https://sourceforge.net/p/genomecmp/activity/Recent activity for genomecmpenMon, 17 Sep 2018 14:07:44 -0000https://sourceforge.net/p/genomecmp/code/ci/2f674b28e8eee74c398bc20e1ca6c0145d846044/fix threshold setting in webMaciej KulawikMon, 17 Sep 2018 14:07:44 -0000https://sourceforge.net/p/genomecmp/code/ci/2f674b28e8eee74c398bc20e1ca6c0145d846044/https://sourceforge.net/p/genomecmp/code/ci/6714c1c5660cf17a6408bb0c894fb2e249f7cb43/Add new algorithms to webMaciej KulawikThu, 13 Sep 2018 08:31:36 -0000https://sourceforge.net/p/genomecmp/code/ci/6714c1c5660cf17a6408bb0c894fb2e249f7cb43/https://sourceforge.net/p/genomecmp/code/ci/ae81ab268e602213dd9343f34f9839a5b91604c4/add final experimentsMaciej KulawikFri, 01 Jun 2018 17:31:38 -0000https://sourceforge.net/p/genomecmp/code/ci/ae81ab268e602213dd9343f34f9839a5b91604c4/https://sourceforge.net/p/genomecmp/code/ci/0c515772710a575b97fb437701351ca5cf4c8797/add NoSearchMarkersSearcher, add some missing filesMaciej KulawikThu, 24 May 2018 08:34:37 -0000https://sourceforge.net/p/genomecmp/code/ci/0c515772710a575b97fb437701351ca5cf4c8797/https://sourceforge.net/p/genomecmp/code/ci/d3f3571af5c32a6d5f52373ddd6dbd8bf61a035b/add IterativeMarkersDefinerMaciej KulawikWed, 23 May 2018 12:25:18 -0000https://sourceforge.net/p/genomecmp/code/ci/d3f3571af5c32a6d5f52373ddd6dbd8bf61a035b/https://sourceforge.net/p/genomecmp/code/ci/cef35efa4e49968e76087412e9aeed1d828756e2/IterativeMarkersDefiner draftMaciej KulawikTue, 22 May 2018 15:14:03 -0000https://sourceforge.net/p/genomecmp/code/ci/cef35efa4e49968e76087412e9aeed1d828756e2/https://sourceforge.net/p/genomecmp/code/ci/36c9dd55d84540b3ad6344886459396fa0709519/Fix issue with duplicationsMaciej KulawikWed, 16 May 2018 18:05:40 -0000https://sourceforge.net/p/genomecmp/code/ci/36c9dd55d84540b3ad6344886459396fa0709519/https://sourceforge.net/p/genomecmp/code/ci/bc0fb5943c8cd064fffdaab95949be22806978ad/[exp] add new exp framework draftMaciej KulawikTue, 15 May 2018 13:22:48 -0000https://sourceforge.net/p/genomecmp/code/ci/bc0fb5943c8cd064fffdaab95949be22806978ad/https://sourceforge.net/p/genomecmp/code/ci/cf8d3a2759d724b6a25eab5ca35bac08c37287d5/experiments' scriptsMaciej KulawikTue, 15 May 2018 13:22:48 -0000https://sourceforge.net/p/genomecmp/code/ci/cf8d3a2759d724b6a25eab5ca35bac08c37287d5/https://sourceforge.net/p/genomecmp/code/ci/72993f899e2556dd0caeca80bc1d19d11a768025/#610 Fix corner case in Diff, use Diff in DiffDetectorMaciej KulawikTue, 20 Mar 2018 12:28:07 -0000https://sourceforge.net/p/genomecmp/code/ci/72993f899e2556dd0caeca80bc1d19d11a768025/https://sourceforge.net/p/genomecmp/code/ci/41e0bd8d40f09ee01c87bff303d0738f787e3527/#610 Add simple diff implementationMaciej KulawikMon, 19 Mar 2018 22:01:11 -0000https://sourceforge.net/p/genomecmp/code/ci/41e0bd8d40f09ee01c87bff303d0738f787e3527/https://sourceforge.net/p/genomecmp/code/ci/951dadc4a30df016e0d3b444fa4b365171e42ab8/#604 Enable command halting while executing ChunkedXcorr algorithm (also while openmp is used)Maciej KulawikWed, 28 Feb 2018 18:10:27 -0000https://sourceforge.net/p/genomecmp/code/ci/951dadc4a30df016e0d3b444fa4b365171e42ab8/https://sourceforge.net/p/genomecmp/code/ci/0853af75d6f335b347941f91e2230e49f075f773/#598 Integrate BlastMarkersSearcher with web interface, #604 Add command haltingMaciej KulawikWed, 28 Feb 2018 16:31:09 -0000https://sourceforge.net/p/genomecmp/code/ci/0853af75d6f335b347941f91e2230e49f075f773/https://sourceforge.net/p/genomecmp/code/ci/b2a55e62ac4a563674bf6d071a7a2d81ffc1ca71/Add blast-like markers searcherMaciej KulawikThu, 25 Jan 2018 18:29:45 -0000https://sourceforge.net/p/genomecmp/code/ci/b2a55e62ac4a563674bf6d071a7a2d81ffc1ca71/https://sourceforge.net/p/genomecmp/code/ci/cdf02670a78b866a28176a4e2e12967182edfed7/#574 Add rearrangement position to gff-like file.Maciej KulawikTue, 26 Dec 2017 12:02:10 -0000https://sourceforge.net/p/genomecmp/code/ci/cdf02670a78b866a28176a4e2e12967182edfed7/https://sourceforge.net/p/genomecmp/code/ci/205e893a86b19c82d44a9642a4e2d4a0c788e88b/Remove searching for inversed markers in base sequenceMaciej KulawikTue, 26 Dec 2017 12:02:10 -0000https://sourceforge.net/p/genomecmp/code/ci/205e893a86b19c82d44a9642a4e2d4a0c788e88b/https://sourceforge.net/p/genomecmp/code/ci/4d5d19418046903a39fb029887f6405f85da4492/#574 Add some tests for DiffDetectorMaciej KulawikMon, 11 Dec 2017 13:44:45 -0000https://sourceforge.net/p/genomecmp/code/ci/4d5d19418046903a39fb029887f6405f85da4492/https://sourceforge.net/p/genomecmp/code/ci/b04261a0d4f36a823131b326fc454509765998af/#574 Reimplemnt DiffDetector, add rearrangements positions. For now only transpositions and duplications are supported.Maciej KulawikMon, 11 Dec 2017 13:12:26 -0000https://sourceforge.net/p/genomecmp/code/ci/b04261a0d4f36a823131b326fc454509765998af/https://sourceforge.net/p/genomecmp/code/ci/b21e7b92323668c145278c4cb647a66ee83c611e/#574 DiffDetector - add inversions supportMaciej KulawikMon, 11 Dec 2017 13:12:26 -0000https://sourceforge.net/p/genomecmp/code/ci/b21e7b92323668c145278c4cb647a66ee83c611e/https://sourceforge.net/p/genomecmp/code/ci/54f98970a60e0c4c7fd4c559ec2aec500348d65b/#574 DiffDetector - add deletions supportMaciej KulawikMon, 11 Dec 2017 13:12:26 -0000https://sourceforge.net/p/genomecmp/code/ci/54f98970a60e0c4c7fd4c559ec2aec500348d65b/https://sourceforge.net/p/genomecmp/code/ci/f96733c73b108f9e80be3bb9679274db3fb45c9c/#573 Change extension of markers, fix bug in AllAtOnceMarkersDefiner::sieveCandidatesMaciej KulawikSun, 12 Nov 2017 14:37:22 -0000https://sourceforge.net/p/genomecmp/code/ci/f96733c73b108f9e80be3bb9679274db3fb45c9c/https://sourceforge.net/p/genomecmp/code/ci/0f264848883058302ef71f90f7c41e9c73ef6f5a/Parallize ChunkedXcorr::getMarkersSignalsMaciej KulawikSun, 12 Nov 2017 14:37:22 -0000https://sourceforge.net/p/genomecmp/code/ci/0f264848883058302ef71f90f7c41e9c73ef6f5a/https://sourceforge.net/p/genomecmp/code/ci/6e2fadd259d44c3759d9916be4d49da3c456d169/Change factors type from doubleto float in FFTMaciej KulawikSun, 12 Nov 2017 14:37:22 -0000https://sourceforge.net/p/genomecmp/code/ci/6e2fadd259d44c3759d9916be4d49da3c456d169/https://sourceforge.net/p/genomecmp/code/ci/b17d2576548a44adc499888dbbc3ac45d7e5dc29/#460 Fix defining of multiple markers at onceMaciej KulawikThu, 12 Oct 2017 23:53:23 -0000https://sourceforge.net/p/genomecmp/code/ci/b17d2576548a44adc499888dbbc3ac45d7e5dc29/https://sourceforge.net/p/genomecmp/code/ci/35c0ed3c1798ae2fbcd2a4f56630404a62c75dd2/#460 Add some comments to DiffDetectorMaciej KulawikThu, 12 Oct 2017 23:53:23 -0000https://sourceforge.net/p/genomecmp/code/ci/35c0ed3c1798ae2fbcd2a4f56630404a62c75dd2/https://sourceforge.net/p/genomecmp/code/ci/f80b67e097baa82d84cd91828865177b0a8a4270/#420 Use multiple threads in ChunkedXcorr::searchMaciej KulawikThu, 12 Oct 2017 23:53:23 -0000https://sourceforge.net/p/genomecmp/code/ci/f80b67e097baa82d84cd91828865177b0a8a4270/https://sourceforge.net/p/genomecmp/code/ci/4f304c9877f7a61ba99cf05fc2394ee2ce0fcfbe/#460 Add tests for CircosKaryotypeSaver and CircosSegdupSaver, add some commentsMaciej KulawikMon, 02 Oct 2017 11:54:56 -0000https://sourceforge.net/p/genomecmp/code/ci/4f304c9877f7a61ba99cf05fc2394ee2ce0fcfbe/https://sourceforge.net/p/genomecmp/code/ci/3df8b598a95bc61453f33765bfa29aede8ad4aa5/#460 Move CachedMarkersSearcher to separate file, add tests for CachedMarkersSearcher, add some documentationMaciej KulawikThu, 28 Sep 2017 19:37:50 -0000https://sourceforge.net/p/genomecmp/code/ci/3df8b598a95bc61453f33765bfa29aede8ad4aa5/https://sourceforge.net/p/genomecmp/code/ci/d3ad9f43aa14aef983672abb760d41d806916af5/#460 Fix progress in MarkersSearcher, add removing zip file in command callback in genomecmp/views.pyMaciej KulawikMon, 25 Sep 2017 16:40:58 -0000https://sourceforge.net/p/genomecmp/code/ci/d3ad9f43aa14aef983672abb760d41d806916af5/https://sourceforge.net/p/genomecmp/code/ci/5ceb55449d20793c0c13a22b19803d0de99b60e2/#460 Fix number of defined markers by InGroupsMarkerDefiner and OneByOneMarkersDefinerMaciej KulawikMon, 25 Sep 2017 16:40:58 -0000https://sourceforge.net/p/genomecmp/code/ci/5ceb55449d20793c0c13a22b19803d0de99b60e2/https://sourceforge.net/p/genomecmp/code/ci/4fdb1a7b5d6ad837440a13b531c3f48f19290718/#460 change version to 1.0, add ben to allowed hostsMaciej KulawikFri, 22 Sep 2017 08:31:06 -0000https://sourceforge.net/p/genomecmp/code/ci/4fdb1a7b5d6ad837440a13b531c3f48f19290718/https://sourceforge.net/p/genomecmp/code/ci/8827cd3d164a833d8ba1997c38b557a2ec699036/#460 Add InGroupsMarkersSearcher, add SequenceFileValidator, fix FastaFileParserMaciej KulawikTue, 19 Sep 2017 18:54:07 -0000https://sourceforge.net/p/genomecmp/code/ci/8827cd3d164a833d8ba1997c38b557a2ec699036/https://sourceforge.net/p/genomecmp/code/ci/f3656948915c6a142063b0bf94d4af9d0c0cdf21/#460 rename directories: calc -> calc_old, calc_new -> calcMaciej KulawikTue, 19 Sep 2017 18:54:07 -0000https://sourceforge.net/p/genomecmp/code/ci/f3656948915c6a142063b0bf94d4af9d0c0cdf21/https://sourceforge.net/p/genomecmp/code/ci/58512936d3988ecb3a0cf86b0d0b66a8b1a3c117/#460 Use new gencmp library in webMaciej KulawikTue, 19 Sep 2017 18:54:07 -0000https://sourceforge.net/p/genomecmp/code/ci/58512936d3988ecb3a0cf86b0d0b66a8b1a3c117/https://sourceforge.net/p/genomecmp/code/ci/62e8df6f88bab58e0481b3239472763ce9f32f24/#460 Add KnuthMorrisPrattMaciej KulawikTue, 19 Sep 2017 18:54:07 -0000https://sourceforge.net/p/genomecmp/code/ci/62e8df6f88bab58e0481b3239472763ce9f32f24/https://sourceforge.net/p/genomecmp/code/ci/ce9991907b6a20a532f946862bb7bf8deae165be/#460 Add OneByOneMarkersDefinerMaciej KulawikTue, 19 Sep 2017 18:54:07 -0000https://sourceforge.net/p/genomecmp/code/ci/ce9991907b6a20a532f946862bb7bf8deae165be/https://sourceforge.net/p/genomecmp/code/ci/9f1287beca072f390e110642c5f98cb7beffaf20/#460 Add ChunkedXcorrMaciej KulawikSun, 17 Sep 2017 16:01:50 -0000https://sourceforge.net/p/genomecmp/code/ci/9f1287beca072f390e110642c5f98cb7beffaf20/https://sourceforge.net/p/genomecmp/code/ci/af5b20920357616d38dfb7059cbcb79b1bdb28cd/#460 Add TempFilenameManagerMaciej KulawikFri, 15 Sep 2017 15:31:42 -0000https://sourceforge.net/p/genomecmp/code/ci/af5b20920357616d38dfb7059cbcb79b1bdb28cd/https://sourceforge.net/p/genomecmp/code/ci/2cfc4cc6b8413663072ecf8f994a56019a814b85/#460 Add circos data savers, add some missing filesMaciej KulawikFri, 15 Sep 2017 15:31:42 -0000https://sourceforge.net/p/genomecmp/code/ci/2cfc4cc6b8413663072ecf8f994a56019a814b85/https://sourceforge.net/p/genomecmp/code/ci/a00144ea57bfceaa2ef59e6fba7a54869854a539/#460 Fix progressMaciej KulawikWed, 13 Sep 2017 12:42:20 -0000https://sourceforge.net/p/genomecmp/code/ci/a00144ea57bfceaa2ef59e6fba7a54869854a539/https://sourceforge.net/p/genomecmp/code/ci/04e3852043ad669dab13e0671940598a99ce4da3/#460 Add some DiffDetector testsMaciej KulawikWed, 13 Sep 2017 12:42:20 -0000https://sourceforge.net/p/genomecmp/code/ci/04e3852043ad669dab13e0671940598a99ce4da3/https://sourceforge.net/p/genomecmp/code/ci/9b2dd094084db1214c32d099542390250ff7b0f2/#460 Add DiffDetector, add searching of inversed markers in MarkersBasedRearrangementsDetectorMaciej KulawikMon, 11 Sep 2017 21:45:24 -0000https://sourceforge.net/p/genomecmp/code/ci/9b2dd094084db1214c32d099542390250ff7b0f2/https://sourceforge.net/p/genomecmp/code/ci/a0f1221a7d75ab9fe26ba0a162dbeae21b876b01/#460 add InGroupsMarkersDefiner, add SimpleMarkersSearcherMaciej KulawikMon, 11 Sep 2017 21:45:24 -0000https://sourceforge.net/p/genomecmp/code/ci/a0f1221a7d75ab9fe26ba0a162dbeae21b876b01/https://sourceforge.net/p/genomecmp/code/ci/bd883dff239ab2eab1c141402b1c5ed56e2949b8/#460 Add comments to FFT and FFTPlans.Maciej KulawikFri, 08 Sep 2017 12:05:51 -0000https://sourceforge.net/p/genomecmp/code/ci/bd883dff239ab2eab1c141402b1c5ed56e2949b8/https://sourceforge.net/p/genomecmp/code/ci/ea49d2cd881e0dbcb37679771c8cb7fd0d6eb9c2/#460 Fix CommandManagerPy python apiMaciej KulawikWed, 06 Sep 2017 14:55:12 -0000https://sourceforge.net/p/genomecmp/code/ci/ea49d2cd881e0dbcb37679771c8cb7fd0d6eb9c2/https://sourceforge.net/p/genomecmp/code/ci/3c577f8224aa82091527ef0a1cdd5c484f7943ab/#460 add FastXcorr, FFT, FFTPlans, RecursiveRadix2FFTMaciej KulawikWed, 06 Sep 2017 14:12:25 -0000https://sourceforge.net/p/genomecmp/code/ci/3c577f8224aa82091527ef0a1cdd5c484f7943ab/https://sourceforge.net/p/genomecmp/code/ci/390133e8627835e6c7b85338d998100c8f76432a/#460 Add CachedMarkerSearcher, move caching tracking methods to this class from MarkerSearcherMaciej KulawikSun, 03 Sep 2017 21:10:37 -0000https://sourceforge.net/p/genomecmp/code/ci/390133e8627835e6c7b85338d998100c8f76432a/https://sourceforge.net/p/genomecmp/code/ci/fee29db6360b86eadfe3d3b2c9f4004dd7b04bda/#460 fixes inspired by cppcheckMaciej KulawikSun, 03 Sep 2017 20:52:14 -0000https://sourceforge.net/p/genomecmp/code/ci/fee29db6360b86eadfe3d3b2c9f4004dd7b04bda/https://sourceforge.net/p/genomecmp/code/ci/0d50ae291ca200489f360aec4ea062ab482906a7/#460 fix subprogress in GenomeComparator and MarkersSearcher, add logger init to testsMaciej KulawikSun, 03 Sep 2017 20:16:17 -0000https://sourceforge.net/p/genomecmp/code/ci/0d50ae291ca200489f360aec4ea062ab482906a7/https://sourceforge.net/p/genomecmp/code/ci/6437effa73c94df482309d6200829570672ea75f/#460 Change Marker::Locations to std::map, add caching tracking option to MarkersSearcher, add some commentsMaciej KulawikSun, 03 Sep 2017 20:16:17 -0000https://sourceforge.net/p/genomecmp/code/ci/6437effa73c94df482309d6200829570672ea75f/https://sourceforge.net/p/genomecmp/code/ci/cd283b2e80ad1241e251da541638082d0509bc8e/#460 Add MarkersBasedRearrangementsDetector, fix typoMaciej KulawikFri, 01 Sep 2017 14:45:59 -0000https://sourceforge.net/p/genomecmp/code/ci/cd283b2e80ad1241e251da541638082d0509bc8e/https://sourceforge.net/p/genomecmp/code/ci/ffb9337e0a8792105aa9e77ec8406aaa3201b52f/#460 remove GenomeComparator::getSplitedProgressMaciej KulawikFri, 01 Sep 2017 13:24:49 -0000https://sourceforge.net/p/genomecmp/code/ci/ffb9337e0a8792105aa9e77ec8406aaa3201b52f/https://sourceforge.net/p/genomecmp/code/ci/b9fed308ab2b8efbeb13e577f95ff5fa2fdd2f72/#460 Change python callback wrappingMaciej KulawikFri, 01 Sep 2017 13:24:49 -0000https://sourceforge.net/p/genomecmp/code/ci/b9fed308ab2b8efbeb13e577f95ff5fa2fdd2f72/https://sourceforge.net/p/genomecmp/code/ci/dcd0c57cdc7e5725cf77aa42368ad4811a8bda15/#460 Add boost python api draft, add PyCallbackResultsProcessor, use boost::shared_ptr for storing base classes pointersMaciej KulawikWed, 30 Aug 2017 19:30:36 -0000https://sourceforge.net/p/genomecmp/code/ci/dcd0c57cdc7e5725cf77aa42368ad4811a8bda15/https://sourceforge.net/p/genomecmp/code/ci/1e6d3df2f9f77acc6b93efa6b4c8b04dc9bbd66f/#460 Add CommandManagerMaciej KulawikWed, 30 Aug 2017 19:30:36 -0000https://sourceforge.net/p/genomecmp/code/ci/1e6d3df2f9f77acc6b93efa6b4c8b04dc9bbd66f/https://sourceforge.net/p/genomecmp/code/ci/7b8fdcebbd0141e5ef67224660346dcca1212565/#460 Comment CallbackResultsProcessor and CallbackData, add unit tests for the classesMaciej KulawikMon, 28 Aug 2017 18:33:02 -0000https://sourceforge.net/p/genomecmp/code/ci/7b8fdcebbd0141e5ef67224660346dcca1212565/https://sourceforge.net/p/genomecmp/code/ci/fd366c9244909a56bd380abf0f488b07122ee671/#460 Add BaseToComparedPlan unit tests, comment BaseToComparedPlanMaciej KulawikMon, 28 Aug 2017 16:36:48 -0000https://sourceforge.net/p/genomecmp/code/ci/fd366c9244909a56bd380abf0f488b07122ee671/https://sourceforge.net/p/genomecmp/code/ci/3f9a4574760fed0cd4bba23f10b8e04b38cb6b57/#460 Further refactoring. Split GenomeComparator.h into separate files for each major class.Maciej KulawikSun, 27 Aug 2017 20:40:47 -0000https://sourceforge.net/p/genomecmp/code/ci/3f9a4574760fed0cd4bba23f10b8e04b38cb6b57/https://sourceforge.net/p/genomecmp/code/ci/595f1c19206eb5356ca10542daffd5904ffa5ce5/#460 Add PyCallbackResultsProcessorMaciej KulawikThu, 24 Aug 2017 11:10:10 -0000https://sourceforge.net/p/genomecmp/code/ci/595f1c19206eb5356ca10542daffd5904ffa5ce5/https://sourceforge.net/p/genomecmp/code/ci/6b2b3721de8e022cb04c527fe490dc258caf38e0/#460 Add BaseToComparedPlan, remove NamedSequencesById i.a. from parsersMaciej KulawikThu, 24 Aug 2017 11:10:10 -0000https://sourceforge.net/p/genomecmp/code/ci/6b2b3721de8e022cb04c527fe490dc258caf38e0/https://sourceforge.net/p/genomecmp/code/ci/200cccdbfabf1790fdbc8a325f9df58e76304235/#460 add TwoSequenceFilesLoader, remove unique_ptrs in sequence file parsersMaciej KulawikThu, 24 Aug 2017 11:10:10 -0000https://sourceforge.net/p/genomecmp/code/ci/200cccdbfabf1790fdbc8a325f9df58e76304235/https://sourceforge.net/p/genomecmp/code/ci/0908fbeaff20ac1a04c30e867aaf8e51fee296b9/#460 Add new c++ library draftMaciej KulawikTue, 22 Aug 2017 15:11:12 -0000https://sourceforge.net/p/genomecmp/code/ci/0908fbeaff20ac1a04c30e867aaf8e51fee296b9/https://sourceforge.net/p/genomecmp/code/ci/703645be695906cd9a50aadfc129bdaf3d9bab4a/doxyfile, change project namernowak2Thu, 27 Jul 2017 07:42:28 -0000https://sourceforge.net/p/genomecmp/code/ci/703645be695906cd9a50aadfc129bdaf3d9bab4a/https://sourceforge.nethttps%3A//sourceforge.net/projects/genomecmp/files/README.md/downloadgenomecmpThu, 27 Jul 2017 07:19:03 -0000https://sourceforge.net/projects/genomecmp/files/README.md/downloadhttps://sourceforge.net/p/genomecmp/code/ci/f1a9dc02f600d33adf4513b91f4ad940654fa34f/init revision, from antakya.ise.pw.edu.pl, change version to 0.4Maciej KulawikTue, 25 Jul 2017 11:30:22 -0000https://sourceforge.net/p/genomecmp/code/ci/f1a9dc02f600d33adf4513b91f4ad940654fa34f/