Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...
[jalview.git] / src / jalview / analysis / AlignSeq.java
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-08-30 gmungocJAL-2685 tweaks to output spacing, updated TestAlignSeq...
2017-08-30 gmungocJAL-2685 use actual selection for report of pairwise...
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-04-07 gmungocJAL-2393 code tidying for review comments
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle...
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically...
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca...
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with...
2017-02-20 gmungocJAL-2416 remove unused pep, dna alphabets, unused metho...
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62...
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr...
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode...
2016-11-08 tcofoegbuJAL-2292 updated method calls
2016-11-04 tcofoegbuJAL-2292 fix for wrong mapping output in sequence mappi...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2015-10-28 tcofoegbuJAL-1952 bugfix
2015-10-22 tcofoegbuJAL-1479 added basic support for SIFTs mapping - more...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-06-04 gmungocJAL-1750 small tidy of AlignSeq.printMapping (+Junit)
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-01-28 Jim Procter JAL-674 patch to make Mapping.compareTransferredToR...
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-11-18 Jim ProcterJAL-674 make temperature factor, local secondary struct...
2014-11-12 Jim ProcterJAL-674 patch broken getMapping function
2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and...
2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge
2014-10-21 Jim ProcterJAL-674 patch for duplicate row bug
2014-10-21 Jim ProcterJAL-674 patch to ensure existing annotation is properly...
2014-10-21 Jim ProcterJAL-674 JAL-207 getTers for aligned sequences in datase...
2014-10-21 Jim ProcterJAL-674 refactor method to match and transfer annotatio...
2014-09-23 darolmarJAL-1355
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-06-18 Jim ProcterJAL-674 fix the mapping generation algorithm
2012-11-17 jproctermethod to construct sequence mapping for matching posit...
2012-11-17 jprocterconvenience method for performing pairwise alignment
2012-11-17 jprocterformatting and javadoc
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-09-06 jprocterJAL-1013 - employ index parameter rather than hardcode...
2012-09-02 jprocterJAL-1007 refactored code and patched calculation bug
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made...
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made...
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-05-12 jprocterfix for JAL-527
2010-04-30 jprocterjalview 2.5 release banner
2009-11-02 jproctergracefully cope with non-standard nucleotide or amino...
2009-06-08 jprocterapply gpl development license
2008-09-04 jproctermerge from 2_4_Release branch
2007-04-11 jprocterfixed base lookup bug in dna pairwise alignment and...
2007-02-07 amwaterhouseFormatting
2006-12-06 jproctergeneral pairwise substitution score models for pairwise...
2006-12-05 amwaterhousesequence is char []
2006-10-10 amwaterhouseaaIndex replaces aaHash
2006-08-21 amwaterhouseheader updated
2006-07-19 amwaterhouseCheck for all gapped seqs
2006-07-18 amwaterhouseWorks on strings, not seqs
2006-07-07 amwaterhouseSequence numbering maintained
2005-12-15 amwaterhousePrevents confusing extra line being output in Java...
2005-12-06 amwaterhouseafter merge
2005-06-30 amwaterhouseFormatting changes
2005-06-08 amwaterhouseFormatted source
2005-06-08 amwaterhouseGPL license added
2004-11-18 amwaterhousemake variable public
2004-11-02 amwaterhouseJalview Imported Sources start