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JAL-250 prototype ‘hide redundant sequences’ - redundant seqs are represented by...
[jalview.git]
/
src
/
jalview
/
2016-08-02
Jim Procter
JAL-250 prototype ‘hide redundant sequences’ - redundan...
tree
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commitdiff
2016-08-02
Jim Procter
JAL-250 save the less redundant neighbour for each...
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
2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
tree
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commitdiff
2016-07-07
gmungoc
JAL-2110 field 'cf' moved to stack
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 generic rather than specific check for gap...
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 AlignmentUtils.alignCdsAsProtein implemented
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 cross-refs from protein to show cds not non...
tree
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commitdiff
2016-07-06
gmungoc
JAL-2110 fixes and tests for adding dbrefs to EMBL...
tree
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commitdiff
2016-07-04
gmungoc
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 use shared dataset when copying alignment...
tree
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commitdiff
2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 bug fix / test for searchDataset mappings...
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 unused method removed
tree
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commitdiff
2016-07-04
gmungoc
JAL-2110 defensive check in code
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 set reasonable bounds to initial split of...
tree
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commitdiff
2016-07-01
tcofoegbu
JAL-2135 bugfix for error preventing processing of...
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
tree
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commitdiff
2016-07-01
gmungoc
JAL-2110 code/comment tidy
tree
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commitdiff
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