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[jalview.git] / src / jalview / analysis / AlignSeq.java

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

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