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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
2017-08-14 TZVanaaltenJAL-2629 fix expected length error for hmmbuild by... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 add padding for .sto annotations to fix issues... commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2335 choose appropriate alphabet for filtering... commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2335 source formatting commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2335 filterNonStandardResidues configurable for... commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 remove redundant options from HMMER menu commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 add validation for HMMER path commit | commitdiff | tree | snapshot
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterMerge branch 'patch/JAL-2116_java9' into develop commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterMerge branch 'patch/JAL-2116_java9' into releases/Relea... commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2116 switch to java.se.ee https://bugs.openjdk... 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 ProcterMerge branch 'patch/JAL-2663_filterAACons' into develop commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2663 flag and filter to exclude non-standard amino... commit | commitdiff | tree | snapshot
2017-08-14 Jim ProcterJAL-2663 source formatting commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 fix issue where trim termini setting would... commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 hmmalign can now be run from the sequence... commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 add force alphabet type for HMMER commands commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too... commit | commitdiff | tree | snapshot
2017-08-13 TZVanaaltenJAL-2629 add HMMER tab in preferences menu commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2629 delete unnecessary buffer files for hmmer... commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2629 add ability to select HMMs commit | commitdiff | tree | snapshot
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop commit | commitdiff | tree | snapshot
2017-08-10 Jim ProcterMerge branch 'patch/JAL-2116_java9' into releases/Relea... commit | commitdiff | tree | snapshot
2017-08-10 Jim ProcterJAL-2116 try '=' syntax jigsaw-dev.1059479.n5.nabble... commit | commitdiff | tree | snapshot
2017-08-10 Jim ProcterMerge branch 'patch/JAL-2116_java9' into releases/Relea... commit | commitdiff | tree | snapshot
2017-08-10 Jim ProcterJAL-2116 test java 9 only JNLP launch commit | commitdiff | tree | snapshot
2017-08-10 Jim ProcterMerge branch 'patch/JAL-2116_java9' into releases/Relea... commit | commitdiff | tree | snapshot
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