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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/ datamodel
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-2839findWi...
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3072scrollThread' into merge...
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commitdiff
2019-03-04
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3082select...
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2019-03-04
gmungoc
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-3164complementOverview' into...
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commitdiff
2019-03-01
gmungoc
Merge branch 'feature/intervalStoreJ' into merge/JAL...
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commitdiff
2019-03-01
gmungoc
JAL-3140 reduced coupling to intervalstore.jar
feature/intervalStoreJ
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commitdiff
2019-02-28
gmungoc
JAL-3140 confine intervalstore imports to jalview.datam...
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commitdiff
2019-02-24
gmungoc
JAL-3198 SequenceGroup 'bulk constructor' without dupli...
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commitdiff
2019-02-21
gmungoc
JAL-3187 handle no mapping / complement features withou...
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commitdiff
2019-02-20
gmungoc
JAL-3187 read peptide variant from CSQ:HGVSp if present...
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commitdiff
2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
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commitdiff
2019-02-04
hansonr
refactoring for DBMODList
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commitdiff
2019-01-29
hansonr
iterators
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commitdiff
2019-01-26
hansonr
Platform.timecheck calls removed or commented out.
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commitdiff
2019-01-26
hansonr
removing cyclic call
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commitdiff
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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commitdiff
2019-01-21
gmungoc
JAL-3187 unit tests updated and errors caught
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commitdiff
2019-01-21
gmungoc
JAL-3187 findFeaturesAtResidue answer in render order...
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commitdiff
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
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commitdiff
2019-01-17
gmungoc
Merge branch 'develop' into Jalview-BH/JAL-3026-JAL...
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commitdiff
2019-01-16
Jim Procter
Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA...
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2018-12-19
Jim Procter
Merge branch 'features/JAL-1767pcaInProject' into bug...
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commitdiff
2018-12-17
Jim Procter
Merge branch 'bug/JAL-2750' into develop
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commitdiff
2018-12-17
Jim Procter
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
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commitdiff
2018-12-06
Ben Soares
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
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commitdiff
2018-11-29
gmungoc
JAL-3140 NCList now via IntervalStore library
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commitdiff
2018-11-28
gmungoc
JAL-3164 redraw complement overview on hide columns
bug/JAL-3164complementOverview
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commitdiff
2018-11-19
Jim Procter
JAL-3156 JAL-3127 code tidy
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commitdiff
2018-11-19
Jim Procter
JAL-3156 javadoc re JAL-3127 and FIXME to make Alignmen...
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commitdiff
2018-10-17
Jim Procter
Merge branch 'feature/JAL-3063JAXB' into Jalview-BH...
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commitdiff
2018-09-14
gmungoc
JAL-3116 parse EMBL XML with JAXB (todo: update unit...
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commitdiff
2018-09-13
gmungoc
JAL-3116 Uniprot XML unmarshalled using JAXB not Castor
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commitdiff
2018-09-11
Jim Procter
Merge branch 'develop' into releases/Release_2_11_Branch
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commitdiff
2018-09-10
gmungoc
JAL-3099 new method AlignmentI.getVisibleWidth()
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commitdiff
2018-08-27
Ben Soares
JAL-3061 / JAL-3053
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commitdiff
2018-08-16
gmungoc
Merge branch 'bug/JAL-3082selectRegex' into Jalview...
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commitdiff
2018-08-16
gmungoc
JAL-3082 handle regex error, exclusive threshold, unit...
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commitdiff
2018-08-10
gmungoc
JAL-3076 refactor for more efficient scan of 'gene...
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commitdiff
2018-08-02
Ben Soares
JAL-3053
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commitdiff
2018-07-30
bsoares
Fixed bug ignoring "alpha" extended braces in RNA SS...
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commitdiff
2018-07-26
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3072scroll...
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2018-07-25
gmungoc
JAL-3074 don't scroll up/down on drag out of scale...
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commitdiff
2018-07-20
gmungoc
JAL-3048 revised AlignExportSettings dialog with respon...
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commitdiff
2018-07-11
Jim Procter
JAL-3048 refactored export settings to bean+dialog...
Jalview-BH/JAL-3048_exportSettingsrefactor
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commitdiff
2018-07-06
gmungoc
JAL-3032 use Math.min/max not Float.min/max
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commitdiff
2018-07-02
hansonr
JAL-3026 GD#75 Stockholm file load fails
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commitdiff
2018-06-22
gmungoc
JAL-3032 avoid assignments on the same line as synchronized
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commitdiff
2018-06-04
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
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commitdiff
2018-06-02
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
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commitdiff
2018-05-31
gmungoc
JAL-2808 don't capture or report min-max for mixed...
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commitdiff
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
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commitdiff
2018-05-21
gmungoc
JAL-2920 use HGVS notation for protein variant feature
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commitdiff
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
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commitdiff
2018-05-10
Jim Procter
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into...
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commitdiff
2018-05-10
Jim Procter
JAL-2920 simplified logic and added corner cases for...
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commitdiff
2018-05-07
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-05-07
gmungoc
JAL-1767 unit test for save and restore PCA
features/JAL-1767pcaInProject
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commitdiff
2018-05-07
Jim Procter
JAL-2906 apply GPLv3 license source
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commitdiff
2018-05-04
gmungoc
JAL-1767 refactorings to enable faithful restore of...
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commitdiff
2018-04-27
gmungoc
JAL-1767 refactoring and tidying of RotatableCanvas...
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commitdiff
2018-04-26
gmungoc
JAL-2962 code tidying/documentation (non-functional...
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commitdiff
2018-04-23
gmungoc
JAL-2954 more efficient SearchResults.markColumns
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commitdiff
2018-03-16
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
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commitdiff
2018-03-14
gmungoc
JAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
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commitdiff
2018-03-13
gmungoc
JAL-2839 addResult ignores duplicates
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commitdiff
2018-03-09
gmungoc
JAL-2839 Finder refactoring prior to fixing the defect
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commitdiff
2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-03-07
gmungoc
JAL-2925 handle empty annotation when copying group...
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commitdiff
2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
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commitdiff
2018-02-26
Jim Procter
JAL-2920 parse variation and original elements of the...
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commitdiff
2018-02-21
Jim Procter
Merge branch 'bug/JAL-2778again' into releases/Release_...
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commitdiff
2018-02-21
kiramt
JAL-2778 Revert back to old synchronisation
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commitdiff
2018-02-20
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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commitdiff
2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
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commitdiff
2018-02-05
Jim Procter
JAL-2780 JAL-2781 - patch and first test for AlignmentI...
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commitdiff
2018-02-05
kiramt
JAL-2759 Fix errant RangeElementsIterator (unit tests...
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commitdiff
2018-02-05
kiramt
JAL-2759 Rename getBoundedStartIterator
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commitdiff
2018-02-05
kiramt
JAL-2759 Changes to StartRegionIterator after review
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commitdiff
2018-02-05
kiramt
JAL-2788 possible adjustments to sequence accesses
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commitdiff
2018-02-01
kiramt
JAL-2759 use right iterator for getVisibleColsIterator
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commitdiff
2018-01-31
kiramt
JAL-2759 Rationalise VisibleColsIterator and HiddenCols...
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commitdiff
2018-01-31
kiramt
JAL-2759 Generalised HiddenColsIterator naming
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commitdiff
2018-01-31
kiramt
JAL-2759 minor refactor to hiding bitsets
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commitdiff
2018-01-30
kiramt
JAL-2759 Add missing hiddenColumns empty check
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commitdiff
2018-01-30
kiramt
JAL-2759 updateForDeletedRegion no longer needed
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commitdiff
2018-01-30
kiramt
JAL-2759 Rationalising hidden cols cursor, and sorting...
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commitdiff
2018-01-30
kiramt
JAL-2759 comment
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commitdiff
2018-01-30
kiramt
JAL-2759 Additional tests and tweaks to numColumns...
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commitdiff
2018-01-30
kiramt
JAL-2759 Keep numColumns up to date
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commitdiff
2018-01-29
kiramt
JAL-2759 Combine findRegionForColumn code in HiddenColu...
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commitdiff
2018-01-29
kiramt
JAL-2759 numColumns reset
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commitdiff
2018-01-29
kiramt
JAL-2759 remove redundant hiddenColumns.clear()
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commitdiff
2018-01-29
kiramt
JAL-2759 Tidy
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2018-01-29
kiramt
JAL-2759 make a new cursor instead of resetting, update...
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commitdiff
2018-01-29
kiramt
JAL-2759 Fix unintended type change
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2018-01-26
kiramt
JAL-2778 try another way to draw sequences with reduced...
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commitdiff
2018-01-22
kiramt
JAL-2579 Moved locateVisibleStartOfSequence to Sequence...
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commitdiff
2018-01-22
kiramt
JAL-2759 Various minor HiddenColumns updates after...
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