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

2019-07-12	Thomas	JAL-2629 add sort by evalue and bit score	blob \| commitdiff
2019-07-10	tva	JAL-2629 fix incorrect hmmbuild on groups behaviour	blob \| commitdiff \| diff to current
2019-07-03	tva	JAL-2629 can now filter by sequence e-value or bit...	blob \| commitdiff \| diff to current
2019-07-02	tva	JAL-2629 add simple jackhmmer functionality	blob \| commitdiff \| diff to current
2019-06-04	Jim Procter	Merge branch 'develop' into developtomchmmer	blob \| commitdiff \| diff to current
2019-05-28	Ben Soares	JAL-1988 Some TEST code accidentally left in now remove...	blob \| commitdiff \| diff to current
2019-04-11	Jim Procter	Merge branch 'develop' into task/JAL-3130_Java_11_inves...	blob \| commitdiff \| diff to current
2019-03-23	gmungoc	JAL-1889 explicit recalc of geometry for scale left... bug/JAL-1889serverTestSuite	blob \| commitdiff \| diff to current
2019-03-20	Ben Soares	JAL-3130 Lots of deprecation fixes. See utils/deprecat...	blob \| commitdiff \| diff to current
2019-03-20	gmungoc	JAL-3093 fine tuning of SeqPanel tooltip	blob \| commitdiff \| diff to current
2019-03-19	Ben Soares	JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben...	blob \| commitdiff \| diff to current
2019-03-11	gmungoc	Merge branch 'feature/JAL-3127_seqidChainshading' into...	blob \| commitdiff \| diff to current
2019-03-07	gmungoc	Merge branch 'feature/JAL-3180colourAnnotationMenu...	blob \| commitdiff \| diff to current
2019-03-07	gmungoc	JAL-2250 default Apply Colour to All Groups selected	blob \| commitdiff \| diff to current
2019-03-05	gmungoc	Merge remote-tracking branch 'origin/features/JAL-2620a...	blob \| commitdiff \| diff to current
2019-03-04	gmungoc	Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...	blob \| commitdiff \| diff to current
2019-03-01	gmungoc	Merge branch 'feature/JAL-3093wrappedModeTooltips'...	blob \| commitdiff \| diff to current
2019-03-01	gmungoc	Merge branch 'bug/JAL-3158selectionBroadcasts' into...	blob \| commitdiff \| diff to current
2019-02-28	gmungoc	Merge remote-tracking branch 'origin/feature/JAL-3141_b...	blob \| commitdiff \| diff to current
2019-02-28	Jim Procter	Merge branch 'feature/JAL-3141_backupfiles_for211'... merge/develop_feature/JAL-3141_backupfiles_for211	blob \| commitdiff \| diff to current
2019-02-24	gmungoc	JAL-3198 SequenceGroup 'bulk constructor' without dupli...	blob \| commitdiff \| diff to current
2019-02-22	gmungoc	JAL-2915 don't recalculate Overview on scroll to positi...	blob \| commitdiff \| diff to current
2019-01-18	Jim Procter	Merge branch 'feature/JAL-3063jaxbNoCastor' into featur...	blob \| commitdiff \| diff to current
2019-01-04	gmungoc	JAL-3180 fix By Annotation selection state in colour...	blob \| commitdiff \| diff to current
2018-12-14	Ben Soares	JAL-3130 single class testing on CLI with ant [ -Dclass...	blob \| commitdiff \| diff to current
2018-12-06	Ben Soares	JAL-3130 incorporating feature/JAL-3063jaxbNoCastor...	blob \| commitdiff \| diff to current
2018-11-28	gmungoc	JAL-3158 additional calls to reset 'selection changed... bug/JAL-3158selectionBroadcasts	blob \| commitdiff \| diff to current
2018-11-05	Ben Soares	JAL-1988 Investigating...	blob \| commitdiff \| diff to current
2018-10-25	Ben Soares	JAL-3141 Ostensibly all backups working for alignment...	blob \| commitdiff \| diff to current
2018-10-16	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	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
2018-05-28	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
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
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