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JAL-6386 update slivka client for j2s compatibility
[jalview.git] / src / jalview / schemes /
2019-09-26 Jim ProcterJAL-3070 JAL-3066 JAL-2808 allow feature filter definit... tree | commitdiff
2019-07-11 ThomasJAL-2629 hmm search UI and structural improvements... tree | commitdiff
2019-07-02 tvaJAL-2629 hmm match score colour scheme now colours... tree | commitdiff
2019-06-28 tvaJAL-2629 add ability to add background frequencies... tree | commitdiff
2019-06-28 tvaJAL-2629 add file that should have been in previous... tree | commitdiff
2019-06-28 tvaJAL-2629 add HMM Match Score colour scheme tree | commitdiff
2019-06-06 tvaJAL-3285 code changes to HMMER colour schemes not inclu... 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
2019-03-19 Ben SoaresJAL-3130 Merge of JAL-3130_Java_11_investigations-Ben... tree | commitdiff
2019-03-12 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... tree | commitdiff
2019-03-12 gmungocJAL-3127 check for null viewport feature/JAL-3127_seqidChainshading tree | commitdiff
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... tree | commitdiff
2019-03-11 gmungocJAL-3206 strict above/below threshold test restored tree | commitdiff
2019-03-07 gmungocMerge branch 'feature/JAL-3180colourAnnotationMenu... tree | commitdiff
2019-03-07 Ben SoaresJAL-3130 deprecation change preparation tree | commitdiff
2019-03-05 gmungocMerge remote-tracking branch 'origin/features/JAL-2620a... tree | commitdiff
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-3049colour... tree | commitdiff
2019-03-04 gmungocJAL-3206 avoid divide by zero when threshold is graphMi... tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3120restoreFeatureColour' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'bug/JAL-2791exportFilteredFeature' into... tree | commitdiff
2019-02-28 gmungocMerge remote-tracking branch 'origin/feature/JAL-3141_b... tree | commitdiff
2019-02-28 Jim ProcterMerge branch 'feature/JAL-3141_backupfiles_for211'... merge/develop_feature/JAL-3141_backupfiles_for211 tree | commitdiff
2019-02-25 gmungocJAL-3200 fast lookup of DSSP3 notation tree | commitdiff
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA... tree | commitdiff
2019-01-04 gmungocJAL-3180 fix By Annotation selection state in colour... tree | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... tree | commitdiff
2018-12-03 gmungocJAL-3063 Castor removed from codebase tree | commitdiff
2018-12-03 gmungocMerge branch 'feature/JAL-3063JAXB' into feature/JAL... tree | commitdiff
2018-11-20 Jim ProcterJAL-3127 Sequence ID Colour and nominal spanish translation tree | commitdiff
2018-11-19 Jim ProcterJAL-3127 javadoc, don’t darken white when shading resid... tree | commitdiff
2018-11-19 Jim ProcterJAL-3127 drop redundant hidden representative sequences... tree | commitdiff
2018-10-16 Jim ProcterJAL-3127 always look up sequence ID colour from view... tree | commitdiff
2018-10-09 Jim ProcterJAL-3127 Colour sequences by ID - need to check that... tree | commitdiff
2018-10-09 Jim ProcterJAL-3127 pass reference to AlignViewportI when creating... tree | commitdiff
2018-09-27 gmungocJAL-2791 new method to test if feature fails colour... tree | commitdiff
2018-09-21 gmungocJAL-3120 preserve feature colour/mincolour/maxcolour... bug/JAL-3120restoreFeatureColour tree | commitdiff
2018-09-20 gmungocJAL-2843 help text for colour by attribute, feature... tree | commitdiff
2018-09-18 gmungocJAL-3063 Save/Load user defined colours using JAXB tree | commitdiff
2018-06-29 gmungocJAL-3049 JAL-2069 colour icon tooltip including by... tree | commitdiff
2018-05-31 Jim ProcterJAL-1958 use the annotation score for the sequence... tree | commitdiff
2018-05-31 Jim ProcterJAL-1950 JAL-1958 disable per-row score modulation... 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
2018-04-17 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
2018-03-30 gmungocJAL-2938 revisions to implementation details tree | commitdiff
2018-03-23 gmungocJAL-2938 update colour schemes enum for class name... tree | commitdiff
2018-03-23 gmungocJAL-2938 extracted base class for Hmmer colour schems tree | commitdiff
2018-03-16 gmungocJAL-2620 alternative genetic code translation tables tree | commitdiff
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... tree | commitdiff
2018-02-27 gmungocJAL-2668 method name change for clarity tree | commitdiff
2018-02-27 gmungocJAL-2668 fix broken factory method for colour scheme tree | commitdiff
2018-02-27 gmungocJAL-2717 JAL-2668 fixes to HMMER colour scheme display... tree | commitdiff
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer tree | commitdiff
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and... tree | commitdiff
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences tree | commitdiff
2018-01-10 gmungocJAL-1793 update spike branch to latest tree | commitdiff
2017-12-11 gmungocJAL-2843 add colour by attribute, and no value colour... tree | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) tree | commitdiff
2017-11-22 gmungocJAL-2069 Javadoc added only tree | commitdiff
2017-11-16 gmungocJAL-2069 removed unused and redundant thresholdIsMinMax tree | commitdiff
2017-11-15 gmungocJAL-2816 exclude filtered / thresholded out features... tree | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest tree | commitdiff
2017-11-15 gmungocJAL-2835 support filter/colour by nested attribute... tree | commitdiff
2017-11-07 gmungocJAL-2069 update spike with latest tree | commitdiff
2017-11-07 gmungocJAL-2069 corrected overloaded constructor behaviour tree | commitdiff
2017-11-07 gmungocJAL-2069 update spike branch with latest tree | commitdiff
2017-11-07 gmungocJAL-2069 add attributeName and noValueColour to Feature... tree | commitdiff
2017-11-02 gmungocJAL-2808 reverted to develop (attribute filters removed) tree | commitdiff
2017-10-31 gmungocJAL-2808 revised util.matcher package, 2 filter conditi... tree | commitdiff
2017-10-30 gmungocJAL-2808 add attribute filter(s) to FeatureColour tree | commitdiff
2017-10-24 gmungocJAL-2738 update spike branch with latest tree | commitdiff
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-09-15 Jim ProcterJAL-1950 update colour gradient variables to new, more... tree | commitdiff
2017-09-15 Jim ProcterMerge branch 'develop' into trial_merge/JAL-1950 tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1... tree | commitdiff
2017-08-28 TZVanaaltenJAL-2629 HMMER alignment background colour scheme is... tree | commitdiff
2017-08-25 TZVanaaltenJAl-2629 add new HMMER colour scheme class tree | commitdiff
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild... tree | commitdiff
2017-08-22 Jim ProcterJAL-1950 patch after merge tree | commitdiff
2017-08-21 Jim ProcterMerge branch 'develop' into trial_merge/JAL-1950 spike/JAL-1950_hmmer3client tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList tree | commitdiff
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer tree | commitdiff
2017-08-18 Jim ProcterMerge branch 'feature/2588' into merge/develop_feature... tree | commitdiff
2017-08-18 TZVanaaltenJAL-2668 add tests for HMMER commands, annotation and io 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 fix background frequency storage and correct... tree | commitdiff
2017-08-15 TZVanaaltenJAL-2599 fix HMMER scheme not colouring inserts and... tree | commitdiff
2017-08-09 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-07-31 TZVanaaltenJAL-2629 add hmmalign command tree | commitdiff
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder... tree | commitdiff
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 tree | commitdiff
2017-07-24 gmungocJAL-2624 additional tests for FeatureColour.getColour(), tree | commitdiff
2017-07-23 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-07-20 TZVanaaltenJAL-2599 add ability to process RNA HMMer files tree | commitdiff
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