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