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JAL-3690 Let's enable web services (seriously this time)
[jalview.git] / src / jalview / hmmer /
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... tree | commitdiff
2019-07-12 ThomasJAL-2629 can now choose number of jackhmmer iterations merge/JAL-3285_mchmmer_with_211_develop tree | commitdiff
2019-07-12 ThomasJAL-2629 fix faulty label in a MessageManager.getString... tree | commitdiff
2019-07-12 ThomasJAL-2629 hmmer searches now read domain rather than... tree | commitdiff
2019-07-11 ThomasJAL-2629 hmmer searches include seqs past inclusion... tree | commitdiff
2019-07-11 ThomasJAL-2629 hmm search UI and structural improvements... tree | commitdiff
2019-07-10 tvaJAL-2629 fix hmmsearch/jackhmmer assigning incorrect... tree | commitdiff
2019-07-10 tvaJAL-2629 fix hmsearch and jackhmmer not being able... tree | commitdiff
2019-07-10 tvaJAL-2629 hmmsearch # of new sequences now only displaye... tree | commitdiff
2019-07-10 tvaJAL-2629 fix incorrect hmmbuild on groups behaviour tree | commitdiff
2019-07-10 tvaJAL-2629 fix hmmsearch/jackhmmer being unable to search... tree | commitdiff
2019-07-05 tvaJAL-2629 uniquify all hmmer command sequence outputs tree | commitdiff
2019-07-05 tvaJAL-2629 fix file format issues preventing hmmsearch... tree | commitdiff
2019-07-03 tvaJAL-2629 fix search scores being read in incorrectly tree | commitdiff
2019-07-03 tvaJAL-2629 fix hmm on alignment being deleted upon runnin... tree | commitdiff
2019-07-03 tvaJAL-2629 can now filter by sequence e-value or bit... tree | commitdiff
2019-07-02 tvaJAL-2629 add simple jackhmmer functionality tree | commitdiff
2019-06-28 tvaJAL-3336 add better method of determining where data... tree | commitdiff
2019-06-28 tvaJAL-3336 fix hmmsearch failing when parsing score table tree | commitdiff
2019-06-28 tvaJAL-2629 add HMM Match Score colour scheme tree | commitdiff
2019-06-10 tvaJAL-3297 pad gaps in alignment to ensure hmmalign runs tree | commitdiff
2019-06-06 tvaJAL-3285 fix incorrect file paths on HMMAlign/Search... tree | commitdiff
2019-06-06 tvaJAL-3285 add Cygwin environment path fix for Windows tree | commitdiff
2019-06-05 tvaJAL-3285 method call change to HMMBuild not included... tree | commitdiff
2018-07-18 Jim ProcterMerge branch 'features/mchmmer' into features/mchmmer_m... features/mchmmer_merge_JAL-1950 tree | commitdiff
2018-06-06 gmungocJAL-3013 resolve symlink to hmmer binaries folder features/mchmmer tree | commitdiff
2018-06-01 Jim ProcterJAL-3012 JAL-2937 TODO avoid creating data copies by... tree | commitdiff
2018-06-01 Jim ProcterJAL-2937 hmmbuild input data generated via AlignmentVie... tree | commitdiff
2018-05-31 Jim ProcterJAL-1950 JAL-2629 insert gaps into HMM used to search... tree | commitdiff
2018-05-31 Jim ProcterJAL-2629 (probably not right issue) JAL-1950 - make... tree | commitdiff
2018-05-31 Jim ProcterJAL-3011 JAL-2719 JAL-1958 add posterior probability... tree | commitdiff
2018-05-30 gmungocJAL-3005 JAL-2629 file chooser argument for HMM search... tree | commitdiff
2018-05-22 gmungocJAL-2629 method refactor and menu tidying tree | commitdiff
2018-05-15 gmungocJAL-2719 parse bit score annotation from search results tree | commitdiff
2018-05-15 gmungocJAL-2629 JAL-2937 respect 'align automatically' option... tree | commitdiff
2018-05-14 gmungocJAL-2711 show short file names in search database combo box tree | commitdiff
2018-05-10 gmungocJAL-2629 revert to showing Profile parameter even if... tree | commitdiff
2018-05-10 gmungocJAL-2629 default HMMBuild to alignment if not specified... tree | commitdiff
2018-05-10 gmungocJAL-2629 adjust placement and optionality of arguments... tree | commitdiff
2018-05-09 gmungocJAL-2714 HMMSearch cutoff by E-Value, Score or None tree | commitdiff
2018-04-20 gmungocJAL-591 slider scale factor now derived from min-max... tree | commitdiff
2018-04-18 gmungocJAL-2629 corrected cutoff parameter passing to hmmsearch tree | commitdiff
2018-04-17 gmungocMerge branch 'features/mchmmer' of https://source.jalvi... tree | commitdiff
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not... tree | commitdiff
2018-04-17 Mungo CarstairsJAL-2937 working Cygwin bash execution of hmmbuild... tree | commitdiff
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... tree | commitdiff
2018-04-16 gmungocJAL-2937 use preferences for presets, simplify some... tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2937 Cygwin path preference, method refactoring tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2629 more error checking tree | commitdiff
2018-03-30 gmungocJAL-2629 tidy code, factory methods for param sets tree | commitdiff
2018-03-30 gmungocJAL-2629 use correct gap character, revised deletion... tree | commitdiff
2018-03-30 gmungocJAL-2629 Javadoc updates tree | commitdiff
2018-03-30 gmungocJAL-2629 ensure hmm consensus sequence set on alignment... tree | commitdiff
2018-03-30 gmungocJAL-2629 add title to output alignment window tree | commitdiff
2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo tree | commitdiff
2018-03-23 gmungocJAL-2629 pad gaps when exporting alignment as 'database... tree | commitdiff
2018-03-21 gmungocJAL-2629 tweaks to Information annotation updating tree | commitdiff
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and... tree | commitdiff
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... tree | commitdiff
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) tree | commitdiff
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display... tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly tree | commitdiff
2018-02-21 gmungocJAL-2629 simplifying method signatures in Hmmer command... tree | commitdiff
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and... tree | commitdiff
2018-02-19 gmungocJAL-2629 partial refactoring of Hmmer command classes tree | commitdiff
2018-02-19 gmungocJAL-2629 formatting only tree | commitdiff
2017-09-01 TZVanaaltenJAL-2629 fix hmmbuild failing due to RF longer than... features/hmmer tree | commitdiff
2017-09-01 TZVanaaltenJAL-2629 manual curation of HMMs via reference annotati... tree | commitdiff
2017-08-30 TZVanaaltenJAL-2629 fix issue where HMM sequence would be longer... tree | commitdiff
2017-08-30 TZVanaaltenJAL-2629 for multi-job hmmbuilds, group names are now... tree | commitdiff
2017-08-28 TZVanaaltenJAL-2629 HMMER alignment background colour scheme is... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 hmmsearch now adds the E-value as an annotation tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 hmmbuild runs on the alignment by default tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 fix for hmmbuild failing due to whitespace... tree | commitdiff
2017-08-25 TZVanaaltenRevert "jal-2629 fix for hmmbuild failing due to whites... tree | commitdiff
2017-08-25 TZVanaaltenjal-2629 fix for hmmbuild failing due to whitespace... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 adjust log parameter slightly and reduce granu... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 hmmsearch no longer throws an error if no... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 adjust parameter min and max to better suit... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 fix for NPE caused by incorrect initiation... tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 hmmsearch now works for different databases tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 add ability to add and select a DB for hmmsearch tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 add basic parameter adjustment to hmmsearch... tree | commitdiff
2017-08-23 tzvanaaltenJAL-2629 fix for addHMMConsensus failing if no HMM... tree | commitdiff
2017-08-22 TZVanaaltenJAL-2629 add hmmsearch class tree | commitdiff
2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io tree | commitdiff
2017-08-18 TZVanaaltenJAL-2668 HMMFile export method moved to print method tree | commitdiff
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work tree | commitdiff
2017-08-16 TZVanaaltenJAL-2629 fix for hmmbuild not loading a HMM onto the... tree | commitdiff
2017-08-16 TZVanaaltenJAL-2629 add hmmbuild validation check which also gets... tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 prevent hmmbuild from running if there are... tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 add checks for executing hmmer commands as... tree | commitdiff
2017-08-15 tzvanaaltenJAL-2629 fix file loading issues on Mac tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 add HMMER version check tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 exported HMMs are now named correctly tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 fix uniquified sequence names appearing when... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 remove annotation when exporting for hmmbuild tree | commitdiff
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