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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / analysis / AlignSeq.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-06-22 James ProcterJAL-2292 - ensure mapping is built for equal symbols... patch/JAL-2292_caseSensitivePAE commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-08-30 gmungocJAL-2685 tweaks to output spacing, updated TestAlignSeq... commit | commitdiff
2017-08-30 gmungocJAL-2685 use actual selection for report of pairwise... commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-04-07 gmungocJAL-2393 code tidying for review comments commit | commitdiff
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle... commit | commitdiff
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically... commit | commitdiff
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... commit | commitdiff
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with... commit | commitdiff
2017-02-20 gmungocJAL-2416 remove unused pep, dna alphabets, unused metho... commit | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... commit | commitdiff
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr... commit | commitdiff
2017-02-17 gmungocJAL-2416 scoreMatrices removed from ResidueProperties commit | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... commit | commitdiff
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... commit | commitdiff
2016-11-08 tcofoegbuJAL-2292 updated method calls commit | commitdiff
2016-11-04 tcofoegbuJAL-2292 fix for wrong mapping output in sequence mappi... commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2015-10-28 tcofoegbuJAL-1952 bugfix commit | commitdiff
2015-10-22 tcofoegbuJAL-1479 added basic support for SIFTs mapping - more... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin... commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-06-04 gmungocJAL-1750 small tidy of AlignSeq.printMapping (+Junit) commit | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... commit | commitdiff
2015-01-28 Jim Procter JAL-674 patch to make Mapping.compareTransferredToR... commit | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-11-18 Jim ProcterJAL-674 make temperature factor, local secondary struct... commit | commitdiff
2014-11-12 Jim ProcterJAL-674 patch broken getMapping function commit | commitdiff
2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and... commit | commitdiff
2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge commit | commitdiff
2014-10-21 Jim ProcterJAL-674 patch for duplicate row bug commit | commitdiff
2014-10-21 Jim ProcterJAL-674 patch to ensure existing annotation is properly... commit | commitdiff
2014-10-21 Jim ProcterJAL-674 JAL-207 getTers for aligned sequences in datase... commit | commitdiff
2014-10-21 Jim ProcterJAL-674 refactor method to match and transfer annotatio... commit | commitdiff
2014-09-23 darolmarJAL-1355 commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2013-06-18 Jim ProcterJAL-674 fix the mapping generation algorithm commit | commitdiff
2012-11-17 jproctermethod to construct sequence mapping for matching posit... commit | commitdiff
2012-11-17 jprocterconvenience method for performing pairwise alignment commit | commitdiff
2012-11-17 jprocterformatting and javadoc commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-09-06 jprocterJAL-1013 - employ index parameter rather than hardcode... commit | commitdiff
2012-09-02 jprocterJAL-1007 refactored code and patched calculation bug commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made... commit | commitdiff
2011-08-30 jprocterfix for JAL-917 - ensure all sequence strings are made... commit | commitdiff
2010-09-23 jprocterapply jalview code style commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-05-12 jprocterfix for JAL-527 commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-11-02 jproctergracefully cope with non-standard nucleotide or amino... commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2007-04-11 jprocterfixed base lookup bug in dna pairwise alignment and... commit | commitdiff
2007-02-07 amwaterhouseFormatting commit | commitdiff
2006-12-06 jproctergeneral pairwise substitution score models for pairwise... commit | commitdiff
2006-12-05 amwaterhousesequence is char [] commit | commitdiff
2006-10-10 amwaterhouseaaIndex replaces aaHash commit | commitdiff
2006-08-21 amwaterhouseheader updated commit | commitdiff
2006-07-19 amwaterhouseCheck for all gapped seqs commit | commitdiff
2006-07-18 amwaterhouseWorks on strings, not seqs commit | commitdiff
2006-07-07 amwaterhouseSequence numbering maintained commit | commitdiff
2005-12-15 amwaterhousePrevents confusing extra line being output in Java... commit | commitdiff
2005-12-06 amwaterhouseafter merge commit | commitdiff
2005-06-30 amwaterhouseFormatting changes commit | commitdiff
2005-06-08 amwaterhouseFormatted source commit | commitdiff
2005-06-08 amwaterhouseGPL license added commit | commitdiff
2004-11-18 amwaterhousemake variable public commit | commitdiff
2004-11-02 amwaterhouseJalview Imported Sources start commit | commitdiff