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JAL-2629 fix issue where Stockholm file would print two terminators
[jalview.git] / src /
2017-08-25 TZVanaaltenJAL-2629 fix issue where Stockholm file would print... 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 hmmsearch/build/align no longer run after... 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 remove sequence and group HMMER options tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 add basic parameter adjustment to hmmsearch... tree | commitdiff
2017-08-23 tzvanaaltenJAL-2629 selected HMM is now a sequence, not a HMM tree | commitdiff
2017-08-23 tzvanaaltenJAL-2629 fix for addHMMConsensus failing if no HMM... tree | commitdiff
2017-08-23 tzvanaaltenJAL-2629 add logarithmic parameter for logarithmic... tree | commitdiff
2017-08-22 TZVanaaltenJAL-2629 add hmmsearch class tree | commitdiff
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer 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-2599 move fillSymbol method to HMFile tree | commitdiff
2017-08-17 TZVanaaltenJAL-2599 some slight renaming of variables and methods tree | commitdiff
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-08-16 TZVanaaltenJAL-2599 HMM annotation now shows consensus characters... tree | commitdiff
2017-08-16 TZVanaaltenJAL-2599 fix background frequency storage and correct... 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 configure file chooser to select either a... 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
2017-08-15 TZVanaaltenJAL-2599 fix HMMER scheme not colouring inserts and... tree | commitdiff
2017-08-15 TZVanaaltenJAL-2629 the HMMER tab is now disabled when HMMER is... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 remove annotation when exporting for hmmbuild tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 remove gap padding, and now has option to... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 add insert sequence at method on alignment tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 fix expected length error for hmmbuild by... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 add padding for .sto annotations to fix issues... tree | commitdiff
2017-08-14 Jim ProcterJAL-2335 choose appropriate alphabet for filtering... tree | commitdiff
2017-08-14 Jim ProcterJAL-2335 source formatting tree | commitdiff
2017-08-14 Jim ProcterJAL-2335 filterNonStandardResidues configurable for... tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 remove redundant options from HMMER menu tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 add validation for HMMER path tree | commitdiff
2017-08-14 TZVanaaltenJAL-2629 fix incorrect gap insertions on HMM sequence tree | commitdiff
2017-08-14 Jim ProcterMerge branch 'patch/JAL-2663_filterAACons' into develop tree | commitdiff
2017-08-14 Jim ProcterJAL-2663 flag and filter to exclude non-standard amino... tree | commitdiff
2017-08-14 Jim ProcterJAL-2663 source formatting tree | commitdiff
2017-08-13 TZVanaaltenJAL-2629 fix issue where trim termini setting would... tree | commitdiff
2017-08-13 TZVanaaltenJAL-2629 hmmalign can now be run from the sequence... tree | commitdiff
2017-08-13 TZVanaaltenJAL-2629 add force alphabet type for HMMER commands tree | commitdiff
2017-08-13 TZVanaaltenJAL-2629 fix issue where HMM sequences would be too... tree | commitdiff
2017-08-13 TZVanaaltenJAL-2629 add HMMER tab in preferences menu tree | commitdiff
2017-08-11 TZVanaaltenJAL-2629 delete unnecessary buffer files for hmmer... tree | commitdiff
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group tree | commitdiff
2017-08-11 TZVanaaltenJAL-2629 add ability to select HMMs tree | commitdiff
2017-08-11 TZVanaaltenJAL-2599 HMMs can now be dropped onto the desktop tree | commitdiff
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame tree | commitdiff
2017-08-10 gmungocJAL-2660 used saved value of ignoreGapsInConsensus... tree | commitdiff
2017-08-10 tzvanaaltenMerge branch 'features/hmmer' of https://source.jalview... tree | commitdiff
2017-08-10 tzvanaaltenJAL-2629 fix files permission issue on Mac tree | commitdiff
2017-08-09 Jim ProcterJAL-2426 Rfam download suffix tree | commitdiff
2017-08-09 Jim ProcterJAL-2426 JAL-1270 report Xfam download URL used if... tree | commitdiff
2017-08-09 Jim ProcterJAL-2425 raw stockholm download URLs tree | commitdiff
2017-08-09 Jim ProcterJAL-2425 remove overloaded getSequenceRecords method... tree | commitdiff
2017-08-09 TZVanaaltenJAL-2599 fix for issue where info annot would not display tree | commitdiff
2017-08-09 tzvanaaltenJAL-2599 fix for issue where info annot would not display tree | commitdiff
2017-08-09 TZVanaaltenJAL-2629 buffers are now temporary files tree | commitdiff
2017-08-09 TZVanaaltenJAL-2629 removed unnecessary exception throws from... tree | commitdiff
2017-08-09 Jim ProcterMerge branch 'bug/JAL-2634' into develop tree | commitdiff
2017-08-09 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... tree | commitdiff
2017-08-08 TZVanaaltenJAL-2616 fix allowing clan sorting to work tree | commitdiff
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup tree | commitdiff
2017-08-08 TZVanaaltenJAL-2629 add ability to select hmmer binaries folder tree | commitdiff
2017-08-08 gmungocJAL-2560 alternative fix (reinstate lost line of code) tree | commitdiff
2017-08-08 gmungocJAL-2649 JAL-2650 wait for Conservation calc to complet... tree | commitdiff
2017-08-08 gmungocJAL-2650 configure new viewport settings before selecti... tree | commitdiff
2017-08-07 TZVanaaltenJAL-2629 fixed hmmalign failing due to differing sequen... tree | commitdiff
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in... tree | commitdiff
2017-08-07 Jim ProcterMerge branch 'bug/JAL-2592userDefinedScheme' into develop tree | commitdiff
2017-08-04 TZVanaaltenJAL-2599 fixed information annotation buttons not working tree | commitdiff
2017-08-04 TZVanaaltenJAL-2629 hmmbuild now runs on alignments of different... tree | commitdiff
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment tree | commitdiff
2017-08-03 gmungocJAL-2435 test for 'mirror font' option visible (not... tree | commitdiff
2017-08-02 TZVanaaltenJAL-2599 fix for HMM logo not normalising correctly tree | commitdiff
2017-08-02 TZVanaaltenJAL-2599 fix issue where parser exported map annotation... tree | commitdiff
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons tree | commitdiff
2017-08-01 Jim ProcterMerge branch 'bug/JAL-2632' into develop tree | commitdiff
2017-08-01 gmungocJAL-2611 reinstate missed merge - again! tree | commitdiff
2017-08-01 gmungocMerge branch 'feature/JAL-2611' into develop tree | commitdiff
2017-08-01 gmungocMerge branch 'bug/JAL-2630gradColourUpdateOverview... tree | commitdiff
2017-07-31 TZVanaaltenJAL-2629 add hmmalign command tree | commitdiff
2017-07-31 kiramtJAL-2634 Make overview box full height when alignment... bug/JAL-2634 tree | commitdiff
2017-07-31 gmungocJAL-2623 updated Overview/structure on input of thresho... bug/JAL-2630gradColourUpdateOverview tree | commitdiff
2017-07-31 kiramtJAL-2634 Added null test for graphics in AnnotationPane... tree | commitdiff
2017-07-31 gmungocJAL-2622 don't vertical scroll wrapped alignment id... tree | commitdiff
2017-07-31 gmungocJAL-2623 JAL-2015 set Below Threshold on FeatureColour... tree | commitdiff
2017-07-31 gmungocJAL-2630 applet update overview on release of threshold... tree | commitdiff
2017-07-28 kiramtJAL-2632 Added paintAlignment(true) to show cols code tree | commitdiff
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