0.000490) - test_pathways_as_strings: .: (0.000452) - test_rpairs_as_hash: .: (0.000818) - test_rpairs_as_strings: .: (0.000456) - test_rpairs_as_tokens: .: (0.000517) + test_definition: .: (0.002507) + test_entry_id: .: (0.001248) + test_enzymes: .: (0.001185) + test_equation: .: (0.001234) + test_name: .: (0.001213) + test_orthologs_as_hash: .: (0.001379) + test_orthologs_as_strings: .: (0.001787) + test_pathways_as_hash: .: (0.001337) + test_pathways_as_strings: .: (0.001192) + test_rpairs_as_hash: .: (0.001392) + test_rpairs_as_strings: .: (0.001201) + test_rpairs_as_tokens: .: (0.001321) Bio::TestLasergene: - test_methods: .: (0.015583) + test_methods: .: (0.040231) Bio::TestLocations: - test_complement: .: (0.000620) - test_hat: .: (0.000261) - test_normal: .: (0.000280) - test_replace_single_base: .: (0.000224) - test_should_not_modify_argument: .: (0.000251) + test_complement: .: (0.001964) + test_hat: .: (0.000765) + test_normal: .: (0.000669) + test_replace_single_base: .: (0.000596) + test_should_not_modify_argument: .: (0.000530) Bio::TestLocationsRoundTrip: - test_locations_roundtrip: .: (0.007171) - test_locations_to_s: .: (0.003355) + test_locations_roundtrip: .: (0.020767) + test_locations_to_s: .: (0.009671) Bio::TestMEDLINE: - test_authors: .: (0.001760) - test_authors_with_last_name_all_caps: .: (0.000236) - test_authors_with_suffix: .: (0.000237) + test_authors: .: (0.003787) + test_authors_with_last_name_all_caps: .: (0.000564) + test_authors_with_suffix: .: (0.000576) Bio::TestMEDLINE_20146148: - test_ab: .: (0.001624) - test_ad: .: (0.000777) - test_au: .: (0.000694) - test_authors: .: (0.000890) - test_doi: .: (0.000708) - test_dp: .: (0.000717) - test_ip: .: (0.000714) - test_mh: .: (0.000723) - test_pages: .: (0.000792) - test_pg: .: (0.000719) - test_pii: .: (0.000842) - test_pmid: .: (0.000695) - test_pt: .: (0.000954) - test_reference: .: (0.001180) - test_self_new: .: (0.000855) - test_so: .: (0.000702) - test_ta: .: (0.000967) - test_ti: .: (0.000821) - test_ui: .: (0.000762) - test_vi: .: (0.000710) - test_year: .: (0.000758) + test_ab: .: (0.004019) + test_ad: .: (0.002135) + test_au: .: (0.001923) + test_authors: .: (0.002064) + test_doi: .: (0.002571) + test_dp: .: (0.001992) + test_ip: .: (0.002030) + test_mh: .: (0.002005) + test_pages: .: (0.002669) + test_pg: .: (0.002135) + test_pii: .: (0.001947) + test_pmid: .: (0.001989) + test_pt: .: (0.002582) + test_reference: .: (0.003175) + test_self_new: .: (0.002093) + test_so: .: (0.001923) + test_ta: .: (0.002598) + test_ti: .: (0.002192) + test_ui: .: (0.001909) + test_vi: .: (0.001926) + test_year: .: (0.001853) Bio::TestMapSimple: - test_attributes: .: (0.000793) + test_attributes: .: (0.001658) Bio::TestMapping: - test_add_mapping_as_map: .: (0.000667) - test_add_mapping_as_marker: .: (0.000402) - test_contains_marker?: .: (0.000280) - test_mapped_to?: .: (0.000287) - test_mapping_location_comparison: .: (0.000620) - test_mappings_as_map_each: .: (0.000256) - test_mappings_as_marker_each: .: (0.000332) - test_mappings_on: .: (0.000344) - test_multiple_mappings_between_same_marker_and_map: .: (0.000877) - test_positions_on: .: (0.000439) - test_raise_error_kind_of: .: (0.000711) + test_add_mapping_as_map: .: (0.001588) + test_add_mapping_as_marker: .: (0.000848) + test_contains_marker?: .: (0.000633) + test_mapped_to?: .: (0.000605) + test_mapping_location_comparison: .: (0.001639) + test_mappings_as_map_each: .: (0.000620) + test_mappings_as_marker_each: .: (0.000796) + test_mappings_on: .: (0.001505) + test_multiple_mappings_between_same_marker_and_map: .: (0.001814) + test_positions_on: .: (0.000926) + test_raise_error_kind_of: .: (0.001921) Bio::TestMast: - test_check_options_with_empty_opts: .: (0.000734) - test_check_options_with_invalid_opts: .: (0.000435) - test_check_options_with_valid_opts: .: (0.000367) - test_command_to_be_run: .: (0.000389) - test_config_defaults: .: (0.000588) - test_minimal_config: .: (0.000331) - test_more_config: .: (0.000289) - test_run: .: (0.000212) + test_check_options_with_empty_opts: .: (0.001599) + test_check_options_with_invalid_opts: .: (0.000964) + test_check_options_with_valid_opts: .: (0.000853) + test_command_to_be_run: .: (0.000967) + test_config_defaults: .: (0.000763) + test_minimal_config: .: (0.001358) + test_more_config: .: (0.000723) + test_run: .: (0.000509) Bio::TestMastReport: - test_parse_hit_list_with_bad_data: .: (0.001501) - test_report_has_motifs: .: (0.000665) + test_parse_hit_list_with_bad_data: .: (0.002727) + test_report_has_motifs: .: (0.001411) Bio::TestModel: - test_addChain: .: (0.000480) - test_comp: .: (0.000251) - test_each: .: (0.000246) - test_each_chain: .: (0.000203) - test_inspect: .: (0.000200) - test_rehash: .: (0.000469) - test_square_brace: .: (0.000219) - test_to_s: .: (0.000210) + test_addChain: .: (0.001075) + test_comp: .: (0.000603) + test_each: .: (0.000634) + test_each_chain: .: (0.000566) + test_inspect: .: (0.000496) + test_rehash: .: (0.000461) + test_square_brace: .: (0.001028) + test_to_s: .: (0.000577) Bio::TestModelFinder: - test_find_model: .: (0.000537) + test_find_model: .: (0.001138) Bio::TestMotif: - test_creation_and_attributes: .: (0.000526) - test_length: .: (0.000171) + test_creation_and_attributes: .: (0.001321) + test_length: .: (0.000475) Bio::TestMyGraph: - test_cliquishness: .: (0.000955) + test_cliquishness: .: (0.002608) Bio::TestNA: - test_accessor: .: (0.000365) - test_na: .: (0.000176) - test_name: .: (0.000341) - test_names: .: (0.000216) - test_to_re: .: (0.000459) - test_weight: .: (0.000212) - test_weight_rna: .: (0.000190) + test_accessor: .: (0.000937) + test_na: .: (0.000441) + test_name: .: (0.000432) + test_names: .: (0.000415) + test_to_re: .: (0.001530) + test_weight: .: (0.000527) + test_weight_rna: .: (0.000501) Bio::TestNAConstants: - test_NAMES: .: (0.000354) - test_NAMES_1_to_name: .: (0.000172) - test_WEIGHT: .: (0.000191) + test_NAMES: .: (0.000936) + test_NAMES_1_to_name: .: (0.000427) + test_WEIGHT: .: (0.000481) Bio::TestNATranslate: - test_translate: .: (0.000608) - test_translate_1: .: (0.000319) - test_translate_2: .: (0.000217) - test_translate_3: .: (0.000222) - test_translate_4: .: (0.000332) - test_translate_5: .: (0.000209) - test_translate_6: .: (0.000191) + test_translate: .: (0.001364) + test_translate_1: .: (0.000776) + test_translate_2: .: (0.000519) + test_translate_3: .: (0.000498) + test_translate_4: .: (0.000740) + test_translate_5: .: (0.000524) + test_translate_6: .: (0.000522) Bio::TestNCBIDB: - test_fetch: .: (0.000530) - test_p_entry2hash: .: (0.000163) - test_p_subtag2array: .: (0.000136) - test_p_toptag2array: .: (0.000146) + test_fetch: .: (0.001608) + test_p_entry2hash: .: (0.000394) + test_p_subtag2array: .: (0.000412) + test_p_toptag2array: .: (0.000382) Bio::TestNewick: - test_reparse: .: (0.002510) - test_reparse_before_lazy_parsing: .: (0.001033) - test_string_tree: .: (0.001676) + test_reparse: .: (0.006626) + test_reparse_before_lazy_parsing: .: (0.002233) + test_string_tree: .: (0.005019) Bio::TestNewick2: - test_string_tree: .: (0.001297) + test_string_tree: .: (0.003567) Bio::TestNewickPrivate: - test_parse_newick_get_tokens_for_leaf: .: (0.000471) - test_parse_newick_leaf: .: (0.000406) - test_parse_newick_tokenize: .: (0.001013) + test_parse_newick_get_tokens_for_leaf: .: (0.001117) + test_parse_newick_leaf: .: (0.000981) + test_parse_newick_tokenize: .: (0.001865) Bio::TestNexus: - test_nexus: .: (0.022149) + test_nexus: .: (0.065000) Bio::TestOSLine: - test_period_trancation_O63147: .: (0.000794) - test_uncapitalized_letter_Q32725_9POAL: .: (0.000315) + test_period_trancation_O63147: .: (0.001329) + test_uncapitalized_letter_Q32725_9POAL: .: (0.001112) Bio::TestPAMLCodeml::TestCodeml: - test_dump_parameters: .: (0.000447) - test_load_parameters: .: (0.000246) - test_parameters: .: (0.000190) - test_set_default_parameters: .: (0.000226) + test_dump_parameters: .: (0.001114) + test_load_parameters: .: (0.000581) + test_parameters: .: (0.000439) + test_set_default_parameters: .: (0.000564) Bio::TestPAMLCodeml::TestCodemlControlGeneration: - test_control_file_generated: .: (0.001762) - test_expected_parameters_set_in_control_file: .: (0.001525) + test_control_file_generated: .: (0.003452) + test_expected_parameters_set_in_control_file: .: (0.003492) Bio::TestPAMLCodeml::TestCodemlInitialize: - test_new_with_one_argument: .: (0.000448) - test_new_with_parameters: .: (0.000481) - test_new_with_two_argument: .: (0.000235) - test_new_without_argument: .: (0.000204) + test_new_with_one_argument: .: (0.001200) + test_new_with_parameters: .: (0.001173) + test_new_with_two_argument: .: (0.000724) + test_new_without_argument: .: (0.000516) Bio::TestPAMLCodeml::TestCodemlRates: - test_rates_first_position: .: (0.003639) - test_rates_hundred_and_fiftieth_position: .: (0.002818) - test_rates_last_position: .: (0.002694) + test_rates_first_position: .: (0.011118) + test_rates_hundred_and_fiftieth_position: .: (0.007751) + test_rates_last_position: .: (0.007582) Bio::TestPAMLCodeml::TestCodemlReport: - test_alpha: .: (0.020747) - test_tree: .: (0.020254) - test_tree_length: .: (0.020284) - test_tree_log_likelihood: .: (0.020733) + test_alpha: .: (0.066431) + test_tree: .: (0.065425) + test_tree_length: .: (0.065612) + test_tree_log_likelihood: .: (0.065348) Bio::TestPAMLCodeml::TestControlFileUsage: - test_correct_parameters_should_be_loaded: .: (0.001608) - test_parameters_should_be_loaded_from_control: .: (0.000566) + test_correct_parameters_should_be_loaded: .: (0.002878) + test_parameters_should_be_loaded_from_control: .: (0.001508) Bio::TestPAMLCodeml::TestExpectedErrorsThrown: - test_error_thrown_if_seqfile_does_not_specified: .: (0.003189) + test_error_thrown_if_seqfile_does_not_specified: .: (0.007688) Bio::TestPAMLCodemlReportWithModels::TestCodemlModelM0M3: - test_alpha: .: (0.001210) - test_dN_dS: .: (0.000445) - test_kappa: .: (0.000427) - test_lnL: .: (0.000350) - test_m3_classes: .: (0.000507) - test_m3_lnL: .: (0.000355) - test_m3_to_s: .: (0.000360) - test_m3_tree: .: (0.001507) - test_omega: .: (0.000462) - test_to_s: .: (0.000552) - test_tree: .: (0.001491) - test_tree_length: .: (0.000674) + test_alpha: .: (0.002238) + test_dN_dS: .: (0.001176) + test_kappa: .: (0.001026) + test_lnL: .: (0.000946) + test_m3_classes: .: (0.001507) + test_m3_lnL: .: (0.001165) + test_m3_to_s: .: (0.001020) + test_m3_tree: .: (0.004697) + test_omega: .: (0.001052) + test_to_s: .: (0.001012) + test_tree: .: (0.004291) + test_tree_length: .: (0.001572) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSiteM0M3: - test_dN_dS: .: (0.001382) - test_p: .: (0.000871) - test_position: .: (0.000858) - test_probability: .: (0.001277) - test_w: .: (0.001064) + test_dN_dS: .: (0.003000) + test_p: .: (0.002113) + test_position: .: (0.002090) + test_probability: .: (0.002357) + test_w: .: (0.002061) Bio::TestPAMLCodemlReportWithModels::TestCodemlPositiveSitesM0M3: - test_graph: .: (0.001549) - test_graph_omega: .: (0.001209) + test_graph: .: (0.003514) + test_graph_omega: .: (0.002772) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM0M3: - test_descr: .: (0.000747) - test_footer: .: (0.000510) - test_header: .: (0.000451) - test_initialize: .: (0.000486) - test_models: .: (0.000631) - test_nb_sites: .: (0.001497) - test_num_codons: .: (0.000476) - test_num_sequences: .: (0.000431) - test_significant: .: (0.000503) + test_descr: .: (0.001700) + test_footer: .: (0.000964) + test_header: .: (0.000899) + test_initialize: .: (0.001100) + test_models: .: (0.001053) + test_nb_sites: .: (0.003983) + test_num_codons: .: (0.001089) + test_num_sequences: .: (0.001066) + test_significant: .: (0.001023) Bio::TestPAMLCodemlReportWithModels::TestCodemlReportM7M8: - test_models: .: (0.001355) - test_nb_sites: .: (0.000625) - test_significant: .: (0.000509) - test_sites: .: (0.002644) + test_models: .: (0.002407) + test_nb_sites: .: (0.001619) + test_significant: .: (0.001906) + test_sites: .: (0.006165) Bio::TestPDB: - test_accession: .: (0.013379) - test_addModel: .: (0.001778) - test_authors: .: (0.002029) - test_bracket: .: (0.001658) - test_classification: .: (0.002254) - test_dbref: .: (0.002031) - test_definition: .: (0.002011) - test_each: .: (0.001702) - test_each_model: .: (0.001949) - test_entry_id: .: (0.001916) - test_helix: .: (0.002118) - test_inspect: .: (0.006882) - test_jrnl: .: (0.002177) - test_keywords: .: (0.002025) - test_record: .: (0.001678) - test_remark: .: (0.002051) - test_seqres: .: (0.002713) - test_sheet: .: (0.004098) - test_ssbond: .: (0.001693) - test_to_s: .: (0.002721) - test_turn: .: (0.001694) - test_version: .: (0.002054) + test_accession: .: (0.006950) + test_addModel: .: (0.005492) + test_authors: .: (0.004386) + test_bracket: .: (0.004278) + test_classification: .: (0.005566) + test_dbref: .: (0.004819) + test_definition: .: (0.005309) + test_each: .: (0.004494) + test_each_model: .: (0.005254) + test_entry_id: .: (0.004388) + test_helix: .: (0.005319) + test_inspect: .: (0.004449) + test_jrnl: .: (0.004962) + test_keywords: .: (0.004435) + test_record: .: (0.004891) + test_remark: .: (0.005399) + test_seqres: .: (0.006389) + test_sheet: .: (0.008394) + test_ssbond: .: (0.005207) + test_to_s: .: (0.005761) + test_turn: .: (0.005918) + test_version: .: (0.004474) Bio::TestPDBRecord::TestANISOU: - test_U11: .: (0.000601) - test_U12: .: (0.000317) - test_U13: .: (0.000282) - test_U22: .: (0.000270) - test_U23: .: (0.000264) - test_U33: .: (0.000257) - test_altLoc: .: (0.000282) - test_chainID: .: (0.000280) - test_charge: .: (0.000279) - test_element: .: (0.000877) - test_iCode: .: (0.000382) - test_name: .: (0.000328) - test_resName: .: (0.000266) - test_resSeq: .: (0.000250) - test_segID: .: (0.000246) - test_serial: .: (0.000256) + test_U11: .: (0.001417) + test_U12: .: (0.000708) + test_U13: .: (0.000666) + test_U22: .: (0.001532) + test_U23: .: (0.000666) + test_U33: .: (0.000653) + test_altLoc: .: (0.000661) + test_chainID: .: (0.000655) + test_charge: .: (0.000697) + test_element: .: (0.000686) + test_iCode: .: (0.000669) + test_name: .: (0.000660) + test_resName: .: (0.000995) + test_resSeq: .: (0.000669) + test_segID: .: (0.000657) + test_serial: .: (0.000656) Bio::TestPDBRecord::TestATOM: - test_altLoc: .: (0.000491) - test_anisou: .: (0.000202) - test_chainID: .: (0.000201) - test_charge: .: (0.000199) - test_comparable: .: (0.000332) - test_do_parse: .: (0.000275) - test_element: .: (0.000249) - test_iCode: .: (0.000759) - test_name: .: (0.000246) - test_occupancy: .: (0.000368) - test_original_data: .: (0.000225) - test_record_name: .: (0.000262) - test_resName: .: (0.000259) - test_resSeq: .: (0.000188) - test_residue: .: (0.000264) - test_segID: .: (0.000233) - test_serial: .: (0.000188) - test_sigatm: .: (0.000192) - test_tempFactor: .: (0.000277) - test_ter: .: (0.000205) - test_to_a: .: (0.000204) - test_to_s: .: (0.000255) - test_x: .: (0.000327) - test_xyz: .: (0.000532) - test_y: .: (0.000337) - test_z: .: (0.000270) + test_altLoc: .: (0.001123) + test_anisou: .: (0.000510) + test_chainID: .: (0.001467) + test_charge: .: (0.000761) + test_comparable: .: (0.000655) + test_do_parse: .: (0.000482) + test_element: .: (0.000482) + test_iCode: .: (0.000475) + test_name: .: (0.000486) + test_occupancy: .: (0.000775) + test_original_data: .: (0.000507) + test_record_name: .: (0.000495) + test_resName: .: (0.000489) + test_resSeq: .: (0.000482) + test_residue: .: (0.000533) + test_segID: .: (0.000493) + test_serial: .: (0.029164) + test_sigatm: .: (0.000559) + test_tempFactor: .: (0.000770) + test_ter: .: (0.000512) + test_to_a: .: (0.000535) + test_to_s: .: (0.000641) + test_x: .: (0.000665) + test_xyz: .: (0.000691) + test_y: .: (0.000697) + test_z: .: (0.000662) Bio::TestPDBRecord::TestAUTHOR: - test_authorList: .: (0.000541) + test_authorList: .: (0.001167) Bio::TestPDBRecord::TestCAVEAT: - test_comment: .: (0.000560) - test_idcode: .: (0.000283) + test_comment: .: (0.002074) + test_idcode: .: (0.000518) Bio::TestPDBRecord::TestCISPEP: - test_chainID1: .: (0.000536) - test_chainID2: .: (0.000301) - test_icode1: .: (0.000322) - test_icode2: .: (0.000774) - test_measure: .: (0.000313) - test_modNum: .: (0.000324) - test_pep1: .: (0.000261) - test_pep2: .: (0.000281) - test_seqNum1: .: (0.000302) - test_seqNum2: .: (0.000298) - test_serNum: .: (0.000353) + test_chainID1: .: (0.001271) + test_chainID2: .: (0.000652) + test_icode1: .: (0.000627) + test_icode2: .: (0.000659) + test_measure: .: (0.000718) + test_modNum: .: (0.000641) + test_pep1: .: (0.000629) + test_pep2: .: (0.000621) + test_seqNum1: .: (0.000675) + test_seqNum2: .: (0.000647) + test_serNum: .: (0.001845) Bio::TestPDBRecord::TestCOMPND: - test_compound: .: (0.000560) + test_compound: .: (0.001198) Bio::TestPDBRecord::TestCONECT: - test_serial: .: (0.000528) + test_serial: .: (0.001066) Bio::TestPDBRecord::TestCRYST1: - test_a: .: (0.000463) - test_alpha: .: (0.000218) - test_b: .: (0.000228) - test_beta: .: (0.000914) - test_c: .: (0.000248) - test_gamma: .: (0.000222) - test_sGroup: .: (0.000211) - test_z: .: (0.000213) + test_a: .: (0.001174) + test_alpha: .: (0.000550) + test_b: .: (0.000530) + test_beta: .: (0.000540) + test_c: .: (0.000538) + test_gamma: .: (0.000540) + test_sGroup: .: (0.000550) + test_z: .: (0.000538) Bio::TestPDBRecord::TestDBREF: - test_chainID: .: (0.000624) - test_database: .: (0.000381) - test_dbAccession: .: (0.000327) - test_dbIdCode: .: (0.000399) - test_dbseqBegin: .: (0.000412) - test_dbseqEnd: .: (0.000332) - test_idCode: .: (0.000293) - test_idbnsBeg: .: (0.000353) - test_insertBegin: .: (0.000311) - test_insertEnd: .: (0.000307) - test_seqBegin: .: (0.000282) - test_seqEnd: .: (0.000289) + test_chainID: .: (0.002351) + test_database: .: (0.000807) + test_dbAccession: .: (0.000724) + test_dbIdCode: .: (0.000767) + test_dbseqBegin: .: (0.000822) + test_dbseqEnd: .: (0.000735) + test_idCode: .: (0.000718) + test_idbnsBeg: .: (0.000739) + test_insertBegin: .: (0.000731) + test_insertEnd: .: (0.000725) + test_seqBegin: .: (0.000721) + test_seqEnd: .: (0.000719) Bio::TestPDBRecord::TestDefault: - test_text: .: (0.000560) + test_text: .: (0.001264) Bio::TestPDBRecord::TestENDMDL: - test_serial: .: (0.000458) + test_serial: .: (0.001073) Bio::TestPDBRecord::TestEXPDTA: - test_technique: .: (0.000494) + test_technique: .: (0.001039) Bio::TestPDBRecord::TestEnd: - test_serial: .: (0.000429) + test_serial: .: (0.000990) Bio::TestPDBRecord::TestHEADER: - test_classification: .: (0.000553) - test_depDate: .: (0.000281) - test_idCode: .: (0.000223) + test_classification: .: (0.001070) + test_depDate: .: (0.000561) + test_idCode: .: (0.000542) Bio::TestPDBRecord::TestHET: - test_ChainID: .: (0.000572) - test_hetID: .: (0.000255) - test_iCode: .: (0.000274) - test_numHetAtoms: .: (0.000281) - test_seqNum: .: (0.000303) - test_text: .: (0.000223) + test_ChainID: .: (0.001192) + test_hetID: .: (0.000594) + test_iCode: .: (0.001961) + test_numHetAtoms: .: (0.000611) + test_seqNum: .: (0.000573) + test_text: .: (0.000569) Bio::TestPDBRecord::TestHETATM: - test_altLoc: .: (0.000459) - test_anisou: .: (0.000224) - test_chainID: .: (0.000196) - test_charge: .: (0.000205) - test_comparable: .: (0.000308) - test_do_parse: .: (0.000705) - test_element: .: (0.000311) - test_iCode: .: (0.000239) - test_name: .: (0.000193) - test_occupancy: .: (0.000306) - test_original_data: .: (0.000203) - test_record_name: .: (0.000198) - test_resName: .: (0.000194) - test_resSeq: .: (0.000189) - test_residue: .: (0.000193) - test_segID: .: (0.000192) - test_serial: .: (0.000189) - test_sigatm: .: (0.000199) - test_tempFactor: .: (0.000276) - test_ter: .: (0.000224) - test_to_a: .: (0.000590) - test_to_s: .: (0.000272) - test_x: .: (0.000259) - test_xyz: .: (0.000240) - test_y: .: (0.000249) - test_z: .: (0.000243) + test_altLoc: .: (0.001143) + test_anisou: .: (0.000508) + test_chainID: .: (0.000498) + test_charge: .: (0.000489) + test_comparable: .: (0.000647) + test_do_parse: .: (0.000539) + test_element: .: (0.000495) + test_iCode: .: (0.000487) + test_name: .: (0.000482) + test_occupancy: .: (0.002181) + test_original_data: .: (0.000538) + test_record_name: .: (0.000491) + test_resName: .: (0.000484) + test_resSeq: .: (0.000481) + test_residue: .: (0.000522) + test_segID: .: (0.000493) + test_serial: .: (0.000476) + test_sigatm: .: (0.000483) + test_tempFactor: .: (0.000662) + test_ter: .: (0.000482) + test_to_a: .: (0.000515) + test_to_s: .: (0.000628) + test_x: .: (0.000656) + test_xyz: .: (0.001877) + test_y: .: (0.000670) + test_z: .: (0.000639) Bio::TestPDBRecord::TestHYDBND: - test_Chain1: .: (0.000671) - test_ChainH: .: (0.000428) - test_ICode1: .: (0.000355) - test_altLoc1: .: (0.000344) - test_altLoc2: .: (0.000325) - test_altLocH: .: (0.000791) - test_chainID2: .: (0.000457) - test_iCode2: .: (0.000442) - test_iCodeH: .: (0.000487) - test_name1: .: (0.000391) - test_name2: .: (0.000423) - test_nameH: .: (0.000388) - test_resName1: .: (0.000372) - test_resName2: .: (0.000392) - test_resSeq1: .: (0.000395) - test_resSeq2: .: (0.000592) - test_resSeqH: .: (0.000434) - test_sym1: .: (0.000404) - test_sym2: .: (0.000355) + test_Chain1: .: (0.001587) + test_ChainH: .: (0.000832) + test_ICode1: .: (0.000812) + test_altLoc1: .: (0.000861) + test_altLoc2: .: (0.000866) + test_altLocH: .: (0.000806) + test_chainID2: .: (0.000810) + test_iCode2: .: (0.001642) + test_iCodeH: .: (0.000817) + test_name1: .: (0.000777) + test_name2: .: (0.000826) + test_nameH: .: (0.000830) + test_resName1: .: (0.000795) + test_resName2: .: (0.000788) + test_resSeq1: .: (0.000827) + test_resSeq2: .: (0.000878) + test_resSeqH: .: (0.000804) + test_sym1: .: (0.000795) + test_sym2: .: (0.001640) Bio::TestPDBRecord::TestKEYWDS: - test_keywds: .: (0.000605) + test_keywds: .: (0.001125) Bio::TestPDBRecord::TestLINK: - test_altLoc1: .: (0.000738) - test_altLoc2: .: (0.000351) - test_chainID1: .: (0.000335) - test_chainID2: .: (0.000350) - test_iCode1: .: (0.000349) - test_iCode2: .: (0.000344) - test_name1: .: (0.000337) - test_name2: .: (0.000882) - test_resName1: .: (0.000303) - test_resName2: .: (0.000280) - test_resSeq1: .: (0.000279) - test_resSeq2: .: (0.000274) - test_sym1: .: (0.000279) - test_sym2: .: (0.000271) + test_altLoc1: .: (0.001316) + test_altLoc2: .: (0.000722) + test_chainID1: .: (0.000704) + test_chainID2: .: (0.000699) + test_iCode1: .: (0.000805) + test_iCode2: .: (0.000773) + test_name1: .: (0.000706) + test_name2: .: (0.000697) + test_resName1: .: (0.001811) + test_resName2: .: (0.000721) + test_resSeq1: .: (0.000694) + test_resSeq2: .: (0.000744) + test_sym1: .: (0.000686) + test_sym2: .: (0.000691) Bio::TestPDBRecord::TestMASTER: - test_numConect: .: (0.000536) - test_numCoord: .: (0.000335) - test_numHelix: .: (0.000319) - test_numHet: .: (0.000308) - test_numRemark: .: (0.000260) - test_numSeq: .: (0.000212) - test_numSheet: .: (0.000686) - test_numSite: .: (0.000210) - test_numTer: .: (0.000201) - test_numTurn: .: (0.000202) - test_numXform: .: (0.000199) + test_numConect: .: (0.001203) + test_numCoord: .: (0.000552) + test_numHelix: .: (0.000543) + test_numHet: .: (0.000541) + test_numRemark: .: (0.000547) + test_numSeq: .: (0.000571) + test_numSheet: .: (0.000547) + test_numSite: .: (0.000588) + test_numTer: .: (0.000539) + test_numTurn: .: (0.000559) + test_numXform: .: (0.000533) Bio::TestPDBRecord::TestMODEL: - test_serial: .: (0.000526) + test_serial: .: (0.001030) Bio::TestPDBRecord::TestMODRES: - test_chainID: .: (0.000569) - test_comment: .: (0.000293) - test_iCode: .: (0.000264) - test_idCode: .: (0.000275) - test_resName: .: (0.000272) - test_seqNum: .: (0.000276) - test_stdRes: .: (0.000284) + test_chainID: .: (0.001195) + test_comment: .: (0.000623) + test_iCode: .: (0.000602) + test_idCode: .: (0.000611) + test_resName: .: (0.000603) + test_seqNum: .: (0.000608) + test_stdRes: .: (0.000606) Bio::TestPDBRecord::TestMTRIX1: - test_Mn1: .: (0.000770) - test_Mn2: .: (0.000283) - test_Mn3: .: (0.000277) - test_Vn: .: (0.000292) - test_iGiven: .: (0.000255) - test_serial: .: (0.000254) + test_Mn1: .: (0.002207) + test_Mn2: .: (0.000556) + test_Mn3: .: (0.000498) + test_Vn: .: (0.000504) + test_iGiven: .: (0.000516) + test_serial: .: (0.000496) Bio::TestPDBRecord::TestMTRIX2: - test_Mn1: .: (0.000602) - test_Mn2: .: (0.000289) - test_Mn3: .: (0.000295) - test_Vn: .: (0.000287) - test_iGiven: .: (0.000243) - test_serial: .: (0.000278) + test_Mn1: .: (0.001181) + test_Mn2: .: (0.000519) + test_Mn3: .: (0.000512) + test_Vn: .: (0.000551) + test_iGiven: .: (0.000522) + test_serial: .: (0.000508) Bio::TestPDBRecord::TestMTRIX3: - test_Mn1: .: (0.000540) - test_Mn2: .: (0.000237) - test_Mn3: .: (0.000231) - test_Vn: .: (0.000277) - test_iGiven: .: (0.000307) - test_serial: .: (0.000243) + test_Mn1: .: (0.001053) + test_Mn2: .: (0.001539) + test_Mn3: .: (0.000538) + test_Vn: .: (0.000500) + test_iGiven: .: (0.000509) + test_serial: .: (0.000536) Bio::TestPDBRecord::TestOBSLTE: - test_idCode: .: (0.000539) - test_rIdCode: .: (0.000265) - test_repDate: .: (0.000234) + test_idCode: .: (0.001212) + test_rIdCode: .: (0.000564) + test_repDate: .: (0.000544) Bio::TestPDBRecord::TestORIGX1: - test_On1: .: (0.000519) - test_On2: .: (0.000244) - test_On3: .: (0.000230) - test_Tn: .: (0.000223) + test_On1: .: (0.001171) + test_On2: .: (0.000508) + test_On3: .: (0.000499) + test_Tn: .: (0.000489) Bio::TestPDBRecord::TestREVDAT: - test_modDate: .: (0.001035) - test_modId: .: (0.000261) - test_modNum: .: (0.000468) - test_modType: .: (0.000292) - test_record: .: (0.000697) + test_modDate: .: (0.002125) + test_modId: .: (0.000596) + test_modNum: .: (0.000615) + test_modType: .: (0.000554) + test_record: .: (0.000554) Bio::TestPDBRecord::TestRemarkN: - test_remarkNum: .: (0.000429) - test_text: .: (0.000224) + test_remarkNum: .: (0.001061) + test_text: .: (0.000536) Bio::TestPDBRecord::TestSCALE1: - test_Sn1: .: (0.000488) - test_Sn2: .: (0.000224) - test_Sn3: .: (0.000217) - test_Un: .: (0.000269) + test_Sn1: .: (0.001054) + test_Sn2: .: (0.000496) + test_Sn3: .: (0.000482) + test_Un: .: (0.000529) Bio::TestPDBRecord::TestSCALE2: - test_Sn1: .: (0.000541) - test_Sn2: .: (0.000230) - test_Sn3: .: (0.000213) - test_Un: .: (0.000225) + test_Sn1: .: (0.001032) + test_Sn2: .: (0.000495) + test_Sn3: .: (0.001523) + test_Un: .: (0.000540) Bio::TestPDBRecord::TestSCALE3: - test_Sn1: .: (0.000474) - test_Sn2: .: (0.000240) - test_Sn3: .: (0.000233) - test_Un: .: (0.000221) + test_Sn1: .: (0.001082) + test_Sn2: .: (0.000524) + test_Sn3: .: (0.000507) + test_Un: .: (0.000493) Bio::TestPDBRecord::TestSEQADV: - test_chainID: .: (0.000674) - test_conflict: .: (0.000294) - test_database: .: (0.000284) - test_dbIdCode: .: (0.000275) - test_dbRes: .: (0.000272) - test_dbSeq: .: (0.000276) - test_iCode: .: (0.000288) - test_idCode: .: (0.000266) - test_resName: .: (0.000384) - test_seqNum: .: (0.000323) + test_chainID: .: (0.001230) + test_conflict: .: (0.000706) + test_database: .: (0.000660) + test_dbIdCode: .: (0.000655) + test_dbRes: .: (0.000655) + test_dbSeq: .: (0.000646) + test_iCode: .: (0.000762) + test_idCode: .: (0.000673) + test_resName: .: (0.000699) + test_seqNum: .: (0.000711) Bio::TestPDBRecord::TestSEQRES: - test_chainID: .: (0.000956) - test_numRes: .: (0.000322) - test_resName: .: (0.000312) + test_chainID: .: (0.001232) + test_numRes: .: (0.000644) + test_resName: .: (0.000711) Bio::TestPDBRecord::TestSHEET: - test_curAtom: .: (0.000759) - test_curChainId: .: (0.000431) - test_curICode: .: (0.000445) - test_curResName: .: (0.000383) - test_curResSeq: .: (0.000430) - test_endChainID: .: (0.000387) - test_endICode: .: (0.000399) - test_endResName: .: (0.000456) - test_endSeqNum: .: (0.000428) - test_initChainID: .: (0.000814) - test_initICode: .: (0.000379) - test_initResName: .: (0.000358) - test_initSeqNum: .: (0.000361) - test_numStrands: .: (0.000321) - test_prevAtom: .: (0.000315) - test_prevChainId: .: (0.000372) - test_prevICode: .: (0.000352) - test_prevResName: .: (0.000305) - test_prevResSeq: .: (0.000312) - test_sense: .: (0.000741) - test_sheetID: .: (0.000316) - test_strand: .: (0.000310) + test_curAtom: .: (0.001376) + test_curChainId: .: (0.000853) + test_curICode: .: (0.000893) + test_curResName: .: (0.000879) + test_curResSeq: .: (0.000832) + test_endChainID: .: (0.001726) + test_endICode: .: (0.000872) + test_endResName: .: (0.000822) + test_endSeqNum: .: (0.000828) + test_initChainID: .: (0.000871) + test_initICode: .: (0.000830) + test_initResName: .: (0.000825) + test_initSeqNum: .: (0.000831) + test_numStrands: .: (0.000939) + test_prevAtom: .: (0.000872) + test_prevChainId: .: (0.000833) + test_prevICode: .: (0.000876) + test_prevResName: .: (0.000865) + test_prevResSeq: .: (0.000871) + test_sense: .: (0.000862) + test_sheetID: .: (0.000833) + test_strand: .: (0.000824) Bio::TestPDBRecord::TestSIGATM: - test_altLoc: .: (0.000630) - test_chainID: .: (0.000287) - test_charge: .: (0.000266) - test_element: .: (0.000263) - test_iCode: .: (0.000263) - test_name: .: (0.000256) - test_resName: .: (0.000255) - test_resSeq: .: (0.000250) - test_segID: .: (0.000263) - test_serial: .: (0.000568) - test_sigOcc: .: (0.000306) - test_sigTemp: .: (0.000292) - test_sigX: .: (0.000249) - test_sigY: .: (0.000340) - test_sigZ: .: (0.000247) + test_altLoc: .: (0.001391) + test_chainID: .: (0.000688) + test_charge: .: (0.000676) + test_element: .: (0.000667) + test_iCode: .: (0.000696) + test_name: .: (0.000682) + test_resName: .: (0.000668) + test_resSeq: .: (0.000654) + test_segID: .: (0.000658) + test_serial: .: (0.001854) + test_sigOcc: .: (0.000669) + test_sigTemp: .: (0.000649) + test_sigX: .: (0.000681) + test_sigY: .: (0.001161) + test_sigZ: .: (0.000663) Bio::TestPDBRecord::TestSIGUIJ: - test_SigmaU11: .: (0.000500) - test_SigmaU12: .: (0.000259) - test_SigmaU13: .: (0.000262) - test_SigmaU22: .: (0.000251) - test_SigmaU23: .: (0.000262) - test_SigmaU33: .: (0.000305) - test_altLoc: .: (0.000779) - test_chainID: .: (0.000300) - test_charge: .: (0.000344) - test_element: .: (0.000310) - test_iCode: .: (0.000325) - test_name: .: (0.000360) - test_resName: .: (0.000351) - test_resSeq: .: (0.000530) - test_segID: .: (0.000315) - test_serial: .: (0.000294) + test_SigmaU11: .: (0.001329) + test_SigmaU12: .: (0.000694) + test_SigmaU13: .: (0.000676) + test_SigmaU22: .: (0.000672) + test_SigmaU23: .: (0.000667) + test_SigmaU33: .: (0.000670) + test_altLoc: .: (0.000673) + test_chainID: .: (0.000662) + test_charge: .: (0.000666) + test_element: .: (0.000689) + test_iCode: .: (0.001665) + test_name: .: (0.000666) + test_resName: .: (0.000689) + test_resSeq: .: (0.001066) + test_segID: .: (0.000667) + test_serial: .: (0.000656) Bio::TestPDBRecord::TestSITE: - test_chainID1: .: (0.000629) - test_chainID2: .: (0.000316) - test_chainID3: .: (0.000696) - test_chainID4: .: (0.000382) - test_iCode1: .: (0.000374) - test_iCode2: .: (0.000317) - test_iCode3: .: (0.000347) - test_iCode4: .: (0.000353) - test_numRes: .: (0.000357) - test_resName1: .: (0.000350) - test_resName2: .: (0.000372) - test_resName3: .: (0.000364) - test_resName4: .: (0.000453) - test_seq1: .: (0.000356) - test_seq2: .: (0.000352) - test_seq3: .: (0.000619) - test_seq4: .: (0.000375) - test_seqNum: .: (0.000352) - test_siteID: .: (0.000342) + test_chainID1: .: (0.001399) + test_chainID2: .: (0.000751) + test_chainID3: .: (0.000741) + test_chainID4: .: (0.000734) + test_iCode1: .: (0.000746) + test_iCode2: .: (0.001782) + test_iCode3: .: (0.000759) + test_iCode4: .: (0.000729) + test_numRes: .: (0.000721) + test_resName1: .: (0.000720) + test_resName2: .: (0.000723) + test_resName3: .: (0.000774) + test_resName4: .: (0.000732) + test_seq1: .: (0.000719) + test_seq2: .: (0.000715) + test_seq3: .: (0.001021) + test_seq4: .: (0.000752) + test_seqNum: .: (0.001534) + test_siteID: .: (0.000784) Bio::TestPDBRecord::TestSLTBRG: - test_altLoc1: .: (0.000639) - test_altLoc2: .: (0.000279) - test_atom1: .: (0.000273) - test_atom2: .: (0.000263) - test_chainID1: .: (0.000261) - test_chainID2: .: (0.000264) - test_iCode1: .: (0.000272) - test_iCode2: .: (0.000263) - test_resName1: .: (0.000256) - test_resName2: .: (0.000913) - test_resSeq1: .: (0.000264) - test_resSeq2: .: (0.000253) - test_sym1: .: (0.000270) - test_sym2: .: (0.000260) + test_altLoc1: .: (0.001254) + test_altLoc2: .: (0.000627) + test_atom1: .: (0.000650) + test_atom2: .: (0.000625) + test_chainID1: .: (0.000618) + test_chainID2: .: (0.000613) + test_iCode1: .: (0.000613) + test_iCode2: .: (0.000636) + test_resName1: .: (0.000611) + test_resName2: .: (0.000613) + test_resSeq1: .: (0.000614) + test_resSeq2: .: (0.001714) + test_sym1: .: (0.000653) + test_sym2: .: (0.000604) Bio::TestPDBRecord::TestSOURCE: - test_srcName: .: (0.000550) + test_srcName: .: (0.001256) Bio::TestPDBRecord::TestSPRSDE: - test_idCode: .: (0.000580) - test_sIdCode: .: (0.000292) - test_sprsdeDate: .: (0.000263) + test_idCode: .: (0.001125) + test_sIdCode: .: (0.000556) + test_sprsdeDate: .: (0.000541) Bio::TestPDBRecord::TestTER: - test_chainID: .: (0.000532) - test_iCode: .: (0.000270) - test_resName: .: (0.000273) - test_resSeq: .: (0.000261) - test_serial: .: (0.000259) + test_chainID: .: (0.001093) + test_iCode: .: (0.000555) + test_resName: .: (0.000554) + test_resSeq: .: (0.000541) + test_serial: .: (0.000546) Bio::TestPDBRecord::TestTITLE: - test_title: .: (0.000591) + test_title: .: (0.001045) Bio::TestPDBRecord::TestTVECT: - test_serial: .: (0.000580) - test_t1: .: (0.000282) - test_t2: .: (0.000261) - test_t3: .: (0.000257) - test_text: .: (0.000270) + test_serial: .: (0.002089) + test_t1: .: (0.000562) + test_t2: .: (0.000541) + test_t3: .: (0.000530) + test_text: .: (0.000547) Bio::TestPROSITE: - test_ac: .: (0.004056) - test_cc: .: (0.003677) - test_de: .: (0.003323) - test_division: .: (0.003478) - test_dr: .: (0.090993) - test_dt: .: (0.011833) - test_false_neg: .: (0.026455) - test_false_pos: .: (0.004119) - test_false_positive_sequences: .: (0.004001) - test_list_falsenegative: .: (0.033020) - test_list_falsepositive: .: (0.033302) - test_list_potentialhit: .: (0.033727) - test_list_truepositive: .: (0.034914) - test_list_unknown: .: (0.034634) - test_list_xref: .: (0.033055) - test_ma: .: (0.004098) - test_max_repeat: .: (0.004442) - test_name: .: (0.003947) - test_nr: .: (0.003659) - test_pa: .: (0.003386) - test_pa2re: .: (0.004174) - test_partial: .: (0.003794) - test_pdb_xref: .: (0.003211) - test_pdoc_xref: .: (0.007100) - test_positive: .: (0.004063) - test_positive_hits: .: (0.003642) - test_positive_sequences: .: (0.003761) - test_release: .: (0.004644) - test_ru: .: (0.003839) - test_self_pa2re: .: (0.004509) - test_site: .: (0.003981) - test_skip_flag: .: (0.003879) - test_swissprot_release_number: .: (0.004368) - test_swissprot_release_sequences: .: (0.004522) - test_taxon_range: .: (0.003777) - test_total: .: (0.003320) - test_total_hits: .: (0.004310) - test_total_sequences: .: (0.004379) - test_unknown: .: (0.004203) - test_unknown_hits: .: (0.004499) - test_unknown_sequences: .: (0.004213) + test_ac: .: (0.009659) + test_cc: .: (0.008375) + test_de: .: (0.008897) + test_division: .: (0.008709) + test_dr: .: (0.087033) + test_dt: .: (0.008179) + test_false_neg: .: (0.008701) + test_false_pos: .: (0.021448) + test_false_positive_sequences: .: (0.035711) + test_list_falsenegative: .: (0.265041) + test_list_falsepositive: .: (0.095150) + test_list_potentialhit: .: (0.093218) + test_list_truepositive: .: (0.099954) + test_list_unknown: .: (0.093305) + test_list_xref: .: (0.092660) + test_ma: .: (0.008196) + test_max_repeat: .: (0.009370) + test_name: .: (0.009004) + test_nr: .: (0.009820) + test_pa: .: (0.008436) + test_pa2re: .: (0.008803) + test_partial: .: (0.010375) + test_pdb_xref: .: (0.010455) + test_pdoc_xref: .: (0.009330) + test_positive: .: (0.010228) + test_positive_hits: .: (0.009582) + test_positive_sequences: .: (0.009978) + test_release: .: (0.008866) + test_ru: .: (0.009436) + test_self_pa2re: .: (0.009142) + test_site: .: (0.009421) + test_skip_flag: .: (0.009263) + test_swissprot_release_number: .: (0.009862) + test_swissprot_release_sequences: .: (0.008569) + test_taxon_range: .: (0.009176) + test_total: .: (0.009711) + test_total_hits: .: (0.009128) + test_total_sequences: .: (0.020437) + test_unknown: .: (0.009360) + test_unknown_hits: .: (0.010073) + test_unknown_sequences: .: (0.010882) Bio::TestPROSITEConst: - test_delimiter: .: (0.000530) - test_tagsize: .: (0.000223) + test_delimiter: .: (0.001199) + test_tagsize: .: (0.000437) Bio::TestPTS1: - test_function_set: .: (0.000501) - test_function_set_number_1: .: (0.000259) - test_function_set_number_2: .: (0.000222) - test_function_set_number_3: .: (0.000225) - test_function_show: .: (0.000221) + test_function_set: .: (0.001044) + test_function_set_number_1: .: (0.000527) + test_function_set_number_2: .: (0.000565) + test_function_set_number_3: .: (0.000503) + test_function_show: .: (0.000457) Bio::TestPTS1Constant: - test_FUNCTION: .: (0.000969) + test_FUNCTION: .: (0.000933) Bio::TestPTS1New: - test_fungi: .: (0.000437) - test_general: .: (0.000216) - test_metazoa: .: (0.000205) + test_fungi: .: (0.001019) + test_general: .: (0.000484) + test_metazoa: .: (0.002040) Bio::TestQualifier: - test_qualifier: .: (0.000408) - test_value: .: (0.000193) + test_qualifier: .: (0.001035) + test_value: .: (0.000420) Bio::TestREBASE: - test_methods: .: (0.002469) + test_methods: .: (0.004432) Bio::TestRPSBlast::TestRPSBlastHSP: - test_align_len: .: (0.006191) - test_bit_score: .: (0.001335) - test_evalue: .: (0.001262) - test_gaps: .: (0.001400) - test_hit_from: .: (0.001870) - test_hit_to: .: (0.001456) - test_hseq: .: (0.001366) - test_identity: .: (0.001442) - test_midline: .: (0.001390) - test_percent_identity: .: (0.001992) - test_positive: .: (0.001535) - test_qseq: .: (0.001367) - test_query_from: .: (0.001443) - test_query_to: .: (0.001344) - test_score: .: (0.001898) + test_align_len: .: (0.007684) + test_bit_score: .: (0.003352) + test_evalue: .: (0.003277) + test_gaps: .: (0.003418) + test_hit_from: .: (0.003598) + test_hit_to: .: (0.005456) + test_hseq: .: (0.003474) + test_identity: .: (0.003240) + test_midline: .: (0.003523) + test_percent_identity: .: (0.004664) + test_positive: .: (0.004041) + test_qseq: .: (0.003499) + test_query_from: .: (0.003418) + test_query_to: .: (0.003331) + test_score: .: (0.005006) Bio::TestRPSBlast::TestRPSBlastReport: - test_db: .: (0.001432) - test_hits_size: .: (0.002962) - test_iterations_size: .: (0.003478) - test_program: .: (0.001119) - test_query_def: .: (0.002654) - test_query_len: .: (0.003079) - test_version: .: (0.001161) - test_version_date: .: (0.001094) - test_version_number: .: (0.001126) + test_db: .: (0.003758) + test_hits_size: .: (0.007416) + test_iterations_size: .: (0.008593) + test_program: .: (0.003475) + test_query_def: .: (0.006920) + test_query_len: .: (0.006899) + test_version: .: (0.002818) + test_version_date: .: (0.005800) + test_version_number: .: (0.002898) Bio::TestRPSBlast::TestRPSBlastReportHit: - test_bit_score: .: (0.001646) - test_definition: .: (0.002072) - test_evalue: .: (0.001462) - test_hsps_size: .: (0.001359) - test_identity: .: (0.001591) - test_lap_at: .: (0.001478) - test_len: .: (0.002835) - test_midline: .: (0.001468) - test_overlap: .: (0.001428) - test_query_end: .: (0.001506) - test_query_seq: .: (0.001581) - test_query_start: .: (0.002631) - test_target_def: .: (0.001558) - test_target_end: .: (0.001455) - test_target_len: .: (0.001378) - test_target_seq: .: (0.001501) - test_target_start: .: (0.002148) + test_bit_score: .: (0.004195) + test_definition: .: (0.003504) + test_evalue: .: (0.003464) + test_hsps_size: .: (0.004896) + test_identity: .: (0.004223) + test_lap_at: .: (0.003774) + test_len: .: (0.003420) + test_midline: .: (0.005552) + test_overlap: .: (0.004690) + test_query_end: .: (0.003729) + test_query_seq: .: (0.003701) + test_query_start: .: (0.003659) + test_target_def: .: (0.005049) + test_target_end: .: (0.003794) + test_target_len: .: (0.003455) + test_target_seq: .: (0.003692) + test_target_start: .: (0.003644) Bio::TestRPSBlast::TestRPSBlastSplitter: - test_entry_pos: .: (0.001155) - test_get_entry: .: (0.001063) - test_rewind: .: (0.000309) - test_skip_leader: .: (0.000554) + test_entry_pos: .: (0.003781) + test_get_entry: .: (0.002536) + test_rewind: .: (0.000550) + test_skip_leader: .: (0.001026) Bio::TestReference: - test_abstract: .: (0.000524) - test_affiliations: .: (0.000241) - test_authors: .: (0.000225) - test_format_bibitem: .: (0.000357) - test_format_bibtex: .: (0.000545) - test_format_bibtex_with_arguments: .: (0.001007) - test_format_cell: .: (0.000317) - test_format_current: .: (0.000249) - test_format_endnote: .: (0.000289) - test_format_general: .: (0.000283) - test_format_genome_biol: .: (0.000263) - test_format_genome_res: .: (0.000259) - test_format_nar: .: (0.000255) - test_format_nature: .: (0.000295) - test_format_rd: .: (0.000259) - test_format_science: .: (0.000362) - test_format_trends: .: (0.000273) - test_issue: .: (0.000904) - test_journal: .: (0.000352) - test_mesh: .: (0.000194) - test_pages: .: (0.000198) - test_pubmed: .: (0.000192) - test_pubmed_url: .: (0.000197) - test_url: .: (0.000193) - test_volume: .: (0.000185) - test_year: .: (0.000185) + test_abstract: .: (0.001041) + test_affiliations: .: (0.000485) + test_authors: .: (0.000478) + test_format_bibitem: .: (0.000759) + test_format_bibtex: .: (0.002222) + test_format_bibtex_with_arguments: .: (0.001101) + test_format_cell: .: (0.000598) + test_format_current: .: (0.000585) + test_format_endnote: .: (0.000714) + test_format_general: .: (0.000713) + test_format_genome_biol: .: (0.000639) + test_format_genome_res: .: (0.000759) + test_format_nar: .: (0.000645) + test_format_nature: .: (0.000748) + test_format_rd: .: (0.000650) + test_format_science: .: (0.003141) + test_format_trends: .: (0.000550) + test_issue: .: (0.000522) + test_journal: .: (0.002034) + test_mesh: .: (0.000512) + test_pages: .: (0.000463) + test_pubmed: .: (0.000462) + test_pubmed_url: .: (0.000489) + test_url: .: (0.000454) + test_volume: .: (0.000449) + test_year: .: (0.000443) Bio::TestReference_noURL: - test_format_endnote: .: (0.000604) - test_url: .: (0.000203) + test_format_endnote: .: (0.001331) + test_url: .: (0.000473) Bio::TestReferences: - test_append: .: (0.001178) - test_each: .: (0.000299) + test_append: .: (0.003450) + test_each: .: (0.000627) Bio::TestRelation: - test_comparison_operator: .: (0.000613) - test_uniq: .: (0.000327) + test_comparison_operator: .: (0.001320) + test_uniq: .: (0.000673) Bio::TestResidue: - test_addAtom: .: (0.000785) - test_each: .: (0.000505) - test_each_atom: .: (0.000442) - test_get_residue_id_from_atom: .: (0.001288) - test_het_atom: .: (0.000400) - test_iCode: .: (0.000355) - test_inspect: .: (0.000748) - test_resSeq: .: (0.000334) - test_sort: .: (0.000401) - test_square_bracket: .: (0.000368) - test_to_s: .: (0.000577) - test_update_resudue_id: .: (0.000336) + test_addAtom: .: (0.001777) + test_each: .: (0.001077) + test_each_atom: .: (0.003245) + test_get_residue_id_from_atom: .: (0.001006) + test_het_atom: .: (0.000755) + test_iCode: .: (0.000902) + test_inspect: .: (0.001184) + test_resSeq: .: (0.000821) + test_sort: .: (0.000951) + test_square_bracket: .: (0.002617) + test_to_s: .: (0.002133) + test_update_resudue_id: .: (0.000836) Bio::TestResidueFinder: - test_each_residue: .: (0.001426) - test_find_residue: .: (0.000371) - test_residues: .: (0.000313) + test_each_residue: .: (0.001281) + test_find_residue: .: (0.000723) + test_residues: .: (0.000766) Bio::TestRestrictionEnzyme::TestAnalysis: - test_cut: .: (0.262042) - test_cut_from_bio_sequence_na: .: (0.074391) - test_cut_without_permutations: .: (0.049025) - test_view_ranges: .: (0.049537) + test_cut: .: (0.741789) + test_cut_from_bio_sequence_na: .: (0.177835) + test_cut_without_permutations: .: (0.118426) + test_view_ranges: .: (0.127292) Bio::TestRestrictionEnzyme::TestAnalysisCalculatedCuts: - test_cuts: .: (0.002870) - test_cuts_after_remove_incomplete_cuts: .: (0.001938) - test_strands_for_display: .: (0.006860) - test_strands_for_display_current: .: (0.001466) + test_cuts: .: (0.007242) + test_cuts_after_remove_incomplete_cuts: .: (0.004444) + test_strands_for_display: .: (0.022682) + test_strands_for_display_current: .: (0.004410) Bio::TestRestrictionEnzyme::TestAnalysisSequenceRange: - test_fragments: .: (0.001214) - test_fragments_for_display_1: .: (0.001813) - test_fragments_for_display_10: .: (0.002927) - test_fragments_for_display_2: .: (0.001882) - test_fragments_for_display_3: .: (0.004166) - test_fragments_for_display_4: .: (0.002155) - test_fragments_for_display_5: .: (0.002234) - test_fragments_for_display_6: .: (0.001544) - test_fragments_for_display_7: .: (0.001662) - test_fragments_for_display_8: .: (0.001410) - test_fragments_for_display_9: .: (0.001851) + test_fragments: .: (0.003107) + test_fragments_for_display_1: .: (0.004848) + test_fragments_for_display_10: .: (0.006518) + test_fragments_for_display_2: .: (0.004942) + test_fragments_for_display_3: .: (0.007878) + test_fragments_for_display_4: .: (0.005796) + test_fragments_for_display_5: .: (0.004360) + test_fragments_for_display_6: .: (0.003706) + test_fragments_for_display_7: .: (0.003732) + test_fragments_for_display_8: .: (0.003955) + test_fragments_for_display_9: .: (0.003580) Bio::TestRestrictionEnzyme::TestCutRanges: - test_obj_2: .: (0.000951) - test_obj_3: .: (0.000776) - test_obj_7: .: (0.000534) - test_obj_z: .: (0.000593) + test_obj_2: .: (0.002024) + test_obj_3: .: (0.001571) + test_obj_7: .: (0.001812) + test_obj_z: .: (0.001457) Bio::TestRestrictionEnzyme::TestCutSymbol: - test_methods: .: (0.001027) + test_methods: .: (0.001901) Bio::TestRestrictionEnzyme::TestDenseIntArray: - test_bracket: .: (0.000756) - test_bracket_eq: .: (0.000374) - test_concat: .: (0.000318) - test_delete: .: (0.000309) - test_dup: .: (0.000398) - test_each: .: (0.000398) - test_eqeq: .: (0.000294) - test_eqeq_false: .: (0.000288) - test_eqeq_other: .: (0.000275) - test_eqeq_self: .: (0.000228) - test_include?: .: (0.000263) - test_internal_data: .: (0.000585) - test_internal_data_eq: .: (0.000292) - test_length: .: (0.000237) - test_ltlt: .: (0.000256) - test_ltlt_larger: .: (0.000242) - test_ltlt_middle: .: (0.000247) - test_plus: .: (0.000356) - test_plus_error: .: (0.000465) - test_push: .: (0.000280) - test_reverse_each: .: (0.000366) - test_self_bracket: .: (0.000236) - test_self_new: .: (0.000285) - test_size: .: (0.000237) - test_sort!: .: (0.000226) - test_to_a: .: (0.000257) - test_uniq!: .: (0.000234) - test_unshift: .: (0.000395) + test_bracket: .: (0.001474) + test_bracket_eq: .: (0.000741) + test_concat: .: (0.000684) + test_delete: .: (0.000635) + test_dup: .: (0.001531) + test_each: .: (0.000945) + test_eqeq: .: (0.000629) + test_eqeq_false: .: (0.000585) + test_eqeq_other: .: (0.000496) + test_eqeq_self: .: (0.000488) + test_include?: .: (0.000572) + test_internal_data: .: (0.000537) + test_internal_data_eq: .: (0.000643) + test_length: .: (0.000513) + test_ltlt: .: (0.000597) + test_ltlt_larger: .: (0.000594) + test_ltlt_middle: .: (0.000589) + test_plus: .: (0.000702) + test_plus_error: .: (0.000705) + test_push: .: (0.001160) + test_reverse_each: .: (0.000924) + test_self_bracket: .: (0.000547) + test_self_new: .: (0.000569) + test_size: .: (0.000515) + test_sort!: .: (0.000491) + test_to_a: .: (0.000563) + test_uniq!: .: (0.000533) + test_unshift: .: (0.000732) Bio::TestRestrictionEnzyme::TestDoubleStranded: - test_argument_error: .: (0.014053) - test_complement: .: (0.009342) - test_complement_with_cut_symbols: .: (0.009664) - test_cut_locations: .: (0.009149) - test_cut_locations_in_enzyme_notation: .: (0.008744) - test_primary: .: (0.008907) - test_primary_with_cut_symbols: .: (0.009544) - test_to_re: .: (0.008939) + test_argument_error: .: (0.025784) + test_complement: .: (0.023470) + test_complement_with_cut_symbols: .: (0.024701) + test_cut_locations: .: (0.023428) + test_cut_locations_in_enzyme_notation: .: (0.023254) + test_primary: .: (0.023121) + test_primary_with_cut_symbols: .: (0.024231) + test_to_re: .: (0.022622) Bio::TestRestrictionEnzyme::TestDoubleStrandedAlignedStrands: - test_align: .: (0.002514) - test_align_with_cuts: .: (0.001978) - test_argument_error: .: (0.002473) - test_ds: .: (0.002087) + test_align: .: (0.005970) + test_align_with_cuts: .: (0.004971) + test_argument_error: .: (0.005690) + test_ds: .: (0.005164) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPair: - test_argument_error: .: (0.001027) - test_complement: .: (0.000498) - test_contents: .: (0.000506) - test_primary: .: (0.000468) + test_argument_error: .: (0.002458) + test_complement: .: (0.001143) + test_contents: .: (0.001534) + test_primary: .: (0.001128) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationPairInEnzymeNotation: - test_argument_error: .: (0.000879) - test_complement: .: (0.000737) - test_contents: .: (0.000610) - test_primary: .: (0.000519) + test_argument_error: .: (0.001988) + test_complement: .: (0.001128) + test_contents: .: (0.001123) + test_primary: .: (0.001070) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocations: - test_complement: .: (0.000662) - test_contents: .: (0.000393) - test_primary: .: (0.000373) + test_complement: .: (0.001393) + test_contents: .: (0.001360) + test_primary: .: (0.000815) Bio::TestRestrictionEnzyme::TestDoubleStrandedCutLocationsInEnzymeNotation: - test_complement: .: (0.000680) - test_complement_to_array_index: .: (0.000642) - test_complement_to_array_index_class: .: (0.000482) - test_contents: .: (0.000636) - test_primary: .: (0.000334) - test_primary_to_array_index: .: (0.000487) - test_primary_to_array_index_class: .: (0.000447) - test_to_array_index: .: (0.001033) - test_to_array_index_class: .: (0.000878) + test_complement: .: (0.001480) + test_complement_to_array_index: .: (0.001312) + test_complement_to_array_index_class: .: (0.001186) + test_contents: .: (0.000907) + test_primary: .: (0.000847) + test_primary_to_array_index: .: (0.001318) + test_primary_to_array_index_class: .: (0.001176) + test_to_array_index: .: (0.003225) + test_to_array_index_class: .: (0.002336) Bio::TestRestrictionEnzyme::TestRestrictionEnzyme: - test_enzyme_name: .: (0.000957) - test_rebase: .: (0.000340) + test_enzyme_name: .: (0.002509) + test_rebase: .: (0.000790) Bio::TestRestrictionEnzyme::TestSingleStrand: - test_argument_error: .: (0.002217) - test_creation_with_no_cuts: .: (0.001017) - test_cut_locations: .: (0.001283) - test_cut_locations_in_enzyme_notation: .: (0.001025) - test_orientation: .: (0.001051) - test_pattern: .: (0.001137) - test_pattern_palindromic?: .: (0.001694) - test_stripped: .: (0.001105) - test_to_re: .: (0.000956) - test_with_cut_symbols: .: (0.001357) - test_with_spaces: .: (0.001192) + test_argument_error: .: (0.004814) + test_creation_with_no_cuts: .: (0.003285) + test_cut_locations: .: (0.002734) + test_cut_locations_in_enzyme_notation: .: (0.002697) + test_orientation: .: (0.002516) + test_pattern: .: (0.003220) + test_pattern_palindromic?: .: (0.003175) + test_stripped: .: (0.002464) + test_to_re: .: (0.002203) + test_with_cut_symbols: .: (0.003200) + test_with_spaces: .: (0.003019) Bio::TestRestrictionEnzyme::TestSingleStrandComplement: - test_argument_error: .: (0.002252) - test_creation_with_no_cuts: .: (0.001034) - test_cut_locations: .: (0.001055) - test_cut_locations_in_enzyme_notation: .: (0.001377) - test_orientation: .: (0.001034) - test_pattern: .: (0.001120) - test_pattern_palindromic?: .: (0.001771) - test_stripped: .: (0.001030) - test_to_re: .: (0.000913) - test_with_cut_symbols: .: (0.001407) - test_with_spaces: .: (0.001694) + test_argument_error: .: (0.005293) + test_creation_with_no_cuts: .: (0.002749) + test_cut_locations: .: (0.002722) + test_cut_locations_in_enzyme_notation: .: (0.002687) + test_orientation: .: (0.002990) + test_pattern: .: (0.002772) + test_pattern_palindromic?: .: (0.003170) + test_stripped: .: (0.003088) + test_to_re: .: (0.002188) + test_with_cut_symbols: .: (0.002752) + test_with_spaces: .: (0.003576) Bio::TestRestrictionEnzyme::TestSingleStrandCutLocationsInEnzymeNotation: - test_argument_error: .: (0.001339) - test_initialize_with_pattern: .: (0.000995) - test_max: .: (0.000415) - test_min: .: (0.000374) - test_to_array_index: .: (0.000442) + test_argument_error: .: (0.002695) + test_initialize_with_pattern: .: (0.001966) + test_max: .: (0.000801) + test_min: .: (0.000756) + test_to_array_index: .: (0.000946) Bio::TestRestrictionEnzyme::TestSortedNumArray: - test_bracket: .: (0.000673) - test_bracket_eq: .: (0.000342) - test_concat: .: (0.000279) - test_delete: .: (0.000243) - test_dup: .: (0.000338) - test_each: .: (0.000397) - test_eqeq: .: (0.000258) - test_eqeq_false: .: (0.000274) - test_eqeq_other: .: (0.000246) - test_eqeq_self: .: (0.000195) - test_include?: .: (0.000227) - test_internal_data_hash: .: (0.000422) - test_internal_data_hash_eq: .: (0.000250) - test_length: .: (0.000189) - test_ltlt: .: (0.000223) - test_ltlt_noeffect: .: (0.000237) - test_plus: .: (0.000233) - test_plus_error: .: (0.000344) - test_private_push_element: .: (0.000302) - test_private_push_element_intermediate: .: (0.000303) - test_private_push_element_last: .: (0.000256) - test_private_push_element_noeffect: .: (0.000245) - test_private_sorted_keys: .: (0.000229) - test_private_unshift_element: .: (0.000244) - test_private_unshift_element_first: .: (0.000252) - test_private_unshift_element_intermediate: .: (0.000231) - test_private_unshift_element_noeffect: .: (0.000225) - test_push: .: (0.000455) - test_reverse_each: .: (0.000397) - test_self_bracket: .: (0.000237) - test_self_new: .: (0.000246) - test_size: .: (0.000201) - test_sort!: .: (0.000201) - test_to_a: .: (0.000212) - test_uniq!: .: (0.000194) - test_unshift: .: (0.000232) + test_bracket: .: (0.001859) + test_bracket_eq: .: (0.000753) + test_concat: .: (0.000566) + test_delete: .: (0.000516) + test_dup: .: (0.000721) + test_each: .: (0.000916) + test_eqeq: .: (0.000528) + test_eqeq_false: .: (0.000482) + test_eqeq_other: .: (0.000447) + test_eqeq_self: .: (0.000446) + test_include?: .: (0.000517) + test_internal_data_hash: .: (0.000464) + test_internal_data_hash_eq: .: (0.000555) + test_length: .: (0.000447) + test_ltlt: .: (0.000525) + test_ltlt_noeffect: .: (0.000567) + test_plus: .: (0.000505) + test_plus_error: .: (0.000653) + test_private_push_element: .: (0.000527) + test_private_push_element_intermediate: .: (0.000543) + test_private_push_element_last: .: (0.000544) + test_private_push_element_noeffect: .: (0.000524) + test_private_sorted_keys: .: (0.000467) + test_private_unshift_element: .: (0.000515) + test_private_unshift_element_first: .: (0.000544) + test_private_unshift_element_intermediate: .: (0.000568) + test_private_unshift_element_noeffect: .: (0.000527) + test_push: .: (0.000545) + test_reverse_each: .: (0.000905) + test_self_bracket: .: (0.000458) + test_self_new: .: (0.000568) + test_size: .: (0.000469) + test_sort!: .: (0.000993) + test_to_a: .: (0.000470) + test_uniq!: .: (0.000445) + test_unshift: .: (0.000574) Bio::TestRestrictionEnzyme::TestStringFormatting: - test_add_spacing: .: (0.000542) - test_left_padding: .: (0.000289) - test_right_padding: .: (0.000285) - test_strip_padding: .: (0.000324) + test_add_spacing: .: (0.001197) + test_left_padding: .: (0.000678) + test_right_padding: .: (0.000669) + test_strip_padding: .: (0.000695) Bio::TestSOFT: - test_dataset: .: (0.020308) - test_series: .: (0.022558) + test_dataset: .: (0.059691) + test_series: .: (0.042494) Bio::TestSOSUIReport: - test_entry_id: .: (0.000677) - test_prediction: .: (0.000349) - test_tmh: .: (0.000332) - test_tmhs: .: (0.000407) + test_entry_id: .: (0.002186) + test_prediction: .: (0.000783) + test_tmh: .: (0.000757) + test_tmhs: .: (0.000874) Bio::TestSOSUIReportConst: - test_delimiter: .: (0.000419) - test_rs: .: (0.000201) + test_delimiter: .: (0.000921) + test_rs: .: (0.000504) Bio::TestSOSUITMH: - test_grade: .: (0.000928) - test_range: .: (0.000366) - test_sequence: .: (0.000336) + test_grade: .: (0.001330) + test_range: .: (0.000769) + test_sequence: .: (0.000815) Bio::TestSampleGraph: - test_bellman_ford: .: (0.001007) - test_bfs_shortest_path: .: (0.000422) - test_breadth_first_search: .: (0.000484) - test_depth_first_search: .: (0.000661) - test_dijkstra: .: (0.000536) - test_dump_list: .: (0.000935) - test_dump_matrix: .: (0.000723) - test_extract_subgraph_by_label: .: (0.000583) - test_extract_subgraph_by_list: .: (0.000549) - test_extract_subgraph_retains_disconnected_nodes: .: (0.000446) - test_small_world_aka_node_degree_histogram: .: (0.000418) - test_to_matrix: .: (0.001154) - test_to_matrix_fixed_index: .: (0.000695) - test_undirected_cliquishness: .: (0.000871) + test_bellman_ford: .: (0.003419) + test_bfs_shortest_path: .: (0.001039) + test_breadth_first_search: .: (0.000984) + test_depth_first_search: .: (0.001709) + test_dijkstra: .: (0.001304) + test_dump_list: .: (0.001259) + test_dump_matrix: .: (0.002465) + test_extract_subgraph_by_label: .: (0.001149) + test_extract_subgraph_by_list: .: (0.001199) + test_extract_subgraph_retains_disconnected_nodes: .: (0.000890) + test_small_world_aka_node_degree_histogram: .: (0.000814) + test_to_matrix: .: (0.002043) + test_to_matrix_fixed_index: .: (0.001407) + test_undirected_cliquishness: .: (0.001797) Bio::TestScf_version_2: - test_complement: .: (0.021147) - test_seq: .: (0.019224) - test_to_biosequence: .: (0.019320) + test_complement: .: (0.064325) + test_seq: .: (0.060338) + test_to_biosequence: .: (0.060544) Bio::TestScf_version_3: - test_complement: .: (0.066431) - test_seq: .: (0.065944) - test_to_biosequence: .: (0.066315) + test_complement: .: (0.203246) + test_seq: .: (0.198388) + test_to_biosequence: .: (0.201026) Bio::TestSequence: - test_AA_new_blank_sequence: .: (0.000564) - test_AA_new_sequence_all_legal_symbols: .: (0.000281) - test_AA_new_sequence_removes_whitespace: .: (0.000255) - test_AA_new_sequence_upcases_symbols: .: (0.000256) - test_DNA_new_blank_sequence: .: (0.000242) - test_DNA_new_sequence_downcases_symbols: .: (0.000293) - test_DNA_new_sequence_removes_whitespace: .: (0.000250) - test_NA_randomize_with_counts: .: (0.001828) - test_NA_randomize_with_counts_and_block: .: (0.002354) - test_RNA_new_sequence: .: (0.000219) - test_ambiguous_dna_sequence_complement: .: (0.000197) - test_ambiguous_rna_sequence_complement: .: (0.000184) - test_amino_acid_codes: .: (0.000256) - test_amino_acid_molecular_weight: .: (0.000429) - test_amino_acid_names: .: (0.000617) - test_amino_acid_randomize_can_be_chained: .: (0.003026) - test_amino_acid_randomize_has_same_composition: .: (0.001378) - test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.003059) - test_dna_composition: .: (0.000360) - test_dna_gc_percent: .: (0.000400) - test_dna_molecular_weight: .: (0.000502) - test_dna_pikachu: .: (0.000261) - test_dna_sequence_complement: .: (0.000229) - test_dna_sequence_translate: .: (0.001521) - test_dna_to_re: .: (0.000422) - test_element_reference_operator_with_one_argument: .: (0.000230) - test_element_reference_operator_with_two_arguments: .: (0.000270) - test_invalid_nucleic_acid_illegal_bases: .: (0.000314) - test_invalid_nucleic_acid_illegal_bases_more: .: (0.000342) - test_nucleic_acid_names: .: (0.000279) - test_randomize_dna_can_be_chained: .: (0.000801) - test_randomize_dna_retains_composition: .: (0.000963) - test_randomize_dna_with_block: .: (0.005062) - test_rna_composition: .: (0.000348) - test_rna_gc_percent: .: (0.000408) - test_rna_molecular_weight: .: (0.000506) - test_rna_pikachu: .: (0.000290) - test_rna_sequence_complement: .: (0.000321) - test_rna_sequence_translate: .: (0.000866) - test_rna_to_re: .: (0.000423) - test_total: .: (0.000721) - test_two_consecutive_dna_randomizations_not_equal: .: (0.000720) - test_valid_dna_sequence_illegal_bases: .: (0.000245) + test_AA_new_blank_sequence: .: (0.001088) + test_AA_new_sequence_all_legal_symbols: .: (0.000496) + test_AA_new_sequence_removes_whitespace: .: (0.000469) + test_AA_new_sequence_upcases_symbols: .: (0.000525) + test_DNA_new_blank_sequence: .: (0.000465) + test_DNA_new_sequence_downcases_symbols: .: (0.000473) + test_DNA_new_sequence_removes_whitespace: .: (0.000461) + test_NA_randomize_with_counts: .: (0.004942) + test_NA_randomize_with_counts_and_block: .: (0.005860) + test_RNA_new_sequence: .: (0.000499) + test_ambiguous_dna_sequence_complement: .: (0.000507) + test_ambiguous_rna_sequence_complement: .: (0.000491) + test_amino_acid_codes: .: (0.000769) + test_amino_acid_molecular_weight: .: (0.000989) + test_amino_acid_names: .: (0.000642) + test_amino_acid_randomize_can_be_chained: .: (0.007698) + test_amino_acid_randomize_has_same_composition: .: (0.003465) + test_consecutive_amino_acid_randomizes_are_not_equal: .: (0.004384) + test_dna_composition: .: (0.000766) + test_dna_gc_percent: .: (0.000760) + test_dna_molecular_weight: .: (0.000929) + test_dna_pikachu: .: (0.000530) + test_dna_sequence_complement: .: (0.000508) + test_dna_sequence_translate: .: (0.002173) + test_dna_to_re: .: (0.000887) + test_element_reference_operator_with_one_argument: .: (0.000630) + test_element_reference_operator_with_two_arguments: .: (0.000583) + test_invalid_nucleic_acid_illegal_bases: .: (0.001529) + test_invalid_nucleic_acid_illegal_bases_more: .: (0.000892) + test_nucleic_acid_names: .: (0.000631) + test_randomize_dna_can_be_chained: .: (0.002128) + test_randomize_dna_retains_composition: .: (0.001569) + test_randomize_dna_with_block: .: (0.001794) + test_rna_composition: .: (0.001588) + test_rna_gc_percent: .: (0.000752) + test_rna_molecular_weight: .: (0.000909) + test_rna_pikachu: .: (0.000499) + test_rna_sequence_complement: .: (0.000619) + test_rna_sequence_translate: .: (0.001521) + test_rna_to_re: .: (0.000813) + test_total: .: (0.000550) + test_two_consecutive_dna_randomizations_not_equal: .: (0.001462) + test_valid_dna_sequence_illegal_bases: .: (0.000476) Bio::TestSequenceAA: - test_codes: .: (0.000574) - test_molecular_weight: .: (0.000450) - test_names: .: (0.000265) - test_to_re: .: (0.000348) - test_to_s: .: (0.000195) + test_codes: .: (0.001975) + test_molecular_weight: .: (0.001175) + test_names: .: (0.000621) + test_to_re: .: (0.000778) + test_to_s: .: (0.000470) Bio::TestSequenceAACompat: - test_aa_self_randomize: .: (0.000643) + test_aa_self_randomize: .: (0.001373) Bio::TestSequenceAANew: - test_new: .: (0.000448) - test_new_n: .: (0.000484) - test_new_r: .: (0.000279) - test_new_t: .: (0.000255) + test_new: .: (0.000949) + test_new_n: .: (0.000494) + test_new_r: .: (0.000475) + test_new_t: .: (0.000516) Bio::TestSequenceCommon::TestSequenceCommon: - test_composition: .: (0.000545) - test_concat: .: (0.000214) - test_push: .: (0.000188) - test_seq: .: (0.000189) - test_splicing: .: (0.000403) - test_sum: .: (0.000193) - test_to_s: .: (0.000171) - test_to_str: .: (0.000188) - test_total: .: (0.000254) - test_window_search: .: (0.001067) + test_composition: .: (0.001407) + test_concat: .: (0.000483) + test_push: .: (0.001187) + test_seq: .: (0.000452) + test_splicing: .: (0.000916) + test_sum: .: (0.000446) + test_to_s: .: (0.000411) + test_to_str: .: (0.000428) + test_total: .: (0.000503) + test_window_search: .: (0.001596) Bio::TestSequenceCommon::TestSequenceCommonNormalize: - test_no_normalize: .: (0.000477) - test_normalize_A: .: (0.000255) - test_normalize_a: .: (0.000250) + test_no_normalize: .: (0.001006) + test_normalize_A: .: (0.000609) + test_normalize_a: .: (0.000565) Bio::TestSequenceCommon::TestSequenceCommonRandomize: - test_randomize: .: (0.005450) - test_randomize_with_block: .: (0.010929) - test_randomize_with_hash: .: (0.003372) - test_randomize_with_hash_block: .: (0.078421) + test_randomize: .: (0.006613) + test_randomize_with_block: .: (0.025490) + test_randomize_with_hash: .: (0.008419) + test_randomize_with_hash_block: .: (0.073760) Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2: test_randomize_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:324:in `test_randomize_equiprobability' =============================================================================== -: (0.016118) +: (0.028234) test_randomize_with_hash_equiprobability: O =============================================================================== Omission: test randomly failing skipped [test_randomize_with_hash_equiprobability(Bio::TestSequenceCommon::TestSequenceCommonRandomizeChi2)] /build/reproducible-path/ruby-bio-2.0.5/test/unit/bio/sequence/test_common.rb:330:in `test_randomize_with_hash_equiprobability' =============================================================================== -: (0.012286) +: (0.019496) Bio::TestSequenceCommon::TestSequenceCommonSubseq: - test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.012723) - test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000329) - test_subseq_returns_subsequence: .: (0.000229) - test_to_s_returns_self_as_string: .: (0.000261) + test_subseq_returns_RuntimeError_blank_sequence_default_end: .: (0.023195) + test_subseq_returns_RuntimeError_start_less_than_one: .: (0.000634) + test_subseq_returns_subsequence: .: (0.000494) + test_to_s_returns_self_as_string: .: (0.000644) Bio::TestSequenceCommon::TestSequenceCommonWindowSearch: - test_window_search_with_width_3_default_step_no_residual: .: (0.000610) - test_window_search_with_width_3_step_two_with_residual: .: (0.001971) + test_window_search_with_width_3_default_step_no_residual: .: (0.001166) + test_window_search_with_width_3_step_two_with_residual: .: (0.000583) Bio::TestSequenceCompat::TestSequenceCommonCompat: - test_to_fasta: .: (0.000776) + test_to_fasta: .: (0.024593) Bio::TestSequenceCompat::TestSequenceCompat: - test_to_s: .: (0.000528) + test_to_s: .: (0.001072) Bio::TestSequenceCompat::TestSequenceNACompat: - test_aa_self_randomize: .: (0.000720) - test_na_self_randomize: .: (0.000440) + test_aa_self_randomize: .: (0.019399) + test_na_self_randomize: .: (0.001046) Bio::TestSequenceDBLink: - test_database: .: (0.000485) - test_id: .: (0.000206) - test_secondary_ids: .: (0.000219) + test_database: .: (0.001047) + test_id: .: (0.000437) + test_secondary_ids: .: (0.000445) Bio::TestSequenceDBLinkClassMethods: - test_parse_embl_DR_line: .: (0.000562) - test_parse_uniprot_DR_line: .: (0.001141) + test_parse_embl_DR_line: .: (0.020728) + test_parse_uniprot_DR_line: .: (0.000868) Bio::TestSequenceFormatFormatterFasta_numeric: - test_output: .: (0.002302) - test_output_width_35: .: (0.001370) - test_output_width_nil: .: (0.000754) + test_output: .: (0.040227) + test_output_width_35: .: (0.002036) + test_output_width_nil: .: (0.024474) Bio::TestSequenceFormatFormatterQual: - test_output: .: (0.000978) - test_output_after_adding_sequence: .: (0.000752) - test_output_after_truncating_sequence: .: (0.000454) - test_output_from_error_probabilities: .: (0.009123) - test_output_width45: .: (0.000880) - test_output_with_converting_score_phred2solexa: .: (0.005226) - test_output_with_converting_score_solexa2phred: .: (0.001367) - test_output_with_default_score: .: (0.000806) + test_output: .: (0.014212) + test_output_after_adding_sequence: .: (0.001886) + test_output_after_truncating_sequence: .: (0.001258) + test_output_from_error_probabilities: .: (0.024058) + test_output_width45: .: (0.001727) + test_output_with_converting_score_phred2solexa: .: (0.005085) + test_output_with_converting_score_solexa2phred: .: (0.002550) + test_output_with_default_score: .: (0.002225) Bio::TestSequenceMasker: - test_mask: .: (0.000804) - test_mask_with_enumerator: .: (0.000515) - test_mask_with_enumerator_empty_mask_char: .: (0.000940) - test_mask_with_enumerator_excess: .: (0.001379) - test_mask_with_enumerator_longer_mask_char: .: (0.000395) - test_mask_with_enumerator_shorter: .: (0.000581) - test_mask_with_error_probability: .: (0.000359) - test_mask_with_quality_score: .: (0.000338) + test_mask: .: (0.001595) + test_mask_with_enumerator: .: (0.001079) + test_mask_with_enumerator_empty_mask_char: .: (0.000998) + test_mask_with_enumerator_excess: .: (0.003665) + test_mask_with_enumerator_longer_mask_char: .: (0.000996) + test_mask_with_enumerator_shorter: .: (0.001507) + test_mask_with_error_probability: .: (0.000997) + test_mask_with_quality_score: .: (0.001616) Bio::TestSequenceNA: - test_at_content: .: (0.001712) - test_at_skew: .: (0.000666) - test_codon_usage: .: (0.000400) - test_complement: .: (0.000217) - test_dna: .: (0.000203) - test_dna!: .: (0.000186) - test_forward_complement: .: (0.000300) - test_gc_content: .: (0.000595) - test_gc_percent: .: (0.000422) - test_gc_skew: .: (0.001504) - test_iliegal_bases: .: (0.000271) - test_molecular_weight: .: (0.000445) - test_names: .: (0.000420) - test_reverse_complement: .: (0.000377) - test_rna: .: (0.000227) - test_rna!: .: (0.000211) - test_splicing: .: (0.000388) - test_to_re: .: (0.000581) - test_to_s: .: (0.000256) + test_at_content: .: (0.002373) + test_at_skew: .: (0.001809) + test_codon_usage: .: (0.000753) + test_complement: .: (0.000625) + test_dna: .: (0.000569) + test_dna!: .: (0.000558) + test_forward_complement: .: (0.000899) + test_gc_content: .: (0.002613) + test_gc_percent: .: (0.001194) + test_gc_skew: .: (0.002406) + test_iliegal_bases: .: (0.000633) + test_molecular_weight: .: (0.001005) + test_names: .: (0.000813) + test_reverse_complement: .: (0.000929) + test_rna: .: (0.000566) + test_rna!: .: (0.000540) + test_splicing: .: (0.001701) + test_to_re: .: (0.000981) + test_to_s: .: (0.000476) Bio::TestSequenceNACommon: - test_composition: .: (0.000663) - test_concat: .: (0.000268) - test_push: .: (0.000243) - test_seq: .: (0.000222) - test_splicing: .: (0.001946) - test_sum: .: (0.000207) - test_to_s: .: (0.000171) - test_to_str: .: (0.000168) - test_total: .: (0.000203) - test_window_search: .: (0.000788) + test_composition: .: (0.001464) + test_concat: .: (0.000509) + test_push: .: (0.000473) + test_seq: .: (0.000472) + test_splicing: .: (0.000839) + test_sum: .: (0.000519) + test_to_s: .: (0.000482) + test_to_str: .: (0.000463) + test_total: .: (0.000547) + test_window_search: .: (0.002947) Bio::TestSequenceNANew: - test_new: .: (0.000520) - test_new_n: .: (0.000748) - test_new_r: .: (0.000257) - test_new_t: .: (0.000201) + test_new: .: (0.001143) + test_new_n: .: (0.000536) + test_new_r: .: (0.000481) + test_new_t: .: (0.000477) Bio::TestSequenceNATranslation: - test_translate: .: (0.000937) - test_translate_0: .: (0.002421) - test_translate_1: .: (0.000654) - test_translate_2: .: (0.000616) - test_translate_3: .: (0.000586) - test_translate_4: .: (0.000655) - test_translate_5: .: (0.000687) - test_translate_6: .: (0.000611) - test_translate_7: .: (0.001216) - test_translate_given_codon_table: .: (0.108843) - test_translate_n1: .: (0.001374) - test_translate_n2: .: (0.001399) - test_translate_n3: .: (0.001058) - test_translate_unknown_o: .: (0.000654) - test_translate_unknown_x: .: (0.000561) + test_translate: .: (0.002194) + test_translate_0: .: (0.004869) + test_translate_1: .: (0.001474) + test_translate_2: .: (0.001311) + test_translate_3: .: (0.001256) + test_translate_4: .: (0.002358) + test_translate_5: .: (0.001373) + test_translate_6: .: (0.001487) + test_translate_7: .: (0.003126) + test_translate_given_codon_table: .: (0.284321) + test_translate_n1: .: (0.003371) + test_translate_n2: .: (0.003630) + test_translate_n3: .: (0.002773) + test_translate_unknown_o: .: (0.001483) + test_translate_unknown_x: .: (0.001369) Bio::TestSequenceQualityScore::TestConverter: - test_convert_nothing: .: (0.000511) - test_convert_scores_from_phred_to_solexa: .: (0.001373) - test_convert_scores_from_solexa_to_phred: .: (0.000506) + test_convert_nothing: .: (0.001159) + test_convert_scores_from_phred_to_solexa: .: (0.003256) + test_convert_scores_from_solexa_to_phred: .: (0.001234) Bio::TestSequenceQualityScore::TestPhred: - test_convert_nothing: .: (0.000495) - test_convert_scores_from_phred: .: (0.000278) - test_convert_scores_from_phred_to_solexa: .: (0.001271) - test_convert_scores_from_solexa: .: (0.000486) - test_convert_scores_from_solexa_to_phred: .: (0.000540) - test_convert_scores_to_phred: .: (0.000214) - test_convert_scores_to_solexa: .: (0.001283) - test_p2q: .: (0.000671) - test_phred_p2q: .: (0.000375) - test_phred_q2p: .: (0.013170) - test_q2p: .: (0.012096) - test_quality_score_type: .: (0.000281) - test_self_convert_scores_to_solexa: .: (0.001036) - test_self_p2q: .: (0.000427) - test_self_q2p: .: (0.016753) + test_convert_nothing: .: (0.001057) + test_convert_scores_from_phred: .: (0.000559) + test_convert_scores_from_phred_to_solexa: .: (0.003387) + test_convert_scores_from_solexa: .: (0.001208) + test_convert_scores_from_solexa_to_phred: .: (0.001176) + test_convert_scores_to_phred: .: (0.000445) + test_convert_scores_to_solexa: .: (0.003658) + test_p2q: .: (0.001371) + test_phred_p2q: .: (0.000935) + test_phred_q2p: .: (0.033089) + test_q2p: .: (0.034808) + test_quality_score_type: .: (0.000515) + test_self_convert_scores_to_solexa: .: (0.002822) + test_self_p2q: .: (0.001046) + test_self_q2p: .: (0.033850) Bio::TestSequenceQualityScore::TestSolexa: - test_convert_nothing: .: (0.000560) - test_convert_scores_from_phred: .: (0.001516) - test_convert_scores_from_phred_to_solexa: .: (0.001035) - test_convert_scores_from_solexa: .: (0.000332) - test_convert_scores_from_solexa_to_phred: .: (0.000842) - test_convert_scores_to_phred: .: (0.000501) - test_convert_scores_to_solexa: .: (0.000202) - test_p2q: .: (0.000632) - test_q2p: .: (0.013100) - test_quality_score_type: .: (0.000287) - test_self_convert_scores_to_phred: .: (0.000813) - test_self_p2q: .: (0.000568) - test_self_q2p: .: (0.014284) - test_solexa_p2q: .: (0.000761) - test_solexa_q2p: .: (0.012255) + test_convert_nothing: .: (0.001268) + test_convert_scores_from_phred: .: (0.002736) + test_convert_scores_from_phred_to_solexa: .: (0.003236) + test_convert_scores_from_solexa: .: (0.000439) + test_convert_scores_from_solexa_to_phred: .: (0.001184) + test_convert_scores_to_phred: .: (0.002034) + test_convert_scores_to_solexa: .: (0.000540) + test_p2q: .: (0.001524) + test_q2p: .: (0.046534) + test_quality_score_type: .: (0.000554) + test_self_convert_scores_to_phred: .: (0.001296) + test_self_p2q: .: (0.001562) + test_self_q2p: .: (0.037056) + test_solexa_p2q: .: (0.001461) + test_solexa_q2p: .: (0.037139) Bio::TestSequenceRuby3::TestSequenceCommon: - test_capitalize: .: (0.000622) - test_center: .: (0.000259) - test_chomp: .: (0.000427) - test_chop: .: (0.000345) - test_delete: .: (0.000245) - test_delete_prefix: .: (0.000256) - test_delete_suffix: .: (0.000292) - test_downcase: .: (0.000242) - test_each_char: .: (0.000399) - test_each_char_enum: .: (0.000348) - test_each_grapheme_cluster: .: (0.001089) - test_each_grapheme_cluster_enum: .: (0.000444) - test_each_line: .: (0.000352) - test_each_line_enum: .: (0.000461) - test_gsub: .: (0.000322) - test_gsub_with_block: .: (0.001058) - test_ljust: .: (0.000277) - test_lstrip: .: (0.000302) - test_multiply: .: (0.000316) - test_next: .: (0.000270) - test_reverse: .: (0.000252) - test_rjust: .: (0.000269) - test_rstrip: .: (0.000261) - test_slice: .: (0.000272) - test_slice2: .: (0.000291) - test_split: .: (0.000339) - test_squeeze: .: (0.000262) - test_strip: .: (0.000256) - test_sub: .: (0.000324) - test_sub_with_block: .: (0.000595) - test_succ: .: (0.000270) - test_swapcase: .: (0.000258) - test_tr: .: (0.000277) - test_tr_s: .: (0.000278) - test_upcase: .: (0.000280) + test_capitalize: .: (0.001332) + test_center: .: (0.000732) + test_chomp: .: (0.000788) + test_chop: .: (0.000765) + test_delete: .: (0.000603) + test_delete_prefix: .: (0.000626) + test_delete_suffix: .: (0.001728) + test_downcase: .: (0.000636) + test_each_char: .: (0.001513) + test_each_char_enum: .: (0.000931) + test_each_grapheme_cluster: .: (0.002286) + test_each_grapheme_cluster_enum: .: (0.000952) + test_each_line: .: (0.000946) + test_each_line_enum: .: (0.000819) + test_gsub: .: (0.000746) + test_gsub_with_block: .: (0.002542) + test_ljust: .: (0.000715) + test_lstrip: .: (0.000648) + test_multiply: .: (0.000616) + test_next: .: (0.000590) + test_reverse: .: (0.000638) + test_rjust: .: (0.000613) + test_rstrip: .: (0.000580) + test_slice: .: (0.000585) + test_slice2: .: (0.000570) + test_split: .: (0.000867) + test_squeeze: .: (0.000592) + test_strip: .: (0.000571) + test_sub: .: (0.000640) + test_sub_with_block: .: (0.001430) + test_succ: .: (0.000631) + test_swapcase: .: (0.000586) + test_tr: .: (0.000606) + test_tr_s: .: (0.001045) + test_upcase: .: (0.000689) Bio::TestSequenceRuby3::TestSequenceCommonPartition: - test_partition: .: (0.000865) - test_partition_nomatch: .: (0.000402) - test_partition_sep_TSeq: .: (0.000329) - test_partition_sep_regexp: .: (0.000357) + test_partition: .: (0.001466) + test_partition_nomatch: .: (0.000840) + test_partition_sep_TSeq: .: (0.000778) + test_partition_sep_regexp: .: (0.000815) Bio::TestSequenceRuby3::TestSequenceCommonRpartition: - test_rpartition: .: (0.000583) - test_rpartition_nomatch: .: (0.000326) - test_rpartition_sep_TSeq: .: (0.000335) - test_rpartition_sep_regexp: .: (0.000338) + test_rpartition: .: (0.001548) + test_rpartition_nomatch: .: (0.000810) + test_rpartition_sep_TSeq: .: (0.000817) + test_rpartition_sep_regexp: .: (0.000874) Bio::TestShRNA: - test_blocK_it: .: (0.054469) - test_blocK_it_: .: (0.058666) - test_blocK_it_BLOCK_IT: .: (0.054970) - test_blocK_it_BLOCK_iT: .: (0.053602) - test_blocK_it_piGene: .: (0.054969) - test_bottom_strand: .: (0.053236) - test_bottom_strand_class: .: (0.053753) - test_bottom_strand_nil: .: (0.055042) - test_design: .: (0.054175) - test_design_BLOCK_IT: .: (0.055074) - test_report: .: (0.055384) - test_report_before_design: .: (0.054098) - test_top_strand: .: (0.054873) - test_top_strand_class: .: (0.054114) - test_top_strand_nil: .: (0.054186) + test_blocK_it: .: (0.160138) + test_blocK_it_: .: (0.158013) + test_blocK_it_BLOCK_IT: .: (0.161096) + test_blocK_it_BLOCK_iT: .: (0.155262) + test_blocK_it_piGene: .: (0.152336) + test_bottom_strand: .: (0.156710) + test_bottom_strand_class: .: (0.156303) + test_bottom_strand_nil: .: (0.152120) + test_design: .: (0.154944) + test_design_BLOCK_IT: .: (0.158903) + test_report: .: (0.154354) + test_report_before_design: .: (0.154449) + test_top_strand: .: (0.160013) + test_top_strand_class: .: (0.161777) + test_top_strand_nil: .: (0.158482) Bio::TestShRNANew: - test_new: .: (0.000898) + test_new: .: (0.002965) Bio::TestSiRNA: - test_antisense_size: .: (0.000490) - test_design: .: (0.054306) - test_design_reynolds: .: (0.068734) - test_design_uitei: .: (0.054313) - test_max_gc_percent: .: (0.000271) - test_min_gc_percent: .: (0.000212) - test_reynolds: .: (0.066571) - test_reynolds?: .: (0.000395) - test_uitei: .: (0.056923) - test_uitei?: .: (0.000381) + test_antisense_size: .: (0.001018) + test_design: .: (0.161007) + test_design_reynolds: .: (0.195153) + test_design_uitei: .: (0.160386) + test_max_gc_percent: .: (0.000573) + test_min_gc_percent: .: (0.000608) + test_reynolds: .: (0.197416) + test_reynolds?: .: (0.000763) + test_uitei: .: (0.158388) + test_uitei?: .: (0.000694) Bio::TestSiRNANew: - test_new: .: (0.000883) + test_new: .: (0.001953) Bio::TestSiRNAPair: - test_antisense: .: (0.054867) - test_gc_percent: .: (0.053983) - test_report: .: (0.057389) - test_rule: .: (0.055205) - test_sense: .: (0.054349) - test_start: .: (0.056187) - test_stop: .: (0.054947) - test_target: .: (0.057821) + test_antisense: .: (0.156382) + test_gc_percent: .: (0.160176) + test_report: .: (0.163220) + test_rule: .: (0.160663) + test_sense: .: (0.160573) + test_start: .: (0.160099) + test_stop: .: (0.162279) + test_target: .: (0.160596) Bio::TestSiRNAPairNew: - test_new: .: (0.000937) + test_new: .: (0.002252) Bio::TestSim4Report: - test_all_hits: .: (0.002227) - test_each: .: (0.000647) - test_each_hit: .: (0.000780) - test_hits: .: (0.000506) - test_num_hits: .: (0.000407) - test_query_def: .: (0.000425) - test_query_id: .: (0.000836) - test_query_len: .: (0.002915) - test_seq1: .: (0.000787) + test_all_hits: .: (0.003019) + test_each: .: (0.002166) + test_each_hit: .: (0.001598) + test_hits: .: (0.001136) + test_num_hits: .: (0.000882) + test_query_def: .: (0.000962) + test_query_id: .: (0.000891) + test_query_len: .: (0.000881) + test_seq1: .: (0.001683) Bio::TestSim4Report2: - test_all_hits: .: (0.001472) - test_each: .: (0.001057) - test_each_hit: .: (0.002032) - test_hits: .: (0.002005) - test_num_hits: .: (0.000486) - test_query_def: .: (0.000417) - test_query_id: .: (0.000435) - test_query_len: .: (0.000437) - test_seq1: .: (0.000570) + test_all_hits: .: (0.003611) + test_each: .: (0.001430) + test_each_hit: .: (0.002629) + test_hits: .: (0.001237) + test_num_hits: .: (0.001080) + test_query_def: .: (0.001021) + test_query_id: .: (0.000991) + test_query_len: .: (0.001082) + test_seq1: .: (0.001324) Bio::TestSim4Report4: - test_all_hits: .: (0.001544) - test_each: .: (0.000597) - test_each_hit: .: (0.000893) - test_hits: .: (0.000647) - test_num_hits: .: (0.000998) - test_query_def: .: (0.000476) - test_query_id: .: (0.000426) - test_query_len: .: (0.000416) - test_seq1: .: (0.000571) + test_all_hits: .: (0.003614) + test_each: .: (0.002248) + test_each_hit: .: (0.001574) + test_hits: .: (0.001375) + test_num_hits: .: (0.001099) + test_query_def: .: (0.001131) + test_query_id: .: (0.001051) + test_query_len: .: (0.001051) + test_seq1: .: (0.006515) Bio::TestSim4ReportHit: - test_align: .: (0.001821) - test_complement?: .: (0.001601) - test_definition: .: (0.001146) - test_each: .: (0.000811) - test_exons: .: (0.000749) - test_hit_id: .: (0.000416) - test_hsps: .: (0.000710) - test_introns: .: (0.001581) - test_len: .: (0.000968) - test_query_def: .: (0.000559) - test_query_id: .: (0.000397) - test_query_len: .: (0.000827) - test_segmentpairs: .: (0.000814) - test_seq1: .: (0.000563) - test_seq2: .: (0.000552) - test_target_def: .: (0.000412) - test_target_id: .: (0.000406) - test_target_len: .: (0.000978) + test_align: .: (0.002592) + test_complement?: .: (0.001053) + test_definition: .: (0.000903) + test_each: .: (0.001970) + test_exons: .: (0.002076) + test_hit_id: .: (0.001106) + test_hsps: .: (0.003055) + test_introns: .: (0.002120) + test_len: .: (0.001139) + test_query_def: .: (0.001065) + test_query_id: .: (0.001024) + test_query_len: .: (0.001125) + test_segmentpairs: .: (0.001998) + test_seq1: .: (0.001451) + test_seq2: .: (0.002405) + test_target_def: .: (0.001466) + test_target_id: .: (0.001026) + test_target_len: .: (0.000997) Bio::TestSim4ReportHit2: - test_align: .: (0.001017) - test_complement?: .: (0.000422) - test_definition: .: (0.000388) - test_each: .: (0.001343) - test_exons: .: (0.000794) - test_hit_id: .: (0.000467) - test_hsps: .: (0.002066) - test_introns: .: (0.002405) - test_len: .: (0.001011) - test_query_def: .: (0.000957) - test_query_id: .: (0.000852) - test_query_len: .: (0.000763) - test_segmentpairs: .: (0.001768) - test_seq1: .: (0.001285) - test_seq2: .: (0.001135) - test_target_def: .: (0.000994) - test_target_id: .: (0.004392) - test_target_len: .: (0.002320) + test_align: .: (0.002095) + test_complement?: .: (0.001013) + test_definition: .: (0.001017) + test_each: .: (0.001874) + test_exons: .: (0.002865) + test_hit_id: .: (0.001465) + test_hsps: .: (0.001919) + test_introns: .: (0.001799) + test_len: .: (0.000962) + test_query_def: .: (0.000944) + test_query_id: .: (0.000954) + test_query_len: .: (0.001044) + test_segmentpairs: .: (0.002867) + test_seq1: .: (0.001513) + test_seq2: .: (0.001302) + test_target_def: .: (0.001062) + test_target_id: .: (0.000970) + test_target_len: .: (0.000859) Bio::TestSim4ReportHit4: - test_align: .: (0.001015) - test_complement?: .: (0.000411) - test_definition: .: (0.000475) - test_each: .: (0.000886) - test_exons: .: (0.001354) - test_hit_id: .: (0.000625) - test_hsps: .: (0.001182) - test_introns: .: (0.000848) - test_len: .: (0.000373) - test_query_def: .: (0.000369) - test_query_id: .: (0.000356) - test_query_len: .: (0.000967) - test_segmentpairs: .: (0.001133) - test_seq1: .: (0.000492) - test_seq2: .: (0.000465) - test_target_def: .: (0.000373) - test_target_id: .: (0.000363) - test_target_len: .: (0.000405) + test_align: .: (0.002291) + test_complement?: .: (0.000954) + test_definition: .: (0.001850) + test_each: .: (0.002632) + test_exons: .: (0.002373) + test_hit_id: .: (0.001170) + test_hsps: .: (0.002168) + test_introns: .: (0.003084) + test_len: .: (0.001274) + test_query_def: .: (0.000970) + test_query_id: .: (0.000912) + test_query_len: .: (0.000895) + test_segmentpairs: .: (0.002393) + test_seq1: .: (0.001257) + test_seq2: .: (0.001285) + test_target_def: .: (0.002156) + test_target_id: .: (0.001178) + test_target_len: .: (0.001044) Bio::TestSim4ReportSegment: - test_from: .: (0.000438) - test_self_new: .: (0.000691) - test_seq: .: (0.000170) - test_to: .: (0.000149) + test_from: .: (0.001188) + test_self_new: .: (0.000716) + test_seq: .: (0.000499) + test_to: .: (0.000479) Bio::TestSim4ReportSegmentPair2_exon: - test_align_len: .: (0.000798) - test_direction: .: (0.000632) - test_hit_from: .: (0.000596) - test_hit_to: .: (0.000524) - test_hseq: .: (0.000512) - test_midline: .: (0.000856) - test_percent_identity: .: (0.000653) - test_qseq: .: (0.000719) - test_query_from: .: (0.000553) - test_query_to: .: (0.000527) - test_seq1: .: (0.000644) - test_seq2: .: (0.000613) + test_align_len: .: (0.002198) + test_direction: .: (0.001508) + test_hit_from: .: (0.002707) + test_hit_to: .: (0.001600) + test_hseq: .: (0.001504) + test_midline: .: (0.001475) + test_percent_identity: .: (0.001527) + test_qseq: .: (0.001463) + test_query_from: .: (0.002487) + test_query_to: .: (0.001920) + test_seq1: .: (0.001760) + test_seq2: .: (0.001620) Bio::TestSim4ReportSegmentPair2_intron: - test_align_len: .: (0.000933) - test_direction: .: (0.000568) - test_hit_from: .: (0.000531) - test_hit_to: .: (0.000517) - test_hseq: .: (0.000527) - test_midline: .: (0.001005) - test_percent_identity: .: (0.000681) - test_qseq: .: (0.000536) - test_query_from: .: (0.000511) - test_query_to: .: (0.000515) - test_seq1: .: (0.000624) - test_seq2: .: (0.000752) + test_align_len: .: (0.002147) + test_direction: .: (0.001649) + test_hit_from: .: (0.001579) + test_hit_to: .: (0.001897) + test_hseq: .: (0.001551) + test_midline: .: (0.001626) + test_percent_identity: .: (0.001474) + test_qseq: .: (0.001523) + test_query_from: .: (0.001454) + test_query_to: .: (0.002717) + test_seq1: .: (0.002507) + test_seq2: .: (0.001863) Bio::TestSim4ReportSegmentPair4_exon: - test_align_len: .: (0.001060) - test_direction: .: (0.000684) - test_hit_from: .: (0.000723) - test_hit_to: .: (0.000730) - test_hseq: .: (0.000656) - test_midline: .: (0.001129) - test_percent_identity: .: (0.000846) - test_qseq: .: (0.000811) - test_query_from: .: (0.000681) - test_query_to: .: (0.000660) - test_seq1: .: (0.001101) - test_seq2: .: (0.001034) + test_align_len: .: (0.002764) + test_direction: .: (0.002085) + test_hit_from: .: (0.003063) + test_hit_to: .: (0.002646) + test_hseq: .: (0.002182) + test_midline: .: (0.001890) + test_percent_identity: .: (0.001931) + test_qseq: .: (0.001803) + test_query_from: .: (0.003533) + test_query_to: .: (0.002044) + test_seq1: .: (0.002121) + test_seq2: .: (0.002130) Bio::TestSim4ReportSegmentPair4_intron: - test_align_len: .: (0.000925) - test_direction: .: (0.000648) - test_hit_from: .: (0.001027) - test_hit_to: .: (0.000918) - test_hseq: .: (0.000662) - test_midline: .: (0.000649) - test_percent_identity: .: (0.000617) - test_qseq: .: (0.000945) - test_query_from: .: (0.000810) - test_query_to: .: (0.000630) - test_seq1: .: (0.000696) - test_seq2: .: (0.001066) + test_align_len: .: (0.004057) + test_direction: .: (0.001990) + test_hit_from: .: (0.001959) + test_hit_to: .: (0.001945) + test_hseq: .: (0.001786) + test_midline: .: (0.002951) + test_percent_identity: .: (0.002433) + test_qseq: .: (0.001843) + test_query_from: .: (0.001881) + test_query_to: .: (0.001775) + test_seq1: .: (0.003189) + test_seq2: .: (0.002932) Bio::TestSim4ReportSegmentPair4_intron1: - test_align_len: .: (0.001019) - test_direction: .: (0.000654) - test_hit_from: .: (0.000623) - test_hit_to: .: (0.000612) - test_hseq: .: (0.001253) - test_midline: .: (0.000932) - test_percent_identity: .: (0.000694) - test_qseq: .: (0.000676) - test_query_from: .: (0.000732) - test_query_to: .: (0.004481) - test_seq1: .: (0.001014) - test_seq2: .: (0.000753) + test_align_len: .: (0.002593) + test_direction: .: (0.001889) + test_hit_from: .: (0.003065) + test_hit_to: .: (0.002643) + test_hseq: .: (0.001865) + test_midline: .: (0.001859) + test_percent_identity: .: (0.001864) + test_qseq: .: (0.003030) + test_query_from: .: (0.002578) + test_query_to: .: (0.001939) + test_seq1: .: (0.002140) + test_seq2: .: (0.002193) Bio::TestSim4ReportSegmentPair_exon: - test_align_len: .: (0.000768) - test_direction: .: (0.001870) - test_hit_from: .: (0.000621) - test_hit_to: .: (0.001024) - test_hseq: .: (0.003145) - test_midline: .: (0.000678) - test_percent_identity: .: (0.000526) - test_qseq: .: (0.000649) - test_query_from: .: (0.000545) - test_query_to: .: (0.000522) - test_seq1: .: (0.001218) - test_seq2: .: (0.001031) + test_align_len: .: (0.002712) + test_direction: .: (0.001456) + test_hit_from: .: (0.001439) + test_hit_to: .: (0.001366) + test_hseq: .: (0.001448) + test_midline: .: (0.001406) + test_percent_identity: .: (0.001388) + test_qseq: .: (0.002510) + test_query_from: .: (0.001880) + test_query_to: .: (0.001435) + test_seq1: .: (0.001737) + test_seq2: .: (0.001630) Bio::TestSim4ReportSegmentPair_intron: - test_align_len: .: (0.000812) - test_direction: .: (0.000537) - test_hit_from: .: (0.000526) - test_hit_to: .: (0.000503) - test_hseq: .: (0.001102) - test_midline: .: (0.000790) - test_percent_identity: .: (0.000501) - test_qseq: .: (0.000490) - test_query_from: .: (0.000491) - test_query_to: .: (0.000488) - test_seq1: .: (0.001142) - test_seq2: .: (0.001182) + test_align_len: .: (0.002124) + test_direction: .: (0.002363) + test_hit_from: .: (0.001786) + test_hit_to: .: (0.001409) + test_hseq: .: (0.001510) + test_midline: .: (0.001394) + test_percent_identity: .: (0.001343) + test_qseq: .: (0.001391) + test_query_from: .: (0.002408) + test_query_to: .: (0.001746) + test_seq1: .: (0.001661) + test_seq2: .: (0.001769) Bio::TestSim4ReportSeqDesc: - test_definition: .: (0.000745) - test_entry_id: .: (0.000196) - test_filename: .: (0.000199) - test_len: .: (0.000307) - test_self_new: .: (0.000290) - test_self_parse: .: (0.000283) + test_definition: .: (0.001106) + test_entry_id: .: (0.000529) + test_filename: .: (0.000506) + test_len: .: (0.000502) + test_self_new: .: (0.000567) + test_self_parse: .: (0.000728) Bio::TestTMHMMReport: - test_entry_id: .: (0.000942) - test_exp_aas_in_tmhs: .: (0.000620) - test_exp_first_60aa: .: (0.000989) - test_helix: .: (0.000737) - test_predicted_tmhs: .: (0.000572) - test_query_len: .: (0.000567) - test_tmhs: .: (0.000597) - test_to_s: .: (0.001418) - test_total_prob_of_N_in: .: (0.000619) + test_entry_id: .: (0.003293) + test_exp_aas_in_tmhs: .: (0.001700) + test_exp_first_60aa: .: (0.001640) + test_helix: .: (0.001892) + test_predicted_tmhs: .: (0.002703) + test_query_len: .: (0.001644) + test_tmhs: .: (0.001785) + test_to_s: .: (0.002360) + test_total_prob_of_N_in: .: (0.001879) Bio::TestTMHMMReport_reports: - test_reports: .: (0.000466) + test_reports: .: (0.001089) Bio::TestTMHMMTMH: - test_entry_id: .: (0.000838) - test_pos: .: (0.000607) - test_range: .: (0.001060) - test_status: .: (0.000600) - test_version: .: (0.000571) + test_entry_id: .: (0.002574) + test_pos: .: (0.001746) + test_range: .: (0.001667) + test_status: .: (0.001729) + test_version: .: (0.001655) Bio::TestTargetPReport: - test_cleavage_site_prediction: .: (0.000703) - test_cutoff: .: (0.000444) - test_entry_id: .: (0.000492) - test_length: .: (0.000473) - test_loc: .: (0.000811) - test_name: .: (0.000403) - test_networks: .: (0.000387) - test_prediction: .: (0.000432) - test_query_len: .: (0.000396) - test_query_sequences: .: (0.000482) - test_rc: .: (0.000461) - test_version: .: (0.000401) + test_cleavage_site_prediction: .: (0.001830) + test_cutoff: .: (0.001266) + test_entry_id: .: (0.001166) + test_length: .: (0.001130) + test_loc: .: (0.001172) + test_name: .: (0.001119) + test_networks: .: (0.001103) + test_prediction: .: (0.001281) + test_query_len: .: (0.001255) + test_query_sequences: .: (0.002074) + test_rc: .: (0.001143) + test_version: .: (0.001122) Bio::TestTargetPReportConst: - test_delimiter: .: (0.000392) - test_rs: .: (0.000158) + test_delimiter: .: (0.001043) + test_rs: .: (0.000429) Bio::TestTogoWSAccessWait: - test_reset_togows_access_wait: .: (0.000347) - test_togows_access_wait: .: (2.005731) + test_reset_togows_access_wait: .: (0.000910) + test_togows_access_wait: .: (2.005558) Bio::TestTogoWSREST: - test_debug: .: (0.000986) - test_debug_default: .: (0.000347) - test_internal_http: .: (0.000359) + test_debug: .: (0.002211) + test_debug_default: .: (0.001949) + test_internal_http: .: (0.002037) Bio::TestTogoWSRESTclassMethod: - test_convert: .: (0.000392) - test_entry: .: (0.000233) - test_entry_database_list: .: (0.000190) - test_new: .: (0.000423) - test_new_with_uri_object: .: (0.000449) - test_new_with_uri_string: .: (0.000858) - test_retrieve: .: (0.000191) - test_search: .: (0.000174) - test_search_database_list: .: (0.000167) + test_convert: .: (0.001998) + test_entry: .: (0.001129) + test_entry_database_list: .: (0.001002) + test_new: .: (0.002022) + test_new_with_uri_object: .: (0.002354) + test_new_with_uri_string: .: (0.002355) + test_retrieve: .: (0.001029) + test_search: .: (0.001076) + test_search_database_list: .: (0.001016) Bio::TestTogoWSRESTprivate: - test_make_path: .: (0.000892) - test_prepare_return_value: .: (0.000442) + test_make_path: .: (0.005350) + test_prepare_return_value: .: (0.002223) Bio::TestTopologicalSort: - test_dfs_topological_sort: .: (0.000816) + test_dfs_topological_sort: .: (0.004373) Bio::TestTree: - test_get_edge_distance: .: (0.000502) - test_get_edge_distance_string: .: (0.000303) - test_get_node_name: .: (0.000545) - test_initialize: .: (0.000247) - test_options: .: (0.000223) - test_root: .: (0.000172) - test_root=: .: (0.000214) + test_get_edge_distance: .: (0.002480) + test_get_edge_distance_string: .: (0.001660) + test_get_node_name: .: (0.001195) + test_initialize: .: (0.001235) + test_options: .: (0.001204) + test_root: .: (0.000955) + test_root=: .: (0.001212) Bio::TestTree2: - test_add_edge: .: (0.000724) - test_add_node: .: (0.000479) - test_adjacency_matrix: .: (0.000484) - test_adjacency_matrix_with_block: .: (0.000565) - test_adjacent_nodes: .: (0.000580) - test_adjacent_nodes_nonexistent: .: (0.000369) - test_ancestors: .: (0.000367) - test_children: .: (0.000339) - test_clear: .: (0.000359) - test_clear_node: .: (0.000454) - test_clear_node_nonexistent: .: (0.000729) - test_collect_edge!: .: (0.000606) - test_collect_node!: .: (0.000597) - test_concat: .: (0.000612) - test_descendents: .: (0.000795) - test_distance_matrix: .: (0.001210) - test_each_edge: .: (0.000475) - test_each_node: .: (0.000431) - test_each_out_edge: .: (0.000421) - test_each_out_edge_chimpanzee: .: (0.000402) - test_each_out_edge_human: .: (0.000380) - test_each_out_edge_mammals: .: (0.000458) - test_each_out_edge_nonexistent: .: (0.000475) - test_each_out_edge_primates: .: (0.001127) - test_each_out_edge_rat: .: (0.000412) - test_each_out_edge_rodents: .: (0.000522) - test_edges: .: (0.000365) - test_get_edge: .: (0.000835) - test_get_edge_indirect: .: (0.000397) - test_get_edge_merged: .: (0.000353) - test_get_edge_nonexistent: .: (0.000761) - test_get_node_bootstrap: .: (0.000322) - test_get_node_bootstrap_string=: .: (0.000313) - test_get_node_by_name: .: (0.000479) - test_get_node_by_name_noexistent: .: (0.000313) - test_include?: .: (0.000550) - test_include_nonexistent: .: (0.000356) - test_insert_node: .: (0.000733) - test_leaves: .: (0.000462) - test_leaves_noargs: .: (0.000357) - test_lowest_common_ancestor: .: (0.000778) - test_nodes: .: (0.000440) - test_number_of_edges: .: (0.000399) - test_number_of_nodes: .: (0.000340) - test_out_degree: .: (0.000465) - test_out_degree_nonexistent: .: (0.000331) - test_out_edges: .: (0.000401) - test_out_edges_mammals: .: (0.000485) - test_out_edges_nonexistent: .: (0.000340) - test_out_edges_primates: .: (0.000586) - test_out_edges_rodents: .: (0.001018) - test_parent: .: (0.000502) - test_path: .: (0.000377) - test_remove_edge: .: (0.000357) - test_remove_edge_if: .: (0.000406) - test_remove_edge_if_nothing_removed: .: (0.000487) - test_remove_edge_nonexistent: .: (0.000809) - test_remove_node: .: (0.000458) - test_remove_node_if: .: (0.000343) - test_remove_node_if_false: .: (0.000378) - test_remove_node_nonexistent: .: (0.000369) - test_remove_nonsense_nodes: .: (0.000898) - test_subtree: .: (0.000708) - test_subtree_with_all_paths: .: (0.000657) - test_total_distance: .: (0.000310) + test_add_edge: .: (0.005665) + test_add_node: .: (0.002476) + test_adjacency_matrix: .: (0.002478) + test_adjacency_matrix_with_block: .: (0.002638) + test_adjacent_nodes: .: (0.002717) + test_adjacent_nodes_nonexistent: .: (0.001770) + test_ancestors: .: (0.002208) + test_children: .: (0.001884) + test_clear: .: (0.002124) + test_clear_node: .: (0.002589) + test_clear_node_nonexistent: .: (0.004249) + test_collect_edge!: .: (0.003246) + test_collect_node!: .: (0.003393) + test_concat: .: (0.003172) + test_descendents: .: (0.002300) + test_distance_matrix: .: (0.005965) + test_each_edge: .: (0.002694) + test_each_node: .: (0.002486) + test_each_out_edge: .: (0.004109) + test_each_out_edge_chimpanzee: .: (0.002217) + test_each_out_edge_human: .: (0.002212) + test_each_out_edge_mammals: .: (0.002596) + test_each_out_edge_nonexistent: .: (0.002344) + test_each_out_edge_primates: .: (0.003620) + test_each_out_edge_rat: .: (0.002291) + test_each_out_edge_rodents: .: (0.002883) + test_edges: .: (0.002026) + test_get_edge: .: (0.006234) + test_get_edge_indirect: .: (0.001866) + test_get_edge_merged: .: (0.001846) + test_get_edge_nonexistent: .: (0.001711) + test_get_node_bootstrap: .: (0.001798) + test_get_node_bootstrap_string=: .: (0.001805) + test_get_node_by_name: .: (0.003423) + test_get_node_by_name_noexistent: .: (0.002115) + test_include?: .: (0.002503) + test_include_nonexistent: .: (0.001767) + test_insert_node: .: (0.005383) + test_leaves: .: (0.002333) + test_leaves_noargs: .: (0.001951) + test_lowest_common_ancestor: .: (0.002104) + test_nodes: .: (0.001817) + test_number_of_edges: .: (0.001709) + test_number_of_nodes: .: (0.001693) + test_out_degree: .: (0.002541) + test_out_degree_nonexistent: .: (0.001724) + test_out_edges: .: (0.002264) + test_out_edges_mammals: .: (0.002661) + test_out_edges_nonexistent: .: (0.003675) + test_out_edges_primates: .: (0.002935) + test_out_edges_rodents: .: (0.002899) + test_parent: .: (0.002176) + test_path: .: (0.002220) + test_remove_edge: .: (0.002120) + test_remove_edge_if: .: (0.002266) + test_remove_edge_if_nothing_removed: .: (0.002443) + test_remove_edge_nonexistent: .: (0.002722) + test_remove_node: .: (0.002479) + test_remove_node_if: .: (0.002009) + test_remove_node_if_false: .: (0.002253) + test_remove_node_nonexistent: .: (0.002819) + test_remove_nonsense_nodes: .: (0.002240) + test_subtree: .: (0.002680) + test_subtree_with_all_paths: .: (0.004095) + test_total_distance: .: (0.001135) Bio::TestTreeEdge: - test_distance: .: (0.000425) - test_distance=: .: (0.000242) - test_distance_string: .: (0.000166) - test_distance_string=: .: (0.000239) - test_initialize: .: (0.000286) - test_inspect: .: (0.000215) - test_to_s: .: (0.000168) + test_distance: .: (0.001100) + test_distance=: .: (0.000728) + test_distance_string: .: (0.000455) + test_distance_string=: .: (0.000671) + test_initialize: .: (0.000648) + test_inspect: .: (0.000530) + test_to_s: .: (0.000449) Bio::TestTreeNode: - test_bootstrap: .: (0.000356) - test_bootstrap=: .: (0.000677) - test_bootstrap_string: .: (0.000153) - test_bootstrap_string=: .: (0.000271) - test_initialize: .: (0.000205) - test_inspect: .: (0.000210) - test_name: .: (0.000172) - test_to_s: .: (0.000154) + test_bootstrap: .: (0.001844) + test_bootstrap=: .: (0.000737) + test_bootstrap_string: .: (0.000421) + test_bootstrap_string=: .: (0.000786) + test_initialize: .: (0.000579) + test_inspect: .: (0.000575) + test_name: .: (0.000510) + test_to_s: .: (0.000425) Bio::TestUniProt: - test_gene_name: .: (0.009625) + test_gene_name: .: (0.027630) Bio::TestUniProtKB: - test_ac: .: (0.009770) - test_accession: .: (0.018038) - test_cc: .: (0.012331) - test_cc_alternative_products: .: (0.012675) - test_cc_database: .: (0.012755) - test_cc_mass_spectrometry: .: (0.012404) - test_de: .: (0.010149) - test_dr: .: (0.014082) - test_dr_with_key: .: (0.012722) - test_dr_with_key_empty: .: (0.012272) - test_dt: .: (0.046730) - test_dt_annotation: .: (0.047677) - test_dt_created: .: (0.032597) - test_dt_sequence: .: (0.009401) - test_entry: .: (0.008943) - test_ft: .: (0.023556) - test_gene_name: .: (0.009620) - test_gene_names: .: (0.008841) - test_gn: .: (0.009051) - test_gn_old_parser: .: (0.009011) - test_gn_uniprot_parser: .: (0.009077) - test_id_line: .: (0.009039) - test_id_line_data_class: .: (0.011348) - test_id_line_entry_name: .: (0.009417) - test_id_line_molecule_type: .: (0.011213) - test_id_line_sequence_length: .: (0.009051) - test_kw: .: (0.009181) - test_molecule: .: (0.008802) - test_oc: .: (0.009777) - test_og_1: .: (0.008608) - test_og_2: .: (0.009248) - test_og_3: .: (0.009153) - test_og_4: .: (0.009209) - test_og_5: .: (0.010439) - test_og_6: .: (0.010250) - test_os: .: (0.009874) - test_os_access: .: (0.009553) - test_os_access2: .: (0.011440) - test_ox: .: (0.010180) - test_protein_name: .: (0.009717) - test_ref: .: (0.022725) - test_seq: .: (0.010026) - test_sequence_length: .: (0.009363) - test_sq: .: (0.010175) - test_sq_crc64: .: (0.009761) - test_sq_len: .: (0.010062) - test_sq_mw: .: (0.009737) - test_synonyms: .: (0.010048) + test_ac: .: (0.028681) + test_accession: .: (0.026468) + test_cc: .: (0.037087) + test_cc_alternative_products: .: (0.056004) + test_cc_database: .: (0.037316) + test_cc_mass_spectrometry: .: (0.037008) + test_de: .: (0.027407) + test_dr: .: (0.039864) + test_dr_with_key: .: (0.038826) + test_dr_with_key_empty: .: (0.036684) + test_dt: .: (0.026587) + test_dt_annotation: .: (0.027089) + test_dt_created: .: (0.028081) + test_dt_sequence: .: (0.075161) + test_entry: .: (0.118160) + test_ft: .: (0.164386) + test_gene_name: .: (0.028191) + test_gene_names: .: (0.026210) + test_gn: .: (0.027592) + test_gn_old_parser: .: (0.026641) + test_gn_uniprot_parser: .: (0.027443) + test_id_line: .: (0.027495) + test_id_line_data_class: .: (0.028181) + test_id_line_entry_name: .: (0.026609) + test_id_line_molecule_type: .: (0.027459) + test_id_line_sequence_length: .: (0.025683) + test_kw: .: (0.027006) + test_molecule: .: (0.025645) + test_oc: .: (0.027238) + test_og_1: .: (0.032627) + test_og_2: .: (0.026549) + test_og_3: .: (0.026889) + test_og_4: .: (0.025987) + test_og_5: .: (0.026815) + test_og_6: .: (0.027472) + test_os: .: (0.026505) + test_os_access: .: (0.025857) + test_os_access2: .: (0.027829) + test_ox: .: (0.026419) + test_protein_name: .: (0.027447) + test_ref: .: (0.064631) + test_seq: .: (0.027515) + test_sequence_length: .: (0.030865) + test_sq: .: (0.027779) + test_sq_crc64: .: (0.026554) + test_sq_len: .: (0.027550) + test_sq_mw: .: (0.026316) + test_synonyms: .: (0.027452) Bio::TestUniProtKB_CC: - test_allergen: .: (0.000776) - test_alternative_products_access_as_hash: .: (0.000476) - test_alternative_products_ai: .: (0.000624) - test_alternative_products_apu: .: (0.000967) - test_alternative_products_as: .: (0.001014) - test_alternative_products_rf: .: (0.000256) - test_biophysicochemical_properties: .: (0.000954) - test_biotechnology: .: (0.000504) - test_catalytic_activity: .: (0.000672) - test_caution: .: (0.000473) - test_cofactor: .: (0.000415) - test_developmental_stage: .: (0.000501) - test_disease: .: (0.000667) - test_domain: .: (0.001121) - test_enzyme_regulation: .: (0.000425) - test_function: .: (0.000467) - test_induction: .: (0.000413) - test_interaction: .: (0.000562) - test_mass_spectrometry: .: (0.000597) - test_miscellaneous: .: (0.000393) - test_pathway: .: (0.000458) - test_pharmaceutical: .: (0.000442) - test_polymorphism: .: (0.000975) - test_ptm: .: (0.000432) - test_rna_editing: .: (0.000575) - test_similarity: .: (0.000402) - test_subcellular_location: .: (0.000466) - test_subunit: .: (0.000322) - test_tissue_specificity: .: (0.000516) - test_toxic_dose: .: (0.000412) - test_web_resource: .: (0.000601) + test_allergen: .: (0.001757) + test_alternative_products_access_as_hash: .: (0.001234) + test_alternative_products_ai: .: (0.001629) + test_alternative_products_apu: .: (0.002666) + test_alternative_products_as: .: (0.001692) + test_alternative_products_rf: .: (0.000491) + test_biophysicochemical_properties: .: (0.003929) + test_biotechnology: .: (0.001301) + test_catalytic_activity: .: (0.001081) + test_caution: .: (0.001159) + test_cofactor: .: (0.001061) + test_developmental_stage: .: (0.001214) + test_disease: .: (0.001731) + test_domain: .: (0.001976) + test_enzyme_regulation: .: (0.002043) + test_function: .: (0.001535) + test_induction: .: (0.000964) + test_interaction: .: (0.001354) + test_mass_spectrometry: .: (0.001798) + test_miscellaneous: .: (0.001173) + test_pathway: .: (0.001405) + test_pharmaceutical: .: (0.001243) + test_polymorphism: .: (0.002793) + test_ptm: .: (0.001278) + test_rna_editing: .: (0.001852) + test_similarity: .: (0.001156) + test_subcellular_location: .: (0.001422) + test_subunit: .: (0.001000) + test_tissue_specificity: .: (0.001232) + test_toxic_dose: .: (0.001079) + test_web_resource: .: (0.001726) Bio::TestUniProtKB_CC_WEB_RESOURCE_since_rel12_2: - test_cc_web_resource: .: (0.001212) + test_cc_web_resource: .: (0.003524) Bio::TestUniProtKB_DE_since_rel14_0: - test_private_parse_DE_line_rel14: .: (0.001174) - test_protein_name: .: (0.003283) - test_synonyms: .: (0.001025) + test_private_parse_DE_line_rel14: .: (0.003076) + test_protein_name: .: (0.002205) + test_synonyms: .: (0.002691) Bio::TestUniProtKB_ID_since_rel9_0: - test_aalen: .: (0.000516) - test_entry: .: (0.000250) - test_entry_id: .: (0.000243) - test_entry_name: .: (0.000238) - test_id_line: .: (0.000239) - test_molecule: .: (0.000235) - test_sequence_length: .: (0.000929) + test_aalen: .: (0.001337) + test_entry: .: (0.000845) + test_entry_id: .: (0.000722) + test_entry_name: .: (0.000631) + test_id_line: .: (0.000617) + test_molecule: .: (0.000660) + test_sequence_length: .: (0.000631) Bio::TestUniProtKB_P03589: - test_ac: .: (0.006779) - test_accession: .: (0.001156) - test_cc: .: (0.002286) - test_cc_alternative_products: .: (0.001514) - test_cc_database: .: (0.001314) - test_cc_mass_spectrometry: .: (0.001875) - test_de: .: (0.000997) - test_dr: .: (0.001778) - test_dr_with_key: .: (0.001548) - test_dr_with_key_empty: .: (0.001869) - test_dt: .: (0.000898) - test_dt_annotation: .: (0.000937) - test_dt_created: .: (0.001216) - test_dt_sequence: .: (0.000928) - test_entry: .: (0.000945) - test_ft: .: (0.001703) - test_gene_name: .: (0.000948) - test_gene_names: .: (0.001347) - test_gn: .: (0.000986) - test_gn_old_parser: .: (0.000959) - test_gn_uniprot_parser: .: (0.001406) - test_id_line: .: (0.001055) - test_id_line_data_class: .: (0.000855) - test_id_line_entry_name: .: (0.001449) - test_id_line_sequence_length: .: (0.001371) - test_kw: .: (0.001087) - test_oc: .: (0.000955) - test_oh: .: (0.002104) - test_os: .: (0.000935) - test_os_access: .: (0.000896) - test_os_access2: .: (0.001648) - test_ox: .: (0.000905) - test_protein_name: .: (0.000952) - test_protein_name_after_calling_de: .: (0.001687) - test_ref: .: (0.001033) - test_seq: .: (0.001662) - test_sequence_length: .: (0.001501) - test_sq: .: (0.000927) - test_sq_crc64: .: (0.000894) - test_sq_len: .: (0.001648) - test_sq_mw: .: (0.001077) - test_synonyms: .: (0.001594) + test_ac: .: (0.007105) + test_accession: .: (0.007803) + test_cc: .: (0.004622) + test_cc_alternative_products: .: (0.004459) + test_cc_database: .: (0.005644) + test_cc_mass_spectrometry: .: (0.004415) + test_de: .: (0.003240) + test_dr: .: (0.005996) + test_dr_with_key: .: (0.005641) + test_dr_with_key_empty: .: (0.005062) + test_dt: .: (0.003087) + test_dt_annotation: .: (0.003917) + test_dt_created: .: (0.003253) + test_dt_sequence: .: (0.002870) + test_entry: .: (0.003151) + test_ft: .: (0.004721) + test_gene_name: .: (0.003243) + test_gene_names: .: (0.003266) + test_gn: .: (0.004322) + test_gn_old_parser: .: (0.003247) + test_gn_uniprot_parser: .: (0.003115) + test_id_line: .: (0.004201) + test_id_line_data_class: .: (0.002954) + test_id_line_entry_name: .: (0.002993) + test_id_line_sequence_length: .: (0.003769) + test_kw: .: (0.003653) + test_oc: .: (0.003162) + test_oh: .: (0.006297) + test_os: .: (0.003458) + test_os_access: .: (0.003067) + test_os_access2: .: (0.003075) + test_ox: .: (0.003902) + test_protein_name: .: (0.003250) + test_protein_name_after_calling_de: .: (0.003208) + test_ref: .: (0.004526) + test_seq: .: (0.005062) + test_sequence_length: .: (0.004038) + test_sq: .: (0.003450) + test_sq_crc64: .: (0.003035) + test_sq_len: .: (0.003210) + test_sq_mw: .: (0.004172) + test_synonyms: .: (0.003318) Bio::TestUniProtKB_P28907: - test_ac: .: (0.025599) - test_accession: .: (0.003408) - test_cc: .: (0.004286) - test_cc_alternative_products: .: (0.012263) - test_cc_database: .: (0.004787) - test_cc_mass_spectrometry: .: (0.005708) - test_de: .: (0.004092) - test_dr: .: (0.009778) - test_dr_with_key: .: (0.008383) - test_dr_with_key_empty: .: (0.008471) - test_dt: .: (0.003449) - test_dt_annotation: .: (0.003253) - test_dt_created: .: (0.003166) - test_dt_sequence: .: (0.003309) - test_entry: .: (0.003467) - test_ft: .: (0.006661) - test_gene_name: .: (0.004130) - test_gene_names: .: (0.003630) - test_gn: .: (0.007248) - test_gn_old_parser: .: (0.004528) - test_gn_uniprot_parser: .: (0.004173) - test_id_line: .: (0.003771) - test_id_line_data_class: .: (0.004231) - test_id_line_entry_name: .: (0.003558) - test_id_line_sequence_length: .: (0.003660) - test_kw: .: (0.005099) - test_oc: .: (0.004484) - test_os: .: (0.003602) - test_os_access: .: (0.004335) - test_os_access2: .: (0.004208) - test_ox: .: (0.004195) - test_protein_name: .: (0.004459) - test_protein_name_after_calling_de: .: (0.003810) - test_ref: .: (0.005549) - test_seq: .: (0.004242) - test_sequence_length: .: (0.003571) - test_sq: .: (0.003505) - test_sq_crc64: .: (0.003891) - test_sq_len: .: (0.003954) - test_sq_mw: .: (0.003958) - test_synonyms: .: (0.003968) - test_synonyms_after_calling_de: .: (0.004204) + test_ac: .: (0.011882) + test_accession: .: (0.009900) + test_cc: .: (0.014328) + test_cc_alternative_products: .: (0.013866) + test_cc_database: .: (0.013041) + test_cc_mass_spectrometry: .: (0.014121) + test_de: .: (0.010415) + test_dr: .: (0.032921) + test_dr_with_key: .: (0.025598) + test_dr_with_key_empty: .: (0.025280) + test_dt: .: (0.010182) + test_dt_annotation: .: (0.009967) + test_dt_created: .: (0.009629) + test_dt_sequence: .: (0.009416) + test_entry: .: (0.009910) + test_ft: .: (0.019215) + test_gene_name: .: (0.010943) + test_gene_names: .: (0.010398) + test_gn: .: (0.009604) + test_gn_old_parser: .: (0.009984) + test_gn_uniprot_parser: .: (0.010527) + test_id_line: .: (0.010759) + test_id_line_data_class: .: (0.010079) + test_id_line_entry_name: .: (0.010079) + test_id_line_sequence_length: .: (0.010131) + test_kw: .: (0.010659) + test_oc: .: (0.010424) + test_os: .: (0.010706) + test_os_access: .: (0.009737) + test_os_access2: .: (0.009957) + test_ox: .: (0.009997) + test_protein_name: .: (0.011185) + test_protein_name_after_calling_de: .: (0.010852) + test_ref: .: (0.015703) + test_seq: .: (0.010441) + test_sequence_length: .: (0.009677) + test_sq: .: (0.009924) + test_sq_crc64: .: (0.011151) + test_sq_len: .: (0.010870) + test_sq_mw: .: (0.009839) + test_synonyms: .: (0.010612) + test_synonyms_after_calling_de: .: (0.011232) Bio::TestUniProtKB_P49144: - test_ac: .: (0.108954) - test_accession: .: (0.002607) - test_cc: .: (0.002997) - test_cc_alternative_products: .: (0.003141) - test_cc_database: .: (0.002808) - test_cc_mass_spectrometry: .: (0.002325) - test_de: .: (0.002135) - test_dr: .: (0.003036) - test_dr_with_key: .: (0.003073) - test_dr_with_key_empty: .: (0.002997) - test_dt: .: (0.001546) - test_dt_annotation: .: (0.001572) - test_dt_created: .: (0.001650) - test_dt_sequence: .: (0.001629) - test_entry: .: (0.002126) - test_ft: .: (0.004036) - test_gene_name: .: (0.002126) - test_gene_names: .: (0.001707) - test_gn: .: (0.002119) - test_gn_old_parser: .: (0.001612) - test_gn_uniprot_parser: .: (0.001922) - test_id_line: .: (0.004594) - test_id_line_data_class: .: (0.001671) - test_id_line_entry_name: .: (0.002022) - test_id_line_sequence_length: .: (0.001575) - test_kw: .: (0.002070) - test_oc: .: (0.002067) - test_os: .: (0.001632) - test_os_access: .: (0.002134) - test_os_access2: .: (0.001595) - test_ox: .: (0.002111) - test_protein_name: .: (0.001652) - test_protein_name_after_calling_de: .: (0.002158) - test_ref: .: (0.002318) - test_seq: .: (0.002126) - test_sequence_length: .: (0.002057) - test_sq: .: (0.001858) - test_sq_crc64: .: (0.002334) - test_sq_len: .: (0.001848) - test_sq_mw: .: (0.002014) - test_synonyms: .: (0.002263) - test_synonyms_after_calling_de: .: (0.001908) + test_ac: .: (0.007617) + test_accession: .: (0.004578) + test_cc: .: (0.015099) + test_cc_alternative_products: .: (0.008897) + test_cc_database: .: (0.007047) + test_cc_mass_spectrometry: .: (0.008086) + test_de: .: (0.006348) + test_dr: .: (0.008849) + test_dr_with_key: .: (0.009314) + test_dr_with_key_empty: .: (0.009456) + test_dt: .: (0.004816) + test_dt_annotation: .: (0.005183) + test_dt_created: .: (0.004613) + test_dt_sequence: .: (0.005457) + test_entry: .: (0.004662) + test_ft: .: (0.011757) + test_gene_name: .: (0.005419) + test_gene_names: .: (0.004408) + test_gn: .: (0.004506) + test_gn_old_parser: .: (0.004472) + test_gn_uniprot_parser: .: (0.005545) + test_id_line: .: (0.004318) + test_id_line_data_class: .: (0.005184) + test_id_line_entry_name: .: (0.004438) + test_id_line_sequence_length: .: (0.005570) + test_kw: .: (0.005693) + test_oc: .: (0.004843) + test_os: .: (0.005609) + test_os_access: .: (0.004290) + test_os_access2: .: (0.005424) + test_ox: .: (0.004458) + test_protein_name: .: (0.005473) + test_protein_name_after_calling_de: .: (0.004550) + test_ref: .: (0.006380) + test_seq: .: (0.006074) + test_sequence_length: .: (0.004498) + test_sq: .: (0.005443) + test_sq_crc64: .: (0.004413) + test_sq_len: .: (0.005768) + test_sq_mw: .: (0.004526) + test_synonyms: .: (0.005821) + test_synonyms_after_calling_de: .: (0.004730) Bio::TestUniProtKB_Ref: - test_RA: .: (0.000883) - test_RC: .: (0.001038) - test_RG: .: (0.000673) - test_RL: .: (0.000597) - test_RN: .: (0.000706) - test_RP: .: (0.000591) - test_RT: .: (0.001067) - test_RX: .: (0.000591) - test_ref: .: (0.000689) + test_RA: .: (0.002524) + test_RC: .: (0.001514) + test_RG: .: (0.001526) + test_RL: .: (0.001435) + test_RN: .: (0.002420) + test_RP: .: (0.001717) + test_RT: .: (0.001479) + test_RX: .: (0.001468) + test_ref: .: (0.001587) Bio::TestUniProtKB_SwissProtRel41_0: - test_multiple_RP_lines: .: (0.000611) + test_multiple_RP_lines: .: (0.002442) Bio::TestUniProtKB_SwissProtRel41_1: - test_alternative_products: .: (0.001503) - test_alternative_products_with_ft: .: (0.001669) + test_alternative_products: .: (0.002588) + test_alternative_products_with_ft: .: (0.004256) Bio::TestUniProtKB_SwissProtRel41_10: - test_RC_lines: .: (0.000740) + test_RC_lines: .: (0.001878) Bio::TestUniProtKB_SwissProtRel41_20: - test_CC_allergen: .: (0.001221) - test_RL_lines: .: (0.000325) + test_CC_allergen: .: (0.001953) + test_RL_lines: .: (0.000778) Bio::TestUniProtKB_SwissProtRel42_6: - test_CC_rna_editing: .: (0.001237) + test_CC_rna_editing: .: (0.003038) Bio::TestUniProtKB_UniProtRel1_12: - test_DOI_in_RX_line: .: (0.000543) - test_RG_line: .: (0.000342) + test_DOI_in_RX_line: .: (0.001299) + test_RG_line: .: (0.000802) Bio::TestUniProtKB_UniProtRel2_0: - test_GN_line: .: (0.001096) + test_GN_line: .: (0.003878) Bio::TestUniProtKB_UniProtRel2_1: - test_CC_mass_spectrometry: .: (0.000822) + test_CC_mass_spectrometry: .: (0.001646) Bio::TestUniProtKB_UniProtRel2_3: - test_DR_PDB: .: (0.000491) - test_RL_line: .: (0.000326) + test_DR_PDB: .: (0.001176) + test_RL_line: .: (0.000716) Bio::TestUniProtKB_UniProtRel3_4: - test_CC_biophysiochemical_properties: .: (0.001539) - test_RP_line: .: (0.001033) + test_CC_biophysiochemical_properties: .: (0.003819) + test_RP_line: .: (0.002184) Bio::TestUniProtKB_UniProtRel3_5: - test_entry_name_format: .: (0.000348) + test_entry_name_format: .: (0.000835) Bio::TestUniProtKB_UniProtRel4_0: - test_CC_interaction: .: (0.000624) - test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.000493) - test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.000474) - test_CC_interaction_isoform: .: (0.000426) - test_CC_interaction_no_gene_name: .: (0.000418) - test_CC_interaction_self_association: .: (0.000482) + test_CC_interaction: .: (0.001514) + test_CC_interaction_Different_isoforms_of_the_current_protein_are_shown_to_interact_with_the_same_protein: .: (0.001142) + test_CC_interaction_The_source_organisms_of_the_interacting_proteins_are_different: .: (0.001224) + test_CC_interaction_isoform: .: (0.001033) + test_CC_interaction_no_gene_name: .: (0.000962) + test_CC_interaction_self_association: .: (0.001133) Bio::TestUniProtKB_UniProtRel5_0: - test_DR_line: .: (0.000598) + test_DR_line: .: (0.002460) Bio::TestUniProtKB_UniProtRel5_4: - test_multiple_cofactors: .: (0.000887) + test_multiple_cofactors: .: (0.001666) Bio::TestUniProtKB_UniProtRel6_0: - test_OG_line: .: (0.000890) + test_OG_line: .: (0.002295) Bio::TestUniProtKB_UniProtRel6_1: - test_FT_metal: .: (0.000680) + test_FT_metal: .: (0.001680) Bio::TestUniProtKB_UniProtRel6_5: - test_HI_line: .: (0.000642) + test_HI_line: .: (0.001570) Bio::TestUniProtKB_UniProtRel7_0: - test_CC_copyright_statement: .: (0.000625) - test_DT_line: .: (0.000896) + test_CC_copyright_statement: .: (0.002398) + test_DT_line: .: (0.000889) Bio::TestUniProtKB_UniProtRel7_6: - test_10000aa: .: (0.008200) + test_10000aa: .: (0.023458) Bio::TestUniProtKB_UniProtRel8_0: - test_CC_alternative_products: .: (0.001738) - test_CC_web_resource: .: (0.000265) - test_FT_VER_SEQ: .: (0.000446) - test_OH_line_exception: .: (0.000498) - test_OH_lines: .: (0.000750) + test_CC_alternative_products: .: (0.004266) + test_CC_web_resource: .: (0.000447) + test_FT_VER_SEQ: .: (0.001009) + test_OH_line_exception: .: (0.001222) + test_OH_lines: .: (0.001950) Bio::TestUtils: - test_centreOfGravity: .: (0.001611) - test_dihedral_angle: .: (0.000897) - test_distance: .: (0.000778) - test_geometricCentre: .: (0.001207) - test_rad2deg: .: (0.000469) + test_centreOfGravity: .: (0.003770) + test_dihedral_angle: .: (0.002290) + test_distance: .: (0.002083) + test_geometricCentre: .: (0.002641) + test_rad2deg: .: (0.001045) Bio::TestWeightedGraph: - test_bellman_ford_on_negative_weighted_graph: .: (0.000658) - test_dijkstra_on_weighted_graph: .: (0.000292) + test_bellman_ford_on_negative_weighted_graph: .: (0.001475) + test_dijkstra_on_weighted_graph: .: (0.000720) -Finished in 34.541725139 seconds. +Finished in 88.321390416 seconds. ------------------------------------------------------------------------------- 3941 tests, 21601 assertions, 0 failures, 0 errors, 0 pendings, 2 omissions, 0 notifications 100% passed ------------------------------------------------------------------------------- -114.09 tests/s, 625.36 assertions/s +44.62 tests/s, 244.57 assertions/s ┌──────────────────────────────────────────────────────────────────────────────┐ │ dh_ruby --install finished │ @@ -5533,12 +5569,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/27617/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27617/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/28256 and its subdirectories -I: Current time: Thu Dec 5 01:20:09 -12 2024 -I: pbuilder-time-stamp: 1733404809 +I: removing directory /srv/workspace/pbuilder/27617 and its subdirectories +I: Current time: Fri Dec 6 03:25:50 +14 2024 +I: pbuilder-time-stamp: 1733405150