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Merge branch 'develop' into features/mchmmer
[jalview.git] / src / jalview / gui / AlignFrame.java
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer blob | commitdiff
2018-02-19 gmungocJAL-2629 refactoring of Hmmer preferences blob | commitdiff | diff to current
2018-01-10 gmungocJAL-1793 update spike branch to latest blob | commitdiff | diff to current
2017-12-08 gmungocJAL-2843 refactor / tidy for feature filter input/output blob | commitdiff | diff to current
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere... blob | commitdiff | diff to current
2017-10-27 gmungocJAL-1793 spike branch updated to latest blob | commitdiff | diff to current
2017-10-27 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop blob | commitdiff | diff to current
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2727closeAllFreeMemory' into... blob | commitdiff | diff to current
2017-10-24 gmungocJAL-2738 update spike branch with latest blob | commitdiff | diff to current
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... blob | commitdiff | diff to current
2017-10-20 gmungocPush 1793 latest to spike branch blob | commitdiff | diff to current
2017-10-19 gmungocJAL-2755 find gene loci for fetched xrefs where possible blob | commitdiff | diff to current
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes blob | commitdiff | diff to current
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence blob | commitdiff | diff to current
2017-09-12 gmungocJAL-2727 ensure ViewportRanges (and gapcounts) are... blob | commitdiff | diff to current
2017-09-01 gmungocJAL-2488 remove finalize methods blob | commitdiff | diff to current
2017-08-29 Jim ProcterJAL-2698 spawn a thread to test for and raise auto... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 hmmsearch/build/align no longer run after... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add ability to add and select a DB for hmmsearch blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add basic parameter adjustment to hmmsearch... blob | commitdiff | diff to current
2017-08-23 tzvanaaltenJAL-2629 selected HMM is now a sequence, not a HMM blob | commitdiff | diff to current
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer blob | commitdiff | diff to current
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu blob | commitdiff | diff to current
2017-08-15 TZVanaaltenJAL-2629 the HMMER tab is now disabled when HMMER is... blob | commitdiff | diff to current
2017-08-14 TZVanaaltenJAL-2629 remove redundant options from HMMER menu blob | commitdiff | diff to current
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop blob | commitdiff | diff to current
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame blob | commitdiff | diff to current
2017-08-10 tzvanaaltenJAL-2629 fix files permission issue on Mac blob | commitdiff | diff to current
2017-08-09 TZVanaaltenJAL-2599 fix for issue where info annot would not display blob | commitdiff | diff to current
2017-08-09 tzvanaaltenJAL-2599 fix for issue where info annot would not display blob | commitdiff | diff to current
2017-08-09 TZVanaaltenJAL-2629 removed unnecessary exception throws from... blob | commitdiff | diff to current
2017-08-09 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-08 TZVanaaltenJAL-2629 add ability to select hmmer binaries folder blob | commitdiff | diff to current
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in... blob | commitdiff | diff to current
2017-08-07 Jim ProcterMerge branch 'bug/JAL-2592userDefinedScheme' into develop blob | commitdiff | diff to current
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment blob | commitdiff | diff to current
2017-08-02 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons blob | commitdiff | diff to current
2017-07-31 TZVanaaltenJAL-2629 add hmmalign command blob | commitdiff | diff to current
2017-07-28 kiramtJAL-2632 Added paintAlignment(true) to show cols code blob | commitdiff | diff to current
2017-07-27 TZVanaaltenJAL-2629 implement hmmbuild blob | commitdiff | diff to current
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... blob | commitdiff | diff to current
2017-07-25 TZVanaaltenJAL-2629 add non-functional HMMER menu blob | commitdiff | diff to current
2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not... blob | commitdiff | diff to current
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 blob | commitdiff | diff to current
2017-07-20 TZVanaaltenJAL-2616 remove statistical analysis from AlignFrame blob | commitdiff | diff to current
2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files blob | commitdiff | diff to current
2017-07-19 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics... features/hmmer_statistics blob | commitdiff | diff to current
2017-07-12 TZVanaaltentest HMM annotaTION blob | commitdiff | diff to current
2017-07-04 gmungocJAL-147 remove redundant calls to update overview panel blob | commitdiff | diff to current
2017-07-04 gmungocJAL-2608 tidy up OverviewPanel when closed blob | commitdiff | diff to current
2017-06-29 gmungocJAL-147 improved wrapped scrolling (including Overview... blob | commitdiff | diff to current
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations blob | commitdiff | diff to current
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-06-26 gmungocJAL-1858 ensure full redraw on 'remove all selections' blob | commitdiff | diff to current
2017-06-23 TZVanaaltenadd HMMER colour scheme blob | commitdiff | diff to current
2017-06-22 TZVanaaltenfully integrate HMMER3 file format into Jalview blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2592 distinguish "User Defined" (scheme name) from... bug/JAL-2592userDefinedScheme blob | commitdiff | diff to current
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea... blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 Further refactoring (still incomplete) blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 More refactoring (incomplete) blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 More rationalising of hiddencols blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage blob | commitdiff | diff to current
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2536' into develop blob | commitdiff | diff to current
2017-05-16 kiramtJAL-2536 Overview window sizing not subject to min... bug/JAL-2536 blob | commitdiff | diff to current
2017-05-15 kiramtMerge remote-tracking branch 'origin/develop' into... blob | commitdiff | diff to current
2017-05-12 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... blob | commitdiff | diff to current
2017-05-11 kiramtJAL-2491 Unit tests and updates blob | commitdiff | diff to current
2017-05-08 gmungocJAL-1632 i18n for warning messages blob | commitdiff | diff to current
2017-05-08 kiramtJAL-2491 Started moving other scrolling fns into viewpo... blob | commitdiff | diff to current
2017-05-05 kiramtMerge remote-tracking branch blob | commitdiff | diff to current
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges blob | commitdiff | diff to current
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside... blob | commitdiff | diff to current
2017-04-25 kiramtJAL-2388 Working hidden regions hide/show in desktop blob | commitdiff | diff to current
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... blob | commitdiff | diff to current
2017-04-12 gmungocJAL-1632 removed check for aligned sequences for Tree... blob | commitdiff | diff to current
2017-04-12 gmungocJAL-1632 one PCA/Tree per panel, closed when panel... blob | commitdiff | diff to current
2017-04-07 gmungocMerge branch 'develop' into features/JAL-2393customMatrices blob | commitdiff | diff to current
2017-04-05 gmungocJAL-2361 simplify constructors, select unsaved but... blob | commitdiff | diff to current
2017-03-31 gmungocMerge branch 'develop' into bug/JAL-2431splitFrameNewView bug/JAL-2431splitFrameNewView blob | commitdiff | diff to current
2017-03-30 gmungocJAL-1608 leave Create Group, Remove Group menu items... blob | commitdiff | diff to current
2017-03-29 gmungocMerge branch 'develop' into bug/JAL-1608createGroups blob | commitdiff | diff to current
2017-03-24 gmungocJAL-1632 TreeChooser renamed CalculationChooser, text... blob | commitdiff | diff to current
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... blob | commitdiff | diff to current
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices blob | commitdiff | diff to current
2017-03-16 kiramtJAL-2388 Applied ViewportRanges to code blob | commitdiff | diff to current
2017-03-15 gmungocJAL-2431 show cDNA consensus after New View in split... blob | commitdiff | diff to current
2017-02-27 kiramtJAL-2388 Make startRes,startSeq,endRes,endSeq private... blob | commitdiff | diff to current
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... blob | commitdiff | diff to current
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