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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignSeq.java
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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diff to current
2023-06-22
James Procter
JAL-2292 - ensure mapping is built for equal symbols...
patch/JAL-2292_caseSensitivePAE
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commitdiff
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diff to current
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
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diff to current
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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diff to current
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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diff to current
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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commitdiff
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diff to current
2017-08-30
gmungoc
JAL-2685 tweaks to output spacing, updated TestAlignSeq...
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diff to current
2017-08-30
gmungoc
JAL-2685 use actual selection for report of pairwise...
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commitdiff
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diff to current
2017-08-16
Jim Procter
JAL-2418 source formatting
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commitdiff
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diff to current
2017-06-09
gmungoc
JAL-2446 merged to spike branch
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diff to current
2017-04-07
gmungoc
JAL-2393 code tidying for review comments
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commitdiff
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diff to current
2017-03-29
gmungoc
JAL-2416 revert to '*' not '-' in score matrix, handle...
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commitdiff
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diff to current
2017-03-27
gmungoc
JAL-2416 score matrix gap symbol (if any) dynamically...
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diff to current
2017-03-24
gmungoc
JAL-838 move two callers off Comparison.PID and depreca...
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commitdiff
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diff to current
2017-02-20
gmungoc
JAL-2416 replaced dependency on ResidueProperties with...
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diff to current
2017-02-20
gmungoc
JAL-2416 remove unused pep, dna alphabets, unused metho...
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diff to current
2017-02-18
gmungoc
JAL-2416 better encapsulated 'constants' for BLOSUM62...
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commitdiff
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diff to current
2017-02-17
gmungoc
JAL-2416 removed DNA and PAM250 matrices from ResiduePr...
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diff to current
2017-02-17
gmungoc
JAL-2416 scoreMatrices removed from ResidueProperties
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commitdiff
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diff to current
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
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diff to current
2017-02-13
gmungoc
JAL-1632 first cut of Tree chooser dialog and ScoreMode...
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commitdiff
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diff to current
2016-11-08
tcofoegbu
JAL-2292 updated method calls
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commitdiff
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diff to current
2016-11-04
tcofoegbu
JAL-2292 fix for wrong mapping output in sequence mappi...
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diff to current
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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commitdiff
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diff to current
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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commitdiff
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diff to current
2016-10-05
Jim Procter
JAL-2189 source formatting
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commitdiff
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diff to current
2015-10-28
tcofoegbu
JAL-1952 bugfix
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commitdiff
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diff to current
2015-10-22
tcofoegbu
JAL-1479 added basic support for SIFTs mapping - more...
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commitdiff
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diff to current
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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commitdiff
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diff to current
2015-10-14
tcofoegbu
JAL-1926 added supporting model changes to enable savin...
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commitdiff
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diff to current
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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commitdiff
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diff to current
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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commitdiff
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diff to current
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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commitdiff
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diff to current
2015-06-04
gmungoc
JAL-1750 small tidy of AlignSeq.printMapping (+Junit)
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commitdiff
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diff to current
2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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commitdiff
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diff to current
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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diff to current
2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
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commitdiff
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diff to current
2015-01-28
Jim Procter
JAL-674 patch to make Mapping.compareTransferredToR...
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commitdiff
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diff to current
2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
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commitdiff
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diff to current
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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commitdiff
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diff to current
2014-11-18
Jim Procter
JAL-674 make temperature factor, local secondary struct...
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commitdiff
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diff to current
2014-11-12
Jim Procter
JAL-674 patch broken getMapping function
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commitdiff
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diff to current
2014-10-30
Jim Procter
JAL-674 return original and replacement sequences and...
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commitdiff
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diff to current
2014-10-21
Jim Procter
JAL-674 JAL-1551 imports dropped during merge
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commitdiff
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diff to current
2014-10-21
Jim Procter
JAL-674 patch for duplicate row bug
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commitdiff
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diff to current
2014-10-21
Jim Procter
JAL-674 patch to ensure existing annotation is properly...
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commitdiff
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diff to current
2014-10-21
Jim Procter
JAL-674 JAL-207 getTers for aligned sequences in datase...
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commitdiff
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diff to current
2014-10-21
Jim Procter
JAL-674 refactor method to match and transfer annotatio...
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commitdiff
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diff to current
2014-09-23
darolmar
JAL-1355
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commitdiff
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diff to current
2014-06-06
Jim Procter
JAL-1517 source formatting
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commitdiff
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diff to current
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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commitdiff
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diff to current
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
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diff to current
2014-06-05
Jim Procter
Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
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diff to current
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
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commitdiff
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diff to current
2014-02-18
Jim Procter
Merge branch 'JAL-1445' into develop
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commitdiff
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diff to current
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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commitdiff
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diff to current
2013-06-18
Jim Procter
JAL-674 fix the mapping generation algorithm
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commitdiff
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diff to current
2012-11-17
jprocter
method to construct sequence mapping for matching posit...
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commitdiff
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diff to current
2012-11-17
jprocter
convenience method for performing pairwise alignment
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commitdiff
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diff to current
2012-11-17
jprocter
formatting and javadoc
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commitdiff
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diff to current
2012-10-22
jprocter
Jalview 2.8 Source Header
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commitdiff
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diff to current
2012-10-03
jprocter
formatting
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commitdiff
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diff to current
2012-09-06
jprocter
JAL-1013 - employ index parameter rather than hardcode...
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commitdiff
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diff to current
2012-09-02
jprocter
JAL-1007 refactored code and patched calculation bug
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commitdiff
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diff to current
2011-10-10
jprocter
update author list in license for (JAL-826)
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commitdiff
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diff to current
2011-09-27
jprocter
apply version 2.7 copyright
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commitdiff
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diff to current
2011-08-30
jprocter
fix for JAL-917 - ensure all sequence strings are made...
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commitdiff
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diff to current
2011-08-30
jprocter
fix for JAL-917 - ensure all sequence strings are made...
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commitdiff
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diff to current
2010-09-23
jprocter
apply jalview code style
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commitdiff
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diff to current
2010-09-23
jprocter
Jalview 2.6 source licence
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commitdiff
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diff to current
2010-05-12
jprocter
fix for JAL-527
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commitdiff
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diff to current
2010-04-30
jprocter
jalview 2.5 release banner
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commitdiff
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diff to current
2009-11-02
jprocter
gracefully cope with non-standard nucleotide or amino...
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commitdiff
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diff to current
2009-06-08
jprocter
apply gpl development license
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diff to current
2008-09-04
jprocter
merge from 2_4_Release branch
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commitdiff
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diff to current
2007-04-11
jprocter
fixed base lookup bug in dna pairwise alignment and...
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diff to current
2007-02-07
amwaterhouse
Formatting
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diff to current
2006-12-06
jprocter
general pairwise substitution score models for pairwise...
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commitdiff
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2006-12-05
amwaterhouse
sequence is char []
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diff to current
2006-10-10
amwaterhouse
aaIndex replaces aaHash
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diff to current
2006-08-21
amwaterhouse
header updated
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commitdiff
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diff to current
2006-07-19
amwaterhouse
Check for all gapped seqs
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diff to current
2006-07-18
amwaterhouse
Works on strings, not seqs
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commitdiff
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diff to current
2006-07-07
amwaterhouse
Sequence numbering maintained
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commitdiff
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diff to current
2005-12-15
amwaterhouse
Prevents confusing extra line being output in Java...
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commitdiff
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diff to current
2005-12-06
amwaterhouse
after merge
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commitdiff
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diff to current
2005-06-30
amwaterhouse
Formatting changes
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commitdiff
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diff to current
2005-06-08
amwaterhouse
Formatted source
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commitdiff
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diff to current
2005-06-08
amwaterhouse
GPL license added
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commitdiff
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diff to current
2004-11-18
amwaterhouse
make variable public
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commitdiff
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diff to current
2004-11-02
amwaterhouse
Jalview Imported Sources
start
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diff to current