JAL-1632 add score model params to PCAModel and PCA constructors
[jalview.git] / src / jalview / gui / Jalview2XML.java
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,
2016-11-28 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
2016-07-24 Jim ProcterJAL-2154 keep track of incomplete sequences and report...
2016-07-24 Jim ProcterJAL-2154 systematic pattern for defining/resolving...
2016-07-23 Jim ProcterJAL-2154 patch the hack (Jalview2XML tests pass)
2016-07-20 gmungocJAL-2154 poke JSeq start/end into Vamsas sequence
2016-07-20 gmungocJAL-2023 avoid writing / loading empty mappings
2016-07-11 gmungocfile format enum wip changes
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-29 gmungocJAL-1369 fix bug reloading a project with group sequenc...
2016-06-27 gmungoctidied loop with generic iteration / loop variable
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
2016-06-21 Jim ProcterJAL-1369 mark reference sequence & view state and resto...
2016-06-21 Jim ProcterJAL-1369 project XML efficiency TODO
2016-06-21 Jim ProcterJAL-1369 dead code TODO?
2016-06-21 Jim ProcterJAL-1369 ensure *real* alignment’s metadata written...
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi...
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-05-09 gmungocJAL-2018 export graduated feature colours correctly
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset
2016-02-24 gmungocJAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list...
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-10-05 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-25 gmungocJAL-1815 restore split frame geometry correctly includi...
2015-09-22 Jim ProcterMerge branch 'develop' into Release_2_9_0b1_Branch
2015-09-16 gmungocJAL-1885 small fix to isVersionStringLaterThan plus...
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-09-03 gmungocJAL-1690 scaleProteinAsCdna new optional attribute...
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries...
2015-07-23 Jim ProcterMerge branch 'features/JAL-1759jmolUpdate' into develop
2015-07-23 Jim ProcterJAL-1759 formatting

2015-07-23 Jim ProcterJAL-1759 reinstate changes from bdfde6ef989da0702cef90f...
2015-07-23 Jim ProcterJAL-1759 formatting
2015-07-08 gmungocJAL-1759 merge from develop
2015-07-07 tcofoegbuJAL-1769 fixed output to jalview (.jpv) file in headles...
2015-07-03 gmungocJAL-892 1 second delay for correct initial rendering...
2015-06-30 gmungocJAL=1759 fix Jmol state command bug; remove debug output
2015-06-22 gmungocJAL-892 tidy Varna panel names; JAL-1789 simplified...
2015-06-19 gmungocJAL-892 check viewer is linked to alignment panel on...
2015-06-18 gmungocJAL-892 JAL-1779 save/restore Varna viewer to/from...
2015-06-18 gmungocJAL-1781 annotation.sequenceRef now sequence id not... features/JAL-1781annotationXmlIds
2015-06-17 gmungocJAL-1588 restore ChimeraViewFrame geometry as well
2015-06-10 gmungocMerge remote-tracking branch
2015-06-10 gmungocJAL-1764 save Chimera/Jmol state as separate entries...
2015-04-30 tcofoegbuJAL-1717 updated the PDBEntry model and updated the...
2015-04-08 gmungocJAL-1691 applet SplitFrame scrolling; pull up of 5...
2015-04-01 gmungocJAL-1264 reinstate Show annotations menu item
2015-03-30 gmungocJAL-1596 refactoring to allow unit tests to start and...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
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