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JAL-2629 some tidying of Hmmer commands (wip)
[jalview.git]
/
src
/
jalview
/
analysis
/
2017-03-06
gmungoc
JAL-2428 correct order of processing in joinClusters()
tree
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commitdiff
2017-03-06
gmungoc
JAL-2428 separate TreeModel from TreeBuilder/NJTree...
tree
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commitdiff
2017-03-03
gmungoc
JAL-2428 use BitSet for clusters and done flags
tree
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commitdiff
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
tree
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commitdiff
2017-02-28
gmungoc
JAL-1632 'includeGaps' applied to FeatureDistanceModel...
tree
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commitdiff
2017-02-27
gmungoc
JAL-2416 seqspace.scm and PIDDistanceModel replaced...
tree
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commitdiff
2017-02-27
gmungoc
JAL-838 ScoreMatrix now respects SimilarityParams!
tree
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commitdiff
2017-02-27
gmungoc
JAL-838 tests for PID calculation with parameter options
tree
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commitdiff
2017-02-27
gmungoc
JAL-1632 similarity options on TreeChooser panel affect...
tree
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commitdiff
2017-02-27
gmungoc
JAL-1632 add score model params to PCAModel and PCA...
tree
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commitdiff
2017-02-27
gmungoc
JAL-1632 refactored NJTree constructor to include Simil...
tree
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commitdiff
2017-02-27
gmungoc
JAL-2403 JAL-838 remove unused methods and unneeded...
tree
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commitdiff
2017-02-24
gmungoc
JAL-838 added 'SeqSpace' PID mode, added parameters...
tree
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commitdiff
2017-02-24
gmungoc
JAL-1403 preserve range of distance scores for similarity
tree
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commitdiff
2017-02-24
gmungoc
JAL-2403 PIDModel added (wip)
tree
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commitdiff
2017-02-24
gmungoc
JAL-2403 code tidy
tree
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commitdiff
2017-02-24
gmungoc
JAL-1483 PIDModel potential replacement for PIDDistance...
tree
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commitdiff
2017-02-24
gmungoc
JAL-838 first version of PID parameters model
tree
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commitdiff
2017-02-24
gmungoc
JAL-2403 remove unused ScoreMatrix.symmetric
tree
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commitdiff
2017-02-24
gmungoc
JAL-2403 JAL-1483 push 'reverseRange' inside Matrix
tree
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commitdiff
2017-02-23
gmungoc
JAL-2403 JAL-1483 changes to ScoreModelI hierarchy...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 ScoreMatrix.getMatrix() returns a defensive...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 support roundtrip print/parse of ScoreMatrix
tree
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commitdiff
2017-02-21
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 quality calculation now only depends on loaded...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 more validation in ScoreMatrix constructor
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commitdiff
2017-02-20
gmungoc
JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix...
tree
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commitdiff
2017-02-20
gmungoc
JAL-2416 replaced dependency on ResidueProperties with...
tree
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commitdiff
2017-02-20
gmungoc
JAL-2416 remove unused pep, dna alphabets, unused metho...
tree
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commitdiff
2017-02-18
gmungoc
JAL-2416 better encapsulated 'constants' for BLOSUM62...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 BLOSUM62 removed from ResidueProperties
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 removed DNA and PAM250 matrices from ResiduePr...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 scoreMatrices removed from ResidueProperties
tree
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commitdiff
2017-02-17
gmungoc
JAL-2413 extracted new method SetUtils.countDisjunction()
tree
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commitdiff
2017-02-17
gmungoc
JAL-2423 refactored method to build panel title for...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 order score models by order of addition rather...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 redundant 'implements' removed
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 extract method refactoring of FeatureScoreMode...
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 constants for "NJ", "AV"
tree
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commitdiff
2017-02-14
gmungoc
Parsing moved to (new) ScoreMatrixFile, drag and drop...
tree
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commitdiff
2017-02-13
gmungoc
JAL-2416 allow alphabet symbol (optional) in first...
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
tree
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commitdiff
2017-02-13
gmungoc
JAL-1632 first cut of Tree chooser dialog and ScoreMode...
tree
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commitdiff
2017-02-09
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
features/JAL-2379pcaMemory
tree
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commitdiff
2017-02-07
gmungoc
JAL-2379 removed unused commented code
tree
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commitdiff
2017-02-06
gmungoc
JAL-2379 computePairwiseScores() moved to ScoreMatrix
tree
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commitdiff
2017-02-03
gmungoc
JAL-2379 'direct' pairwise score calculation for PCA...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2379pcaMemory
tree
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commitdiff
2017-01-26
gmungoc
JAL-2380 code tidy after review
tree
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commitdiff
2017-01-17
gmungoc
JAL-2379 use SparseMatrix for encoded sequences, tidy...
tree
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commitdiff
2017-01-04
gmungoc
JAL-2371 CollectionColourScheme wraps ColourSchemeI
tree
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commitdiff
2016-12-16
gmungoc
JAL-1705 JAL-98 use SortedMap as more accurate type...
tree
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commitdiff
2016-12-05
gmungoc
Merge branch 'features/JAL-1933_occupancy' into feature...
tree
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commitdiff
2016-12-04
Jim Procter
JAL-1933 show occupancy count as a tooltip
tree
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commitdiff
2016-12-04
Jim Procter
JAL-1933 switch from gap count to occupancy
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commitdiff
2016-12-02
gmungoc
Merge branch 'features/JAL-1933_occupancy' into feature...
tree
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commitdiff
2016-12-02
gmungoc
JAL-1933 gap value as description; minor formatting
tree
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commitdiff
2016-12-01
Jim Procter
JAL-1933 update the bounds for the Gap annotation row...
tree
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commitdiff
2016-12-01
Jim Procter
JAL-1933 basic hack to get gap counts shown as an annot...
tree
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commitdiff
2016-11-23
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-22
Jim Procter
Merge branch 'features/JAL-1738_JAL-345_selectionfromhi...
tree
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commitdiff
2016-11-17
gmungoc
JAL-98 ProfilesI container for profiles for columns
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commitdiff
2016-11-11
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2016-11-08
gmungoc
JAL-2295 make RangeComparator a top level class for...
tree
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commitdiff
2016-11-08
tcofoegbu
JAL-2292 updated method calls
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commitdiff
2016-11-04
tcofoegbu
JAL-2292 fix for wrong mapping output in sequence mappi...
tree
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commitdiff
2016-11-03
gmungoc
JAL-2310 don't double-count sequence matches; code...
tree
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commitdiff
2016-11-02
Jim Procter
JAL-1738 JAL-345 fix for JAL-2302 only report Matches...
tree
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commitdiff
2016-11-02
gmungoc
JAL-98 JAL-1854 encapsulate 'magic number' threshold...
tree
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commitdiff
2016-11-02
gmungoc
JAL-98 ProfileI interface for Profile
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commitdiff
2016-11-02
gmungoc
JAL-98 Profile and ResidueCount moved from analysis...
tree
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commitdiff
2016-11-02
gmungoc
JAL-98 wording "negatively conserved" now "absence...
tree
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commitdiff
2016-11-01
gmungoc
Conservation now using ResidueCount; tests added
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commitdiff
2016-11-01
gmungoc
JAL-98 typo in javadoc
tree
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commitdiff
2016-10-28
Jim Procter
JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
tree
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commitdiff
2016-10-25
gmungoc
JAL-98 javadoc corrected
tree
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commitdiff
2016-10-25
gmungoc
JAL-98 javadoc added
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commitdiff
2016-10-25
gmungoc
JAL-98 minor fixes to / tests for annotation derivation
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commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
tree
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commitdiff
2016-10-25
gmungoc
JAL-98 small efficiency fix + commenting
tree
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commitdiff
2016-10-25
gmungoc
JAL-98 javadoc / comments updated
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commitdiff
2016-10-24
gmungoc
JAL-98 fixme comment removed - nothing to do
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commitdiff
2016-10-24
gmungoc
JAL-98 ResidueCount 100% test coverage (and bug fixes!)
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commitdiff
2016-10-06
gmungoc
Merge branch 'develop' into bug/JAL-98consensusMemory
tree
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
tree
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commitdiff
2016-10-05
Jim Procter
JAL-2189 source formatting
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commitdiff
2016-10-03
gmungoc
JAL-98 use Profile to store consensus, ResidueCount...
tree
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commitdiff
2016-10-03
Jim Procter
JAL-2210 hack to remove EMBL from Protein crossrefs...
tree
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commitdiff
2016-10-03
Jim Procter
JAL-2210 explicit ‘doNotAdd’ list to prevent sequences...
tree
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commitdiff
2016-10-02
Jim Procter
JAL-2210 two pass attempt to import retrieved sequences...
tree
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commitdiff
2016-10-02
Jim Procter
JAL-2210 try to merge all sequences referenced by a...
tree
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commitdiff
2016-10-02
Jim Procter
JAL-2210 comments
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commitdiff
2016-10-02
Jim Procter
JAL-2210 discover candidate dataset sequences for an...
tree
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commitdiff
2016-10-01
Jim Procter
JAL-2210 factored out code for processing cross-referen...
tree
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commitdiff
2016-10-01
Jim Procter
JAL-2210 refactor code to remove from a list of dbrefs...
tree
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commitdiff
2016-09-30
Jim Procter
JAL-2210 some DBRef xref/ref correspondences may add...
tree
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commitdiff
2016-09-30
Jim Procter
JAL-2210 CrossRef.findInDataset should search for prese...
tree
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commitdiff
2016-09-30
gmungoc
Merge branch 'develop' into bug/JAL-98consensusMemory
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