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JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time...
[jalview.git] / src / jalview / analysis /
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 tree | commitdiff
2022-02-03 Jim ProcterJAL-2305 comments re testFindXrefSequences_withFetch... tree | commitdiff
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2020-10-29 Jim Procter JAL-3759 exclude hidden columns when processing... tree | commitdiff
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11... tree | commitdiff
2020-10-28 Jim Procterfix for JAL-3765 tree | commitdiff
2020-10-27 Jim ProcterJAL-3700 JAL-3748 JAL-3763 don’t add stop codon via... tree | commitdiff
2020-10-22 gmungocJAL-3763 always make a new dataset sequence for CDS... tree | commitdiff
2020-10-20 Jim Procterfix for JAL-3765 tree | commitdiff
2020-10-08 gmungocJAL-3763 always make a new dataset sequence for CDS... tree | commitdiff
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... tree | commitdiff
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop tree | commitdiff
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490 tree | commitdiff
2020-06-29 Jim ProcterMerge branch 'bug/JAL-3490findSpanHiddenGaps' into... tree | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2020-02-18 Mungo CarstairsJAL-3536 JAL-3187 don't create duplicate CDS-to-protein... bug/JAL-3536getCrossrefTwice tree | commitdiff
2020-01-28 gmungocJAL-3187 one more obsolete method removed tree | commitdiff
2019-12-12 gmungocJAL-3490 unit test for ignore hidden regions with selec... tree | commitdiff
2019-12-11 gmungocJAL-3490 tests for skip hidden regions (and a bug fix) tree | commitdiff
2019-12-11 gmungocJAL-3490 revised layout and search algorithm (more... tree | commitdiff
2019-11-29 gmungocJAL-3490 Finder match across entirely gapped hidden... 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
2019-08-22 gmungocJAL-3187 one more obsolete method removed tree | commitdiff
2019-08-09 gmungocJAL-3187 removal of variant feature (non-virtual) trans... tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-18 gmungocJAL-3313 don't double count mapped codons tree | commitdiff
2019-06-17 gmungocJAL-3187 update alignAs code and unit tests for 'shared... tree | commitdiff
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures 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
2019-04-18 hansonrexplicit Hashtable objects tree | commitdiff
2019-04-11 Jim ProcterMerge branch 'develop' into task/JAL-3130_Java_11_inves... tree | commitdiff
2019-04-04 gmungocJAL-3220 unneeded main methods removed tree | commitdiff
2019-03-27 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-03-27 gmungocJAL-2620 improved error reporting on failure to load... 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 gmungocJAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test... tree | commitdiff
2019-03-07 gmungocMerge branch 'feature/JAL-3205symmetricCalc' into develop 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-2839findWi... tree | commitdiff
2019-03-03 gmungocJAL-3205 faster calculation with symmetric score matrix tree | commitdiff
2019-02-28 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into merge... tree | commitdiff
2019-02-27 gmungocJAL-3202 discard zero percentages in extracted profile tree | commitdiff
2019-02-20 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into feature... 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 gmungocMerge branch 'feature/JAL-3143ensemblJSON' into trialMerge tree | commitdiff
2019-01-26 hansonrJalview.isJS() --> Platform.isJS(), DBRefEntry[] -... tree | commitdiff
2019-01-25 hansonrJSON refactoring tree | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... tree | commitdiff
2019-01-18 gmungocJAL-3143 'id' not 'ID' attribute drives generation... tree | commitdiff
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug... tree | commitdiff
2018-10-17 Jim ProcterMerge branch 'feature/JAL-3063JAXB' into Jalview-BH... tree | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch tree | commitdiff
2018-09-06 Jim ProcterJAL-3105 reallocate quality and consensus annotation... tree | commitdiff
2018-08-30 Jim ProcterJAL-3092 make sure base pair counter is always moved... tree | commitdiff
2018-06-27 hansonrConsensus LOGO done tree | commitdiff
2018-06-22 gmungocJAL-3032 avoid assignments on the same line as synchronized tree | commitdiff
2018-06-21 gmungocJAL-3032 round Quality score for tooltip (as it becomes... tree | commitdiff
2018-06-20 hansonrJAL-3032 for (var var tree | commitdiff
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject tree | commitdiff
2018-05-07 gmungocJAL-1767 save PCA D and E vectors instead of 'details... 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 remove Change Parameters menu from PCA panel tree | commitdiff
2018-04-26 gmungocJAL-2962 code tidying/documentation (non-functional... tree | commitdiff
2018-04-25 gmungocJAL-1767 minor field tidying prior to functional changes tree | commitdiff
2018-03-19 gmungocJAL-2620 parse genetic code tables from standard file... tree | commitdiff
2018-03-16 gmungocJAL-2620 alternative genetic code translation tables tree | commitdiff
2018-03-14 gmungocJAL-2933 pass viewport in Finder constructor, find... bug/JAL-2839findWithHidden tree | commitdiff
2018-03-14 gmungocJAL-2933 gui and applet Finder hold a FinderI per viewport tree | commitdiff
2018-03-14 gmungocJAL-2839 refactored out getNextVisibleSequenceRegion tree | commitdiff
2018-03-13 gmungocJAL-2839 refactored analysis.Finder and tests 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
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666 tree | commitdiff
2018-02-09 gmungocJAL-2789 code format changes only (before functional... tree | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... tree | commitdiff
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge tree | commitdiff
2018-02-05 gmungocJAL-2897 more informative description on synonymous... 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
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon... tree | commitdiff
2018-01-30 gmungocJAL-2897 formatting change only prior to functional... tree | commitdiff
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759 tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
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