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JAL-2074 reinstated xerces-impl.jar
[jalview.git]
/
src
/
2016-05-04
gmungoc
JAL-2092 hide columns with/without feature
tree
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commitdiff
2016-05-04
gmungoc
Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into...
tree
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commitdiff
2016-05-04
tcofoegbu
merge
tree
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commitdiff
2016-05-04
tcofoegbu
JAL-1563 JAL-2091 Added total result count to Uniprot...
tree
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commitdiff
2016-05-04
gmungoc
JAL-2090 removed test for Java > 1.1 to enable transparency
tree
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commitdiff
2016-05-03
gmungoc
JAL-2050 hide introns also when fetching Ensembl xrefs...
tree
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commitdiff
2016-05-03
tcofoegbu
JAL-2091 disable pagination buttons during initialisation
tree
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commitdiff
2016-05-03
tcofoegbu
JAL-1563 JAL-2091 Added generic pagination for FTS...
tree
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commitdiff
2016-05-02
tcofoegbu
JAL-1563 Fixed Uniprot FTS result-set count error,...
tree
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commitdiff
2016-04-29
tcofoegbu
merge
tree
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commitdiff
2016-04-29
tcofoegbu
JAL-1563 house keeping/updated API doc for new method...
merge/JAL-1563_uniprot-free-text-search
tree
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commitdiff
2016-04-29
tcofoegbu
JAL-1563 Further increased swing timer for search textf...
tree
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commitdiff
2016-04-29
gmungoc
JAL-2051 better checking of retrieved / duplicated...
tree
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commitdiff
2016-04-29
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 need visible and actual sequence limits for...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 fix bounds when no hidden regions, and when...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 scale origin relative to start of reference...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-966 JAL-1553 todo: remove UI components from Colum...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2016-04-29
Jim Procter
JAL-192 ‘efficiently’ locate visible bounds for a seque...
tree
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commitdiff
2016-04-29
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2016-04-29
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-04-28
tcofoegbu
JAL-1563 increased swing timer for search action from...
tree
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commitdiff
2016-04-28
gmungoc
JAL-2083 removed use of reflection for Groovy
tree
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commitdiff
2016-04-28
tcofoegbu
JAL-1563 Implemented hack to make table both scrollable...
tree
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commitdiff
2016-04-27
tcofoegbu
JAL-1563 Added Id (Uniprot Id) to the dynamic column...
tree
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commitdiff
2016-04-27
Jim Procter
JAL-192 fix off-by-one for alignment ruler with no...
tree
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commitdiff
2016-04-27
Jim Procter
JAL-192 show reference sequence position and residue...
tree
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commitdiff
2016-04-27
tcofoegbu
JAL-1563 Added fix to prevent swing timer from reinitia...
tree
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commitdiff
2016-04-27
Jim Procter
JAL-1366 JAL-2086 reinstate bolding of reference sequence
tree
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commitdiff
2016-04-27
Jim Procter
JAL-2085 JAL-2086 fix hiddenRepSequence and new referen...
tree
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commitdiff
2016-04-27
tcofoegbu
JAL-1563 Modified Uniprot data column configurations...
tree
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commitdiff
2016-04-27
tcofoegbu
re-enabled new uniprot sequence fetcher on spike branch
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2079 fix broken cherry-pick conflict merge
tree
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commitdiff
2016-04-26
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2079 use new service to retrieve Rfam Seed alignment
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2079 disable RFAM(Full) source until we can retriev...
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2079 update URL for RFAM and PFAM sources
tree
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commitdiff
2016-04-26
tcofoegbu
merge
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2079 allow prefix+<XFAMID>+suffix type URL signature
tree
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commitdiff
2016-04-26
tcofoegbu
JAL-1563 reverted to old uniprot fetcher to enable...
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2077 reinstate JAL-1554 fix for left-then-right...
tree
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commitdiff
2016-04-26
Jim Procter
JAL-2077 reinstate annotation label popup by handling...
tree
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commitdiff
2016-04-26
gmungoc
JAL-1981 catch any exception when setting QuaQua look...
tree
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commitdiff
2016-04-26
Jim Procter
Merge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4
groovy/JAL-2074_upgradeto2.4.4
tree
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commitdiff
2016-04-26
tcofoegbu
merge
tree
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commitdiff
2016-04-26
tcofoegbu
JAL-2071 improvement to get column data files as InputS...
tree
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commitdiff
2016-04-26
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-04-26
tcofoegbu
JAL-2071 changed extension for data column config files
tree
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commitdiff
2016-04-26
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-04-26
tcofoegbu
JAL-2071 resolved fts data column config file path...
tree
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commitdiff
2016-04-26
tcofoegbu
JAL-2071 House keeping
tree
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commitdiff
2016-04-26
tcofoegbu
JAL-2071 improvement to reduce webservice requests...
tree
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commitdiff
2016-04-25
Jim Procter
JAL-2074 disable security manager at start up re: lopic...
tree
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commitdiff
2016-04-25
tcofoegbu
develop merge
tree
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commitdiff
2016-04-25
tcofoegbu
develop merge
tree
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commitdiff
2016-04-25
tcofoegbu
JAL-2071 added unit tests for FTSRestClient
features/JAL-1563_uniprot-free-text-search
tree
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commitdiff
2016-04-25
gmungoc
JAL-1812 JAL-2068 only allow one Groovy console open...
tree
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commitdiff
2016-04-24
Jim Procter
JAL-1551 JAL-2077 formatting
tree
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commitdiff
2016-04-24
Jim Procter
JAL-2077 - reinstate popups on osx
tree
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commitdiff
2016-04-24
Jim Procter
Merge branch 'JAL-2075_features_hiddeng' into develop
tree
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commitdiff
2016-04-24
Jim Procter
JAL-2075 make GroovyConsole a singleton so tests requir...
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 fix: use AlignmentView.getVisibleContigs and...
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 findPosition for SeqCigar (with test)
tree
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commitdiff
2016-04-23
Jim Procter
JAL-2075 formatting
tree
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commitdiff
2016-04-22
tcofoegbu
JAL-1563 JAL-2071 Update and completed implementation...
tree
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commitdiff
2016-04-22
tcofoegbu
JAL-2071 further refactoring, optimisation, and house...
tree
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commitdiff
2016-04-22
gmungoc
JAL-1812 JAL-2068 add Run Groovy Script to AlignFrame...
tree
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commitdiff
2016-04-22
gmungoc
JAL-2068 code and test for case of minValue == maxValue
tree
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commitdiff
2016-04-22
gmungoc
JAL-2068 framework and example scripts for pluggable...
tree
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commitdiff
2016-04-22
gmungoc
JAL-2068 Javadoc added
tree
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commitdiff
2016-04-22
gmungoc
JAL-2068 redundant implements clauses removed
tree
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commitdiff
2016-04-22
gmungoc
JAL-2068 convenience helper method for graduated score...
tree
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commitdiff
2016-04-20
Jim Procter
fix for JAL-2072
tree
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commitdiff
2016-04-19
tcofoegbu
JAL-2071 architectural improvement for Plugable Free...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2041 add ID,clinical_significance to feature attrib...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2041 clinical_significance shown on sequence featur...
tree
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commitdiff
2016-04-14
gmungoc
JAL-1421 typed map / lists, explicit imports, method...
tree
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commitdiff
2016-04-14
gmungoc
JAL-2049 small refactor of constructors to avoid code...
tree
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commitdiff
2016-04-14
gmungoc
JAL-1421 type parameter added to some collections
tree
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commitdiff
2016-04-14
gmungoc
JAL-2049 revised computePeptideVariants to transfer...
tree
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commitdiff
2016-04-14
gmungoc
JAL-1705 refactored/utility methods to detect e.g....
tree
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commitdiff
2016-04-14
gmungoc
JAL-1270 JAL-653 use 'parse immediately' FeaturesFile...
tree
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commitdiff
2016-04-13
Jim Procter
JAL-2046 fix: patched SeqsetUtils so sequence features...
tree
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commitdiff
2016-04-13
Jim Procter
Merge branch 'bug/JAL-2046_ds_sharing_features_broken...
tree
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commitdiff
2016-04-13
tcofoegbu
JAL-1270 more fix for failing Functional test
tree
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commitdiff
2016-04-13
tcofoegbu
merge
tree
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commitdiff
2016-04-13
tcofoegbu
JAL-2047 delay to allow table model initilisation to...
tree
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commitdiff
2016-04-12
gmungoc
JAL-2050 only hide introns if exons are present! Remove...
tree
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commitdiff
2016-04-12
gmungoc
JAL-2049 separate protein variant per dna variant ...
tree
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commitdiff
2016-04-11
gmungoc
JAL-1705 code/comment tidy only
tree
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commitdiff
2016-04-11
gmungoc
JAL-2051 fetch Ensembl Gene accessions one at a time
tree
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commitdiff
2016-04-11
tcofoegbu
merge
tree
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commitdiff
2016-04-11
tcofoegbu
JAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
tree
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commitdiff
2016-04-11
gmungoc
JAL-1705 (new preference option to) hide introns when...
tree
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commitdiff
2016-04-08
Jim Procter
Merge branch 'feature/JAL-2050_intronhidden' into develop
tree
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commitdiff
2016-04-08
Jim Procter
JAL-2050 JAL-1722 new getSelectedRange() method to...
tree
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commitdiff
2016-04-08
Jim Procter
JAL-2053 fix erratic hidden column marker display
tree
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commitdiff
2016-04-08
Jim Procter
JAL-2053 JAL-1551 javadoc and simpler code
tree
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commitdiff
2016-04-07
Jim Procter
JAL-1722 fix: don’t draw visible regions outside viewpo...
tree
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commitdiff
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