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JAL-1632 add score model params to PCAModel and PCA constructors
[jalview.git] / src / jalview / datamodel /
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy... tree | commitdiff
2017-02-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... tree | commitdiff
2017-02-20 Jim ProcterMerge branch 'features/JAL-2379pcaMemory' into develop tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 new contains methods for seq and seq,apos tree | commitdiff
2017-02-15 Jim ProcterJAL-2374 javadoc - qualify that sequence argument to... tree | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... tree | commitdiff
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... tree | commitdiff
2017-02-09 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory tree | commitdiff
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup... tree | commitdiff
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader... tree | commitdiff
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1 tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2379pcaMemory tree | commitdiff
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-19 gmungocJAL-2370 corrected applet mouse drag, refactored into... tree | commitdiff
2017-01-17 gmungocJAL-2370 fix bug when hiding a range including two... tree | commitdiff
2017-01-17 gmungocJAL-2379 use SparseMatrix for encoded sequences, tidy... tree | commitdiff
2017-01-09 gmungocJAL-2371 pull up isNucleotide to SequenceCollectionI tree | commitdiff
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-06 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-05 gmungocJAL-2374 fix popup out by one and multiple groups bugs tree | commitdiff
2017-01-05 gmungocJAL-2371 tests added tree | commitdiff
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI tree | commitdiff
2016-12-21 gmungocJAL-2360 Javadoc and test cases for findAnnotation tree | commitdiff
2016-12-14 gmungocJAL-2360 added check for null annotations array tree | commitdiff
2016-12-12 gmungocJAL-2360 simplify nucleotide flag, remove setter tree | commitdiff
2016-11-30 gmungocJAL-2344 use ".cif" for saved mmCIF file (and refactor... tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-24 Jim ProcterJAL-2325 apply license to new source files tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop tree | commitdiff
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi... tree | commitdiff
2016-11-21 gmungocMerge branch 'develop' into bug/JAL-2323disulfideOverview tree | commitdiff
2016-11-18 gmungocJAL-98 with the two types missing from last commit... bug/JAL-98consensusMemory tree | commitdiff
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns tree | commitdiff
2016-11-17 gmungocJAL-2327 add isContactFeature tree | commitdiff
2016-11-16 gmungocJAL-2324 fix and tests for comparison of Float.NaN... tree | commitdiff
2016-11-10 tcofoegbuBugfix to enable accurate chain extraction/association... tree | commitdiff
2016-11-04 gmungocJAL-966 JAL-1854 removed redundant methods / modifiers... tree | commitdiff
2016-11-02 Jim ProcterJAL-345 javadoc and note about JAL-2300 tree | commitdiff
2016-11-02 Jim ProcterJAL-354 JAL-1738 add returns SearchResultMatchI instanc... tree | commitdiff
2016-11-02 Jim ProcterJAL-966 JAL-345 JAL-1738 decontaminate SearchResultI... tree | commitdiff
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold... tree | commitdiff
2016-11-02 gmungocJAL-98 ProfileI interface for Profile tree | commitdiff
2016-11-02 gmungocJAL-98 Profile and ResidueCount moved from analysis... tree | commitdiff
2016-11-01 Jim ProcterJAL-1738 JAL-345 fix broken calculation of newly marked... tree | commitdiff
2016-10-30 Jim ProcterJAL-345 JAL-1738 SearchResultI method to mark columns... tree | commitdiff
2016-10-30 Jim ProcterJAL-966 clarify javadoc for SearchResultsI.getResults tree | commitdiff
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... tree | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch tree | commitdiff
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch' tree | commitdiff
2016-10-24 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory tree | commitdiff
2016-10-14 gmungocMerge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties tree | commitdiff
2016-10-06 gmungocJAL-2254 map error text in root node of EMBL XML response tree | commitdiff
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory tree | commitdiff
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties tree | commitdiff
2016-10-06 gmungocJAL-2245 checks for null added (in case EMBL fetch... tree | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 apply license tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting tree | commitdiff
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties tree | commitdiff
2016-10-05 Jim ProcterRevert "JAL-2245 Castor mapping and code changes for... tree | commitdiff
2016-10-05 gmungocJAL-2245 defence against NullPointer if no EMBL data... tree | commitdiff
2016-10-04 gmungocMerge branch 'bug/JAL-2245enaXmlChange' into develop tree | commitdiff
2016-10-04 gmungocJAL-2245 Castor mapping and code changes for change... bug/JAL-2245enaXmlChange tree | commitdiff
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase... tree | commitdiff
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad... tree | commitdiff
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount... tree | commitdiff
2016-10-03 Jim ProcterJAL-2210 need to add both transcript and product, and... tree | commitdiff
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list: tree | commitdiff
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc... tree | commitdiff
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries tree | commitdiff
2016-09-27 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro... tree | commitdiff
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources... tree | commitdiff
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen... tree | commitdiff
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... tree | commitdiff
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat... tree | commitdiff
2016-09-19 gmungocJAL-2172 test and code updates for readonly selection... tree | commitdiff
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds... tree | commitdiff
2016-09-13 gmungocJAL-2196 refactor PDBEntry.getProperty,setProperty... tree | commitdiff
2016-09-13 gmungocJAL-1803 extracted class ChainId to jalview.util.CaseIn... tree | commitdiff
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157 tree | commitdiff
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry tree | commitdiff
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid... tree | commitdiff
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs tree | commitdiff
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and... tree | commitdiff
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as... tree | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:... tree | commitdiff
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns... tree | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... tree | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum tree | commitdiff
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings tree | commitdiff
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from... tree | commitdiff
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB tree | commitdiff
2016-08-25 gmungocJAL-1854 missing case break statements added tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision... tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... tree | commitdiff
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