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JAL-2154 always check dataset sequence for sequence instance exists in dataset before...
[jalview.git]
/
src
/
jalview
/
2016-08-22
Jim Procter
JAL-2154 always check dataset sequence for sequence...
tree
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commitdiff
2016-08-19
Jim Procter
JAL-2154 - possible patch .. but leads to new stringify...
tree
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commitdiff
2016-08-19
Jim Procter
JAL-2154 reorder the dataset sequences according to...
tree
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commitdiff
2016-08-19
Jim Procter
JAL-2154 belt-and-braces patch:
tree
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commitdiff
2016-08-19
Jim Procter
JAL-2154 verify mapping’s sequenceI ref has been resolv...
tree
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commitdiff
2016-08-19
Jim Procter
JAL-2154 refactor setSequenceAt to replaceSequenceAt...
tree
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commitdiff
2016-08-16
Jim Procter
JAL-2154 make sure any new sequences via DBRefEntry...
tree
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commitdiff
2016-08-16
Jim Procter
JAL-2154 always resolve dataset sequences when creating...
tree
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commitdiff
2016-08-13
Jim Procter
JAL-2154 refactor CrossRef UI code to its own class
tree
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commitdiff
2016-08-13
Jim Procter
JAL-2154 ignore all but the primary source resolved...
tree
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commitdiff
2016-08-13
Jim Procter
JAL-2154 make sure we wait for constructor thread to...
tree
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commitdiff
2016-08-11
Jim Procter
JAL-2154 jalview.gui.SequenceFetcher.fetchAndShow(db...
tree
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commitdiff
2016-08-11
Jim Procter
JAL-2154 JAL-1993 relocate show dbchooser action out...
tree
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commitdiff
2016-08-07
Jim Procter
JAL-2154 add in missing class for createDatasetAlignmen...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 make sure codon mappings between sequences...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 todo
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 use convenience method
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 make sure all sequences referenced via DBRefEn...
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2154 test for CDS->protein map
tree
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commitdiff
2016-08-04
Jim Procter
JAL-2046 stack trace for implementation warning
tree
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commitdiff
2016-08-04
gmungoc
JAL-2008 handle fast mouse drag of feature ordering...
tree
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commitdiff
2016-08-04
gmungoc
JAL-2015 convert Color from colour picker to FeatureColour
tree
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commitdiff
2016-08-02
Jim Procter
JAL-2046 additional logic to suppress spurious implemen...
tree
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commitdiff
2016-08-02
Jim Procter
JAL-2034 show greyed out image during overview update
tree
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commitdiff
2016-08-02
Jim Procter
Merge branch 'develop' into efficiency/JAL-2034_JAL...
tree
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commitdiff
2016-08-02
Jim Procter
JAL-2068 reinstated false return value for notifyWorking
tree
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commitdiff
2016-08-02
Jim Procter
Merge branch 'develop' into efficiency/JAL-2034_JAL...
tree
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commitdiff
2016-08-01
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2016-08-01
tcofoegbu
JAL-2164 bugfix to convert insCodes of '\000' to '...
tree
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commitdiff
2016-08-01
Jim Procter
Merge branch 'bug/JAL-2154projectMappings' into develop
tree
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commitdiff
2016-08-01
Jim Procter
JAL-1772 make sure we actually return reference to...
tree
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commitdiff
2016-07-29
Jim Procter
JAL-2164 JAL-1772 explodeViews can be static, so make...
tree
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commitdiff
2016-07-29
Jim Procter
JAL-2154 disable visual delay only after completed...
tree
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commitdiff
2016-07-29
Jim Procter
JAL-2154 register any new dataset codon frames only...
tree
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commitdiff
2016-07-29
Jim Procter
JAL-2154 only include mappings in dbref/alcodon in...
tree
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commitdiff
2016-07-27
Jim Procter
JAL-2154 toString for forward references
tree
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commitdiff
2016-07-27
Jim Procter
JAL-2163 set title for the alignframe from restored...
patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles
tree
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commitdiff
2016-07-27
Jim Procter
JAL-2156 resolve and add complementary views for saveAl...
tree
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commitdiff
2016-07-27
Jim Procter
JAL-2156 refactor saveState & saveAlignment to common...
tree
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commitdiff
2016-07-27
Jim Procter
JAL-2156 getter for AlignFrame(s) held in a splitframe
tree
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commitdiff
2016-07-26
Jim Procter
JAL-2157 todo: verify parser/file format enums and...
tree
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commitdiff
2016-07-26
tcofoegbu
JAL-2157 bugfix for issues from enum refactoring
tree
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commitdiff
2016-07-25
tcofoegbu
JAL-2157 bugfix for regression from commit 82a6c8e2e25b...
tree
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commitdiff
2016-07-24
Jim Procter
JAL-2154 formatting
tree
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commitdiff
2016-07-24
Jim Procter
JAL-2154 keep track of incomplete sequences and report...
tree
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commitdiff
2016-07-24
Jim Procter
JAL-2154 systematic pattern for defining/resolving...
tree
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commitdiff
2016-07-23
Jim Procter
JAL-2154 patch the hack (Jalview2XML tests pass)
tree
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commitdiff
2016-07-22
tcofoegbu
JAL-2148 Bugfix in structureImportSettings string-to...
tree
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commitdiff
2016-07-21
tcofoegbu
Resolve merge conflict for StructureImportSettings
tree
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commitdiff
2016-07-21
tcofoegbu
JAL-2148 fix to heuristically determine chain terminati...
tree
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commitdiff
2016-07-21
Jim Procter
Merge branch 'apifix/JAL-1926_JAL-2106' into develop
tree
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commitdiff
2016-07-20
gmungoc
JAL-2154 poke JSeq start/end into Vamsas sequence
tree
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commitdiff
2016-07-20
Jim Procter
JAL-1926 JAL-2106 fix name for flag controlling additio...
tree
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commitdiff
2016-07-20
Jim Procter
JAL-1926 JAL-2106 don’t use PDB database constant as...
tree
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commitdiff
2016-07-20
Jim Procter
JAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMA...
tree
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commitdiff
2016-07-20
Jim Procter
JAL-1926 JAL-2106 remove startRes/endRes fields - not...
tree
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commitdiff
2016-07-20
gmungoc
JAL-2023 stronger check for whether to start cdna consensus
tree
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commitdiff
2016-07-20
gmungoc
JAL-2023 avoid writing / loading empty mappings
tree
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commitdiff
2016-07-20
gmungoc
JAL-2023 JAL-1681 fixed bug in computing '+' for co...
tree
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commitdiff
2016-07-20
gmungoc
JAL-2068 AnnotationWorker create/update annotation...
tree
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commitdiff
2016-07-19
gmungoc
JAL-2068 small refactor to reuse shared method
tree
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commitdiff
2016-07-19
gmungoc
JAL-2068 update rather than recreate AlignmentAnnotatio...
tree
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commitdiff
2016-07-19
gmungoc
JAL-391 corrected handling of gapped sequences
tree
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commitdiff
2016-07-19
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-07-19
tcofoegbu
JAL-1919 set default structure file format to mmCIF...
tree
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commitdiff
2016-07-19
Jim Procter
Merge branch 'develop' into efficiency/JAL-2034_JAL...
tree
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commitdiff
2016-07-18
Jim Procter
Merge branch 'develop' of source.jalview.org/git/jalvie...
tree
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commitdiff
2016-07-18
Jim Procter
JAL-666 patch JAL-1947 in applet where overview is...
tree
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commitdiff
2016-07-18
gmungoc
JAL-2105 check content of Ensembl REST ping response
tree
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commitdiff
2016-07-18
gmungoc
JAL-2099 ensure initial setting of scaleAbove reaches...
tree
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commitdiff
2016-07-18
gmungoc
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-07-18
gmungoc
JAL-2099 JAL-2100 port scale number / hidden column...
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2068 scale annotation display character to width...
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2121 cleanup TODO
tree
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commitdiff
2016-07-18
gmungoc
JAL-2015 restore check for null colour in paint()
tree
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commitdiff
2016-07-18
Jim Procter
Merge branch 'features/JAL-2068groovyAnnotationWorker...
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2145 improvement: ensure conservation calculation...
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2145 documentation of getWidth()
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2145 JAL-1551 formatting
tree
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commitdiff
2016-07-18
Jim Procter
JAL-2145 fix: build alignments before building AlignFra...
tree
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commitdiff
2016-07-14
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-07-14
tcofoegbu
JAL-1919 house-keeping
tree
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commitdiff
2016-07-14
Jim Procter
fix for JAL-2147
tree
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commitdiff
2016-07-14
Jim Procter
JAL-2147 findMappingsBetweenSequenceAndOthers for scopi...
tree
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commitdiff
2016-07-14
Jim Procter
JAL-1115 change implementation to avoid possibility...
tree
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commitdiff
2016-07-14
Jim Procter
JAL-1270 test coverage TODO Alignment.append(AlignmentI)
tree
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commitdiff
2016-07-14
Jim Procter
JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
tree
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commitdiff
2016-07-13
Jim Procter
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-07-13
tcofoegbu
JAL-2135 minor house-keeping
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2144 TODO - new methods for canonicalisation and...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 avoid potential race condition where user...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 TODO for JAL-2131
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 javadoc and TODO re shortcomings of implementation
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 javadoc
tree
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commitdiff
2016-07-12
Jim Procter
JAL-2110 scalability todo
tree
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commitdiff
2016-07-12
Jim Procter
JAL-1381 JAL-2110 efficiency TODO
tree
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commitdiff
2016-07-12
tcofoegbu
JAL-2135 NPE bugfix when parsing a structure file with...
tree
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commitdiff
2016-07-09
gmungoc
Merge branch 'develop' into features/JAL-2110_crossRefD...
features/JAL-2110_crossRefDuplications
tree
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commitdiff
2016-07-08
tcofoegbu
JAL-1919 Fixed failing tests, enabled HETATM processing...
tree
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commitdiff
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