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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / analysis /
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-10-17 James ProcterJAL-4134 TODO printNode update for columnTrees tree | commitdiff
2023-10-17 James ProcterJAL-4134 JAL-4302 remove unnecessary casts tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring... tree | commitdiff
2023-07-05 James ProcterMerge branch 'patch/JAL-2292_caseSensitivePAE' into... tree | commitdiff
2023-06-22 James ProcterJAL-4213 - document the addReferenceAnnotations method... tree | commitdiff
2023-06-22 James ProcterJAL-2292 - ensure mapping is built for equal symbols... patch/JAL-2292_caseSensitivePAE tree | commitdiff
2023-05-22 James ProcterJAL-4134 catch NPE - though in principle this should... tree | commitdiff
2023-05-22 James ProcterJAL-1551 spotless tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply tree | commitdiff
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic... tree | commitdiff
2023-05-15 James ProcterJAL-4182 patch - map selection group onto sequence... tree | commitdiff
2023-05-13 James ProcterJAL-2349 JAL-3855 helper method to make it easy to... tree | commitdiff
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... tree | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-4147 - revised annotation label display... tree | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... tree | commitdiff
2023-02-27 James ProcterJAL-4134 fix more of the egregious SeqNode/BinaryNode... tree | commitdiff
2023-02-27 James ProcterJAL-4134 use average distance between PAE elements... tree | commitdiff
2023-02-27 James ProcterJAL-4134 compute normalised dot product for contact... tree | commitdiff
2023-02-23 James ProcterJAL-4134 group columns using a tree cut - seems to... tree | commitdiff
2023-02-23 James ProcterJAL-4134 - brutal hack to build a tree clustering colum... tree | commitdiff
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with... tree | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options tree | commitdiff
2022-10-29 Jim ProcterMerge branch 'features/JAL-4061_and_JAL-4062_findselect... tree | commitdiff
2022-10-17 Jim ProcterJAL-2349 JAL-3855 Integrate pAE retrieval in StructureF... tree | commitdiff
2022-09-15 Jim ProcterJAL-4061 use alignment panel’s feature renderer to... tree | commitdiff
2022-09-15 Jim ProcterJAL-4061 support incremental search of features tree | commitdiff
2022-09-15 Jim ProcterJAL-4061 tests, bugfixes and TODOs for matching feature... tree | commitdiff
2022-09-14 Jim ProcterJAL-4061 JAL-4062 Find can now search features tree | commitdiff
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
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