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

2018-05-15	gmungoc	JAL-1264 exclude score-only from 'Add Reference Annotat...	blob \| commitdiff
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
2018-04-24	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	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
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
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