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[jalview.git] / src / jalview / gui / Jalview2XML.java

2016-09-04	Jim Procter	JAL-1919 preserve filename on restore of project so...	blob \| commitdiff
2016-09-04	Jim Procter	JAL-1803 recover type field faithfully for mmCIF/PDB...	blob \| commitdiff \| diff to current
2016-09-04	Jim Procter	JAL-1803 restore property array for a sequence’s associ...	blob \| commitdiff \| diff to current
2016-08-19	Jim Procter	JAL-2154 - possible patch .. but leads to new stringify...	blob \| commitdiff \| diff to current
2016-08-19	Jim Procter	JAL-2154 reorder the dataset sequences according to...	blob \| commitdiff \| diff to current
2016-08-19	Jim Procter	JAL-2154 belt-and-braces patch:	blob \| commitdiff \| diff to current
2016-08-19	Jim Procter	JAL-2154 verify mapping’s sequenceI ref has been resolv...	blob \| commitdiff \| diff to current
2016-08-01	Jim Procter	Merge branch 'bug/JAL-2154projectMappings' into develop	blob \| commitdiff \| diff to current
2016-08-01	Jim Procter	JAL-1772 make sure we actually return reference to...	blob \| commitdiff \| diff to current
2016-07-29	Jim Procter	JAL-2154 disable visual delay only after completed...	blob \| commitdiff \| diff to current
2016-07-29	Jim Procter	JAL-2154 register any new dataset codon frames only...	blob \| commitdiff \| diff to current
2016-07-29	Jim Procter	JAL-2154 only include mappings in dbref/alcodon in...	blob \| commitdiff \| diff to current
2016-07-27	Jim Procter	JAL-2154 toString for forward references	blob \| commitdiff \| diff to current
2016-07-27	Jim Procter	JAL-2163 set title for the alignframe from restored... patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles	blob \| commitdiff \| diff to current
2016-07-27	Jim Procter	JAL-2156 resolve and add complementary views for saveAl...	blob \| commitdiff \| diff to current
2016-07-27	Jim Procter	JAL-2156 refactor saveState & saveAlignment to common...	blob \| commitdiff \| diff to current
2016-07-24	Jim Procter	JAL-2154 formatting	blob \| commitdiff \| diff to current
2016-07-24	Jim Procter	JAL-2154 keep track of incomplete sequences and report...	blob \| commitdiff \| diff to current
2016-07-24	Jim Procter	JAL-2154 systematic pattern for defining/resolving...	blob \| commitdiff \| diff to current
2016-07-23	Jim Procter	JAL-2154 patch the hack (Jalview2XML tests pass)	blob \| commitdiff \| diff to current
2016-07-20	gmungoc	JAL-2154 poke JSeq start/end into Vamsas sequence	blob \| commitdiff \| diff to current
2016-07-20	gmungoc	JAL-2023 avoid writing / loading empty mappings	blob \| commitdiff \| diff to current
2016-06-29	gmungoc	Merge branch 'develop' into features/JAL-2110_crossRefD...	blob \| commitdiff \| diff to current
2016-06-29	gmungoc	JAL-1369 fix bug reloading a project with group sequenc...	blob \| commitdiff \| diff to current
2016-06-27	gmungoc	tidied loop with generic iteration / loop variable	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	Merge branch 'features/JAL-2110_crossRefDuplications...	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	Merge branch 'features/JAL-1956_featureStyles' into...	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	JAL-1369 mark reference sequence & view state and resto...	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	JAL-1369 project XML efficiency TODO	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	JAL-1369 dead code TODO?	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	JAL-1369 ensure real alignment’s metadata written...	blob \| commitdiff \| diff to current
2016-06-19	Jim Procter	JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...	blob \| commitdiff \| diff to current
2016-05-13	gmungoc	JAL-2105 capture Ensembl data version, check REST versi...	blob \| commitdiff \| diff to current
2016-05-10	gmungoc	Merge branch 'develop' into features/JAL-1956_featureStyles	blob \| commitdiff \| diff to current
2016-05-09	gmungoc	JAL-2018 export graduated feature colours correctly	blob \| commitdiff \| diff to current
2016-03-07	gmungoc	JAL-2023 CDS sequences added to / share alignment dataset	blob \| commitdiff \| diff to current
2016-02-24	gmungoc	JAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 hold AlignedCodonFrame collections as list...	blob \| commitdiff \| diff to current
2015-11-21	gmungoc	JAL-653 JAL-1968 FeaturesFile now handles Jalview or...	blob \| commitdiff \| diff to current
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-09-25	gmungoc	JAL-1815 restore split frame geometry correctly includi...	blob \| commitdiff \| diff to current
2015-09-16	gmungoc	JAL-1885 small fix to isVersionStringLaterThan plus...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-03	gmungoc	JAL-1690 scaleProteinAsCdna new optional attribute...	blob \| commitdiff \| diff to current
2015-08-07	tcofoegbu	JAL-1824 updated caching procedure for pdb entries...	blob \| commitdiff \| diff to current
2015-07-23	Jim Procter	Merge branch 'features/JAL-1759jmolUpdate' into develop	blob \| commitdiff \| diff to current
2015-07-23	Jim Procter	JAL-1759 formatting	blob \| commitdiff \| diff to current
2015-07-23	Jim Procter	JAL-1759 reinstate changes from bdfde6ef989da0702cef90f...	blob \| commitdiff \| diff to current
2015-07-23	Jim Procter	JAL-1759 formatting	blob \| commitdiff \| diff to current
2015-07-08	gmungoc	JAL-1759 merge from develop	blob \| commitdiff \| diff to current
2015-07-07	tcofoegbu	JAL-1769 fixed output to jalview (.jpv) file in headles...	blob \| commitdiff \| diff to current
2015-07-03	gmungoc	JAL-892 1 second delay for correct initial rendering...	blob \| commitdiff \| diff to current
2015-06-30	gmungoc	JAL=1759 fix Jmol state command bug; remove debug output	blob \| commitdiff \| diff to current
2015-06-22	gmungoc	JAL-892 tidy Varna panel names; JAL-1789 simplified...	blob \| commitdiff \| diff to current
2015-06-19	gmungoc	JAL-892 check viewer is linked to alignment panel on...	blob \| commitdiff \| diff to current
2015-06-18	gmungoc	JAL-892 JAL-1779 save/restore Varna viewer to/from...	blob \| commitdiff \| diff to current
2015-06-18	gmungoc	JAL-1781 annotation.sequenceRef now sequence id not... features/JAL-1781annotationXmlIds	blob \| commitdiff \| diff to current
2015-06-17	gmungoc	JAL-1588 restore ChimeraViewFrame geometry as well	blob \| commitdiff \| diff to current
2015-06-10	gmungoc	Merge remote-tracking branch	blob \| commitdiff \| diff to current
2015-06-10	gmungoc	JAL-1764 save Chimera/Jmol state as separate entries...	blob \| commitdiff \| diff to current
2015-04-30	tcofoegbu	JAL-1717 updated the PDBEntry model and updated the...	blob \| commitdiff \| diff to current
2015-04-08	gmungoc	JAL-1691 applet SplitFrame scrolling; pull up of 5...	blob \| commitdiff \| diff to current
2015-04-01	gmungoc	JAL-1264 reinstate Show annotations menu item	blob \| commitdiff \| diff to current
2015-03-30	gmungoc	JAL-1596 refactoring to allow unit tests to start and...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-02-19	gmungoc	JAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor	blob \| commitdiff \| diff to current
2015-01-27	gmungoc	JAL-1588 new class renamed	blob \| commitdiff \| diff to current
2015-01-26	gmungoc	Merge branch 'features/JAL-1588saveChimeraSession'...	blob \| commitdiff \| diff to current
2015-01-26	gmungoc	JAL-1588 restoring saved Chimera session(s)	blob \| commitdiff \| diff to current
2015-01-23	gmungoc	JAL-1588 first working (?) restore of Chimera session...	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-1551 JAL-962 formatting and code change ripples...	blob \| commitdiff \| diff to current
2015-01-23	Jim Procter	JAL-1628 drop getShowAnnotation accessor in favour...	blob \| commitdiff \| diff to current
2015-01-09	gmungoc	JAL-1588 check Chimera session file still exists	blob \| commitdiff \| diff to current
2015-01-08	gmungoc	JAL-1588 part work save/restore of Chimera session	blob \| commitdiff \| diff to current
2015-01-07	gmungoc	JAL-1588 refactoring to StructureViewerBase and related	blob \| commitdiff \| diff to current
2015-01-06	gmungoc	JAL-1588 refactoring prior to 'save Chimera project'	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-12-09	gmungoc	JAL-1616 loading of datasets from XML patched	blob \| commitdiff \| diff to current
2014-12-09	gmungoc	JAL-1616 loading of datasets from XML patched Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-12-05	Charles Ofoegbu	JAL-1605 merge commit	blob \| commitdiff \| diff to current
2014-12-05	Charles Ofoegbu	Change the Html export to utilize svg	blob \| commitdiff \| diff to current
2014-11-27	Jim Procter	Merge branch 'patchJAL-674_offset' into develop	blob \| commitdiff \| diff to current
2014-11-27	Jim Procter	JAL-1177 JAL-905 cannot recover sequences from dataset...	blob \| commitdiff \| diff to current
2014-11-27	Jim Procter	JAL-674 avoid writing \0 for chain code	blob \| commitdiff \| diff to current
2014-11-14	Charles Ofoegbu	House keeping	blob \| commitdiff \| diff to current
2014-11-14	Jim Procter	Merge branch 'develop' into JAL-1483_featureBasedTreeCalc	blob \| commitdiff \| diff to current
2014-11-03	Jim Procter	JAL-1578 JAL-674 store/restore alignment annotation...	blob \| commitdiff \| diff to current
2014-10-30	Jim Procter	JAL-674 register PDB IDs when ever they are resolved...	blob \| commitdiff \| diff to current
2014-10-30	Jim Procter	JAL-1551 format and tidy	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1482 feature renderer and manipulation code refacto...	blob \| commitdiff \| diff to current
2014-08-08	j.procter@dundee...	JAL-1483 move show sequence feature and sequence featur...	blob \| commitdiff \| diff to current
2014-07-02	Jim Procter	JAL-1333 JAL-1527 refactors to create core structure...	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
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