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Resolved diffs from 2.8.3
2015-03-09 Jim ProcterMerge branch 'features/JAL-1565_jpred4' into develop
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2015-03-09 Jim ProcterJAL-1565 loading a concise file causes insertions to...
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2015-03-06 Jim ProcterMerge branch 'features/JAL-845splitPaneMergeDevelop...
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2015-03-06 Jim ProcterMerge branch 'develop' into features/JAL-845splitPaneMergeDe...
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2015-03-06 Jim ProcterJAL-1683 bump version for r2.8.3 branch
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2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
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2015-03-06 Jim Procterreassign features already created/documented for 2...
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2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
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2015-03-06 Jim ProcterMerge commit '6797d65989b01c8fa5bdeaf6a66e35279b66a7f7...
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2015-03-05 Jim ProcterJAL-1678 fix replace token for launchApp in a buildwq
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2015-03-05 Jim ProcterJAL-1678 fix replace token for launchApp in a buildwq
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2015-03-05 Jim ProcterJAL-1213 JAL-1395 add Jmol to JalviewLite classpath...
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2015-03-05 Jim ProcterJAL-1678 add version parameter to example files in...
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2015-03-05 Jim ProcterJAL-1678 add version parameter to example files in...
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2015-03-05 Jim ProcterMerge branch 'bug/JAL-1643_File-chooser-improvement...
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2015-03-05 Jim ProcterJAL-1643 add quaqua libs as OSX specific resources
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2015-02-27 Jim ProcterMerge branch 'bug/addcustomlaunchdesktopparams' into...
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2015-02-27 Jim ProcterJAL-1678 - patch to make sure we only compare positions...
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2015-02-27 Jim Procterfix for JAL-1678
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2015-02-12 Jim ProcterJAL-1350 added to 2.9 release notes
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2015-02-12 Jim ProcterJAL-1350 document changed behaviour
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2015-02-12 Jim ProcterJAL-1350 forgot to remove empty test
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2015-02-12 Jim ProcterJAL-1350 pass the columnselection rather then selected...
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2015-02-12 Jim ProcterJAL-1350 cloned method and tested equivalence for using...
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2015-02-12 Jim ProcterJAL-1115 switch to lists in SequenceGroup
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2015-02-12 Jim ProcterJAL-1115 typecast
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2015-02-12 Jim Procterjavadoc
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2015-02-12 Jim ProcterJAL-1115 List rather than vector for sequence groups...
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2015-02-11 Jim ProcterJAL-1655 JAL-845 special support to set column width...
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2015-02-11 Jim ProcterJAL-845 avoid OOBException when method is called with...
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2015-02-11 Jim ProcterJAL-969 use AlignViewportI interface instance where...
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2015-02-11 Jim ProcterJAL-1654 allow font to be specified without modifying...
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2015-02-10 Jim Procternote about preserving/reinstating custom grid geometry...
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2015-02-10 Jim ProcterJAL-1640 make font-size changes modify grid size again
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2015-02-10 Jim ProcterJAL-845 - portability patch - workaround for lastToken...
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2015-02-10 Jim Procteradded comment to @gmungoc todo about referencing PDB...
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2015-02-10 Jim ProcterJAL-845 @mungoc TODO comments - addAlignment needs...
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2015-02-10 Jim ProcterJAL-1382 slightly more efficient detection of non-gap...
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2015-02-10 Jim ProcterJAL-1382 @mungo TODO done: use StringUtils for delete...
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2015-02-10 Jim ProcterJAL-966 @mungo TODO complete: List rather than bare...
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2015-02-09 Jim ProcterMerge branch 'features/JAL-845splitPaneMergeDevelop...
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2015-02-09 Jim ProcterMerge branch 'develop' into JAL-1640_stylesettings
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2015-02-06 Jim ProcterMerge branch 'bug/JAL-1643_File-chooser-improvement...
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2015-02-06 Jim ProcterJAL-1640 new menu allowing view settings to be transferred...
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2015-02-06 Jim ProcterJAL-1640 Desktop.getAlignmentPanel and Desktop.getViewports...
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2015-02-06 Jim ProcterJAL-1551 formatting
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2015-02-06 Jim ProcterJAL-1640 more properties moved to style bean and rationalisa...
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2015-02-06 Jim ProcterJAL-1551 formatting
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2015-02-06 Jim ProcterJAL-1640 JAL-966 is for boolean getter on AlignViewportI
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2015-02-05 Jim ProcterJAL-1643 jarred up the quaqua native libraries and...
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2015-02-05 Jim ProcterJAL-1643 added quaqua filechooser and jni libraries...
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2015-02-05 Jim ProcterJAL-1643 correct version of quaqua (8) plus THIRDPARTYLIB...
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2015-02-05 Jim ProcterJAL-1643 renamed quaqua library to add version number
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2015-02-02 Jim ProcterJAL-1640 setStyle method and associated tests (required...
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2015-02-02 Jim ProcterJAL-966 allow access to viewport interface from alignPanel
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2015-02-02 Jim ProcterJAL-1640 getters and setters for viewStyleI - note...
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2015-02-02 Jim ProcterJAL-1640 copy constructor test and implementation by...
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2015-02-02 Jim ProcterJAL-715 tweaks for SRBS description string parsing
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2015-02-02 Jim ProcterJAL-1161 JAL-1606 note about awt/swing dependency in...
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2015-02-02 Jim ProcterJAL-1640 JAL-1551 formatting/imports/remove dead code
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2015-02-02 Jim ProcterJAL-1640 updates to use get/setter on viewportI: efficiencie...
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2015-02-02 Jim ProcterJAL-1640 separated style operations into a new ViewStyle...
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2015-01-28 Jim ProcterJAL-1565 automatically mark query sequence as the sequence...
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2015-01-28 Jim Procter JAL-674 patch to make Mapping.compareTransferredToRefPDB...
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2015-01-27 Jim ProcterJAL-674 JAL-1270 added settings to ensure temperature...
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2015-01-23 Jim ProcterMerge branch 'feature_29/JAL-1372_referenceseq' into...
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2015-01-23 Jim ProcterJAL-1541 changed assert to JUnit assert - test now...
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2015-01-23 Jim ProcterJAL-1551 formatting
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2015-01-23 Jim ProcterJAL-1286 don't print an exception if a non-gzip stream...
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2015-01-23 Jim ProcterJAL-1551 crlf changes
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2015-01-23 Jim ProcterJAL-969 hasHiddenRows is now an interface method
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2015-01-23 Jim ProcterJAL-969 drop the hiddenColumns flag in favour of checking...
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2015-01-23 Jim ProcterMerge branch 'develop' into feature_29/JAL-1372_referenceseq
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2015-01-23 Jim ProcterJAL-1628 tweak signature of core annotation printer...
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2015-01-23 Jim ProcterJAL-1551 formatting/imports
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2015-01-23 Jim ProcterJAL-1551 JAL-962 formatting and code change ripples...
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2015-01-23 Jim ProcterJAL-1551 source code formatting
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2015-01-23 Jim ProcterJAL-969 javadoc and mark interface overrides for clarity
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2015-01-23 Jim ProcterJAL-1628 drop getShowAnnotation accessor in favour...
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2015-01-22 Jim ProcterJAL-1372 JAL-1169 documentation for new commands HIDE_INSERT...
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2015-01-21 Jim ProcterMerge branch 'develop' into feature_29/JAL-1372_referenceseq
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2015-01-21 Jim Proctertidy up class files that shouldn't be in repo
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2015-01-20 Jim ProcterJAL-1304 revamped annotation file documentation structure...
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2015-01-18 Jim ProcterJAL-1372 i18n and tweaking set/unset representative...
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2015-01-18 Jim ProcterJAL-1628 formatting
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2015-01-18 Jim ProcterJAL-1628 employ new AnnotationFile reader method to...
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2015-01-18 Jim ProcterJAL-1628 new entry point for reading annotation files...
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2015-01-18 Jim ProcterJAL-1628 formatting and javadoc
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2015-01-18 Jim ProcterJAL-1628 method to hide insertions to current sequence...
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2015-01-18 Jim ProcterJAL-1628 wrappers for common checks on ColumnSelection
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2015-01-18 Jim ProcterJAL-1628 ColumnSelection method to hide insertions...
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2015-01-18 Jim ProcterJAL-1628 new method to get a list of insertions in...
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2015-01-18 Jim Procteralways use interface rather than field access
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2015-01-18 Jim ProcterJAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
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2015-01-09 Jim ProcterMerge branch 'JAL-1372_referenceseq' into feature_29...
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2015-01-09 Jim ProcterMerge branch 'JAL-1483_29dev' into develop
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2015-01-09 Jim ProcterJAL-1483 formatting
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2015-01-09 Jim ProcterJAL-1483 remember to look at base dataset sequence...
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2015-01-08 Jim ProcterMerge branch 'JAL-1483_29dev' into develop
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2015-01-07 Jim ProcterMerge branch 'develop' into JAL-1483_29dev
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