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JAL-3070 refactored Client specific code from jalview.ws.jws2.MSA* as implementors...
[jalview.git]
/
src
/
2018-03-07
gmungoc
JAL-2629 storage and lifecycle of alignment/group HMM...
tree
|
commitdiff
2018-03-01
gmungoc
JAL-2629 revising hmmer annotation updating (wip)
tree
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commitdiff
2018-02-28
gmungoc
JAL-2924 no tooltip over null annotation positions
bug/JAL-2924nullTooltip
tree
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commitdiff
2018-02-28
gmungoc
JAL-2629 some tidying of Hmmer commands (wip)
tree
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commitdiff
2018-02-27
gmungoc
JAL-2668 method name change for clarity
tree
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commitdiff
2018-02-27
gmungoc
JAL-2668 fix broken factory method for colour scheme
tree
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commitdiff
2018-02-27
gmungoc
JAL-2717 JAL-2668 fixes to HMMER colour scheme display...
tree
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commitdiff
2018-02-27
Jim Procter
Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104
tree
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commitdiff
2018-02-27
Jim Procter
fix for JAL-2922 - update states all at once and then...
tree
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commitdiff
2018-02-26
Jim Procter
JAL-2920 parse variation and original elements of the...
tree
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commitdiff
2018-02-26
gmungoc
JAL-2599 test coverage and bug fixes for 'minimal file...
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 corrected case-insensitive symbol indexing
tree
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commitdiff
2018-02-23
Jim Procter
Merge branch 'features/JAL-2885UniprotHttps' into relea...
tree
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commitdiff
2018-02-23
gmungoc
JAL-2599 parser and datamodel use primitive double...
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 xfam https
features/JAL-2885UniprotHttps
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 XFAM_DOMAIN->XFAM_BASEURL
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 Ensembl* -> https
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
tree
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commitdiff
2018-02-23
Jim Procter
JAL-2885 renamed base URL getter from getDomain..
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy tests, refactor hmmer node mapping slightly
tree
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commitdiff
2018-02-22
Jim Procter
Merge branch 'feature/JAL-984splitAdjuster' into releas...
tree
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commitdiff
2018-02-22
Jim Procter
JAL-984 ID width adjuster needs to be white !
tree
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commitdiff
2018-02-22
Jim Procter
Merge branch 'bug/JAL-2666' into releases/Release_2_10_...
tree
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commitdiff
2018-02-22
Jim Procter
Merge branch 'feature/JAL-984splitAdjuster' into releas...
tree
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commitdiff
2018-02-22
Jim Procter
JAL-984 remove all references to idwidth.gif and use...
tree
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commitdiff
2018-02-22
Jim Procter
Merge branch 'feature/JAL-984splitAdjuster' into releas...
tree
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commitdiff
2018-02-22
Jim Procter
JAL-294 remove unneeded paint() method
tree
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commitdiff
2018-02-22
Jim Procter
JAL-984 remove commented/unnecessary if clause
tree
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commitdiff
2018-02-22
gmungoc
JAL-2629 tidy unit tests, constants etc
tree
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commitdiff
2018-02-21
Jim Procter
Merge branch 'bug/JAL-2778again' into releases/Release_...
tree
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commitdiff
2018-02-21
Jim Procter
JAL-2778 reinstate transparent windows to avoid ugly...
bug/JAL-2778again
tree
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commitdiff
2018-02-21
gmungoc
JAL-2629 simplifying method signatures in Hmmer command...
tree
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commitdiff
2018-02-21
kiramt
JAL-2778 Adjust cursor changes in overview panel
tree
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commitdiff
2018-02-21
kiramt
JAL-2778 Revert back to old synchronisation
tree
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commitdiff
2018-02-20
gmungoc
JAL-2629 removed SequenceI.get/setLastPosition and...
tree
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commitdiff
2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-02-20
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-02-19
gmungoc
JAL-2629 refactoring of Hmmer preferences
tree
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commitdiff
2018-02-19
gmungoc
JAL-2629 partial refactoring of Hmmer command classes
tree
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commitdiff
2018-02-19
gmungoc
JAL-2629 formatting only
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2780 JAL-2781 don’t create a mapping if sequence...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2780 JAL-2781 only create a mapping entry or write...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 JAL-2780 include sequence start number when...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 refactor ‘trim retrieved sequence’ preference...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 null local siftsClient variable if exception...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 refactor StructureSelectionManager.siftsClient...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 FIXME: value of sourceType parameter always...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 refactor possibly non-functional ‘extract...
tree
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commitdiff
2018-02-13
Jim Procter
JAL-2781 tidy up comments on getMapping/computeMapping
tree
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commitdiff
2018-02-12
Jim Procter
JAL-2780 JAL-2781 ahem - add a semicolon if there isn...
tree
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commitdiff
2018-02-11
Jim Procter
JAL-2781 use SIFTs mapping rather than maxChain AlignSe...
tree
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commitdiff
2018-02-11
Jim Procter
JAL-2780 JAL-2781 use PDBe numbering to map between...
tree
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commitdiff
2018-02-11
Jim Procter
JAL-2781 mark aligned positions via StructureMapping...
tree
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commitdiff
2018-02-11
Jim Procter
JAL-2780 JAL-2781 include a Mapping object in Structure...
tree
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commitdiff
2018-02-11
Jim Procter
JAL-2780 JAL-2781 UNASSIGNED positions marked as Intege...
tree
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commitdiff
2018-02-09
gmungoc
JAL-2789 avoid using transcript (with no UTR) as CDS...
bug/JAL-2666
tree
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commitdiff
2018-02-09
gmungoc
JAL-2789 code format changes only (before functional...
tree
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commitdiff
2018-02-09
gmungoc
JAL-2666 fix failure to scroll split alignment of height 1
tree
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commitdiff
2018-02-09
Jim Procter
Use the “PDBe” or “PDB” numbering (starts from 1, corre...
tree
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commitdiff
2018-02-09
Jim Procter
JAL-2780 JAL-2781 should always ensure SIFTS mappings...
tree
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commitdiff
2018-02-08
gmungoc
JAL-2666 basic initial fix for split screen scroll bug
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2902 catch case where viewer is closed (therefore...
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2902 thread off dialog close op to avoid deadlock...
tree
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commitdiff
2018-02-07
gmungoc
JAL-2808 ensure pattern field re-enabled when needed...
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2902 - isBusy and hasMapping methods so client...
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2780 JAL-2781 fix javadoc in line with behaviour...
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to...
tree
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commitdiff
2018-02-07
Jim Procter
JAL-2780 JAL-2781 don’t assume contiguous mapping to...
tree
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commitdiff
2018-02-06
kiramt
Merge branch 'develop' into feature/JAL-2759
feature/JAL-2759
tree
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commitdiff
2018-02-05
Jim Procter
JAL-2780 JAL-2781 programmatically select structures...
tree
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commitdiff
2018-02-05
Jim Procter
JAL-2780 JAL-2871 only look up current table view once
tree
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commitdiff
2018-02-05
Jim Procter
JAL-2780 JAL-2781 - patch and first test for AlignmentI...
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Fix errant RangeElementsIterator (unit tests...
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Rename getBoundedStartIterator
tree
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commitdiff
2018-02-05
kiramt
JAL-2759 Changes to StartRegionIterator after review
tree
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commitdiff
2018-02-05
kiramt
JAL-2788 possible adjustments to sequence accesses
tree
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
tree
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commitdiff
2018-02-05
gmungoc
Merge branch 'spikes/mungo' into trialMerge
tree
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commitdiff
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
tree
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commitdiff
2018-02-02
gmungoc
JAL-984 merged to spikes-mungo
tree
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commitdiff
2018-02-02
gmungoc
Merge branch 'feature/JAL-984splitAdjuster' into featur...
tree
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commitdiff
2018-02-02
gmungoc
JAL-2899 asynchronous Jmol colour updates
bug/JAL-2899
tree
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commitdiff
2018-02-02
gmungoc
JAL-984 use cursor for drag regions to adjust annotatio...
tree
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commitdiff
2018-02-02
gmungoc
JAL-984 better behaved panel height adjuster
tree
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commitdiff
2018-02-01
gmungoc
JAL-2899 update structure and overview on slider drag...
tree
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commitdiff
2018-02-01
kiramt
JAL-2759 Added in JAL-2851 fix
tree
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commitdiff
2018-02-01
kiramt
JAL-2759 use right iterator for getVisibleColsIterator
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 Rationalise VisibleColsIterator and HiddenCols...
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 Generalised HiddenColsIterator naming
tree
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commitdiff
2018-01-31
gmungoc
JAL-2792 added tooltip to menu items in case of truncation
tree
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commitdiff
2018-01-31
kiramt
JAL-2759 minor refactor to hiding bitsets
tree
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commitdiff
2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Add missing hiddenColumns empty check
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 updateForDeletedRegion no longer needed
tree
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commitdiff
2018-01-30
gmungoc
JAL-2897 generate peptide variants for synonymous codon...
tree
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commitdiff
2018-01-30
gmungoc
JAL-2897 formatting change only prior to functional...
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Rationalising hidden cols cursor, and sorting...
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 comment
tree
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commitdiff
2018-01-30
kiramt
JAL-2759 Additional tests and tweaks to numColumns...
tree
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commitdiff
next