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Merge branch 'features/JAL-845splitPaneMergeDevelop' into merge_JAL-845_JAL-1640
[jalview.git]
/
src
/
jalview
/
analysis
/
2015-02-09
Jim Procter
Merge branch 'features/JAL-845splitPaneMergeDevelop...
tree
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commitdiff
2015-02-09
gmungoc
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2015-02-03
gmungoc
JAL-845 code/refactoring/tests related to linking DNA...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
Merge branch 'bug/JAL-1644_Finder-logic-improvement...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
JAL-1644 added null check for sequence description...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
Merge commit
tree
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commitdiff
2015-02-02
Charles Ofoegbu
JAL-1644 revised Finder's implementation to use a flag...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
Merge branch 'bug/JAL-1644_Finder-logic-improvement...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
JAL-1644 improvment of finder logic to include the...
tree
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commitdiff
2015-01-30
gmungoc
JAL-845 linked protein/dna 'slave' further PoC function...
features/JAL-845linkedProteinDnaEditing
tree
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commitdiff
2015-01-28
Jim Procter
JAL-674 patch to make Mapping.compareTransferredToR...
tree
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commitdiff
2015-01-22
gmungoc
JAL-1619 refactoring / tests to support 'align linked...
tree
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commitdiff
2015-01-19
gmungoc
JAL-1619 refactored cDNA translation; modified codon...
tree
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commitdiff
2015-01-18
gmungoc
JAL-1619 refactoring wip
tree
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commitdiff
2015-01-17
gmungoc
JAL-1619 further refactoring
tree
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commitdiff
2015-01-16
gmungoc
JAL-1619 refactoring in progress for Dna translation
tree
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commitdiff
2015-01-14
gmungoc
JAL-1619 Javadoc
tree
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commitdiff
2015-01-12
gmungoc
JAL-1619 load/align cDNA for protein (wip)
tree
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commitdiff
2015-01-07
Jim Procter
JAL-1483 patches to make test case pass: hamming distan...
tree
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commitdiff
2015-01-07
Jim Procter
JAL-1483 source formatting
tree
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commitdiff
2015-01-07
Jim Procter
JAL-1483 refactor NJTree constructor to allow preconfig...
tree
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commitdiff
2015-01-07
Jim Procter
JAL-1483 organise imports
tree
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commitdiff
2015-01-04
gmungoc
JAL-1619 first draft of 'linked protein and cDNA'
tree
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commitdiff
2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
tree
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commitdiff
2014-12-16
gmungoc
JAL-1619 don't copy hidden or RNA SS annotations to...
tree
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commitdiff
2014-12-12
gmungoc
JAL-845 don't translate hidden annotation (plus formatting)
tree
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commitdiff
2014-11-27
Jim Procter
JAL-674 add sequence associated annotation rows to...
tree
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commitdiff
2014-11-23
Jim Procter
Merge branch 'JAL-1569_wuss_vienna_broke' into develop
tree
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commitdiff
2014-11-23
Jim Procter
Merge branch 'JAL-1569_wuss_vienna_broke' into Release_...
tree
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commitdiff
2014-11-23
Jim Procter
JAL-1152 avoid NPE on null alignment annotation vector
tree
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commitdiff
2014-11-20
Jim Procter
JAL-1569 remove log output during RNA secondary structu...
tree
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commitdiff
2014-11-18
Jim Procter
JAL-674 make temperature factor, local secondary struct...
tree
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commitdiff
2014-11-14
Jim Procter
Merge branch 'develop' into JAL-1483_featureBasedTreeCalc
tree
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commitdiff
2014-11-12
Jim Procter
JAL-674 patch broken getMapping function
tree
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commitdiff
2014-11-04
gmungoc
JAL-1152 annotation sort algorithm optimisation
tree
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commitdiff
2014-11-03
gmungoc
Merge branch 'features/JAL-1152annotationSorting' of...
tree
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commitdiff
2014-11-03
gmungoc
JAL-1152 annotation sorting preferences and help docume...
tree
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commitdiff
2014-11-03
Jim Procter
Merge branch 'develop' into features/JAL-1152annotation...
tree
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commitdiff
2014-10-31
gmungoc
JAL-1152 bug fix for 'no sort' case + tests for autocal...
tree
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commitdiff
2014-10-31
gmungoc
JAL-1152 menu tweaks plus new option to put Autocalc...
tree
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commitdiff
2014-10-30
gmungoc
JAL-1152 with sticky annotation sort order that updates...
tree
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commitdiff
2014-10-30
Jim Procter
JAL-674 return original and replacement sequences and...
tree
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commitdiff
2014-10-30
gmungoc
JAL-1152 prototype of new Annotations menu with sort...
tree
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commitdiff
2014-10-23
gmungoc
JAL-1264 further refactoring and tests
tree
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commitdiff
2014-10-21
Jim Procter
JAL-674 JAL-1551 imports dropped during merge
tree
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commitdiff
2014-10-21
Jim Procter
JAL-674 patch for duplicate row bug
tree
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commitdiff
2014-10-21
Jim Procter
JAL-674 patch to ensure existing annotation is properly...
tree
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commitdiff
2014-10-21
Jim Procter
JAL-674 JAL-207 getTers for aligned sequences in datase...
tree
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commitdiff
2014-10-21
Jim Procter
JAL-674 refactor method to match and transfer annotatio...
tree
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commitdiff
2014-09-23
darolmar
JAL-1355
tree
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commitdiff
2014-08-08
j.procter@dundee...
JAL-1483 reformatting and use new feature renderer...
tree
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commitdiff
2014-06-13
Jim Procter
Merge branch 'Release_2_8_2_Branch' into JAL-1483_featu...
tree
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commitdiff
2014-06-06
Jim Procter
JAL-1517 source formatting
tree
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commitdiff
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
tree
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commitdiff
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
tree
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commitdiff
2014-06-05
Jim Procter
Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
tree
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commitdiff
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
tree
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commitdiff
2014-05-02
Jim Procter
Merge branch 'JAL-1397' into develop
tree
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commitdiff
2014-05-01
Jim Procter
make sure valid value for non-gapped calculation with...
tree
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commitdiff
2014-04-21
Jim Procter
Merge branch 'jims_marckhacks' into develop
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 don't include empty columns if no upstream...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1483 cut and paste from SW score model to allow...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-736 hack to show the conserved property values...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1427 make sure we are working with dataset sequence...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1481 relevant todo re warning user for broken regex
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 improved test and patched off by one that...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1466 new calculation menu option to recover the...
tree
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commitdiff
2014-04-21
Jim Procter
JAL-1473 refactor score matrices and tree score calcula...
tree
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commitdiff
2014-02-25
Jim Procter
Merge branch 'JAL-1454_patch' into develop
tree
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commitdiff
2014-02-25
Jim Procter
JAL-1454 catch exceptions during calculation and report...
tree
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commitdiff
2014-02-18
Jim Procter
Merge branch 'JAL-1445' into develop
tree
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commitdiff
2014-02-03
Jim Procter
Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
tree
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commitdiff
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
tree
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commitdiff
2013-10-16
Jim Procter
Merge branch 'JAL-1395' into develop
tree
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commitdiff
2013-10-16
Jim Procter
JAL-1395 do not calculate non-gap consensus when no...
tree
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commitdiff
2013-10-15
Jim Procter
JAL-1159 Merging 2.8.1 patches and Anne Menards work...
tree
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commitdiff
2013-10-14
Jim Procter
Merge branch 'develop' into dev_from_2_8_1
tree
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commitdiff
2013-09-03
Jim Procter
JAL-1373 tweak precision calculation so alignments...
tree
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commitdiff
2013-09-03
Jim Procter
JAL-920 compute a consensus for single sequence
tree
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commitdiff
2013-09-02
Jim Procter
Merge branch 'JAL-1373_precision' into develop
tree
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commitdiff
2013-09-02
Jim Procter
JAL-1373 generate percentages with appropriate precision
tree
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commitdiff
2013-09-02
Jim Procter
JAL-1373 pass size of sequence set to consensus renderi...
tree
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commitdiff
2013-06-18
Jim Procter
JAL-674 fix the mapping generation algorithm
tree
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commitdiff
2013-06-18
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
tree
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commitdiff
2013-06-17
Jim Procter
Merge branch 'JAL-1312_ambiguity_na' into develop
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1035 option to allow 'STOP' codon to translate...
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1312 rewrite of code for first reported exception...
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1318 - route warnings to stderr (need to find a...
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1318 avoid failure if SequenceI objects don't have...
tree
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commitdiff
2013-06-17
Jim Procter
JAL-966 avoid using java.util.Vector
tree
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commitdiff
2012-12-07
jprocter
consensus secondary structure algorithm (possibly came...
tree
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commitdiff
2012-12-07
jprocter
revised RNA stem/loop processing code that copes with...
tree
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commitdiff
2012-12-07
jprocter
update authors for RNA processing routines
tree
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commitdiff
2012-12-07
jprocter
formatting
tree
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commitdiff
2012-11-17
jprocter
method to construct sequence mapping for matching posit...
tree
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commitdiff
2012-11-17
jprocter
convenience method for performing pairwise alignment
tree
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commitdiff
2012-11-17
jprocter
formatting and javadoc
tree
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commitdiff
2012-11-15
jprocter
source formatting
tree
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commitdiff
2012-11-15
jprocter
Merge branch 'develop' into menard
tree
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commitdiff
2012-11-08
jprocter
tidy imports
tree
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commitdiff
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