git://source.jalview.org / jalview.git / history
? search:
summary | shortlog | log | commit | commitdiff | tree
first ⋅ prev ⋅ next
Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / analysis /
2024-10-04 Jim Procterfix for JAL-4471 - secondary structure similarity tree... tree | commitdiff
2024-09-16 Jim ProcterJAL-4392 autohide the secondary structure consensus... tree | commitdiff
2024-09-03 Jim ProcterJAL-4386 remove magic string in registerScoreModel... tree | commitdiff
2024-08-29 Jim ProcterJAL-4446 improved reporting of progress, and transition... tree | commitdiff
2024-08-05 Jim ProcterJAL-4446 .. missing methods for cancellable pasimap tree | commitdiff
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks tree | commitdiff
2024-07-29 Jim ProcterJAL-4443 patch out pasimap in GUI for JalviewJS and... tree | commitdiff
2024-05-24 Jim ProcterJAL-4159 fix PairwiseAlignmentPanelTest - reinstate... tree | commitdiff
2024-05-24 Jim ProcterJAL-4257 JAL-4159 JAL-789 tidy up passing of score... tree | commitdiff
2024-05-24 James ProcterJAL-789 pairwise alignment via calculations dialog... tree | commitdiff
2024-05-24 James ProcterJAL-4366 compute coverage on each side of the pairwise... tree | commitdiff
2024-05-23 MorellThomasFix PaSiMap taking scoreModels input and allow AlignSeq... tree | commitdiff
2024-05-21 Jim ProcterJAL-4159 connectivity should be computed for the sequen... tree | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4159_pasimap tree | commitdiff
2024-05-15 Renia CorreyaJAL-4386 Added preferences for secondary structure... tree | commitdiff
2024-05-15 Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure tree | commitdiff
2024-05-13 Renia CorreyaJAL-4386 - Implementation of substitution matrix and... tree | commitdiff
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure tree | commitdiff
2024-04-30 Renia CorreyaJAL-4386 Comparing secondary structure similarity direc... tree | commitdiff
2024-04-26 Renia CorreyaJAL-4386 Drop down for secondary structure sources... tree | commitdiff
2024-04-24 Renia CorreyaJAL-4386 PCA/Tree Calculation for Secondary Structures... tree | commitdiff
2024-04-18 MorellThomasMerge branch 'test/progressBar' into feature/JAL-4159_p... tree | commitdiff
2024-04-18 MorellThomasImplemented ProgressBar for PaSiMap tree | commitdiff
2024-04-16 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... tree | commitdiff
2024-04-12 MorellThomasinlcude progress tree | commitdiff
2024-03-15 MorellThomasFix output of all dimensions tree | commitdiff
2024-03-15 MorellThomasAlogirthm working, but still giving slightly off results tree | commitdiff
2024-03-13 Renia CorreyaJAL-4386_Added changes in similarity score calculation... tree | commitdiff
2024-03-08 Renia CorreyaJAL-4386 Added further checks for sequences that have... tree | commitdiff
2024-03-08 Renia CorreyaJAL-4386 Calculate tree using secondary structure annot... tree | commitdiff
2024-03-07 MorellThomasInlcude 8 dimensions tree | commitdiff
2024-03-06 MorellThomasFix PaSiMap on selected sequences tree | commitdiff
2024-03-06 MorellThomasTest version to switch branches tree | commitdiff
2024-01-31 MorellThomasFix output points column labels tree | commitdiff
2024-01-10 MorellThomasFixed PaSiMap output columns tree | commitdiff
2023-12-04 MorellThomasNew GPCAPanel button : output pairwise alignments ... tree | commitdiff
2023-12-01 MorellThomasApplying adjustablenw_params.patch (JAL-4159) tree | commitdiff
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
2023-10-01 MorellThomasFix Reset Button for PaSiMap and issue with indelfreeAs... tree | commitdiff
2023-09-18 MorellThomasFix buttons on the PaSiMap plot window tree | commitdiff
2023-09-16 MorellThomasCorrectly working implementation of the PaSiMap pipeline tree | commitdiff
2023-09-16 MorellThomasAlmost working tree | commitdiff
2023-09-08 MorellThomasProperly integrated endGaps option for AlignSeq.traceAl... tree | commitdiff
2023-09-07 MorellThomasMerge branch 'hardcode' tree | commitdiff
2023-09-07 MorellThomasImplemented least-squares optimisation in ccAnalysis tree | commitdiff
2023-09-04 James ProcterJAL-4159 JAL-4257 simple test for default gap parameter... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-08-04 MorellThomasFix alignment and score calculation for cc_analysis tree | commitdiff
2023-07-22 MorellThomasImplement MSA, scoring and counting the connections tree | commitdiff
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring... tree | commitdiff
2023-07-09 MorellThomasCopied PCA files to PaSiMap analogues and changed all... 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... 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... 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... 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
next