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