JAL-1803 JAL-2106 patch tests for tighter PDB Primary DBRef definition
[jalview.git] / src /
2016-07-12 Jim ProcterJAL-2110 javadoc
2016-07-12 Jim ProcterJAL-2110 scalability todo
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with...
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing...
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct...
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap...
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL...
2016-07-06 gmungocJAL-2110 cross-refs from protein to show cds not non...
2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL...
2016-07-04 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment...
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when...
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying...
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings...
2016-07-04 gmungocJAL-2110 unused method removed
2016-07-04 gmungocJAL-2110 defensive check in code
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-07-01 gmungocJAL-2110 set reasonable bounds to initial split of...
2016-07-01 tcofoegbuJAL-2135 bugfix for error preventing processing of...
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results...
2016-07-01 gmungocJAL-2110 code/comment tidy
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-30 tcofoegbuJAL-2074 Improvement to StructureChooser and FTS interf...
2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN...
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-29 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-29 tcofoegbuJAL-1479 improved Sifts PID calculation for determining...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-29 gmungocJAL-1369 fix bug reloading a project with group sequenc...
2016-06-28 tcofoegbuJAL-1479 minor refactor and housekeeping
2016-06-28 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-28 tcofoegbuJAL-1479 improved SiftsClient test coverage and impleme...
2016-06-27 gmungoctidied loop with generic iteration / loop variable
2016-06-27 gmungocJAL-2133 refactored duplicated code to AlignmentViewport
2016-06-27 gmungocJAL-1270 unit tests for HiddenSequences
2016-06-24 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-24 tcofoegbuJAL-1960 updated unit test to include the test case...
2016-06-23 gmungocJAL-2130 now simply viewer.dispose() to close down...
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter...
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds...
2016-06-23 Jim ProcterJAL-2110 clarify javadoc
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref...
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein()
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method
2016-06-22 gmungocJAL-2015 fixed bug in copy constructor and added tests
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
2016-06-22 gmungocJAL-1982 defensive test for null array of annotations
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context...
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
2016-06-21 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie...
2016-06-21 gmungocJAL-2074 suppress prompt to save closed Groovy script...
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
2016-06-21 gmungocJAL-2074 reuse Groovy window when reopening; rebind...
2016-06-21 Jim ProcterJAL-1369 mark reference sequence & view state and resto...
2016-06-21 Jim ProcterJAL-1369 project XML efficiency TODO
2016-06-21 Jim ProcterJAL-1369 dead code TODO?
2016-06-21 Jim ProcterJAL-1369 ensure *real* alignment’s metadata written...
2016-06-21 Jim ProcterJAL-1369 make sure the fake AlignmentI produced by...
2016-06-21 Jim ProcterJAL-1369 HUGE WARNING: datamodel.HiddenSequences is...
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs...
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs...
2016-06-20 Jim ProcterJAL-1369 updated project schema - flag on JSeq to mark...
2016-06-20 Jim ProcterJAL-2065 port patch to applet
2016-06-20 Jim ProcterJAL-1551 tidy
2016-06-20 Jim ProcterJAL-1551 tidy
2016-06-20 Jim ProcterJAL-2065 don’t pass stale group reference
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus...
2016-06-20 Jim ProcterJAL-2065 check position lies within group before gettin...
2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-2068groovyAnno... features/JAL-2068groovyAnnotationWorker
2016-06-20 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-20 tcofoegbuJAL-1823 Deleted two obsolete methods in PopupMenu...
2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-1812_JAL-2083_... features/JAL-1812_JAL-2083_groovyBinding
2016-06-20 gmungocJAL-2130 call viewer.dispose() on closing Jmol
2016-06-20 gmungocJAL-1667 updated PDB example query to a valid id (witho...
2016-06-20 Jim ProcterJAL-2110 catch case when updateDBRef argument has null...
2016-06-20 Jim ProcterJAL-2110 List now used for AlignCodonFrame references
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor...
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
2016-06-17 tcofoegbuJAL-1823 Updated tooltip to reflect how a specific...
2016-06-17 tcofoegbuJAL-1976 clear message if export is cancelled at 'Rende...
2016-06-17 tcofoegbuJAL-1976 improved exception handler.
2016-06-17 tcofoegbuJAL-1976 added an intermediate message between a user...
2016-06-16 gmungocJAL-1993 close sequence fetcher when opening database...
2016-06-16 Jim ProcterJAL-2110 todo - select mappings involving sequences...
2016-06-16 Jim ProcterJAL-2110 equals and hashcode should check fromSeq
2016-06-16 Jim ProcterJAL-2110 throw implementation error if not given a...
2016-06-16 Jim ProcterJAL-2110 typo caused infinite loop
2016-06-16 gmungocJAL-2112 optimisation of EMBL CDS parsing
2016-06-16 gmungocJAL-1993 hide sequence fetcher dialogue until database...
2016-06-15 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-15 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-06-15 tcofoegbuJAL-2002 disabled 'Best Uniport Coverage' filter. JAL...
2016-06-15 gmungocJAL-2025 unit tests added
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