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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
analysis
/
CrossRef.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
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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diff to current
2022-02-03
Jim Procter
JAL-2305 comments re testFindXrefSequences_withFetch...
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diff to current
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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diff to current
2019-08-09
gmungoc
JAL-3187 removal of variant feature (non-virtual) trans...
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commitdiff
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diff to current
2019-02-04
hansonr
refactoring for DBMODList
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diff to current
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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diff to current
2018-06-22
gmungoc
JAL-3032 avoid assignments on the same line as synchronized
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commitdiff
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diff to current
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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diff to current
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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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
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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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
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
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commitdiff
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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
2016-10-03
Jim Procter
JAL-2210 hack to remove EMBL from Protein crossrefs...
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commitdiff
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diff to current
2016-10-03
Jim Procter
JAL-2210 explicit ‘doNotAdd’ list to prevent sequences...
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commitdiff
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diff to current
2016-10-02
Jim Procter
JAL-2210 two pass attempt to import retrieved sequences...
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commitdiff
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diff to current
2016-10-02
Jim Procter
JAL-2210 try to merge all sequences referenced by a...
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commitdiff
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diff to current
2016-10-02
Jim Procter
JAL-2210 comments
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commitdiff
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diff to current
2016-10-02
Jim Procter
JAL-2210 discover candidate dataset sequences for an...
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commitdiff
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diff to current
2016-10-01
Jim Procter
JAL-2210 factored out code for processing cross-referen...
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commitdiff
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diff to current
2016-10-01
Jim Procter
JAL-2210 refactor code to remove from a list of dbrefs...
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commitdiff
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diff to current
2016-09-30
Jim Procter
JAL-2210 some DBRef xref/ref correspondences may add...
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diff to current
2016-09-30
Jim Procter
JAL-2210 CrossRef.findInDataset should search for prese...
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commitdiff
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diff to current
2016-08-29
Jim Procter
JAL-2154 filter out dbrefs that already match primary...
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commitdiff
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diff to current
2016-08-29
Jim Procter
JAL-2154 refactor if (for easier breakpoint) and formatting
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commitdiff
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diff to current
2016-08-26
Jim Procter
JAL-2154 check that xref is a coding xref before adding...
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commitdiff
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diff to current
2016-08-25
Jim Procter
JAL-2154 copy and paste error
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commitdiff
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diff to current
2016-08-25
Jim Procter
Merge branch 'refactor/JAL-2106_sourceDbRef_revision...
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commitdiff
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diff to current
2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
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commitdiff
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diff to current
2016-08-22
Jim Procter
JAL-2154 verify recovered xref sequence not already...
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commitdiff
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diff to current
2016-08-22
Jim Procter
JAL-2154 regression warning - should never recover...
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commitdiff
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diff to current
2016-08-16
Jim Procter
JAL-2154 make sure any new sequences via DBRefEntry...
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commitdiff
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diff to current
2016-08-16
Jim Procter
JAL-2154 always resolve dataset sequences when creating...
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commitdiff
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diff to current
2016-08-04
Jim Procter
JAL-2154 make sure codon mappings between sequences...
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commitdiff
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diff to current
2016-08-04
Jim Procter
JAL-2154 todo
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commitdiff
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diff to current
2016-08-04
Jim Procter
JAL-2154 use convenience method
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commitdiff
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diff to current
2016-07-07
gmungoc
JAL-2110 field 'cf' moved to stack
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commitdiff
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diff to current
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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commitdiff
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diff to current
2016-07-04
gmungoc
JAL-2110 bug fix / test for searchDataset mappings...
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commitdiff
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diff to current
2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
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commitdiff
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diff to current
2016-06-23
Jim Procter
JAL-2110 make indirect xref searches work by not filter...
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commitdiff
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diff to current
2016-06-23
Jim Procter
JAL-2110 warning message when routine finds non-ds...
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commitdiff
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diff to current
2016-06-23
Jim Procter
JAL-2110 clarify javadoc
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commitdiff
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diff to current
2016-06-23
Jim Procter
JAL-2110 refactor to split SequenceFetcher from x-ref...
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commitdiff
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diff to current
2016-06-23
Jim Procter
JAL-2110 use SequenceI.isProtein()
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commitdiff
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diff to current
2016-06-22
Jim Procter
JAL-2110 remove hardwired detection of search context...
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commitdiff
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diff to current
2016-06-14
gmungoc
JAL-2110 fixes to dbref resolution and mappings, use...
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diff to current
2016-06-09
gmungoc
JAL-2110 work in progress
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commitdiff
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diff to current
2016-06-03
gmungoc
JAL-2110 random stuff
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diff to current
2016-05-20
gmungoc
JAL-2110 unit tests for and minor refactoring of CrossRef
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diff to current
2016-04-29
gmungoc
JAL-2051 better checking of retrieved / duplicated...
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commitdiff
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diff to current
2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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commitdiff
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diff to current
2016-03-21
gmungoc
JAL-2029 further fixes to get correct xrefs and xrefs...
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commitdiff
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diff to current
2016-03-21
gmungoc
JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
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commitdiff
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diff to current
2016-03-11
gmungoc
JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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commitdiff
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diff to current
2016-02-19
gmungoc
JAL-1705 refactor show products, set initial split...
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commitdiff
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diff to current
2016-02-12
gmungoc
JAL-1705 various refactoring towards Uniprot-to-Ensembl...
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commitdiff
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diff to current
2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
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commitdiff
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diff to current
2016-01-27
gmungoc
JAL-1705 add exon name to features and render on peptid...
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commitdiff
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diff to current
2016-01-23
gmungoc
JAL-1705 compute peptide variants from dna; add "conseq...
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commitdiff
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diff to current
2016-01-21
gmungoc
JAL-1705 get xrefs only for dna/peptide; code tidy
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commitdiff
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diff to current
2015-11-30
gmungoc
JAL-1421 generics loop syntax; 'bug?' comment added
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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
2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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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
2015-04-13
gmungoc
JAL-1693 make exon alignment for get-xref splitframe...
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commitdiff
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diff to current
2015-03-30
gmungoc
JAL-1264 remove broken applet build dependencies
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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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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
2014-06-06
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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commitdiff
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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
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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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
2012-06-13
jprocter
javatidy
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commitdiff
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diff to current
2012-06-12
jprocter
JAL-1115 refactor base collection for Alignment from...
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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
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
2010-04-30
jprocter
jalview 2.5 release banner
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commitdiff
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diff to current
2009-06-19
jprocter
debug
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commitdiff
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diff to current
2009-06-08
jprocter
apply gpl development license
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commitdiff
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diff to current
2009-02-06
jprocter
fix occasional nullpointer ref when seq ID retrieval...
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commitdiff
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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
2008-08-19
jprocter
better check for molecule type when identifying interna...
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commitdiff
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diff to current
2008-08-06
jprocter
extra checks for datasetsequence for when getDbRefs...
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commitdiff
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diff to current
2007-11-16
jprocter
refactor abstract sequence fetching and DBSource machin...
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commitdiff
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diff to current
2007-11-12
jprocter
crossrefs have properly updated pdbId lists
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commitdiff
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diff to current
2007-09-07
jprocter
formatting and ensure that dataset is actually searched...
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commitdiff
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diff to current
2007-08-01
jprocter
null pointer exception bug fix
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