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

2016-12-16	gmungoc	JAL-2360 refactoring for JalviewColourScheme enum,	blob \| commitdiff
2016-12-12	gmungoc	JAL-2361 extract methods to (re-)build colour menu	blob \| commitdiff \| diff to current
2016-12-09	gmungoc	JAL-1895 suppress RNA interaction colour option	blob \| commitdiff \| diff to current
2016-12-07	gmungoc	JAL-2344 handle null format, simplify JalviewFileChoose...	blob \| commitdiff \| diff to current
2016-11-29	gmungoc	JAL-2344 FileFormat.isStructureFile replaces	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
2016-11-25	gmungoc	JAL-2344 use .equals() to compare FileFormatI objects	blob \| commitdiff \| diff to current
2016-11-24	tcofoegbu	JAL-2326 updated references of JOptionPane to JvOptionPane	blob \| commitdiff \| diff to current
2016-11-24	gmungoc	Further tweaks to get tests passing	blob \| commitdiff \| diff to current
2016-11-24	gmungoc	FileFormatI further tweaks, clean compile	blob \| commitdiff \| diff to current
2016-11-22	Jim Procter	Merge branch 'features/JAL-1738_JAL-345_selectionfromhi...	blob \| commitdiff \| diff to current
2016-11-22	Jim Procter	JAL-1738 JAL-345 changed keystroke to ‘B’ (with modifie...	blob \| commitdiff \| diff to current
2016-11-14	tcofoegbu	JAL-2322 Refactored unified architecture for data ...	blob \| commitdiff \| diff to current
2016-11-11	tcofoegbu	JAL-2277 Refactored out duplicated method - printUnwrap...	blob \| commitdiff \| diff to current
2016-11-02	Jim Procter	JAL-345 JAL-1738 menu item, AlignFrame action listener...	blob \| commitdiff \| diff to current
2016-11-01	tcofoegbu	JAL-2280 refactored and improved structure file identif...	blob \| commitdiff \| diff to current
2016-10-28	Jim Procter	JAL-966 SearchResultsI now on viewmodels.AlignmentViewp...	blob \| commitdiff \| diff to current
2016-10-27	tcofoegbu	JAL-2280 Improvement to enable drag'n'drop association...	blob \| commitdiff \| diff to current
2016-10-26	tcofoegbu	JAL-2284 basic support for exporting BioJS MSA viewer... features/JAL-2284_export-biojsmsa-via-cli	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
2016-10-17	kiramt	acceptDrop call added before getTransferable in alignme... bug/JAL-1552dragndroptake2	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-2189 source formatting	blob \| commitdiff \| diff to current
2016-09-19	gmungoc	JAL-2172 test and code updates for readonly selection...	blob \| commitdiff \| diff to current
2016-09-07	Jim Procter	Merge branch 'develop' into bug/JAL-1803_JAL-2157	blob \| commitdiff \| diff to current
2016-08-31	gmungoc	JAL-2077 test isPopupTrigger in mouseReleased or mouseC...	blob \| commitdiff \| diff to current
2016-08-31	Jim Procter	JAL-2157 JAL-2154 simplify CanshowProducts code to...	blob \| commitdiff \| diff to current
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	Merge branch 'develop' into bug/JAL-2154projectMappings	blob \| commitdiff \| diff to current
2016-08-24	gmungoc	JAL-1424 tidy / recode MessageManager calls to support...	blob \| commitdiff \| diff to current
2016-08-23	gmungoc	JAL-2176 unused field / methods removed	blob \| commitdiff \| diff to current
2016-08-18	gmungoc	JAL-1693 show warning dialog if unable to make CDS...	blob \| commitdiff \| diff to current
2016-08-13	Jim Procter	JAL-2154 refactor CrossRef UI code to its own class	blob \| commitdiff \| diff to current
2016-08-02	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	blob \| commitdiff \| diff to current
2016-07-29	Jim Procter	JAL-2164 JAL-1772 explodeViews can be static, so make...	blob \| commitdiff \| diff to current
2016-07-19	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	blob \| commitdiff \| diff to current
2016-07-18	Jim Procter	JAL-2145 JAL-1551 formatting	blob \| commitdiff \| diff to current
2016-07-18	Jim Procter	JAL-2145 fix: build alignments before building AlignFra...	blob \| commitdiff \| diff to current
2016-07-12	gmungoc	FileFormat enum wip changes	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2144 TODO - new methods for canonicalisation and...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 avoid potential race condition where user...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 TODO for JAL-2131	blob \| commitdiff \| diff to current
2016-07-11	gmungoc	file format enum wip changes	blob \| commitdiff \| diff to current
2016-07-06	gmungoc	JAL-2110 cross-refs from protein to show cds not non...	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	JAL-2110 use shared dataset when copying alignment...	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	Revert "JAL-2110 use shared alignment dataset when...	blob \| commitdiff \| diff to current
2016-07-04	gmungoc	JAL-2110 use shared alignment dataset when copying...	blob \| commitdiff \| diff to current
2016-07-01	gmungoc	JAL-2110 bug fixing and tidying for get cross-refs	blob \| commitdiff \| diff to current
2016-07-01	gmungoc	JAL-2110 add 'products' parameter to filter results...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	Merge branch 'develop' into merge_JAL-2110	blob \| commitdiff \| diff to current
2016-06-22	gmungoc	JAL-1982 defensive test for null array of annotations	blob \| commitdiff \| diff to current
2016-06-22	Jim Procter	JAL-2110 remove hardwired detection of search context...	blob \| commitdiff \| diff to current
2016-06-21	Jim Procter	Merge branch 'features/JAL-2110_crossRefDuplications...	blob \| commitdiff \| diff to current
2016-06-20	Jim Procter	Merge branch 'develop' into features/JAL-1812_JAL-2083_... features/JAL-1812_JAL-2083_groovyBinding	blob \| commitdiff \| diff to current
2016-06-14	gmungoc	JAL-2110 fixes to dbref resolution and mappings, use...	blob \| commitdiff \| diff to current
2016-06-09	gmungoc	JAL-2110 work in progress	blob \| commitdiff \| diff to current
2016-06-09	gmungoc	Merge branch 'develop' into features/JAL-2110_makeSense...	blob \| commitdiff \| diff to current
2016-06-06	tcofoegbu	JAL-1944 bugfix for wrong alignment numbering when...	blob \| commitdiff \| diff to current
2016-06-03	gmungoc	JAL-2110 random stuff	blob \| commitdiff \| diff to current
2016-06-02	gmungoc	Merge branch 'develop' into features/JAL-2110_makeSense...	blob \| commitdiff \| diff to current
2016-06-01	tcofoegbu	Merge branch 'develop' of https://source.jalview.org...	blob \| commitdiff \| diff to current
2016-06-01	tcofoegbu	JAL-1944 updated bugfix implementation	blob \| commitdiff \| diff to current
2016-06-01	gmungoc	JAL-1424 utility to check resource bundle labels used...	blob \| commitdiff \| diff to current
2016-05-31	tcofoegbu	merge	blob \| commitdiff \| diff to current
2016-05-31	tcofoegbu	JAL-1944 fix for visible seqs sometimes been replaced...	blob \| commitdiff \| diff to current
2016-05-31	gmungoc	JAL-2023 adjustments to mappings added for split frame...	blob \| commitdiff \| diff to current
2016-05-30	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	blob \| commitdiff \| diff to current
2016-05-26	gmungoc	JAL-391 add reverse / complement to command history...	blob \| commitdiff \| diff to current
2016-05-26	Jim Procter	JAL-1551 formatting	blob \| commitdiff \| diff to current
2016-05-26	Jim Procter	JAL-1552 refactor shared dataflavor hander	blob \| commitdiff \| diff to current
2016-05-26	Jim Procter	JAL-1552 extra debug logging for dataflavor if drop...	blob \| commitdiff \| diff to current
2016-05-25	Jim Procter	JAL-1522 patch - try to pick best text dataflavor	blob \| commitdiff \| diff to current
2016-05-20	gmungoc	JAL-2110 unit tests for and minor refactoring of CrossRef	blob \| commitdiff \| diff to current
2016-05-03	gmungoc	JAL-2050 hide introns also when fetching Ensembl xrefs...	blob \| commitdiff \| diff to current
2016-05-02	gmungoc	JAL-1812 bind Groovy to Jalview rather than Desktop...	blob \| commitdiff \| diff to current
2016-04-28	gmungoc	JAL-2083 removed use of reflection for Groovy	blob \| commitdiff \| diff to current
2016-04-24	Jim Procter	JAL-2077 - reinstate popups on osx	blob \| commitdiff \| diff to current
2016-04-24	Jim Procter	JAL-2075 make GroovyConsole a singleton so tests requir...	blob \| commitdiff \| diff to current
2016-04-22	gmungoc	JAL-1812 JAL-2068 add Run Groovy Script to AlignFrame...	blob \| commitdiff \| diff to current
2016-04-20	Jim Procter	fix for JAL-2072	blob \| commitdiff \| diff to current
2016-04-11	tcofoegbu	JAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...	blob \| commitdiff \| diff to current
2016-04-11	Jim Procter	Merge branch 'develop' into efficiency/JAL-2034_JAL...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	JAL-1705 ensure the right mapping is used to align...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2016-04-01	gmungoc	JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...	blob \| commitdiff \| diff to current
2016-03-28	gmungoc	JAL-2016 push getFeatureColourScheme(source) into Seque...	blob \| commitdiff \| diff to current
2016-03-28	gmungoc	JAL-2036 update AlignFrame menus when dbreffetcher...	blob \| commitdiff \| diff to current
2016-03-25	Jim Procter	JAL-2034 make Escape/select/deselect operations not...	blob \| commitdiff \| diff to current
2016-03-22	gmungoc	JAL-1705 add xref seqs to 'parent' dataset only if...	blob \| commitdiff \| diff to current
2016-03-15	gmungoc	JAL-2016 FeatureSettingsI now FeatureSettingsModelI	blob \| commitdiff \| diff to current
2016-03-11	gmungoc	JAL-1705 refactoring etc for fetching Ensembl --> Uniprot	blob \| commitdiff \| diff to current
2016-03-07	gmungoc	JAL-2023 CDS sequences added to / share alignment dataset	blob \| commitdiff \| diff to current
2016-03-01	gmungoc	JAL-1705 align CDS and peptide products to transcripts	blob \| commitdiff \| diff to current
2016-02-22	gmungoc	JAL-1705 first pass at applying preset feature colourin...	blob \| commitdiff \| diff to current
2016-02-19	gmungoc	JAL-1705 refactor show products, set initial split...	blob \| commitdiff \| diff to current
2016-02-12	gmungoc	Merge branch 'develop' into	blob \| commitdiff \| diff to current
2016-02-09	tcofoegbu	JAL-1976 Added progress indicators for HTML_SVG and...	blob \| commitdiff \| diff to current
2016-01-29	gmungoc	JAL-1705 copy feature settings when opening a split...	blob \| commitdiff \| diff to current
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