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

2018-02-21	gmungoc	JAL-2629 simplifying method signatures in Hmmer command...	blob \| commitdiff
2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2018-02-19	gmungoc	JAL-2629 refactoring of Hmmer preferences	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
2017-10-27	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
2017-09-22	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
2017-08-25	TZVanaalten	JAL-2629 add ability to add and select a DB for hmmsearch	blob \| commitdiff \| diff to current
2017-08-25	TZVanaalten	JAL-2629 add basic parameter adjustment to hmmsearch...	blob \| commitdiff \| diff to current
2017-08-23	tzvanaalten	JAL-2629 selected HMM is now a sequence, not a HMM	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-18	TZVanaalten	Merge branch 'develop' into features/hmmer	blob \| commitdiff \| diff to current
2017-08-17	TZVanaalten	JAL-2629 add documentation to previous work	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-08-15	TZVanaalten	JAL-2629 selected HMM name now shown in HMMER menu	blob \| commitdiff \| diff to current
2017-08-15	TZVanaalten	JAL-2629 the HMMER tab is now disabled when HMMER is...	blob \| commitdiff \| diff to current
2017-08-14	TZVanaalten	JAL-2629 remove redundant options from HMMER menu	blob \| commitdiff \| diff to current
2017-08-11	TZVanaalten	JAL-2599 HMMs can now be dropped onto the desktop	blob \| commitdiff \| diff to current
2017-08-10	TZVanaalten	JAL-2629 hmmalign now correctly creates a new frame	blob \| commitdiff \| diff to current
2017-08-10	tzvanaalten	JAL-2629 fix files permission issue on Mac	blob \| commitdiff \| diff to current
2017-08-09	TZVanaalten	JAL-2599 fix for issue where info annot would not display	blob \| commitdiff \| diff to current
2017-08-09	tzvanaalten	JAL-2599 fix for issue where info annot would not display	blob \| commitdiff \| diff to current
2017-08-09	TZVanaalten	JAL-2629 removed unnecessary exception throws from...	blob \| commitdiff \| diff to current
2017-08-09	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-08	TZVanaalten	JAL-2629 add ability to select hmmer binaries folder	blob \| commitdiff \| diff to current
2017-08-07	TZVanaalten	JAL-2629 current hmmer commands are now executed in...	blob \| commitdiff \| diff to current
2017-08-07	Jim Procter	Merge branch 'bug/JAL-2592userDefinedScheme' into develop	blob \| commitdiff \| diff to current
2017-08-04	TZVanaalten	JAL-2629 multiple HMMs can now be dropped onto an alignment	blob \| commitdiff \| diff to current
2017-08-02	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-02	TZVanaalten	JAL-2599 fix for information annotation buttons	blob \| commitdiff \| diff to current
2017-07-31	TZVanaalten	JAL-2629 add hmmalign command	blob \| commitdiff \| diff to current
2017-07-28	kiramt	JAL-2632 Added paintAlignment(true) to show cols code	blob \| commitdiff \| diff to current
2017-07-27	TZVanaalten	JAL-2629 implement hmmbuild	blob \| commitdiff \| diff to current
2017-07-27	TZVanaalten	JAL-2629 moved HMM storage location to placeholder...	blob \| commitdiff \| diff to current
2017-07-25	TZVanaalten	JAL-2629 add non-functional HMMER menu	blob \| commitdiff \| diff to current
2017-07-24	tzvanaalten	JAL-2616 add placeholder sequence for HMM, does not...	blob \| commitdiff \| diff to current
2017-07-24	gmungoc	spike branch updated from latest features/JAL-2446	blob \| commitdiff \| diff to current
2017-07-20	TZVanaalten	JAL-2616 remove statistical analysis from AlignFrame	blob \| commitdiff \| diff to current
2017-07-20	TZVanaalten	JAL-2599 add ability to process RNA HMMer files	blob \| commitdiff \| diff to current
2017-07-19	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-07-14	TZVanaalten	add partial button fix to annotation and statistics... features/hmmer_statistics	blob \| commitdiff \| diff to current
2017-07-12	TZVanaalten	test HMM annotaTION	blob \| commitdiff \| diff to current
2017-07-04	gmungoc	JAL-147 remove redundant calls to update overview panel	blob \| commitdiff \| diff to current
2017-07-04	gmungoc	JAL-2608 tidy up OverviewPanel when closed	blob \| commitdiff \| diff to current
2017-06-29	gmungoc	JAL-147 improved wrapped scrolling (including Overview...	blob \| commitdiff \| diff to current
2017-06-29	TZVanaalten	transferred the storage position of the HMM to annotations	blob \| commitdiff \| diff to current
2017-06-27	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-06-26	gmungoc	JAL-1858 ensure full redraw on 'remove all selections'	blob \| commitdiff \| diff to current
2017-06-23	TZVanaalten	add HMMER colour scheme	blob \| commitdiff \| diff to current
2017-06-22	TZVanaalten	fully integrate HMMER3 file format into Jalview	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2592 distinguish "User Defined" (scheme name) from... bug/JAL-2592userDefinedScheme	blob \| commitdiff \| diff to current
2017-06-08	kiramt	JAL-2591 Refactor HiddenColumns to use ArrayList instea...	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 Further refactoring (still incomplete)	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 More refactoring (incomplete)	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 More rationalising of hiddencols	blob \| commitdiff \| diff to current
2017-06-07	kiramt	JAL-2591 simplifying hidden columns usage	blob \| commitdiff \| diff to current
2017-05-29	Jim Procter	Merge branch 'bug/JAL-2536' into develop	blob \| commitdiff \| diff to current
2017-05-16	kiramt	JAL-2536 Overview window sizing not subject to min... bug/JAL-2536	blob \| commitdiff \| diff to current
2017-05-15	kiramt	Merge remote-tracking branch 'origin/develop' into...	blob \| commitdiff \| diff to current
2017-05-12	Jim Procter	Merge branch 'features/JAL-2388OverviewWindow' into...	blob \| commitdiff \| diff to current
2017-05-11	kiramt	JAL-2491 Unit tests and updates	blob \| commitdiff \| diff to current
2017-05-08	gmungoc	JAL-1632 i18n for warning messages	blob \| commitdiff \| diff to current
2017-05-08	kiramt	JAL-2491 Started moving other scrolling fns into viewpo...	blob \| commitdiff \| diff to current
2017-05-05	kiramt	Merge remote-tracking branch	blob \| commitdiff \| diff to current
2017-05-05	kiramt	Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges	blob \| commitdiff \| diff to current
2017-05-02	gmungoc	JAL-2499 JAL-2403 push 'configure for view' inside...	blob \| commitdiff \| diff to current
2017-04-25	kiramt	JAL-2388 Working hidden regions hide/show in desktop	blob \| commitdiff \| diff to current
2017-04-24	kiramt	JAL-2388 Hidden cols separated from column selection...	blob \| commitdiff \| diff to current
2017-04-12	gmungoc	JAL-1632 removed check for aligned sequences for Tree...	blob \| commitdiff \| diff to current
2017-04-12	gmungoc	JAL-1632 one PCA/Tree per panel, closed when panel...	blob \| commitdiff \| diff to current
2017-04-07	gmungoc	Merge branch 'develop' into features/JAL-2393customMatrices	blob \| commitdiff \| diff to current
2017-04-05	gmungoc	JAL-2361 simplify constructors, select unsaved but...	blob \| commitdiff \| diff to current
2017-03-31	gmungoc	Merge branch 'develop' into bug/JAL-2431splitFrameNewView bug/JAL-2431splitFrameNewView	blob \| commitdiff \| diff to current
2017-03-30	gmungoc	JAL-1608 leave Create Group, Remove Group menu items...	blob \| commitdiff \| diff to current
2017-03-29	gmungoc	Merge branch 'develop' into bug/JAL-1608createGroups	blob \| commitdiff \| diff to current
2017-03-24	gmungoc	JAL-1632 TreeChooser renamed CalculationChooser, text...	blob \| commitdiff \| diff to current
2017-03-24	gmungoc	JAL-838 move two callers off Comparison.PID and depreca...	blob \| commitdiff \| diff to current
2017-03-23	gmungoc	Merge branch 'develop' into features/JAL-2393customMatrices	blob \| commitdiff \| diff to current
2017-03-16	kiramt	JAL-2388 Applied ViewportRanges to code	blob \| commitdiff \| diff to current
2017-03-15	gmungoc	JAL-2431 show cDNA consensus after New View in split...	blob \| commitdiff \| diff to current
2017-02-27	kiramt	JAL-2388 Make startRes,startSeq,endRes,endSeq private...	blob \| commitdiff \| diff to current
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