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Merge branch 'features/JAL-653_gffalignments' into features/JAL-653_JAL-1766_htslib_r...
[jalview.git]
/
src
/
jalview
/
analysis
/
2015-06-05
Jim Procter
Merge branch 'develop' into features/JAL-653_gffalignments
tree
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commitdiff
2015-06-05
Jim Procter
JAL-1115 JAL-653 partial introduction of List interface...
tree
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commitdiff
2015-06-04
gmungoc
JAL-1750 small tidy of AlignSeq.printMapping (+Junit)
tree
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commitdiff
2015-06-04
gmungoc
JAL-1544 spelling in javadoc only
tree
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commitdiff
2015-05-29
Jim Procter
Merge branch 'JAL-1755_npe_groupconsensus' into develop
tree
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commitdiff
2015-05-29
Jim Procter
JAL-1755 fix for NPE when setting up temporary variables
tree
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commitdiff
2015-05-15
gmungoc
JAL-1737 ignore non-positional annotations for display
tree
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commitdiff
2015-05-15
gmungoc
JAL-1270 added test for regex actually used; include...
tree
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commitdiff
2015-05-15
gmungoc
JAL-1270 main methods converted to JUnit
tree
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commitdiff
2015-05-12
gmungoc
JAL-1712 fixes/tests for Castor binding and 'show flank...
tree
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commitdiff
2015-04-21
gmungoc
JAL-1693 mappings added back to the original alignment
tree
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commitdiff
2015-04-14
gmungoc
JAL-1693 generate multiple exon sequences for 1-many...
tree
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commitdiff
2015-04-13
gmungoc
JAL-1693 make exon alignment for get-xref splitframe...
tree
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commitdiff
2015-03-30
gmungoc
JAL-1264 remove broken applet build dependencies
tree
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commitdiff
2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
tree
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commitdiff
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
tree
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commitdiff
2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
tree
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commitdiff
2015-02-19
gmungoc
JAL-1665 refactored Sequence.getSequenceFeatures
features/sequenceFeatureRefactor
tree
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commitdiff
2015-02-12
Jim Procter
JAL-1350 cloned method and tested equivalence for using...
tree
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commitdiff
2015-02-12
Jim Procter
JAL-1115 switch to lists in SequenceGroup
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
2015-01-28
Jim Procter
JAL-674 patch to make Mapping.compareTransferredToR...
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
2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
tree
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commitdiff
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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
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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
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commitdiff
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