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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
2015-01-07	Jim Procter	JAL-1483 patches to make test case pass: hamming distance...	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 basic test of sequence similarity score model...	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 source formatting	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 refactor NJTree constructor to allow preconfigured...	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 register feature similarity model	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 null features not displayed	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 check dataset for features if none found on...	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 organise imports	commit \| commitdiff \| tree
2015-01-07	Jim Procter	JAL-1483 making type visible also adds it to registry	commit \| commitdiff \| tree
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 update applet authors list	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 disable desktop 'take snapshot' menu item...	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 dropped jnlp file in help documentation in...	commit \| commitdiff \| tree
2014-12-03	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 updated library licensing info	commit \| commitdiff \| tree
2014-12-03	Jim Procter	JAL-1517 release notes	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1517 typo	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1517 TOC items must be on one line for help2Website	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1602 tweak VM inclusion options	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1517 documentation for 2.8.2 release	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1602 typo in jsonsimple jar	commit \| commitdiff \| tree
2014-12-02	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-02	Jim Procter	JAL-1602 add missing jars to install	commit \| commitdiff \| tree
2014-12-01	Jim Procter	Merge branch 'JAL-1602_282_release' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1602 upgrade to InstallAnywhere 2014 J17 runtimes	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1199 JAL-1569 incremental patch allow non-standard...	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1517 updating author list	commit \| commitdiff \| tree
2014-12-01	Jim Procter	JAL-1517 updating authors list	commit \| commitdiff \| tree
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