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

2016-05-26	Jim Procter	JAL-1552 refactor shared dataflavor hander	blob \| commitdiff
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
2016-05-03	gmungoc	JAL-2050 hide introns also when fetching Ensembl xrefs...	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
2016-04-01	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
2016-03-22	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
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-23	gmungoc	JAL-1705 copy 'show sequence features' setting in ...	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1705 AlignmentUtils method renamed	blob \| commitdiff \| diff to current
2016-01-11	gmungoc	JAL-1989 additional ways to 'mirror' show/hide columns...	blob \| commitdiff \| diff to current
2016-01-11	gmungoc	JAL-1989 more unit tests and encapsulation for ColumnSe...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-391 new Calculate options to Reverse, Reverse Compl...	blob \| commitdiff \| diff to current
2015-11-21	gmungoc	JAL-653 JAL-1968 FeaturesFile now handles Jalview or...	blob \| commitdiff \| diff to current
2015-11-11	tcofoegbu	merge	blob \| commitdiff \| diff to current
2015-10-22	tcofoegbu	JAL-1942 JAL-1479 DBRefFetcher refactor	blob \| commitdiff \| diff to current
2015-10-22	gmungoc	JAL-1932 TrimRegionCommand bug fix, tests and purge...	blob \| commitdiff \| diff to current
2015-10-08	tcofoegbu	merge	blob \| commitdiff \| diff to current
2015-10-07	Jim Procter	JAL-1894 source formatting	blob \| commitdiff \| diff to current
2015-09-30	tcofoegbu	JAL-1912 added support of tcoffee annotation and other...	blob \| commitdiff \| diff to current
2015-09-18	tcofoegbu	JAL-1774 JAL-1506 revised implementaion for clear highl...	blob \| commitdiff \| diff to current
2015-09-18	tcofoegbu	JAL-1506 revised implementation to clear only selected...	blob \| commitdiff \| diff to current
2015-09-17	tcofoegbu	JAL-1774 bugfix for misleading message after trying...	blob \| commitdiff \| diff to current
2015-09-16	tcofoegbu	JAL-1486 off-by-one error bugfix	blob \| commitdiff \| diff to current
2015-09-14	gmungoc	JAL-1865 fixed so initial state of annotation sort...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-06	Jim Procter	JAL-1655 transfer setting option only displayed in...	blob \| commitdiff \| diff to current
2015-09-03	Jim Procter	JAL-1680 JAL-1576 JAL-1233 all conservation and consens...	blob \| commitdiff \| diff to current
2015-09-03	tcofoegbu	JAL-793 use default custom export settings for html...	blob \| commitdiff \| diff to current
2015-09-02	gmungoc	JAL-1843 fixed input/add from textbox; added @Override...	blob \| commitdiff \| diff to current
2015-08-27	gmungoc	JAL-1611 debug sysout suppressed	blob \| commitdiff \| diff to current
2015-08-26	gmungoc	JAL-1830 dropped reference counts for mappings, instead...	blob \| commitdiff \| diff to current
2015-08-25	gmungoc	JAL-1780 just a spelling change	blob \| commitdiff \| diff to current
2015-08-17	gmungoc	JAL-1829 JAL-1830 refactoring for correct mapping ...	blob \| commitdiff \| diff to current
2015-08-10	tcofoegbu	JAL-1486 fixed flatfile output of visible region for...	blob \| commitdiff \| diff to current
2015-07-08	gmungoc	JAL-1759 merge from develop	blob \| commitdiff \| diff to current
2015-07-06	tcofoegbu	Merge branch 'features/1769_headless-mode-test' into...	blob \| commitdiff \| diff to current
2015-07-06	tcofoegbu	JAL-1769 fixed headless execution mode and created...	blob \| commitdiff \| diff to current
2015-07-03	gmungoc	Merge branch 'develop' into features/JAL-892varnaToProject	blob \| commitdiff \| diff to current
2015-07-01	gmungoc	JAL-1802 explanatory comment added	blob \| commitdiff \| diff to current
2015-07-01	gmungoc	JAL-1802 handle slide sequences edits in split frame...	blob \| commitdiff \| diff to current
2015-07-01	gmungoc	Merge branch 'develop' into features/JAL-1759jmolUpdate	blob \| commitdiff \| diff to current
2015-06-29	gmungoc	JAL-1799 adjusted annotation height calculation	blob \| commitdiff \| diff to current
2015-06-26	tcofoegbu	JAL-1641 fixed broken functionalities after refactor	blob \| commitdiff \| diff to current
2015-06-26	gmungoc	Merge branch 'develop' into features/JAL-892varnaToProject	blob \| commitdiff \| diff to current
2015-06-26	gmungoc	Merge branch 'develop' into features/JAL-1759jmolUpdate	blob \| commitdiff \| diff to current
2015-06-26	tcofoegbu	JAL-1780 improvement to ensure export settings dialog...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-19	Jim Procter	JAL-653 JAL-1780 dropped av.setHasHiddenRows() and...	blob \| commitdiff \| diff to current
2015-06-18	Jim Procter	JAL-1780 JAL-653 moved AlignExportSettings reference...	blob \| commitdiff \| diff to current
2015-06-18	gmungoc	JAL-1695 default ENABLE_SPLIT_FRAME to true for desktop	blob \| commitdiff \| diff to current
2015-06-17	Jim Procter	Merge branch 'features/JAL-653_gffalignments' into...	blob \| commitdiff \| diff to current
2015-06-17	Jim Procter	Merge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments	blob \| commitdiff \| diff to current
2015-06-17	tcofoegbu	JAL-1780 more support for export setting for flatfile... features/JAL-1780_export-settings_flatfile	blob \| commitdiff \| diff to current
2015-06-12	tcofoegbu	JAL-1641 refactor	blob \| commitdiff \| diff to current
2015-06-10	gmungoc	Merge branch 'develop' of https://source.jalview.org...	blob \| commitdiff \| diff to current
2015-06-10	tcofoegbu	JAL-1641 updated applet version	blob \| commitdiff \| diff to current
2015-06-10	gmungoc	Merge branch 'develop' of https://source.jalview.org...	blob \| commitdiff \| diff to current
2015-06-10	gmungoc	JAL-1764 save Chimera/Jmol state as separate entries...	blob \| commitdiff \| diff to current
2015-06-09	tcofoegbu	JAL-1488 bug-fix for incorrect start/end position in...	blob \| commitdiff \| diff to current
2015-06-06	Jim Procter	JAL-653 missing imports after rebase	blob \| commitdiff \| diff to current
2015-06-05	tcofoegbu	JAL-1760 JAL-1641 Serialisation of Hidden Seqs and...	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-1482 JAL-653 refactor feature file import code...	blob \| commitdiff \| diff to current
2015-06-01	tcofoegbu	JAL-1641 remove all refs/imports from gui package	blob \| commitdiff \| diff to current
2015-05-29	gmungoc	JAL-1753 declare field with interface type; check for...	blob \| commitdiff \| diff to current
2015-05-29	gmungoc	JAL-1753 duplicated code refactored to new class Progre...	blob \| commitdiff \| diff to current
2015-05-20	tcofoegbu	Merge branch 'features/JAL-1541_BioJsMSA' into develop	blob \| commitdiff \| diff to current
2015-05-20	tcofoegbu	JAL-1541 minor code clean up, and added test for BioJsH...	blob \| commitdiff \| diff to current
2015-05-19	tcofoegbu	Merge branch 'features/JAL-1541_BioJsMSA' into develop	blob \| commitdiff \| diff to current
2015-05-19	tcofoegbu	JAL-1641 Further refactoring of JSON export option...	blob \| commitdiff \| diff to current
2015-05-15	gmungoc	JAL-1737 ignore non-positional annotations for display	blob \| commitdiff \| diff to current
2015-05-11	tcofoegbu	JAL-1641 cherry-picked changes into develop compatible...	blob \| commitdiff \| diff to current
2015-05-01	gmungoc	JAL-1690 refining 'copy format from' as applied to...	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1695 parameter controls whether SplitFrame is enabled	blob \| commitdiff \| diff to current
2015-04-08	gmungoc	JAL-1691 applet SplitFrame scrolling; pull up of 5...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-09	Jim Procter	JAL-1565 loading a concise file causes insertions to...	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
2015-01-26	gmungoc	Merge branch 'features/JAL-1588saveChimeraSession'...	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
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