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2015-06-08	Jim Procter	JAL-1766 test and buggy implementation of fasta index...	commit \| commitdiff \| tree
2015-06-08	Jim Procter	JAL-1766 added a snapshot build of the htsjdk	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-429 remove pointless code from phylip parser	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-653 test for GFF file recognition and alignment...	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-653 GFF recognition for identifyFile and format...	commit \| commitdiff \| tree
2015-06-07	Jim Procter	JAL-653 basic GFF3 alignment import wrapper class	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 make sure dummy sequences created during GFF...	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 first stab at parsing GFF3 pragmas to support...	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 gff version number field	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 test and testdata for importing GFF3 file with...	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 missing imports after rebase	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 test for SequenceDummy methods	commit \| commitdiff \| tree
2015-06-06	Jim Procter	JAL-653 allow a dummy sequence to take on attributes...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	Merge branch 'develop' into features/JAL-653_gffalignments	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 abstract sequence model to support file backed...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 refactor sequence interface to separate concrete...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-845 jim @mungo: should this be in a package local...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 set the warningMessage for the file source...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 GFF attributes parsing mechanism, with first...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 trim initial tab in sequence feature ATTRIBUTES	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 allow dummy sequences to be created if a sequence...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 convenience method to resolve strand attribute...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-1115 JAL-653 partial introduction of List interface...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 JAL-966 TODO and avoid NPE when desktop instance...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 codon frames go on the dataset	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 refactored exonerate full output to separate...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-653 JAL-845 test to check exonerate cDNA-Protein...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-1482 JAL-653 refactor feature file import code...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-1482 refactor setTableData to more sensible name...	commit \| commitdiff \| tree
2015-06-05	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2015-05-29	Jim Procter	Merge branch 'JAL-1755_npe_groupconsensus' into develop	commit \| commitdiff \| tree
2015-05-29	Jim Procter	JAL-1755 fix for NPE when setting up temporary variables	commit \| commitdiff \| tree
2015-05-07	Jim Procter	JAL-1731 fix JPred4 citation in legacy client code	commit \| commitdiff \| tree
2015-05-07	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2015-05-07	Jim Procter	JAL-1601 migrated the JABAWS 2.1 jpred burial representation...	commit \| commitdiff \| tree
2015-04-27	Jim Procter	JAL-1645 Release_2_9 branch build tag	commit \| commitdiff \| tree
2015-03-09	Jim Procter	Merge branch 'features/JAL-1565_jpred4' into Release_2_8_3_B...	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	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
2015-02-06	Jim Procter	Merge branch 'bug/JAL-1643_File-chooser-improvement...	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
2015-01-28	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
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