JAL-3116 clear out whitespace when materialising Sequence object from Uniprot XML
[jalview.git] / src / jalview / gui / Jalview2XML.java
2018-12-20 Jim ProcterJAL-1767 port save/load PCA panel to JAXB - JAL-3063
2018-12-20 Jim ProcterJAL-3171 JAL-3063 merge updates from JAL-1767
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug...
2018-12-14 Jim ProcterJAL-3171 resolve dataset for imported projects via...
2018-12-14 Jim ProcterJAL-3171 register existing dataset for new view
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit...
2018-05-07 gmungocJAL-1767 scheme DoubleMatrix type includes D and E...
2018-05-07 gmungocJAL-1767 JAL-2647 hide 'Input Data..' for PCA loaded...
2018-05-07 gmungocJAL-1767 save PCA D and E vectors instead of 'details...
2018-05-04 gmungocJAL-1767 schema and Castor changes for Save PCA in...
2018-04-27 gmungocJAL-2964 tree@linkToAllViews attribute added to project...
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-01-10 gmungocJAL-1793 update spike branch to latest
2017-12-14 gmungocJAL-2843 save/restore colour feature by attribute,...
2017-12-14 gmungocJAL-2879 save/restore feature sub-attributes in Jalview...
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2727closeAllFreeMemory' into...
2017-10-10 Jim ProcterMerge branch 'codereviews/JAL-1990_IProgressIndicator_j...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-28 gmungocJAL-2036 set menus after fully loading AlignFrame
2017-09-26 kiramtJAL-2674 HiddenColumns interface tidies
2017-09-14 gmungocJAL-2727 null more fields in AlignmentViewport.dispose...
2017-09-01 gmungocJAL-2488 remove finalize methods
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-10 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-08-10 gmungocJAL-2660 used saved value of ignoreGapsInConsensus...
2017-08-08 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-08-08 gmungocJAL-2650 configure new viewport settings before selecti...
2017-07-24 gmungocspike branch updated from latest features/JAL-2446
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea...
2017-06-07 kiramtJAL-2591 More refactoring (incomplete)
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage
2017-06-06 kiramtJAL-2591 Removed getHiddenRegions()==null checks which...
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-15 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-05-05 kiramtMerge remote-tracking branch
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
2017-05-02 kiramtJAL-2491 first addition of new event
2017-04-25 kiramtJAL-2388 Working hidden regions hide/show in desktop
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-04-07 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-03-30 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-03-16 kiramtJAL-2388 Applied ViewportRanges to code
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree...
2017-02-27 kiramtJAL-2388 Make startRes,startSeq,endRes,endSeq private...
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect...
2017-02-14 gmungocMerge branch 'develop' into bug/JAL-2346annotationChoice
2017-01-31 gmungocJAL-2371 rename global/viewportColourScheme to residueS...
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader...
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit...
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-20 gmungocJAL-2383 restore group conservation slider setting...
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-19 gmungocJAL-2383 restore PID colour threshold from project...
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
2016-12-16 gmungocJAL-2360 getColour() renamed to getColourScheme(),...
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum,
2016-12-01 gmungocJAL-2346 save annotation id instead of label with annot...
2016-11-28 gmungocMerge branch 'develop' into trialMerge
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch'
2016-10-14 gmungocMerge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties
2016-10-11 gmungocJAL-2241 check for null jprovider when processing New...
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2036 rebuild menus for each panel before adding...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-09-13 gmungocJAL-2196 refactor PDBEntry.getProperty,setProperty...
2016-09-13 tcofoegbuJAL-2195 bug fix to enable restoring jmol session save...
2016-09-04 Jim ProcterJAL-1919 preserve filename on restore of project so...
2016-09-04 Jim ProcterJAL-1803 recover type field faithfully for mmCIF/PDB...
2016-09-04 Jim ProcterJAL-1803 restore property array for a sequence’s associ...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-19 Jim ProcterJAL-2154 - possible patch .. but leads to new stringify...
2016-08-19 Jim ProcterJAL-2154 reorder the dataset sequences according to...
2016-08-19 Jim ProcterJAL-2154 belt-and-braces patch:
2016-08-19 Jim ProcterJAL-2154 verify mapping’s sequenceI ref has been resolv...
2016-08-01 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into develop
2016-08-01 Jim ProcterJAL-1772 make sure we actually return reference to...
2016-07-29 Jim ProcterJAL-2154 disable visual delay only after completed...
2016-07-29 Jim ProcterJAL-2154 register any new dataset codon frames only...
2016-07-29 Jim ProcterJAL-2154 only include mappings in dbref/alcodon in...
2016-07-27 Jim ProcterJAL-2154 toString for forward references
2016-07-27 Jim ProcterJAL-2163 set title for the alignframe from restored... patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles
2016-07-27 Jim ProcterJAL-2156 resolve and add complementary views for saveAl...
2016-07-27 Jim ProcterJAL-2156 refactor saveState & saveAlignment to common...
2016-07-24 Jim ProcterJAL-2154 formatting
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