JAL-3141 forgot to add this file after extracting the class!
[jalview.git] / test / jalview / analysis /
2018-06-26 Jim ProcterJAL-3035 - jalview-das is no more !
2018-06-04 gmungocJAL-3019 correctly form toRange of 'traversed' MapList
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-09 gmungocJAL-2789 avoid using transcript (with no UTR) as CDS... bug/JAL-2666
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-02-05 gmungocMerge branch 'spikes/mungo' into trialMerge
2018-02-05 gmungocJAL-2897 more informative description on synonymous...
2018-01-30 gmungocJAL-1793 update spike build to latest incl stop and...
2018-01-30 gmungocJAL-2898 show 'stop_gained' variants on peptide sequences
2018-01-30 gmungocJAL-2897 generate peptide variants for synonymous codon...
2017-11-21 kiramtJAL-2759 Remove getVisibleBlocksIterator call
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-27 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-26 Jim ProcterMerge branch 'features/JAL-2685pairwiseSeqLimits' into...
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2617mappedStopCodon' into develop
2017-10-05 gmungocJAL-2738 update spikes/mungo
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript...
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-29 kiramtJAL-2674 finish with iterators for now
2017-09-28 kiramtJAL-2647 more iterators
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi...
2017-09-12 gmungocJAL-2727 first pass of test of memory recovery on close all
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon
2017-08-30 gmungocJAL-2685 tweaks to output spacing, updated TestAlignSeq...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-22 gmungocJAL-2544 unit tests for sort by feature score
2017-05-19 gmungocJAL-2490 performant lookup of features for sorting
2017-05-19 gmungocJAL-2505 unit test for sort by feature density, Javadoc
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF...
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-05-09 gmungocJAL-2403 use preferred factory method to create score...
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges
2017-05-02 Jim ProcterJAL-2424 fixme’s removed
2017-05-02 Jim ProcterJAL-2424 update assert to correct width for normalising...
2017-05-02 Jim ProcterJAL-2424 resolved, assert updated to pass (1f != 1d)
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside...
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-04-11 gmungocJAL-2403 improved ScoreModelI hierarchy as per Kira...
2017-04-10 gmungocJAL-2403 unit tests for PCA.computeSimilarity, signatur...
2017-04-10 gmungocJAL-2416 test updated for reinstatement of '*' row...
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle...
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols...
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min...
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score...
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically...
2017-03-27 gmungocJAL-2416 add score model description field for tooltip...
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices
2017-03-24 gmungocJAL-2416 tests added for ScoreMatrix
2017-03-23 gmungocJAL-2393 updated test for removal of PIDDistanceModel
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel...
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced...
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams!
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters...
2017-02-24 gmungocJAL-2403 PIDModel added (wip)
2017-02-24 gmungocJAL-1483 PIDModel potential replacement for PIDDistance...
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
2017-02-21 gmungocJAL-2416 typo
2017-02-21 gmungocJAL-2416 ScoreMatrix.getMatrix() returns a defensive...
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices
2017-02-21 gmungocJAL-2416 more validation in ScoreMatrix constructor
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
2017-02-20 gmungocJAL-2416 replaced dependency on ResidueProperties with...
2017-02-17 gmungocJAL-2416 score models now held in order added
2017-02-17 gmungocJAL-2403 extract method refactoring of FeatureScoreMode...
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop...
2017-02-13 gmungocJAL-2416 allow alphabet symbol (optional) in first...
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2017-02-06 gmungocJAL-2379 computePairwiseScores() moved to ScoreMatrix
2017-02-03 gmungocJAL-2379 'direct' pairwise score calculation for PCA...
2017-01-16 gmungocJAL-1270 class renamed
2017-01-16 gmungocJAL-1270 tweaks to AlignmentGenerator / client class
2017-01-12 gmungocJAL-1270 renamed AlignmentGenerator, and added peptide...
2016-11-28 gmungocMerge branch 'develop' into trialMerge
2016-11-28 tcofoegbuMerge branch 'features/JAL-2326_JOptionPane-refactoring...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-24 tcofoegbuJAL-2326 added setup method for JvOptionPane in all... features/JAL-2326_JOptionPane-refactoring
2016-11-24 Jim ProcterJAL-2325 apply license to new source files
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi...
2016-11-21 Jim ProcterJAL-2335 failing test for FeatureRendererModel.findFeat...
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-04 gmungocJAL-966 JAL-1854 removed redundant methods / modifiers...
2016-11-04 gmungocJAL-2302 unit tests added for Finder
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold...
2016-11-02 gmungocJAL-98 ProfileI interface for Profile
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis...
2016-11-01 gmungocConservation now using ResidueCount; tests added
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
2016-10-25 gmungocJAL-98 minor fixes to / tests for annotation derivation
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