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JAL-3285 fix incorrect file paths on HMMAlign/Search results
[jalview.git] / src / jalview / datamodel /
2019-06-05 tvaJAL-3285 add unmerged code to AlignmentAnnotation tree | commitdiff
2019-06-05 tvaJAL-3285 add unmerged code to SequenceGroup tree | commitdiff
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... tree | commitdiff
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi... tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3072scrollThread' into merge... tree | commitdiff
2019-03-04 gmungocMerge remote-tracking branch 'origin/bug/JAL-3082select... tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3099alignmentVisibleWidth' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'bug/JAL-3164complementOverview' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL... tree | commitdiff
2019-03-01 gmungocJAL-3140 reduced coupling to intervalstore.jar feature/intervalStoreJ tree | commitdiff
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam... tree | commitdiff
2019-02-24 gmungocJAL-3198 SequenceGroup 'bulk constructor' without dupli... tree | commitdiff
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA... tree | commitdiff
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug... tree | commitdiff
2018-12-17 Jim ProcterMerge branch 'bug/JAL-2750' into develop tree | commitdiff
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures tree | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... tree | commitdiff
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library tree | commitdiff
2018-11-28 gmungocJAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview tree | commitdiff
2018-11-19 Jim ProcterJAL-3156 JAL-3127 code tidy tree | commitdiff
2018-11-19 Jim ProcterJAL-3156 javadoc re JAL-3127 and FIXME to make Alignmen... tree | commitdiff
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit... tree | commitdiff
2018-09-13 gmungocJAL-3116 Uniprot XML unmarshalled using JAXB not Castor tree | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch tree | commitdiff
2018-09-10 gmungocJAL-3099 new method AlignmentI.getVisibleWidth() tree | commitdiff
2018-08-27 Ben SoaresJAL-3061 / JAL-3053 tree | commitdiff
2018-08-16 gmungocJAL-3082 handle regex error, exclusive threshold, unit... tree | commitdiff
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene... tree | commitdiff
2018-08-02 Ben SoaresJAL-3053 tree | commitdiff
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS... tree | commitdiff
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale... tree | commitdiff
2018-07-18 Jim ProcterMerge branch 'features/mchmmer' into features/mchmmer_m... features/mchmmer_merge_JAL-1950 tree | commitdiff
2018-06-05 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-06-04 Jim ProcterJAL-3017 parse multiple variant elements for uniprot... tree | commitdiff
2018-06-02 Jim ProcterJAL-3017 parse multiple variant elements for uniprot... tree | commitdiff
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow individual groups to be remater... tree | commitdiff
2018-06-01 Jim ProcterJAL-1551 formatting tree | commitdiff
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of group without sequences... tree | commitdiff
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of sequences from group... tree | commitdiff
2018-05-31 gmungocJAL-2808 don't capture or report min-max for mixed... tree | commitdiff
2018-05-31 Jim ProcterMerge branch 'spike/JAL-1950_hmmer3client' into feature... tree | commitdiff
2018-05-31 Jim ProcterMerge branch 'develop' into spike/JAL-1950_hmmer3client tree | commitdiff
2018-05-28 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-05-21 gmungocJAL-2920 use HGVS notation for protein variant feature tree | commitdiff
2018-05-11 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue... tree | commitdiff
2018-05-10 Jim ProcterMerge branch 'bug/JAL-2920_uniprotvariantfeature' into... tree | commitdiff
2018-05-10 Jim ProcterJAL-2920 simplified logic and added corner cases for... tree | commitdiff
2018-05-08 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject tree | commitdiff
2018-05-07 Jim ProcterJAL-2906 apply GPLv3 license source tree | commitdiff
2018-05-04 gmungocJAL-1767 refactorings to enable faithful restore of... tree | commitdiff
2018-04-27 gmungocJAL-1767 refactoring and tidying of RotatableCanvas... tree | commitdiff
2018-04-26 gmungocJAL-2962 code tidying/documentation (non-functional... tree | commitdiff
2018-04-23 gmungocJAL-2956 save/restore HMMER profile to/from Jalview... tree | commitdiff
2018-04-23 gmungocJAL-2954 more efficient SearchResults.markColumns tree | commitdiff
2018-04-17 gmungocJAL-2629 choice of hmm profile now a parameter not... tree | commitdiff
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe... tree | commitdiff
2018-04-09 Mungo CarstairsJAL-2629 more error checking tree | commitdiff
2018-03-30 gmungocJAL-2599 MapList from HMM nodes to consensus dataset... tree | commitdiff
2018-03-30 gmungocJAL-2939 field/method naming more consistent tree | commitdiff
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications tree | commitdiff
2018-03-26 gmungocJAL-2939 always store Information profile tree | commitdiff
2018-03-20 gmungocJAL-2629 InformationThread.findOrCreateAnnotation and... tree | commitdiff
2018-03-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-03-16 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db... tree | commitdiff
2018-03-13 gmungocJAL-2839 addResult ignores duplicates tree | commitdiff
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect tree | commitdiff
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group... tree | commitdiff
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... tree | commitdiff
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip) tree | commitdiff
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) tree | commitdiff
2018-02-27 gmungocJAL-2668 method name change for clarity tree | commitdiff
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display... tree | commitdiff
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-26 Jim ProcterJAL-2920 parse variation and original elements of the... tree | commitdiff
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file... tree | commitdiff
2018-02-23 gmungocJAL-2599 corrected case-insensitive symbol indexing tree | commitdiff
2018-02-23 gmungocJAL-2599 parser and datamodel use primitive double... tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly tree | commitdiff
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc tree | commitdiff
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_... tree | commitdiff
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation tree | commitdiff
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and... tree | commitdiff
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... tree | commitdiff
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759 tree | commitdiff
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI... tree | commitdiff
2018-02-05 kiramtJAL-2759 Fix errant RangeElementsIterator (unit tests... tree | commitdiff
2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator tree | commitdiff
2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review tree | commitdiff
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses tree | commitdiff
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