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Merge branch 'develop' into releases/Release_2_10_Branch
[jalview.git]
/
src
/
2016-08-24
gmungoc
JAL-1355 correct 'thereshold' to 'threshold' in message...
tree
|
commitdiff
2016-08-24
gmungoc
JAL-1424 removed unused and duplicated message keys
tree
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commitdiff
2016-08-24
gmungoc
JAL-1424 tidy / recode MessageManager calls to support...
tree
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commitdiff
2016-08-24
gmungoc
JAL-1854 removed pointless method override
tree
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commitdiff
2016-08-24
gmungoc
JAL-1424 removed two redundant (overwritten) setText...
tree
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commitdiff
2016-08-24
gmungoc
JAL-1424 corrected Message bundle lookup key
tree
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commitdiff
2016-08-24
gmungoc
JAL-1424 undo i18n of exception message
tree
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commitdiff
2016-08-24
gmungoc
JAL-1854 declare immutable class as final
tree
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commitdiff
2016-08-24
gmungoc
JAL-1424 recode calls to MessageManager to allow code...
tree
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commitdiff
2016-08-24
gmungoc
JAL-2151 port fix to applet
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 propagate from contig to CDS after constructin...
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 should only add mappings between dataset sequences
tree
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commitdiff
2016-08-23
Jim Procter
JAL-2154 - only copy DBRef from contig to new CDS seque...
tree
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commitdiff
2016-08-23
Jim Procter
Merge branch 'develop' into bug/JAL-2154projectMappings
tree
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commitdiff
2016-08-23
gmungoc
JAL-2176 unused field / methods removed
tree
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commitdiff
2016-08-23
gmungoc
JAL-2174 markColumns() refactored inside ColumnSelection
tree
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commitdiff
2016-08-22
gmungoc
JAL-1448 corrected for backwards compatibility for...
tree
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commitdiff
2016-08-22
gmungoc
JAL-2175 code tidying
tree
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commitdiff
2016-08-22
gmungoc
JAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip
tree
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commitdiff
2016-08-22
Jim Procter
JAL-2154 verify recovered xref sequence not already...
tree
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commitdiff
2016-08-22
Jim Procter
JAL-2154 regression warning - should never recover...
tree
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commitdiff
2016-08-22
Jim Procter
JAL-2154 always check dataset sequence for sequence...
tree
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commitdiff
2016-08-22
gmungoc
JAL-2011 adjust method to fix failing unit test
tree
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commitdiff
2016-08-19
gmungoc
JAL-2174 bug fixes + refactoring to allow + unit tests
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
|
commitdiff
2016-08-18
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-18
gmungoc
JAL-2077 using Platform method to check for Ctrl-down
tree
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commitdiff
2016-08-18
gmungoc
JAL-1445 status message '...not containing...' for...
tree
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commitdiff
2016-08-18
gmungoc
JAL-1693 show warning dialog if unable to make CDS...
tree
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commitdiff
2016-08-18
gmungoc
JAL-1855 fail gracefully if XML has no <sequence> element
tree
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commitdiff
2016-08-18
gmungoc
JAL-2077 handling Cmd-click in scale panel for Mac...
tree
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commitdiff
2016-08-18
gmungoc
JAL-2001 return copy of selection in getSelected()
tree
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commitdiff
2016-08-17
gmungoc
JAL-2146 status message now with formatted residue...
tree
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commitdiff
2016-08-17
gmungoc
JAL-2173 don't remove annotation from hidden columns
tree
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commitdiff
2016-08-17
gmungoc
JAL-2172 reverted to not sorting column selection
tree
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commitdiff
2016-08-17
gmungoc
JAL-2105 rest versions updated to 4.6, change log link...
tree
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commitdiff
2016-08-17
gmungoc
JAL-2172 handle case where column selection is not...
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
2016-08-16
gmungoc
JAL-2171 matching bracket default character for rna...
tree
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commitdiff
2016-08-16
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
tree
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commitdiff
2016-08-15
tcofoegbu
JAL-1128 fix for truncated bottom boarder pixels in...
tree
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commitdiff
2016-08-15
tcofoegbu
JAL-1128 fix for truncated bottom boarder pixels in...
tree
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commitdiff
2016-08-15
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2016-08-15
tcofoegbu
JAL-1919 Added improvement to ensure consistence of...
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
2016-08-12
gmungoc
JAL-1841 count (logo height) is valid pairs only; detec...
tree
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commitdiff
2016-08-12
gmungoc
JAL-1841 bug fixes / code tidy for rna SS rendering...
tree
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commitdiff
2016-08-12
gmungoc
JAL-1841, bug fix in rna SS consensus, additions to...
tree
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commitdiff
2016-08-12
gmungoc
JAL-2171 default SS symbol to existing (if present)
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
2016-08-10
gmungoc
JAL-2124 i18n of 'All' menu item
tree
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commitdiff
2016-08-10
gmungoc
JAL-2124 i18n of "All" menu item
tree
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commitdiff
2016-08-10
gmungoc
JAL-2146 small optimisation (avoid String creation)
tree
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commitdiff
2016-08-10
gmungoc
JAL-2146 show Column no [Sequence no [Residue / pos...
tree
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commitdiff
2016-08-09
Jim Procter
JAL-2154 test for CDS->protein map
tree
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commitdiff
2016-08-08
gmungoc
JAL-1577 rebuild menus when secondary structure manuall...
tree
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commitdiff
2016-08-08
gmungoc
JAL-2168 document '-nonews' parameter
tree
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commitdiff
2016-08-07
Jim Procter
JAL-2068 add the worker to the currently displayed...
patch/JAL-2068_JAL-2169_multiviewannotworker
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
2016-08-05
gmungoc
JAL-2168 skip news feed if parameter "-nonews" is supplied
tree
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commitdiff
2016-08-05
gmungoc
JAL-1448 always use UK locale for formatted date properties
tree
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commitdiff
2016-08-05
gmungoc
JAL-2164 add transferred annotation to sequence
tree
|
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
next