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

2018-11-08	gmungoc	JAL-3048 use JalviewJS compatible JalviewFileChooser...	blob \| commitdiff
2018-11-05	Ben Soares	JAL-1988 Investigating...	blob \| commitdiff \| diff to current
2018-10-31	gmungoc	Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into... feature/JAL-3144noJTree	blob \| commitdiff \| diff to current
2018-10-29	gmungoc	JAL-3144 SequenceFetcher without JDatabaseTree	blob \| commitdiff \| diff to current
2018-10-25	Ben Soares	JAL-3141 Ostensibly all backups working for alignment...	blob \| commitdiff \| diff to current
2018-10-17	Jim Procter	Merge branch 'feature/JAL-3063JAXB' into Jalview-BH...	blob \| commitdiff \| diff to current
2018-10-16	Jim Procter	JAL-3127 use AlignViewportI.addGroup to create & propag...	blob \| commitdiff \| diff to current
2018-10-09	Jim Procter	JAL-3127 pass reference to AlignViewportI when creating...	blob \| commitdiff \| diff to current
2018-10-04	gmungoc	JAL-3132 set status message when over sequence id or...	blob \| commitdiff \| diff to current
2018-09-19	gmungoc	JAL-3063 use JAXB for 'Save as Project' and load projec...	blob \| commitdiff \| diff to current
2018-09-18	gmungoc	JAL-3063 New View via JAXB	blob \| commitdiff \| diff to current
2018-09-18	gmungoc	JAL-3063 temporary extra menu option to save/load proje...	blob \| commitdiff \| diff to current
2018-09-14	gmungoc	JAL-3116 parse EMBL XML with JAXB (todo: update unit...	blob \| commitdiff \| diff to current
2018-09-11	gmungoc	JAL-3048 recoded edit View Name dialog for JalviewJS	blob \| commitdiff \| diff to current
2018-09-11	Jim Procter	Merge branch 'develop' into releases/Release_2_11_Branch	blob \| commitdiff \| diff to current
2018-09-10	gmungoc	JAL-3097 adjust viewport width on hiding columns bug/JAL-3097blankExtraColumns	blob \| commitdiff \| diff to current
2018-09-07	Jim Procter	JAL-3107 update any group associated annotation rows...	blob \| commitdiff \| diff to current
2018-08-27	hansonr	JAL-3026 alignmentFrame.statusBar.setText -> .setStatus	blob \| commitdiff \| diff to current
2018-08-24	hansonr	JAL-3026 Java bug associated with File/String mods	blob \| commitdiff \| diff to current
2018-08-17	gmungoc	JAL-3048 remove obsolete way of handling dialogs in...	blob \| commitdiff \| diff to current
2018-08-14	gmungoc	JAL-3032 tidy AlignmentProperties display for JalviewJS	blob \| commitdiff \| diff to current
2018-08-06	Jim Procter	JAL-3070 TODO for mateusz	blob \| commitdiff \| diff to current
2018-07-23	Jim Procter	Merge branch 'features/mchmmer' into merge/wsinterfaces...	blob \| commitdiff \| diff to current
2018-07-20	Jim Procter	JAL-3070 core service descriptors for JABAWS services...	blob \| commitdiff \| diff to current
2018-07-20	gmungoc	JAL-3048 revised AlignExportSettings dialog with respon...	blob \| commitdiff \| diff to current
2018-07-19	gmungoc	JAL-3048 inlined 1-line methods, small refactor of...	blob \| commitdiff \| diff to current
2018-07-19	gmungoc	JAL-3048 revert saveAs action so it works in Javascript too	blob \| commitdiff \| diff to current
2018-07-11	Jim Procter	JAL-3026 JLabel for alignment properties in jalview-js	blob \| commitdiff \| diff to current
2018-07-11	Jim Procter	Merge branch 'Jalview-BH/JAL-3048_exportSettingsrefacto...	blob \| commitdiff \| diff to current
2018-07-11	Jim Procter	JAL-1551 formatting	blob \| commitdiff \| diff to current
2018-07-11	Jim Procter	JAL-3048 refactored export settings to bean+dialog... Jalview-BH/JAL-3048_exportSettingsrefactor	blob \| commitdiff \| diff to current
2018-07-10	Jim Procter	Merge branch 'Jalview-BH/JAL-3026' of source.jalview...	blob \| commitdiff \| diff to current
2018-07-10	gmungoc	JAL-3048 obsolete method deleted	blob \| commitdiff \| diff to current
2018-07-10	Jim Procter	JAL-3048 switch from 'dialogdata' to DialogRunner for...	blob \| commitdiff \| diff to current
2018-07-03	hansonr	Merge remote-tracking branch 'origin/Jalview-BH/JAL...	blob \| commitdiff \| diff to current
2018-07-02	hansonr	JAL-3026 File...Reload working	blob \| commitdiff \| diff to current
2018-07-02	hansonr	JAL-3026 Java+JavaScript fix for GD#95	blob \| commitdiff \| diff to current
2018-07-02	Jim Procter	JAL-3048 remove TODOs Jalview-BH/JAL-3048_dialogs	blob \| commitdiff \| diff to current
2018-07-02	Jim Procter	JAL-3048 File->VCF load refactored	blob \| commitdiff \| diff to current
2018-07-02	Jim Procter	JAL-3048 AlignFrame -> Save dialog refactored - patched...	blob \| commitdiff \| diff to current
2018-06-29	Jim Procter	JAL-3048 use FileParse to transfer File to NewickFile...	blob \| commitdiff \| diff to current
2018-06-29	Jim Procter	JAL-3048 AlignFrame->File->Load Tree adapted for js	blob \| commitdiff \| diff to current
2018-06-28	Jim Procter	JAL-3048 TODOs for refactoring JalviewFileChooser pattern	blob \| commitdiff \| diff to current
2018-06-28	Jim Procter	JAL-3048 todo and JAL-3026 disable VCF support	blob \| commitdiff \| diff to current
2018-06-28	hansonr	JAL-3032 DND enabled; additional io changes for File...	blob \| commitdiff \| diff to current
2018-06-27	hansonr	JAL-3032 part2 local file reading by JFileChooser	blob \| commitdiff \| diff to current
2018-06-23	hansonr	JAL-3026 JDesktop/JInternalFrames support + relative...	blob \| commitdiff \| diff to current
2018-05-28	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2018-05-28	gmungoc	Merge remote-tracking branch 'origin/releases/Release_2...	blob \| commitdiff \| diff to current
2018-05-23	gmungoc	JAL-2993 AlignFrame listen for keystrokes in OverviewPanel	blob \| commitdiff \| diff to current
2018-05-22	gmungoc	JAL-2629 method refactor and menu tidying	blob \| commitdiff \| diff to current
2018-05-15	gmungoc	JAL-1264 exclude score-only from 'Add Reference Annotat...	blob \| commitdiff \| diff to current
2018-05-14	gmungoc	JAL-2711 show short file names in search database combo box	blob \| commitdiff \| diff to current
2018-05-10	gmungoc	JAL-2629 handle decline 'Add Database'	blob \| commitdiff \| diff to current
2018-05-09	gmungoc	JAL-2984 add pdb as sequence(s) if associate structure...	blob \| commitdiff \| diff to current
2018-04-24	gmungoc	JAL-2616 unused field removed	blob \| commitdiff \| diff to current
2018-04-17	gmungoc	JAL-2629 choice of hmm profile now a parameter not...	blob \| commitdiff \| diff to current
2018-04-16	gmungoc	JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...	blob \| commitdiff \| diff to current
2018-03-30	gmungoc	JAL-2629 combine with/without defaults in one method...	blob \| commitdiff \| diff to current
2018-03-26	gmungoc	JAL-2939 unused action handler methods removed	blob \| commitdiff \| diff to current
2018-03-21	gmungoc	JAL-2629 tweaks to Information annotation updating	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	JAL-2620 alternative genetic code translation tables	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	Merge branch 'bug/JAL-2865removeGC' into develop	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2018-03-07	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	blob \| commitdiff \| diff to current
2018-03-07	gmungoc	JAL-2629 storage and lifecycle of alignment/group HMM...	blob \| commitdiff \| diff to current
2018-02-27	Jim Procter	Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104	blob \| commitdiff \| diff to current
2018-02-21	gmungoc	JAL-2629 simplifying method signatures in Hmmer command...	blob \| commitdiff \| diff to current
2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2018-02-20	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	blob \| commitdiff \| diff to current
2018-02-19	gmungoc	JAL-2629 refactoring of Hmmer preferences	blob \| commitdiff \| diff to current
2018-02-13	Jim Procter	JAL-2781 refactor ‘trim retrieved sequence’ preference...	blob \| commitdiff \| diff to current
2018-01-15	kiramt	JAL-2759 Refactor of hideInsertionsFor after review	blob \| commitdiff \| diff to current
2018-01-10	gmungoc	JAL-2865 unhelpful System.gc() calls removed bug/JAL-2865removeGC	blob \| commitdiff \| diff to current
2018-01-10	gmungoc	JAL-1793 update spike branch to latest	blob \| commitdiff \| diff to current
2017-12-08	gmungoc	JAL-2843 refactor / tidy for feature filter input/output	blob \| commitdiff \| diff to current
2017-12-04	gmungoc	JAL-2850 JAL-1766 option to load contig sequence refere...	blob \| commitdiff \| diff to current
2017-11-08	kiramt	Merge branch 'develop' into feature/JAL-2759	blob \| commitdiff \| diff to current
2017-10-27	gmungoc	JAL-1793 spike branch updated to latest	blob \| commitdiff \| diff to current
2017-10-27	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	blob \| commitdiff \| diff to current
2017-10-26	Jim Procter	Merge branch 'feature/JAL-2488finalize' into develop	blob \| commitdiff \| diff to current
2017-10-26	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	blob \| commitdiff \| diff to current
2017-10-25	Jim Procter	Merge branch 'bug/JAL-2727closeAllFreeMemory' into...	blob \| commitdiff \| diff to current
2017-10-24	gmungoc	JAL-2738 update spike branch with latest	blob \| commitdiff \| diff to current
2017-10-24	gmungoc	Merge branch 'develop' into features/JAL-1793VCF; lambd...	blob \| commitdiff \| diff to current
2017-10-20	gmungoc	Push 1793 latest to spike branch	blob \| commitdiff \| diff to current
2017-10-19	gmungoc	JAL-2755 find gene loci for fetched xrefs where possible	blob \| commitdiff \| diff to current
2017-10-12	Jim Procter	JAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-26	kiramt	JAL-2674 more List<int[]> -> HiddenColumns copy changes	blob \| commitdiff \| diff to current
2017-09-26	kiramt	JAL-2674 Changes to pasting	blob \| commitdiff \| diff to current
2017-09-22	gmungoc	JAL-2738 correct handling of reverse strand genes	blob \| commitdiff \| diff to current
2017-09-21	gmungoc	JAL-2738 PoC of Load VCF file on to gene sequence	blob \| commitdiff \| diff to current
2017-09-12	gmungoc	JAL-2727 ensure ViewportRanges (and gapcounts) are...	blob \| commitdiff \| diff to current
2017-09-01	gmungoc	JAL-2488 remove finalize methods	blob \| commitdiff \| diff to current
2017-08-29	Jim Procter	JAL-2698 spawn a thread to test for and raise auto...	blob \| commitdiff \| diff to current
2017-08-25	TZVanaalten	JAL-2629 add multiple options for running hmmbuild...	blob \| commitdiff \| diff to current
2017-08-25	TZVanaalten	JAL-2629 add adjustable parameters to hmmbuild	blob \| commitdiff \| diff to current
2017-08-25	TZVanaalten	JAL-2629 hmmsearch/build/align no longer run after...	blob \| commitdiff \| diff to current
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