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JAL-1953 redundant tree interface instantiation removed
[jalview.git] / src / jalview / analysis /
2017-12-11 kjvdheideJAL-1953 start on making everything interface based tree | commitdiff
2017-12-05 kjvdheideJAL-2838 Sorting from the alignment view menu now funct... tree | commitdiff
2017-11-08 kjvdheideJAL-2794 Added getter for AlignmentViewport to TreeBuilder tree | commitdiff
2017-11-06 kjvdheideJAL-2794 simplified/clarified associating leaves to... tree | commitdiff
2017-11-02 kjvdheideJAL-2795 Reverted code changes needed to cluster from... tree | commitdiff
2017-11-02 kjvdheideJAL-2795 Forester now NJ-clusters the DistanceMatrix... tree | commitdiff
2017-10-26 kjvdheideMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2017-10-26 kjvdheideAdded getters for scoremodel & scoreparams in TreeBuilder tree | commitdiff
2017-10-26 kjvdheideTreeBuilder now stores the used ScoreModel and ScoreParams tree | commitdiff
2017-10-26 kjvdheidesmall name fixes in TreeBuilder tree | commitdiff
2017-10-26 kjvdheideadded getSeqData to TreeBuilder tree | commitdiff
2017-10-26 kjvdheideAdded full names to the tree algorithm enum tree | commitdiff
2017-10-26 kjvdheideadded abbreviations tree | commitdiff
2017-10-26 kjvdheideadded enum for the different tree algorithms tree | commitdiff
2017-10-26 Jim ProcterMerge branch 'features/JAL-2685pairwiseSeqLimits' into... tree | commitdiff
2017-10-26 kjvdheideremoved accidental added enters, commented out broken... tree | commitdiff
2017-10-25 kjvdheideMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2017-10-11 kjvdheideforester as submodule with InternalFrame + start of... tree | commitdiff
2017-10-11 kjvdheidejust a comment tree | commitdiff
2017-10-10 kjvdheideStart of programmatically creating Aptx trees tree | commitdiff
2017-10-09 kjvdheideFully separated tree GUI from calculation tree | commitdiff
2017-10-05 kjvdheideBlank interfaces added tree | commitdiff
2017-09-27 kjvanderheideproof of concept for passing tree data to archaeopteryx tree | commitdiff
2017-09-04 gmungocJAL-2617 unit tests for CDS + stop codon, CDS with... bug/JAL-2617mappedStopCodon tree | commitdiff
2017-09-01 gmungocJAL-2617 omit stop codon from synthesized CDS sequence tree | commitdiff
2017-08-30 gmungocJAL-2685 tweaks to output spacing, updated TestAlignSeq... tree | commitdiff
2017-08-30 gmungocJAL-2685 use actual selection for report of pairwise... tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 add GPL to main sources tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... tree | commitdiff
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn tree | commitdiff
2017-05-31 gmungocJAL-2574 preparation for Sequence.findFeatures(col1... tree | commitdiff
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures tree | commitdiff
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... tree | commitdiff
2017-05-23 gmungocJAL-2490 find features for export as GFF, JAL-2548... tree | commitdiff
2017-05-22 gmungocJAL-2544 check feature overlaps selection region tree | commitdiff
2017-05-19 gmungocJAL-2544 only include features in selected columns... tree | commitdiff
2017-05-19 gmungocJAL-2490 performant lookup of features for sorting tree | commitdiff
2017-05-19 gmungocJAL-2505 unit test for sort by feature density, Javadoc tree | commitdiff
2017-05-18 gmungocJAL-2490 initial unit tests prior to refactoring tree | commitdiff
2017-05-16 gmungocJAL-2505 refactored method removed tree | commitdiff
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-16 gmungocJAL-2505 set helix number as feature group in SequenceF... tree | commitdiff
2017-05-16 gmungocJAL-2403 simplify instantiation / configuration of... tree | commitdiff
2017-05-15 gmungocJAL-2480 redundant code removed tree | commitdiff
2017-05-12 gmungocJAL-2525 get sequence features for Ontology term(s... tree | commitdiff
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final... tree | commitdiff
2017-05-04 Jim ProcterMerge branch 'features/JAL-2393customMatrices' into... tree | commitdiff
2017-05-04 Jim ProcterMerge branch 'features/JAL-2393customMatrices' into... tree | commitdiff
2017-05-03 Jim ProcterJAL-1933 show occupancy in tooltip for row tree | commitdiff
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside... tree | commitdiff
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-04-27 Jim ProcterJAL-1933 shade occupancy from light grey to black for... tree | commitdiff
2017-04-27 Jim ProcterJAL-1933 don’t show symbol counts under histogram ... tree | commitdiff
2017-04-12 gmungocJAL-2403 public static methods to convert distance... tree | commitdiff
2017-04-11 gmungocJAL-2403 improved ScoreModelI hierarchy as per Kira... tree | commitdiff
2017-04-11 gmungocJAL-2428 Javadoc tree | commitdiff
2017-04-10 gmungocJAL-2403 unit tests for PCA.computeSimilarity, signatur... tree | commitdiff
2017-04-10 gmungocJAL-2403 removed remaining jvCalcMode references from PCA tree | commitdiff
2017-04-09 gmungocJAL-2393 remove unused commented code tree | commitdiff
2017-04-07 gmungocJAL-2393 code tidying for review comments tree | commitdiff
2017-03-29 gmungocJAL-2416 JAL-728 reduced dependency on Blosum62 impleme... tree | commitdiff
2017-03-29 gmungocJAL-2416 revert to '*' not '-' in score matrix, handle... tree | commitdiff
2017-03-29 gmungocJAL-2416 explicit constant for unknown/unknown identity... tree | commitdiff
2017-03-28 gmungocJAL-2403 JAL-2416 pairwise score unexpected symbols... tree | commitdiff
2017-03-28 gmungocJAL-2416 JAL-2403 remove unused '*' row/column from... tree | commitdiff
2017-03-28 gmungocJAL-2403 further test coverage for ScoreMatrix, min... tree | commitdiff
2017-03-27 gmungocJAL-2416 parse score matrices in either NCBI or AAindex... tree | commitdiff
2017-03-27 gmungocJAL-2416 tidy up after switch from ' ' to '-' in score... tree | commitdiff
2017-03-27 gmungocJAL-2416 score matrix gap symbol (if any) dynamically... tree | commitdiff
2017-03-27 gmungocJAL-2416 add score model description field for tooltip... tree | commitdiff
2017-03-27 gmungocJAL-2403 SWDistanceModel now SmithWatermanModel - a... tree | commitdiff
2017-03-27 gmungocJAL-2416 use '-' not space for gap in score matrices tree | commitdiff
2017-03-27 gmungocJAL-2428 unused method deleted tree | commitdiff
2017-03-27 gmungocJAL-2403 PIDDistanceModel deleted as superseded by... tree | commitdiff
2017-03-27 gmungocJAL-2428 pass AlignmentView to TreeModel so Show Input... tree | commitdiff
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin... tree | commitdiff
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... tree | commitdiff
2017-03-23 gmungocJAL-2397 scale PCA by PID to alignment width to match... tree | commitdiff
2017-03-23 gmungocJAL-838 class javadoc added tree | commitdiff
2017-03-23 gmungocJAL-2393 code tidy and comments, PIDDistanceModel depre... tree | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-16 Jim ProcterJAL-1933 refactor parameter for code clarity tree | commitdiff
2017-03-06 gmungocJAL-2428 correct order of processing in joinClusters() tree | commitdiff
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... tree | commitdiff
2017-03-03 gmungocJAL-2428 use BitSet for clusters and done flags tree | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... tree | commitdiff
2017-02-28 gmungocJAL-1632 'includeGaps' applied to FeatureDistanceModel... tree | commitdiff
2017-02-27 gmungocJAL-2416 seqspace.scm and PIDDistanceModel replaced... tree | commitdiff
2017-02-27 gmungocJAL-838 ScoreMatrix now respects SimilarityParams! tree | commitdiff
2017-02-27 gmungocJAL-838 tests for PID calculation with parameter options tree | commitdiff
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... tree | commitdiff
2017-02-27 gmungocJAL-1632 add score model params to PCAModel and PCA... tree | commitdiff
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... tree | commitdiff
2017-02-27 gmungocJAL-2403 JAL-838 remove unused methods and unneeded... tree | commitdiff
2017-02-24 gmungocJAL-838 added 'SeqSpace' PID mode, added parameters... tree | commitdiff
2017-02-24 gmungocJAL-1403 preserve range of distance scores for similarity tree | commitdiff
2017-02-24 gmungocJAL-2403 PIDModel added (wip) tree | commitdiff
2017-02-24 gmungocJAL-2403 code tidy tree | commitdiff
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