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Merge branch 'develop' into releases/Release_2_9_1_Branch
[jalview.git] / src /
2016-07-14 Jim Procterfix for JAL-2147 tree | commitdiff
2016-07-14 Jim ProcterJAL-2147 findMappingsBetweenSequenceAndOthers for scopi... tree | commitdiff
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility... tree | commitdiff
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI) tree | commitdiff
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... tree | commitdiff
2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-07-13 tcofoegbuJAL-2135 minor house-keeping tree | commitdiff
2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 avoid potential race condition where user... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 TODO for JAL-2131 tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 javadoc tree | commitdiff
2016-07-12 Jim ProcterJAL-2110 scalability todo tree | commitdiff
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO tree | commitdiff
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with... tree | commitdiff
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications tree | commitdiff
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... tree | commitdiff
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... tree | commitdiff
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack tree | commitdiff
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap... tree | commitdiff
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented tree | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds tree | commitdiff
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL... tree | commitdiff
2016-07-06 gmungocJAL-2110 cross-refs from protein to show cds not non... tree | commitdiff
2016-07-06 gmungocJAL-2110 fixes and tests for adding dbrefs to EMBL... tree | commitdiff
2016-07-04 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-07-04 gmungocJAL-2110 use shared dataset when copying alignment... tree | commitdiff
2016-07-04 gmungocRevert "JAL-2110 use shared alignment dataset when... tree | commitdiff
2016-07-04 gmungocJAL-2110 use shared alignment dataset when copying... tree | commitdiff
2016-07-04 gmungocJAL-2110 bug fix / test for searchDataset mappings... tree | commitdiff
2016-07-04 gmungocJAL-2110 unused method removed tree | commitdiff
2016-07-04 gmungocJAL-2110 defensive check in code tree | commitdiff
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs tree | commitdiff
2016-07-01 gmungocJAL-2110 set reasonable bounds to initial split of... tree | commitdiff
2016-07-01 tcofoegbuJAL-2135 bugfix for error preventing processing of... tree | commitdiff
2016-07-01 gmungocJAL-2110 add 'products' parameter to filter results... tree | commitdiff
2016-07-01 gmungocJAL-2110 code/comment tidy tree | commitdiff
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-06-30 tcofoegbuJAL-2074 Improvement to StructureChooser and FTS interf... tree | commitdiff
2016-06-30 gmungocJAL-2110 fixes and tests for synthesized EMBLCDSPROTEIN... tree | commitdiff
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser... tree | commitdiff
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-06-29 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-06-29 tcofoegbuJAL-1479 improved Sifts PID calculation for determining... tree | commitdiff
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-06-29 gmungocJAL-1369 fix bug reloading a project with group sequenc... tree | commitdiff
2016-06-28 tcofoegbuJAL-1479 minor refactor and housekeeping tree | commitdiff
2016-06-28 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-06-28 tcofoegbuJAL-1479 improved SiftsClient test coverage and impleme... tree | commitdiff
2016-06-27 gmungoctidied loop with generic iteration / loop variable tree | commitdiff
2016-06-27 gmungocJAL-2133 refactored duplicated code to AlignmentViewport tree | commitdiff
2016-06-27 gmungocJAL-1270 unit tests for HiddenSequences tree | commitdiff
2016-06-24 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-06-24 tcofoegbuJAL-1960 updated unit test to include the test case... tree | commitdiff
2016-06-23 gmungocJAL-2130 now simply viewer.dispose() to close down... tree | commitdiff
2016-06-23 Jim ProcterMerge branch 'develop' into merge_JAL-2110 tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 make indirect xref searches work by not filter... tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 warning message when routine finds non-ds... tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 clarify javadoc tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 refactor to split SequenceFetcher from x-ref... tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 use SequenceI.isProtein() tree | commitdiff
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method tree | commitdiff
2016-06-22 gmungocJAL-2015 fixed bug in copy constructor and added tests tree | commitdiff
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array tree | commitdiff
2016-06-22 gmungocJAL-1982 defensive test for null array of annotations tree | commitdiff
2016-06-22 Jim ProcterJAL-2110 remove hardwired detection of search context... tree | commitdiff
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications... tree | commitdiff
2016-06-21 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... tree | commitdiff
2016-06-21 gmungocJAL-2074 suppress prompt to save closed Groovy script... tree | commitdiff
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into... tree | commitdiff
2016-06-21 gmungocJAL-2074 reuse Groovy window when reopening; rebind... tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 mark reference sequence & view state and resto... tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 project XML efficiency TODO tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 dead code TODO? tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 ensure *real* alignment’s metadata written... tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 make sure the fake AlignmentI produced by... tree | commitdiff
2016-06-21 Jim ProcterJAL-1369 HUGE WARNING: datamodel.HiddenSequences is... tree | commitdiff
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs... tree | commitdiff
2016-06-21 gmungocJAL-2113 tidy up canonicalisation of Uniprot xrefs... tree | commitdiff
2016-06-20 Jim ProcterJAL-1369 updated project schema - flag on JSeq to mark... tree | commitdiff
2016-06-20 Jim ProcterJAL-2065 port patch to applet tree | commitdiff
2016-06-20 Jim ProcterJAL-1551 tidy tree | commitdiff
2016-06-20 Jim ProcterJAL-1551 tidy tree | commitdiff
2016-06-20 Jim ProcterJAL-2065 don’t pass stale group reference tree | commitdiff
2016-06-20 Jim ProcterJAL-2068 avoid ArrayIndexOutOfBounds when consensus... tree | commitdiff
2016-06-20 Jim ProcterJAL-2065 check position lies within group before gettin... tree | commitdiff
2016-06-20 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-06-20 tcofoegbuJAL-1823 Deleted two obsolete methods in PopupMenu... tree | commitdiff
2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-1812_JAL-2083_... features/JAL-1812_JAL-2083_groovyBinding tree | commitdiff
2016-06-20 gmungocJAL-2130 call viewer.dispose() on closing Jmol tree | commitdiff
2016-06-20 gmungocJAL-1667 updated PDB example query to a valid id (witho... tree | commitdiff
2016-06-20 Jim ProcterJAL-2110 catch case when updateDBRef argument has null... tree | commitdiff
2016-06-20 Jim ProcterJAL-2110 List now used for AlignCodonFrame references tree | commitdiff
2016-06-20 Jim ProcterJAL-2110 copy alcodonframes only if copy constructor... tree | commitdiff
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview... tree | commitdiff
2016-06-17 tcofoegbuJAL-1823 Updated tooltip to reflect how a specific... tree | commitdiff
2016-06-17 tcofoegbuJAL-1976 clear message if export is cancelled at 'Rende... tree | commitdiff
2016-06-17 tcofoegbuJAL-1976 improved exception handler. tree | commitdiff
2016-06-17 tcofoegbuJAL-1976 added an intermediate message between a user... tree | commitdiff
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