JAL-2416 remove unused pep, dna alphabets, unused methods, code format
[jalview.git] / src / jalview / datamodel /
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as...
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode...
2017-02-09 gmungocJAL-2405 check for circular reference in SequenceGroup...
2017-01-27 gmungocJAL-2371 CollectionColourScheme renamed ResidueShader...
2017-01-27 gmungocJAL-2360 JAL-2371 updates from review CR-JAL-1
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit...
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-19 gmungocJAL-2370 corrected applet mouse drag, refactored into...
2017-01-17 gmungocJAL-2370 fix bug when hiding a range including two...
2017-01-09 gmungocJAL-2371 pull up isNucleotide to SequenceCollectionI
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit...
2017-01-06 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-05 gmungocJAL-2374 fix popup out by one and multiple groups bugs
2017-01-05 gmungocJAL-2371 tests added
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI
2016-12-21 gmungocJAL-2360 Javadoc and test cases for findAnnotation
2016-12-14 gmungocJAL-2360 added check for null annotations array
2016-12-12 gmungocJAL-2360 simplify nucleotide flag, remove setter
2016-11-30 gmungocJAL-2344 use ".cif" for saved mmCIF file (and refactor...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
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 gmungocMerge branch 'develop' into bug/JAL-2323disulfideOverview
2016-11-18 gmungocJAL-98 with the two types missing from last commit... bug/JAL-98consensusMemory
2016-11-17 gmungocJAL-98 ProfilesI container for profiles for columns
2016-11-17 gmungocJAL-2327 add isContactFeature
2016-11-16 gmungocJAL-2324 fix and tests for comparison of Float.NaN...
2016-11-10 tcofoegbuBugfix to enable accurate chain extraction/association...
2016-11-04 gmungocJAL-966 JAL-1854 removed redundant methods / modifiers...
2016-11-02 Jim ProcterJAL-345 javadoc and note about JAL-2300
2016-11-02 Jim ProcterJAL-354 JAL-1738 add returns SearchResultMatchI instanc...
2016-11-02 Jim ProcterJAL-966 JAL-345 JAL-1738 decontaminate SearchResultI...
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 Jim ProcterJAL-1738 JAL-345 fix broken calculation of newly marked...
2016-10-30 Jim ProcterJAL-345 JAL-1738 SearchResultI method to mark columns...
2016-10-30 Jim ProcterJAL-966 clarify javadoc for SearchResultsI.getResults
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch'
2016-10-24 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-14 gmungocMerge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties
2016-10-06 gmungocJAL-2254 map error text in root node of EMBL XML response
2016-10-06 gmungocMerge branch 'develop' into bug/JAL-98consensusMemory
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-06 gmungocJAL-2245 checks for null added (in case EMBL fetch...
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-05 Jim ProcterRevert "JAL-2245 Castor mapping and code changes for...
2016-10-05 gmungocJAL-2245 defence against NullPointer if no EMBL data...
2016-10-04 gmungocMerge branch 'bug/JAL-2245enaXmlChange' into develop
2016-10-04 gmungocJAL-2245 Castor mapping and code changes for change... bug/JAL-2245enaXmlChange
2016-10-04 gmungocJAL-2232 JAL-2154 update dbrefs to newly created datase...
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad...
2016-10-03 gmungocJAL-98 use Profile to store consensus, ResidueCount...
2016-10-03 Jim ProcterJAL-2210 need to add both transcript and product, and...
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list:
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc...
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries
2016-09-27 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro...
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources...
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen...
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-09-22 gmungocJAL-2216 finalize() refactored so not called programmat...
2016-09-19 gmungocJAL-2172 test and code updates for readonly selection...
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
2016-09-13 gmungocJAL-2196 refactor PDBEntry.getProperty,setProperty...
2016-09-13 gmungocJAL-1803 extracted class ChainId to jalview.util.CaseIn...
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs
2016-09-05 gmungocJAL-2106 corrections to DBRefEntry.isPrimary code and...
2016-09-04 Jim ProcterJAL-1803 chainCode moved onto property hashtable as...
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
2016-08-31 Jim ProcterJAL-2034 fix logic so recalcConservation(true) returns...
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-26 Jim ProcterJAL-2154 drop PDB from Protein db list to remove from...
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB
2016-08-25 gmungocJAL-1854 missing case break statements added
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision...
2016-08-25 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 Jim ProcterJAL-2106 stricter check for 1:1 mapping (same numbering...
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that...
2016-08-24 Jim ProcterJAL-2106 formatting
2016-08-24 Jim ProcterJAL-2106 DBRefEntry.isPrimary() minimal test & implemen...
2016-08-24 Jim ProcterJAL-2106 convenience method to find all dbsource names...
2016-08-24 gmungocJAL-1424 removed unused and duplicated message keys
2016-08-23 Jim ProcterMerge branch 'develop' into bug/JAL-2154projectMappings
2016-08-23 gmungocJAL-2174 markColumns() refactored inside ColumnSelection
2016-08-22 Jim ProcterJAL-2154 always check dataset sequence for sequence...
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