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Граф коммитов

  • 116a6458e3 Allow ValidateGetReverseComplement test to pass, make several changes to deal with even length k-mers again to deal with palindromes and ensure simple paths. evolvedmicrobe_cp 2013-06-30 13:52:48 -0700
  • 71a67e0d7a Removes outdated test evolvedmicrobe_cp 2013-06-30 11:49:58 -0700
  • 23373a70b8 Fixed unit test, now two tests where one sequence "fails" to be assembled and looks like the first. evolvedmicrobe_cp 2013-06-25 13:30:38 -0700
  • e377635017 Updated WIX for final 1.1 release. markjulmar_cp 2013-06-24 15:29:18 -0700
  • cf825516a1 Updated readme files. markjulmar_cp 2013-06-24 11:19:23 -0700
  • 772aa1dbfd Added readme for updates to 1.1. markjulmar_cp 2013-06-24 06:46:15 -0700
  • d9a816f705 Updated copyrights. markjulmar_cp 2013-06-24 06:36:25 -0700
  • 154ff8cdf9 Minor code revisions to checkin. markjulmar_cp 2013-06-24 06:32:38 -0700
  • d63868bafe Missing elements from TFS markjulmar_cp 2013-06-24 06:16:46 -0700
  • ed6045d66e Fixed zipped parser so they could be loaded by reflection, and override base class descriptions evolvedmicrobe_cp 2013-06-21 11:06:35 -0700
  • 88cb99d3c7 Quick fix on removing the zipped extension, now cuts off ".gz" from the end instead of from anywhere in the string. evolvedmicrobe_cp 2013-06-20 10:27:57 -0700
  • 34997894c5 Added assembly test that has a tricky palindromic sequence, which currently instead of returning one sequence returns two incorrect ones. evolvedmicrobe_cp 2013-06-19 20:57:41 -0700
  • f35f3b14e9 Fix bug where array can be resized but still not fit contents of sequences (it used to grow dynamically by a set length when too long, but was not guaranteed to be large enough). evolvedmicrobe_cp 2013-06-12 09:47:11 -0700
  • 955f05ffd4 Include parsers for gzipped FASTA/FASTQ files evolvedmicrobe_cp 2013-06-11 10:50:01 -0700
  • 4c8cb7d090 Fix problem where file format converter checked twice to verify the input format instead of checking the input and export format. evolvedmicrobe_cp 2013-06-07 16:15:01 -0700
  • f6e8d39fdc Made PADENAUtil run in server gc mode evolvedmicrobe_cp 2013-05-27 07:46:43 -0700
  • 61ff248359 Removed Branch evolvedmicrobe_cp 2013-05-19 22:27:52 -0700
  • ad9b12bc4b EnumerableBAMParser evolvedmicrobe_cp 2013-05-19 22:23:14 -0700
  • d7ecc58ea4 Branched from $/bio/bio evolvedmicrobe_cp 2013-05-19 21:54:29 -0700
  • 622a4e0df7 Fixes inability to process unmapped reads in SAM files when converting to/from BAM format. evolvedmicrobe_cp 2013-05-11 11:54:54 -0700
  • d2fd073c60 Changed BAM parser to look for index files of both *.bam.bai and *.bai. evolvedmicrobe_cp 2013-05-10 09:45:21 -0700
  • ee4db8ed57 Added Excel 2013 to string. markjulmar_cp 2013-05-06 13:01:39 -0700
  • e407577275 Improved transation of ambiguous RNA from dstarke. markjulmar_cp 2013-05-06 12:55:26 -0700
  • 882190ce5b Detect EOF in stream and end the sequence rather than throw exception. markjulmar_cp 2013-05-04 08:27:33 -0700
  • 0896c06168 - Moved all web service test cases into Bio.Tests.Web so they can be excluded more easily when no internet connection is available or when services are down. - Added check into DeltaAlignmentParser to remove "Reverse" from ID so we can properly parse position from end of string. - Cleaned up the add-in registration so AddIn folder is not created in tests (because it's not necessary anymore). - Since some of the test aligners show up during other tests (specifically FindParserByFileName), I implemented the SupportedFileTypes so it doesn't thrown an exception. markjulmar_cp 2013-05-04 07:55:07 -0700
  • 05c08ce93a 1) Added argument to command prompt to allow CTRL+C and CTRL+V 2) Bumped version # of the installers 3) Added support for Excel 2013 markjulmar_cp 2013-05-03 14:26:17 -0700
  • d88c9abb27 1) Fixed the Nucmer utility to properly handle forward and reverse strands 2) Added Forward and Reverse properties into the NucmerPairwise Aligner. 3) Fixed unit tests 4) Changed the DeltaAlignment to handle reverse strands and note them with QueryDirection 5) Changed the DeltaAlignmentParser to handle reverse strands (start > end) 6) Bumped the version number on the command line tools 7) Change the copyright to include 2013 markjulmar_cp 2013-05-03 10:22:23 -0700
  • 94a1cd6c37 - Rollback Padena changes due to unit test failures. - Fixed all unit tests to run under VS 2012 and R# - Added unit tests for Newick changes from Nigel markjulmar_cp 2013-05-01 15:17:46 -0700
  • ee180e5baf Fixes and unit test updates. markjulmar_cp 2013-04-12 14:36:07 -0700
  • 10ec32fbb3 Minor improvements to ReadSimulator code. markjulmar_cp 2013-04-12 09:53:42 -0700
  • c8292fe5ce 1) Changed ComparativeGenomeAssembler to use temporary files and paths instead of hardcoded filenames. 2) Updates for Padena from Nigel 3) Unit test fixes 4) Added Try methods to ProteinTranslation 5) Dropped FastAParser buffer size down to avoid OutOfMemory exceptions on 32-bit machines 6) Added echo to console for application logging. 7) Fixed DeltaAlignmentParser to not keep sequence file open after Dispose and removed finalizer. markjulmar_cp 2013-04-12 09:45:34 -0700
  • 340a5cf477 Newick Parser Fix evolvedmicrobe_cp 2013-04-11 13:39:52 -0700
  • 4904e59e1d evolvedmicrobe_cp 2013-04-11 13:37:27 -0700
  • 4b27dcddca Newick File Input Fix evolvedmicrobe_cp 2013-04-11 13:23:35 -0700
  • a834b1f869 Updates to unit tests for new aligner work. markjulmar_cp 2013-04-09 09:46:29 -0700
  • e311923385 Updates to new algorithms to improve performance and memory utilization. markjulmar_cp 2013-04-09 08:43:18 -0700
  • ed36bcbe29 Fixed mummer test cases. markjulmar_cp 2013-04-07 15:53:04 -0700
  • 5a2be02e79 Copy TestData into output directory for new test structures. markjulmar_cp 2013-04-07 10:54:12 -0700
  • f4171e4e35 New solution specific to BioHpc (includes Bio.DLL and Bio.Hpc, DistributeApp and test cases) markjulmar_cp 2013-04-02 15:54:48 -0700
  • 88e2ad5695 Bumped version number to 1.1 for every component Changed copyright dates to reflect new release. markjulmar_cp 2013-04-02 15:50:29 -0700
  • c39d015f39 Moved Silverlight to separate solution with unit tests. Minor cleanup to fix compile warnings and shift to Visual Studio 2012. markjulmar_cp 2013-04-02 07:26:44 -0700
  • 1f6559c8e0 Moved Test Data so we can run unit tests directly in build directory through VS2012 new .testrunner capability. This speeds up the build/test process by 10x and removes the huge TestResult folders we used to have. markjulmar_cp 2013-04-02 06:28:52 -0700
  • 9b1b0735e4 Moved Test Data so we can run unit tests directly in build directory through VS2012 new .testrunner capability. This speeds up the build/test process by 10x and removes the huge TestResult folders we used to have. markjulmar_cp 2013-04-02 06:27:03 -0700
  • c5c6ba08f1 Moved Test Data so we can run unit tests directly in build directory through VS2012 new .testrunner capability. This speeds up the build/test process by 10x and removes the huge TestResult folders we used to have. markjulmar_cp 2013-04-02 06:17:09 -0700
  • aeb28ba6b0 Unit test reshuffling. markjulmar_cp 2013-04-01 18:43:01 -0700
  • 941291dd6a Shifting around Unit test projects. markjulmar_cp 2013-04-01 18:38:39 -0700
  • b50d3d6c1b - Added new alighment algorithms, replaced existing Smith-Waterman and Needleman-Wunsch aligners (renamed to Legacy). - Converted to Visual Studio 2012 unit test formats. - Bumped version of .NET Bio to 1.1 in preparation for next release. - Moved Padena, Pamsam, HPC unit tests into separate libraries - new BioCore.sln for .NET Bio + IO + Unit Tests. markjulmar_cp 2013-04-01 18:26:06 -0700
  • 8f9fa522ad Removed BigList<T> from ContigBuilder markjulmar_cp 2013-03-28 05:12:17 -0700
  • a6b20e084b Removed BigList<T> from ContigBuilder. markjulmar_cp 2013-03-28 05:11:13 -0700
  • b73c4b6a78 Only seeds the random number generator once to avoid repeatedly simulating the same value. Also gets the reverse compliment instead of just the reverse of a simulated sequence if asked. evolvedmicrobe_cp 2013-02-19 13:12:06 -0800
  • 38868687e2 Upgrade: New Version of LabDefaultTemplate.xaml. To upgrade your build definitions, please visit the following link: http://go.microsoft.com/fwlink/?LinkId=254563 [TFS09]\Project Collection Service Accounts 2012-10-01 14:29:18 -0700
  • e62a9dd1f4 Checked in by server upgrade [TFS09]\Project Collection Service Accounts 2012-10-01 14:23:54 -0700
  • 26a1d8ce68 Remove TFS branch to avoid confusing other CodePlex source control systems. bobd00_cp 2012-09-17 10:39:33 -0700
  • 7e997a6e76 Create Bio2 branch for VS2012 / .Net 4.5 integration work bobd00_cp 2012-08-03 00:50:09 -0700
  • 02009d88ec Fix for template version. markjulmar_cp 2012-07-04 06:07:49 -0700
  • 9e58479ac7 Added tooltips to assembly and alignment dialogs. markjulmar_cp 2012-07-02 18:24:16 -0700
  • a28913b39a Added strings and tooltips to dialogs. markjulmar_cp 2012-07-02 18:12:19 -0700
  • 3c796b3581 Various fixes. markjulmar_cp 2012-07-02 16:04:13 -0700
  • 31ad9535ab Enable translation of AmbiguousRNA sequences to AmbiguousProtein sequences Review and apply patch from dstarke bobd00_cp 2012-07-02 14:37:55 -0700
  • d1671efb87 Fixed Bug: 8080 manjus_cp 2012-06-29 15:49:08 -0700
  • 199caa7c08 Fixed Bug id: 8075 manjus_cp 2012-06-27 16:18:31 -0700
  • d900ec4847 1. Added AATree, BigArray, BigList, LongSerialNumbers, Vertex, Edge and Graph classes 2. DeBruijnGraph.cs Added Thread.BeginCriticalRegion and Thread.EndCriticalRegion, this will make sure to bring down the App domain if these Tasks abort unexpectedly. DeBruijnGraph class now extends from Graph class 3. SimplePathContigBuilder.cs Modified to use BigList instead of list. manjus_cp 2012-06-08 13:19:15 -0700
  • b4b2eba073 Removed NodeXL dependency from installer. markjulmar_cp 2012-05-15 12:01:36 -0700
  • 1af5357ca1 Add ToolTip to note that match/mismatch scores are only used for Diagonal (Match x Mismatch) matrix. markjulmar_cp 2012-04-09 13:39:32 -0700
  • ced741a262 Removed hard-coded match value for Smith-Waterman to improve accuracy of alignment. markjulmar_cp 2012-04-07 06:51:43 -0700
  • cce356d062 Minor cleanup of code. markjulmar_cp 2012-04-06 13:03:13 -0700
  • e7b8fa0d6f - Supressed new code analysis messages introduced by newer FxCop. - Sorted alignment algorithms on Assembly dialogs in Excel and Sequence Assembler - Made Smith-Waterman default alignment algorithm for simple assemblies. - Corrected some spelling in comments. markjulmar_cp 2012-04-06 09:06:25 -0700
  • 869ca26c24 - Added MEF export support to WebServices class - Excluded Azure BLAST from MEF - Fixed UI exception in BioExcel related to accessing worksheet during OnLoad (COM error discovered when we turned on UI errors in Excel). - Added override to create Ribbon in BioExcel with try/catch so we can see any errors. markjulmar_cp 2012-04-03 16:36:24 -0700
  • e803a502a8 - Updated version numbers to include build/revision so we can differentiate files. - Added bio.dll into Excel and SequenceAssemblier about dialogs. markjulmar_cp 2012-04-03 11:41:24 -0700
  • aa8a08d58a - Updates to fix failing unit tests - Corrected spelling in several comments. markjulmar_cp 2012-04-03 10:52:09 -0700
  • a3d32e19e9 Updated unit tests for command-line utilities (-help) option to include new version number (1.01) in output text. markjulmar_cp 2012-04-03 06:42:47 -0700
  • c5ad39d045 - Reset PAMSAM algorithm fields when Align is called so same instance can be used multiple times. - Set proper zoom level on alignment/concensus views so sheets look the same as imports. markjulmar_cp 2012-04-03 06:02:34 -0700
  • 24eabff691 Updated readme from Rick. markjulmar_cp 2012-04-02 14:13:04 -0700
  • 0a8b4f0ef0 1) Changed default OpenGap value for all pairwise aligners. 2) Added Open/Extend gap cost defaults for PAMSAM 3) Added complement test to GetReverseComplementedSequence 4) Some spelling fixes 5) Added PAMSAM as dependency to BioExcel to get at IMultipleSequenceAligner 6) Various fixes for BioExcel 7) Added MEF exports to ISequenceRangeParser/Formatter. 8) Changed output of alignment set in BioExcel to improve readability. markjulmar_cp 2012-04-02 14:08:30 -0700
  • 1cbdb96932 - Added new description resource for PAMSAM ISequenceParser.Description (was previously using name) - Changed name of PAMSAM ISequenceParser.Name to "PAMSAM (MUSCLE)". markjulmar_cp 2012-03-30 12:50:00 -0700
  • dad5a3cad5 - Changed license header text to include product name. markjulmar_cp 2012-03-30 12:38:02 -0700
  • 52fbef368c - Secondary change to limit output to a max of 80 per Fasta specification. markjulmar_cp 2012-03-30 08:21:43 -0700
  • 44c798b613 - Changed output to console to be in formal FASTA format. - Limited sequence width to console window size markjulmar_cp 2012-03-30 08:14:44 -0700
  • 7c21b6aec2 - Change welcome screen text for installer to remove "the" markjulmar_cp 2012-03-30 07:10:26 -0700
  • 11961bb4f0 - Set the ControlIdType for our tab to RibbonControlIdType.Office so the text label is properly printed when loading a document. Seems to fix this issue, but it's not documented as necessary. markjulmar_cp 2012-03-29 13:29:55 -0700
  • dda36629e9 - Do not assume email has been supplied to EBI web service. [avoid exception] markjulmar_cp 2012-03-29 12:59:15 -0700
  • 93224a9d29 - Added code to ignore assemblies which cannot be loaded/resolved due to external (missing) references markjulmar_cp 2012-03-29 12:02:24 -0700
  • aa92008122 Added comment about build requirement (Sandcastle) to root readme. markjulmar_cp 2012-03-29 08:35:19 -0700
  • 2f10d0e1c2 - Updated Excel readme for 1.01 with proper spacing for Write.exe - Removed file open check in SFFParser -- sequence assembler app calls FindParserByFileName multiple times which leaves file open. Given our implementation of Parse() we don't need this check. markjulmar_cp 2012-03-29 07:03:17 -0700
  • 20b75aa90a Removed dummy group. markjulmar_cp 2012-03-29 06:14:43 -0700
  • d5ed86bb3f Do not document parameters/values that are missing in the XML. markjulmar_cp 2012-03-29 06:04:43 -0700
  • 9c112509d3 Fix to ensure metadata + ID are stored on generated sequences when using parallel profiler. markjulmar_cp 2012-03-29 06:04:16 -0700
  • 33f995896e Updated readme files from Rick. markjulmar_cp 2012-03-28 15:30:14 -0700
  • f0dbf491d4 Added zero in front of minor number to get directory name to be 1.01 markjulmar_cp 2012-03-28 13:32:30 -0700
  • c7d3778cf6 Changed parser name to make it more obvious in Excel add-in. markjulmar_cp 2012-03-28 12:48:30 -0700
  • e36298add6 Updates for installer 1.01 markjulmar_cp 2012-03-28 12:15:47 -0700
  • 6b7bd24c6a - Installer changes for 1.01 - Changed all assemblies to use v1.01 (1.01.0.0) markjulmar_cp 2012-03-28 08:25:28 -0700
  • 7faf1fc16b - added defaults in constructor to allow Excel to run PAMSAM as ISequenceAligner. - added return result as IAlignedSequences. markjulmar_cp 2012-03-27 13:57:12 -0700
  • a5b83f66bf - Add XML documentation for Bio.Comparative - Fix Bio.HPC XML documentation location - Catch exception when validating alphabet using custom alphabets - Correct documentation tags in Bio.Comparative sources - Change Excel output for imported sequences (GFF/GenBank) - Change position of sequence data inported into Excel to start at column "C" so metadata columns can be auto-sized properly. markjulmar_cp 2012-03-27 13:42:55 -0700
  • cc50394422 - Added sequence extensions to support ConvertToString on any ISequence type (convenience). - Added alphabet extensions to round out missing methods on IAlphabet. - Added unit tests for extensions. markjulmar_cp 2012-03-26 15:21:00 -0700
  • b62e2b46ef - Added (char) cast for /s option values. markjulmar_cp 2012-03-22 12:14:10 -0700
  • 7725c4c4d0 - Added proper help page for SampleClusterApp.exe and Hpc.Bio.Distribute.exe - Renamed Hpc.Bio.Distribute to DistributeApp.exe - Moved splash and help to resources - Added new flag to CommandArguments to allow HelpException to be handled by app for custom help pages - Corrected FxCop rule violation in ClusterSubmitter markjulmar_cp 2012-03-21 03:19:51 -0700
  • 8fee8d6695 - Ensure a valid sequence identifier is always present on generated sequences using the output filename, or first input filename. - Corrected console unit tests based on new output. markjulmar_cp 2012-03-20 15:14:42 -0700
  • d4a7f7e684 - Added new SFF parser and Bio.IO project - Added test cases to support SFF parser - Updated existing test cases for changes in console application output - Added MEF resolver for add-ins. Now searches current directory as well as addin folder (existing known parsers/alphabets/algorithms are excluded) - base interfaces are now marked with [InheritedExport] for MEF so custom parsers/alphabets/algorithms are automatically located and added to global lists. - Corrected some code analysis errors markjulmar_cp 2012-03-19 07:36:22 -0700
  • 6680d073a1 - Corrected output so we never clip string inappropriately. markjulmar_cp 2012-03-13 11:05:45 -0700