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Resolved diffs from 2.8.3
[jalview.git]
/
src
/
jalview
/
2015-02-09
gmungoc
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2015-02-06
gmungoc
JAL-845 further code/tests/refactoring
tree
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commitdiff
2015-02-06
Jim Procter
JAL-1640 new menu allowing view settings to be transfer...
tree
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commitdiff
2015-02-06
Jim Procter
JAL-1640 Desktop.getAlignmentPanel and Desktop.getViewp...
tree
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commitdiff
2015-02-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2015-02-06
Jim Procter
JAL-1640 more properties moved to style bean and ration...
tree
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commitdiff
2015-02-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2015-02-06
Jim Procter
JAL-1640 JAL-966 is for boolean getter on AlignViewportI
tree
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commitdiff
2015-02-05
Charles Ofoegbu
merge commit
tree
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commitdiff
2015-02-04
Charles Ofoegbu
JAL-1643 modified jalviewFileChooser to retain default...
tree
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commitdiff
2015-02-04
Charles Ofoegbu
JAL-1643 Modified JalviewFileChooser to have a more...
tree
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commitdiff
2015-02-03
gmungoc
JAL-845 column mapping speed-up
tree
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commitdiff
2015-02-03
gmungoc
JAL-845 SplitFrame key bindings delegation to AlignFram...
tree
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commitdiff
2015-02-03
gmungoc
JAL-845 preparation for awareness of AlignFrame in...
tree
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commitdiff
2015-02-03
gmungoc
JAL-845 redundant 'map to self' removed from buildSearc...
tree
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commitdiff
2015-02-03
gmungoc
JAL-845 code/refactoring/tests related to linking DNA...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
Merge branch 'bug/JAL-1644_Finder-logic-improvement...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
JAL-1644 added null check for sequence description...
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1640 setStyle method and associated tests (required...
tree
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commitdiff
2015-02-02
Jim Procter
JAL-966 allow access to viewport interface from alignPanel
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1640 getters and setters for viewStyleI - note...
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1640 copy constructor test and implementation by...
tree
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commitdiff
2015-02-02
Jim Procter
JAL-715 tweaks for SRBS description string parsing
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1161 JAL-1606 note about awt/swing dependency in...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
Merge commit
tree
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commitdiff
2015-02-02
Charles Ofoegbu
JAL-1644 revised Finder's implementation to use a flag...
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1640 JAL-1551 formatting/imports/remove dead code
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1640 updates to use get/setter on viewportI: effici...
tree
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commitdiff
2015-02-02
Jim Procter
JAL-1640 separated style operations into a new ViewStyl...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
Merge branch 'bug/JAL-1644_Finder-logic-improvement...
tree
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commitdiff
2015-02-02
Charles Ofoegbu
JAL-1644 improvment of finder logic to include the...
tree
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commitdiff
2015-01-30
gmungoc
JAL-845 linked protein/dna 'slave' further PoC function...
features/JAL-845linkedProteinDnaEditing
tree
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commitdiff
2015-01-28
Jim Procter
JAL-1565 automatically mark query sequence as the seque...
tree
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commitdiff
2015-01-28
Jim Procter
JAL-674 patch to make Mapping.compareTransferredToR...
tree
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commitdiff
2015-01-27
gmungoc
JAL-1588 new class renamed
tree
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commitdiff
2015-01-26
gmungoc
Merge branch 'features/JAL-1588saveChimeraSession'...
tree
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commitdiff
2015-01-26
gmungoc
JAL-1588 restoring saved Chimera session(s)
tree
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commitdiff
2015-01-23
Charles Ofoegbu
Merge branch 'features/JAL-1553_improvement-select...
tree
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commitdiff
2015-01-23
gmungoc
JAL-1588 first working (?) restore of Chimera session...
tree
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commitdiff
2015-01-23
Charles Ofoegbu
JAL-1553 added help documentation and updated Annotatio...
features/JAL-1553_improvement-select-column-by-annotation-row-query-interface
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1286 don't print an exception if a non-gzip stream...
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1551 crlf changes
tree
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commitdiff
2015-01-23
Jim Procter
JAL-969 hasHiddenRows is now an interface method
tree
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commitdiff
2015-01-23
Jim Procter
JAL-969 drop the hiddenColumns flag in favour of checki...
tree
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commitdiff
2015-01-23
Jim Procter
Merge branch 'develop' into feature_29/JAL-1372_referen...
tree
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commitdiff
2015-01-23
gmungoc
JAL-1619 javadoc/tidy
tree
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commitdiff
2015-01-23
gmungoc
JAL-1635 show warning if less than 3 columns selected...
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1628 tweak signature of core annotation printer...
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1551 formatting/imports
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1551 JAL-962 formatting and code change ripples...
tree
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commitdiff
2015-01-23
Charles Ofoegbu
Merge branch 'features/JAL-1553_improvement-select...
tree
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commitdiff
2015-01-23
Charles Ofoegbu
JAL-1553 fixed null pointer exception thrown in SeqCanv...
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1551 source code formatting
tree
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commitdiff
2015-01-23
Jim Procter
JAL-969 javadoc and mark interface overrides for clarity
tree
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commitdiff
2015-01-23
Jim Procter
JAL-1628 drop getShowAnnotation accessor in favour...
tree
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commitdiff
2015-01-22
Charles Ofoegbu
Merge branch 'features/JAL-1553_improvement-select...
tree
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commitdiff
2015-01-22
Charles Ofoegbu
JAL-1553 added applet support for the select-column...
tree
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commitdiff
2015-01-22
gmungoc
JAL-1619 refactoring / tests to support 'align linked...
tree
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commitdiff
2015-01-21
Jim Procter
Merge branch 'develop' into feature_29/JAL-1372_referen...
tree
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commitdiff
2015-01-20
Charles Ofoegbu
clean up
tree
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commitdiff
2015-01-20
Charles Ofoegbu
clean up
tree
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commitdiff
2015-01-20
Charles Ofoegbu
Merge branch 'features/JAL-1553_improvement-select...
tree
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commitdiff
2015-01-20
Charles Ofoegbu
Further abstractions and clean up
tree
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commitdiff
2015-01-20
Charles Ofoegbu
Merge branch 'features/JAL-1553_improvement-select...
tree
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commitdiff
2015-01-20
Charles Ofoegbu
basic house keeping
tree
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commitdiff
2015-01-20
Charles Ofoegbu
Merge branch 'features/JAL-1553_improvement-select...
tree
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commitdiff
2015-01-20
Charles Ofoegbu
JAL-1553 enhancement of column selection by annotation...
tree
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commitdiff
2015-01-19
gmungoc
JAL-1619 refactored cDNA translation; modified codon...
tree
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commitdiff
2015-01-19
gmungoc
JAL-1636 typed collections now in ResidueProperties
tree
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commitdiff
2015-01-19
gmungoc
JAL-1636 fix for mouseover of 'X' in translated protein
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1372 i18n and tweaking set/unset representative...
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 formatting
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 employ new AnnotationFile reader method to...
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 new entry point for reading annotation files...
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 formatting and javadoc
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 method to hide insertions to current sequence...
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 wrappers for common checks on ColumnSelection
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 ColumnSelection method to hide insertions...
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1628 new method to get a list of insertions in...
tree
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commitdiff
2015-01-18
gmungoc
JAL-1619 refactoring wip
tree
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commitdiff
2015-01-18
Jim Procter
JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
tree
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commitdiff
2015-01-17
gmungoc
JAL-1619 further refactoring
tree
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commitdiff
2015-01-16
gmungoc
JAL-1619 refactoring in progress for Dna translation
tree
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commitdiff
2015-01-14
gmungoc
JAL-1619 AlignedCodonFrame in new alignment should...
tree
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commitdiff
2015-01-14
gmungoc
JAL-1619 modified repaint after 'Align As' action
tree
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commitdiff
2015-01-14
gmungoc
JAL-1619 Javadoc
tree
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commitdiff
2015-01-14
gmungoc
JAL-1629 .jar option removed from Alignment File Save...
tree
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commitdiff
2015-01-14
Charles Ofoegbu
Merge branch 'features/JAL-1553_select-columns-by-annot...
tree
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commitdiff
2015-01-14
Charles Ofoegbu
Modified AnnotationColumnChooser to maintain state...
features/JAL-1553_select-columns-by-annotation
tree
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commitdiff
2015-01-13
Charles Ofoegbu
Merge branch 'features/JAL-1553_select-columns-by-annot...
tree
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commitdiff
2015-01-13
Charles Ofoegbu
Refactored AnnotationColumnChoser and AnnotationColorCh...
tree
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commitdiff
2015-01-12
gmungoc
JAL-1619 load/align cDNA for protein (wip)
tree
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commitdiff
2015-01-10
Charles Ofoegbu
JAL-1553 merge commit
tree
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commitdiff
2015-01-10
Charles Ofoegbu
JAL-1553 implementation of column selection by annotati...
tree
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commitdiff
2015-01-09
Jim Procter
Merge branch 'JAL-1372_referenceseq' into feature_29...
tree
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commitdiff
2015-01-09
Jim Procter
JAL-1483 formatting
tree
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commitdiff
2015-01-09
Jim Procter
JAL-1483 remember to look at base dataset sequence...
tree
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commitdiff
2015-01-09
gmungoc
JAL-1588 check Chimera session file still exists
tree
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commitdiff
2015-01-08
gmungoc
JAL-1588 part work save/restore of Chimera session
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commitdiff
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