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jalview.git
2018-02-19 gmungocJAL-2629 partial refactoring of Hmmer command classes commit | commitdiff | tree | snapshot
2018-02-19 gmungocJAL-2629 formatting only commit | commitdiff | tree | snapshot
2017-09-01 TZVanaaltenJAL-2629 fix hmmbuild failing due to RF longer than... features/hmmer commit | commitdiff | tree | snapshot
2017-09-01 TZVanaaltenJAL-2629 fix hmmbuild validation failing if no AlignFra... commit | commitdiff | tree | snapshot
2017-09-01 TZVanaaltenJAL-2629 manual curation of HMMs via reference annotati... commit | commitdiff | tree | snapshot
2017-08-30 TZVanaaltenJAL-2616 HMM-Family alignments can now be filtered... commit | commitdiff | tree | snapshot
2017-08-30 TZVanaaltenJAL-2629 fix issue where HMM sequence would be longer... commit | commitdiff | tree | snapshot
2017-08-30 TZVanaaltenJAL-2629 for multi-job hmmbuilds, group names are now... commit | commitdiff | tree | snapshot
2017-08-29 osboxesJAL-2629 fix incorrect mapping between HMM and columns... commit | commitdiff | tree | snapshot
2017-08-29 osboxesJAL-2629 HMMs dropped on the alignment now map to the... commit | commitdiff | tree | snapshot
2017-08-28 tzvanaaltenJAL-2629 add option to set HMM Logo letter height to... commit | commitdiff | tree | snapshot
2017-08-28 TZVanaaltenJAL-2629 add StringParameter commit | commitdiff | tree | snapshot
2017-08-28 TZVanaaltenJAL-2629 fix HMMER validation fail due to checking... commit | commitdiff | tree | snapshot
2017-08-28 TZVanaaltenJAL-2629 fix issue where HMM would not be added to... commit | commitdiff | tree | snapshot
2017-08-28 TZVanaaltenJAL-2629 HMMER alignment background colour scheme is... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 hmmsearch now adds the E-value as an annotation commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 hmmbuild runs on the alignment by default commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAl-2629 add new HMMER colour scheme class commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 hmm annotation consensus characters are now... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 fix for hmmbuild failing due to whitespace... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenRevert "jal-2629 fix for hmmbuild failing due to whites... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenjal-2629 fix for hmmbuild failing due to whitespace... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 adjust log parameter slightly and reduce granu... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 fix issue where Stockholm file would print... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 hmmsearch no longer throws an error if no... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 adjust parameter min and max to better suit... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 hmmsearch/build/align no longer run after... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 fix for NPE caused by incorrect initiation... commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 hmmsearch now works for different databases commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 add ability to add and select a DB for hmmsearch commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 remove sequence and group HMMER options commit | commitdiff | tree | snapshot
2017-08-25 TZVanaaltenJAL-2629 add basic parameter adjustment to hmmsearch... commit | commitdiff | tree | snapshot
2017-08-23 tzvanaaltenJAL-2629 selected HMM is now a sequence, not a HMM commit | commitdiff | tree | snapshot
2017-08-23 tzvanaaltenJAL-2629 fix for addHMMConsensus failing if no HMM... commit | commitdiff | tree | snapshot
2017-08-23 tzvanaaltenJAL-2629 add logarithmic parameter for logarithmic... commit | commitdiff | tree | snapshot
2017-08-22 TZVanaaltenJAL-2629 add hmmsearch class commit | commitdiff | tree | snapshot
2017-08-21 TZVanaaltenMerge remote-tracking branch 'origin/releases/Release_2... commit | commitdiff | tree | snapshot
2017-08-21 TZVanaaltenMerge remote-tracking branch 'origin/releases/Release_2... commit | commitdiff | tree | snapshot
2017-08-21 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1... commit | commitdiff | tree | snapshot
2017-08-21 Jim ProcterJAL-2675 typo in what's new href commit | commitdiff | tree | snapshot
2017-08-21 TZVanaaltenJAL-2668 fix failing tests caused by HMMER-related... commit | commitdiff | tree | snapshot
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer commit | commitdiff | tree | snapshot
2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io commit | commitdiff | tree | snapshot
2017-08-18 TZVanaaltenJAL-2668 HMMFile export method moved to print method commit | commitdiff | tree | snapshot
2017-08-18 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-18 Jim ProcterJAL-2675 bump version for branch to 2.10.2b1 commit | commitdiff | tree | snapshot
2017-08-18 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-18 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2017-08-18 Jim ProcterJAL-2675 release notes entry for 2.10.2b1, updated... commit | commitdiff | tree | snapshot
2017-08-17 TZVanaaltenJAL-2599 move fillSymbol method to HMFile commit | commitdiff | tree | snapshot
2017-08-17 Jim ProcterJAL-2418 ahem - correct year for what's new releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-17 Jim ProcterJAL-2418 JAL-2116 use single j2se 7+ argumant with... commit | commitdiff | tree | snapshot
2017-08-17 Jim ProcterJAL-2418 JAL-2116 make sure java 8,7 vm args are also... commit | commitdiff | tree | snapshot
2017-08-17 TZVanaaltenJAL-2599 some slight renaming of variables and methods commit | commitdiff | tree | snapshot
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 formatting commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 occupancy row in What’s New commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 mirror fonts option doc tweak commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 whats new for 2.10.2 commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 reclassify some issues to features/bugs resolved commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 typos in release notes commit | commitdiff | tree | snapshot
2017-08-16 Jim ProcterJAL-2418 check groovy script one-liners for restoring... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2599 HMM annotation now shows consensus characters... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2599 fix background frequency storage and correct... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2629 fix for hmmbuild not loading a HMM onto the... commit | commitdiff | tree | snapshot
2017-08-16 TZVanaaltenJAL-2629 add hmmbuild validation check which also gets... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 prevent hmmbuild from running if there are... commit | commitdiff | tree | snapshot
2017-08-15 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-15 Jim ProcterJAL-2116 fix typo in build.xml for j2se element commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 configure file chooser to select either a... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 add checks for executing hmmer commands as... commit | commitdiff | tree | snapshot
2017-08-15 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-15 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-08-15 tzvanaaltenJAL-2629 fix file loading issues on Mac commit | commitdiff | tree | snapshot
2017-08-15 Jim ProcterJAL-2418 bump release to Thursday commit | commitdiff | tree | snapshot
2017-08-15 Jim ProcterMerge branch 'develop' into documentation/JAL-2418_rele... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 add HMMER version check commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 exported HMMs are now named correctly commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 fix uniquified sequence names appearing when... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2599 fix HMMER scheme not colouring inserts and... commit | commitdiff | tree | snapshot
2017-08-15 TZVanaaltenJAL-2629 the HMMER tab is now disabled when HMMER is... commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterMerge branch 'develop' into releases/Release_2_10_2_Branch commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2418 release notes for JAL-2663 commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterMerge branch 'patch/JAL-2335_filterAACons' into develop commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterMerge branch 'patch/JAL-2116_java9' into develop commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2116 add 1.8 1.7 compatible launch string commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 remove annotation when exporting for hmmbuild commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 remove gap padding, and now has option to... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment commit | commitdiff | tree | snapshot
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