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Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor
[jalview.git]
/
src
/
jalview
/
analysis
/
2016-02-12
gmungoc
JAL-2008 avoid unnecessary repaints; signatures changed...
tree
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commitdiff
2016-02-04
gmungoc
Merge branch 'develop' into features/JAL-653_JAL-1766_h...
tree
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commitdiff
2016-02-04
gmungoc
JAL-2005 added (stable) sort methods parameterised by
tree
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commitdiff
2016-02-01
gmungoc
JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
tree
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commitdiff
2016-01-28
gmungoc
JAL-1705 refine feature copying to including 5' and...
tree
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commitdiff
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
tree
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commitdiff
2016-01-27
gmungoc
JAL-1705 add exon name to features and render on peptid...
tree
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commitdiff
2016-01-23
gmungoc
JAL-1705 compute peptide variants from dna; add "conseq...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 transfer features to the dataset sequence...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 features transferred to CDS sequence; makeExon...
tree
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commitdiff
2016-01-21
gmungoc
JAL-1705 get xrefs only for dna/peptide; code tidy
tree
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commitdiff
2015-12-22
gmungoc
JAL-391 new Calculate options to Reverse, Reverse Compl...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame collections changed from...
tree
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commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
tree
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commitdiff
2015-11-30
gmungoc
JAL-1421 generics loop syntax; 'bug?' comment added
tree
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commitdiff
2015-11-30
gmungoc
JAL-653 small comment change only
tree
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commitdiff
2015-11-30
gmungoc
JAL-652 refactored to remove one method
tree
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commitdiff
2015-10-28
tcofoegbu
JAL-1952 bugfix
tree
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commitdiff
2015-10-22
tcofoegbu
JAL-1479 added basic support for SIFTs mapping - more...
tree
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commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
tree
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commitdiff
2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
tree
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commitdiff
2015-10-14
tcofoegbu
JAL-1926 added supporting model changes to enable savin...
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
tree
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commitdiff
2015-10-08
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
tree
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commitdiff
2015-10-07
Jim Procter
JAL-1894 source formatting
tree
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commitdiff
2015-09-22
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
tree
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commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 licencing for new files in src
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
tree
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commitdiff
2015-09-09
gmungoc
JAL-1619 'align protein as cDNA' now leaves unmapped...
tree
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commitdiff
2015-09-07
gmungoc
JAL-1636 translate stop codon as '*', mouseover * as...
tree
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commitdiff
2015-09-07
gmungoc
JAL-1152 check 'autocalculated' not 'null sequenceRef...
tree
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commitdiff
2015-08-17
gmungoc
JAL-1800 separated SearchResults.getCharacters() from...
tree
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commitdiff
2015-08-10
Jim Procter
JAL-736 relocate group associated conservation symbols...
tree
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commitdiff
2015-08-10
Jim Procter
JAL-736 source formatting
tree
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commitdiff
2015-08-07
tcofoegbu
JAL-1824 updated caching procedure for pdb entries...
tree
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commitdiff
2015-07-23
Jim Procter
JAL-1819 use Float.isNaN() to check for NaNs!
tree
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commitdiff
2015-07-08
gmungoc
JAL-1759 merge from develop
tree
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commitdiff
2015-07-01
gmungoc
JAL-1681 more condensed tooltip where codons share...
tree
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commitdiff
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
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