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JAL-1957 JAL-1479 updated SIFTS user docs
[jalview.git]
/
src
/
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
2016-07-22
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
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
2016-07-18
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
2016-06-30
gmungoc
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-06-30
tcofoegbu
JAL-2074 Improvement to StructureChooser and FTS interf...
tree
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commitdiff
2016-06-30
gmungoc
JAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...
tree
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commitdiff
2016-06-30
tcofoegbu
JAL-1919 updated PDBSequenceFetcherTest and JMol parser...
tree
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commitdiff
2016-06-29
gmungoc
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-06-29
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-29
tcofoegbu
JAL-1479 improved Sifts PID calculation for determining...
tree
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commitdiff
2016-06-29
gmungoc
Merge branch 'develop' into features/JAL-2110_crossRefD...
tree
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commitdiff
2016-06-29
gmungoc
JAL-1369 fix bug reloading a project with group sequenc...
tree
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commitdiff
2016-06-28
tcofoegbu
JAL-1479 minor refactor and housekeeping
tree
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commitdiff
2016-06-28
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-28
tcofoegbu
JAL-1479 improved SiftsClient test coverage and impleme...
tree
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commitdiff
2016-06-27
gmungoc
tidied loop with generic iteration / loop variable
tree
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commitdiff
2016-06-27
gmungoc
JAL-2133 refactored duplicated code to AlignmentViewport
tree
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commitdiff
2016-06-27
gmungoc
JAL-1270 unit tests for HiddenSequences
tree
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commitdiff
2016-06-24
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-06-24
tcofoegbu
JAL-1960 updated unit test to include the test case...
tree
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commitdiff
2016-06-23
gmungoc
JAL-2130 now simply viewer.dispose() to close down...
tree
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commitdiff
2016-06-23
Jim Procter
Merge branch 'develop' into merge_JAL-2110
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 make indirect xref searches work by not filter...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 warning message when routine finds non-ds...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 clarify javadoc
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 refactor to split SequenceFetcher from x-ref...
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 use SequenceI.isProtein()
tree
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commitdiff
2016-06-23
Jim Procter
JAL-2110 SequenceI.isProtein method
tree
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commitdiff
2016-06-22
gmungoc
JAL-2015 fixed bug in copy constructor and added tests
tree
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commitdiff
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