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2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... commit | commitdiff | tree | snapshot
2017-07-26 TZVanaaltenJAL-2629 HMMs now map to reference annotation if exists commit | commitdiff | tree | snapshot
2017-07-25 TZVanaaltenJAL-2629 add non-functional HMMER menu commit | commitdiff | tree | snapshot
2017-07-25 TZVanaaltenJAL-2616 add ability to perform random alignments withi... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2616 add placeholder sequence for HMM, does not... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2616 add ability to change location of family and... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2599 add a couple of test files not included in... commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2616 add test class and test files for analyser commit | commitdiff | tree | snapshot
2017-07-24 tzvanaaltenJAL-2599 .hmm parser should now accept older .hmm files commit | commitdiff | tree | snapshot
2017-07-21 TZVanaaltenJAL-2616 add ability to sort Pfam families and HMMs... commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2616 remove statistical analysis from AlignFrame commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2599 small code improvements commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2616 add documentation for probability analyser commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2616 add probability distribution analyser class commit | commitdiff | tree | snapshot
2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files commit | commitdiff | tree | snapshot
2017-07-18 TZVanaaltenJAL-2599 complete documentation for HMM and HMMFile... commit | commitdiff | tree | snapshot
2017-07-18 TZVanaaltenJAL-2599 modified state transition probability storage commit | commitdiff | tree | snapshot
2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics... features/hmmer_statistics commit | commitdiff | tree | snapshot
2017-07-12 TZVanaaltentest HMM annotaTION commit | commitdiff | tree | snapshot
2017-07-11 TZVanaaltencomplete Information Content annotation commit | commitdiff | tree | snapshot
2017-06-29 TZVanaaltenadd information content calculations commit | commitdiff | tree | snapshot
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations commit | commitdiff | tree | snapshot
2017-06-23 TZVanaaltentest HMMER colour scheme commit | commitdiff | tree | snapshot
2017-06-23 TZVanaaltenadd HMMER colour scheme commit | commitdiff | tree | snapshot
2017-06-22 TZVanaaltenfully integrate HMMER3 file format into Jalview commit | commitdiff | tree | snapshot
2017-06-20 TZVanaaltencreate method to test HMM model as string commit | commitdiff | tree | snapshot
2017-06-20 TZVanaaltenrestructure file exporter commit | commitdiff | tree | snapshot
2017-06-15 TZVanaaltenadd tests for HMMFile class commit | commitdiff | tree | snapshot
2017-06-15 TZVanaaltenadd HMMFile class to read and write HMM files commit | commitdiff | tree | snapshot
2017-06-15 TZVanaaltenUpdate HiddenMarkovModel class commit | commitdiff | tree | snapshot
2017-06-09 TZVanaaltenAdd HiddenMarkovModel class commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2418 release notes for JAL-2547, JAL-2563, JAL... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'JAL-2571' into develop commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2398 - updated groovy script for direct field modif... commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2418 JAL-2563 release notes commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterJAL-2418 typo commit | commitdiff | tree | snapshot
2017-05-31 Jim ProcterMerge branch 'develop' into documentation/JAL-2418_rele... commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuJAL-2375 fix unit test to reflect improvement commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuFixed failing tests commit | commitdiff | tree | snapshot
2017-05-31 tcofoegbuJAL-2533 updated unit test to reflect improvement commit | commitdiff | tree | snapshot
2017-05-31 gmungocJAL-2547 handle contact features 'around' a gap correctly commit | commitdiff | tree | snapshot
2017-05-30 kiramtJAL-2573 Fixes for alignment < viewport width, and... JAL-2571 commit | commitdiff | tree | snapshot
2017-05-30 gmungocJAL-2547 tooltip/AmendFeatures on gap straddled by... commit | commitdiff | tree | snapshot
2017-05-30 kiramtJAL-2571 Corrected alignment width/height checks to... commit | commitdiff | tree | snapshot
2017-05-30 gmungocJAL-2570 don't zap group colour scheme when mapping... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2034contextchange' into develop commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2388 release notes commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2520 properly documented as a fixed bug in release... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2465,JAL-2520,JAL-2533 release notes commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2533 update javadoc features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2465 fixed groups for JmolViewerTest.testStructureL... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2536' into develop commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2536 tweak javadoc wording commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2517 release notes commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2517cancelAppletColour' into... commit | commitdiff | tree | snapshot
2017-05-29 Jim Procterrelease notes commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2418 updated JABAWS server in what’s new commit | commitdiff | tree | snapshot
2017-05-29 Jim ProcterJAL-2491 JAL-2526 JAL-2566 JAL-2563 JAL-2547 release... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterMerge branch 'bug/JAL-2491' into develop commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterMerge branch 'bug/JAL-2547tooltipOnGap' into develop commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterMerge branch 'task/JAL-2562_SequenceI.findPosition... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterJAL-2563 failing test to verify SetStatus returns posit... task/JAL-2562_SequenceI.findPosition commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterJAL-2563 test to verify SetStatus returns -1 so mouseOv... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterMerge branch 'task/JAL-2562_SequenceI.findPosition... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterJAL-2547 JAL-2562 rejig SetStatusMessage return value... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterMerge branch 'task/JAL-2562_SequenceI.findPosition... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterJAL-2526 test and documentation for SeqPanel.setStatus... commit | commitdiff | tree | snapshot
2017-05-27 Jim ProcterJAL-2562 javadoc TODO commit | commitdiff | tree | snapshot
2017-05-26 kiramtJAL-2491 Missed port to applet from JAL-1691 bug/JAL-2491 commit | commitdiff | tree | snapshot
2017-05-26 Jim ProcterMerge branch 'documentation/JAL-2418_release2102' into... commit | commitdiff | tree | snapshot
2017-05-26 Jim ProcterJAL-2418 updated JPred documentation and screenshot... commit | commitdiff | tree | snapshot
2017-05-26 Jim ProcterJAL-2418 JAL-2549 JABAWS 2.2 release notes commit | commitdiff | tree | snapshot
2017-05-26 Jim ProcterMerge branch 'features/JAL-2549_updateJABAWSto220'... commit | commitdiff | tree | snapshot
2017-05-26 tcofoegbuJAL-2465 Improvement to re-instate storing recently... commit | commitdiff | tree | snapshot
2017-05-26 tcofoegbuJAL-2465 fix to prevent files loaded from the system... commit | commitdiff | tree | snapshot
2017-05-25 kiramtJAl-2034 Ported to applet bug/JAL-2034contextchange commit | commitdiff | tree | snapshot
2017-05-25 kiramtJAL-2034 don't update overview after click without... commit | commitdiff | tree | snapshot
2017-05-25 kiramtMerge branch 'bug/JAL-2551' into bug/JAL-2034contextchange commit | commitdiff | tree | snapshot
2017-05-24 kiramtJAL-2551 Fix to group colouring when group extent is... bug/JAL-2551 commit | commitdiff | tree | snapshot
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup commit | commitdiff | tree | snapshot
2017-05-23 Jim ProcterJAL-2549 RNAAliFold result to annotation file roundtrip... features/JAL-2549_updateJABAWSto220 commit | commitdiff | tree | snapshot
2017-05-23 Jim ProcterJAL-2549 skip ‘Unrecognised Service’ which resolves... commit | commitdiff | tree | snapshot
2017-05-23 Jim ProcterJAL-2549 replace JABAWS 2.1 with 2.2 client and remove... commit | commitdiff | tree | snapshot
2017-05-23 gmungocJAL-2547 don't show features in tooltip over a gap bug/JAL-2547tooltipOnGap commit | commitdiff | tree | snapshot
2017-05-22 gmungocJAL-2504 update the right feature colour when creating... bug/JAL-2510amendFeatures commit | commitdiff | tree | snapshot
2017-05-22 gmungocJAL-2544 unit tests for sort by feature score commit | commitdiff | tree | snapshot
2017-05-22 gmungocJAL-2544 check feature overlaps selection region commit | commitdiff | tree | snapshot
2017-05-22 kiramtMerge remote-tracking branch 'origin/bug/JAL-2256'... commit | commitdiff | tree | snapshot
2017-05-22 Jim ProcterJAL-2418 patch build - broken htsjdk import commit | commitdiff | tree | snapshot
2017-05-19 gmungocJAL-2526 removed redundant call to Sequence.findPosition() commit | commitdiff | tree | snapshot
2017-05-18 Jim ProcterMerge branch 'bug/JAL-2388_typeCheckAlignView.getUpdate... commit | commitdiff | tree | snapshot
2017-05-18 Jim ProcterJAL-2388 return empty hidden columns for fully visible... commit | commitdiff | tree | snapshot
2017-05-18 kiramtJAL-2256 Corrected AllCols/Rows iterator behaviour... bug/JAL-2256 commit | commitdiff | tree | snapshot
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