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

2017-08-10	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff
2017-08-10	gmungoc	JAL-2660 used saved value of ignoreGapsInConsensus...	blob \| commitdiff \| diff to current
2017-08-08	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-08	gmungoc	JAL-2650 configure new viewport settings before selecti...	blob \| commitdiff \| diff to current
2017-06-27	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-06-08	kiramt	JAL-2591 Refactor HiddenColumns to use ArrayList instea...	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 More refactoring (incomplete)	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 simplifying hidden columns usage	blob \| commitdiff \| diff to current
2017-06-06	kiramt	JAL-2591 Removed getHiddenRegions()==null checks which...	blob \| commitdiff \| diff to current
2017-05-29	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2557 removal of Sequence.sequenceFeatures	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2050 make SequenceFeature.score final, adjust const...	blob \| commitdiff \| diff to current
2017-05-15	kiramt	Merge remote-tracking branch 'origin/develop' into...	blob \| commitdiff \| diff to current
2017-05-05	kiramt	Merge remote-tracking branch	blob \| commitdiff \| diff to current
2017-05-05	kiramt	Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges	blob \| commitdiff \| diff to current
2017-05-02	kiramt	JAL-2491 first addition of new event	blob \| commitdiff \| diff to current
2017-04-25	kiramt	JAL-2388 Working hidden regions hide/show in desktop	blob \| commitdiff \| diff to current
2017-04-24	kiramt	JAL-2388 Hidden cols separated from column selection...	blob \| commitdiff \| diff to current
2017-04-07	gmungoc	Merge branch 'develop' into features/JAL-2393customMatrices	blob \| commitdiff \| diff to current
2017-03-30	gmungoc	Merge branch 'develop' into bug/JAL-2346annotationChoice	blob \| commitdiff \| diff to current
2017-03-23	gmungoc	Merge branch 'develop' into features/JAL-2393customMatrices	blob \| commitdiff \| diff to current
2017-03-16	kiramt	JAL-2388 Applied ViewportRanges to code	blob \| commitdiff \| diff to current
2017-03-06	gmungoc	JAL-2428 separate TreeModel from TreeBuilder/NJTree...	blob \| commitdiff \| diff to current
2017-02-27	kiramt	JAL-2388 Make startRes,startSeq,endRes,endSeq private...	blob \| commitdiff \| diff to current
2017-02-27	gmungoc	JAL-1632 similarity options on TreeChooser panel affect...	blob \| commitdiff \| diff to current
2017-02-14	gmungoc	Merge branch 'develop' into bug/JAL-2346annotationChoice	blob \| commitdiff \| diff to current
2017-01-31	gmungoc	JAL-2371 rename global/viewportColourScheme to residueS...	blob \| commitdiff \| diff to current
2017-01-27	gmungoc	JAL-2371 CollectionColourScheme renamed ResidueShader...	blob \| commitdiff \| diff to current
2017-01-20	gmungoc	Merge branch 'features/JAL-2360colourSchemeApplicabilit...	blob \| commitdiff \| diff to current
2017-01-20	gmungoc	Merge branch 'develop' into features/JAL-2360colourSche...	blob \| commitdiff \| diff to current
2017-01-20	gmungoc	JAL-2383 restore group conservation slider setting...	blob \| commitdiff \| diff to current
2017-01-20	gmungoc	Merge branch 'develop' into features/JAL-2360colourSche...	blob \| commitdiff \| diff to current
2017-01-19	gmungoc	JAL-2383 restore PID colour threshold from project...	blob \| commitdiff \| diff to current
2017-01-04	gmungoc	JAL-2371 CollectionColourScheme wraps ColourSchemeI	blob \| commitdiff \| diff to current
2016-12-16	gmungoc	JAL-2360 getColour() renamed to getColourScheme(),...	blob \| commitdiff \| diff to current
2016-12-16	gmungoc	JAL-2360 refactoring for JalviewColourScheme enum,	blob \| commitdiff \| diff to current
2016-12-01	gmungoc	JAL-2346 save annotation id instead of label with annot...	blob \| commitdiff \| diff to current
2016-11-28	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-24	tcofoegbu	JAL-2326 updated references of JOptionPane to JvOptionPane	blob \| commitdiff \| diff to current
2016-11-02	gmungoc	JAL-98 JAL-1854 encapsulate 'magic number' threshold...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-24	Jim Procter	Merge branch 'releases/Release_2_10_0_Branch'	blob \| commitdiff \| diff to current
2016-10-14	gmungoc	Merge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties	blob \| commitdiff \| diff to current
2016-10-11	gmungoc	JAL-2241 check for null jprovider when processing New...	blob \| commitdiff \| diff to current
2016-10-06	gmungoc	Merge branch 'develop' into task/JAL-2196pdbeProperties	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2036 rebuild menus for each panel before adding...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-10-05	gmungoc	Merge branch 'develop' into task/JAL-2196pdbeProperties	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-1421 typed ResidueProperties.propHash; JAL-2176...	blob \| commitdiff \| diff to current
2016-09-13	gmungoc	JAL-2196 refactor PDBEntry.getProperty,setProperty...	blob \| commitdiff \| diff to current
2016-09-13	tcofoegbu	JAL-2195 bug fix to enable restoring jmol session save...	blob \| commitdiff \| diff to current
2016-09-04	Jim Procter	JAL-1919 preserve filename on restore of project so...	blob \| commitdiff \| diff to current
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
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	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
2016-07-11	gmungoc	file format enum wip changes	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
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-10-05	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-09-25	gmungoc	JAL-1815 restore split frame geometry correctly includi...	blob \| commitdiff \| diff to current
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