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JAL-3690 mark JalviewChangeSupport as deprecated
[jalview.git] / src / jalview / datamodel /
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... tree | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop tree | commitdiff
2020-05-01 gmungocJAL-3613 check sequence overlap when matching search... tree | commitdiff
2020-04-23 Jim ProcterMerge branch 'develop' into alpha/JAL-3362_Jalview_212_... tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-04-21 Jim ProcterJAL-3567 translated rather than imputed peptide tree | commitdiff
2020-04-17 gmungocJAL-3567 unit tests for linked feature tooltips tree | commitdiff
2020-04-16 gmungocJAL-3567 adjust layout of linked feature report, unit... tree | commitdiff
2020-04-16 gmungocJAL-3567 added 'imputed by Jalview' to protein conseque... tree | commitdiff
2020-04-16 gmungocJAL-3567 report mapped location for virtual features... tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2020-02-27 Jim ProcterMerge branch 'bug/JAL-3296changeStartInvalidateCursor... tree | commitdiff
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into... tree | commitdiff
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files tree | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-09-26 Jim ProcterJAL-3070 allow SequenceI.findPositions(0,column+1)... tree | commitdiff
2019-09-26 gmungocJAL-2481 remove code duplication left by merge tree | commitdiff
2019-09-26 Jim ProcterJAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(Alignm... tree | commitdiff
2019-08-22 gmungocMerge branch 'develop' into feature/JAL-3121gffAttributeMap tree | commitdiff
2019-08-22 gmungocJAL-3187 case-insensitive codon variant calculation tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-08-21 gmungocJAL-3187 minor code tidying, todo removal tree | commitdiff
2019-08-13 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... tree | commitdiff
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId() tree | commitdiff
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into tree | commitdiff
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-07-10 Jim ProcterMerge branch 'merge/JAL-3285_mchmmer_with_211_develop... tree | commitdiff
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests tree | commitdiff
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant... tree | commitdiff
2019-07-03 tvaJAL-2629 evalues and bit scores now conserved after... 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-2629 add HMM Match Score colour scheme tree | commitdiff
2019-06-17 gmungocJAL-2792 JAL-3187 linked features (if shown) in Feature... tree | commitdiff
2019-06-17 gmungocJAL-3187 add sequence to feature details table (and... tree | commitdiff
2019-06-13 gmungocJAL-3303 ignore deletions when computing peptide variants tree | commitdiff
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript tree | commitdiff
2019-06-10 tvaJAL-3297 pad gaps in alignment to ensure hmmalign runs tree | commitdiff
2019-06-10 gmungocJAL-3296 ensure sequence cursor reset when sequence... bug/JAL-3296changeStartInvalidateCursor tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 tvaJAL-3291 issue fixed, passing tests added tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
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
2019-04-18 hansonrminor code clean up tree | commitdiff
2019-04-18 hansonrminor code clean up tree | commitdiff
2019-04-03 hansonrj2sNative clean-up. Fixes problem with second try of... 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
2019-03-13 gmungocMerge branch 'develop' into trialMerge 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
2019-02-21 gmungocJAL-3187 handle no mapping / complement features withou... tree | commitdiff
2019-02-20 gmungocJAL-3187 read peptide variant from CSQ:HGVSp if present... tree | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... tree | commitdiff
2019-02-04 hansonrrefactoring for DBMODList tree | commitdiff
2019-01-29 hansonriterators tree | commitdiff
2019-01-26 hansonrPlatform.timecheck calls removed or commented out. tree | commitdiff
2019-01-26 hansonrremoving cyclic call tree | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... tree | commitdiff
2019-01-21 gmungocJAL-3187 unit tests updated and errors caught tree | commitdiff
2019-01-21 gmungocJAL-3187 findFeaturesAtResidue answer in render order... tree | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... tree | commitdiff
2019-01-17 gmungocMerge branch 'develop' into Jalview-BH/JAL-3026-JAL... 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
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH... 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 gmungocMerge branch 'bug/JAL-3082selectRegex' into Jalview... 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
2018-07-26 gmungocMerge remote-tracking branch 'origin/bug/JAL-3072scroll... tree | commitdiff
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale... tree | commitdiff
2018-07-20 gmungocJAL-3048 revised AlignExportSettings dialog with respon... tree | commitdiff
2018-07-18 Jim ProcterMerge branch 'features/mchmmer' into features/mchmmer_m... features/mchmmer_merge_JAL-1950 tree | commitdiff
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