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JAL-2163 set title for the alignframe from restored view state
[jalview.git] / src /
2016-07-27 Jim ProcterJAL-2163 set title for the alignframe from restored... patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles tree | commitdiff
2016-07-27 Jim ProcterJAL-2156 resolve and add complementary views for saveAl... tree | commitdiff
2016-07-27 Jim ProcterJAL-2156 refactor saveState & saveAlignment to common... tree | commitdiff
2016-07-27 Jim ProcterJAL-2156 getter for AlignFrame(s) held in a splitframe tree | commitdiff
2016-07-24 Jim ProcterJAL-2154 formatting tree | commitdiff
2016-07-24 Jim ProcterJAL-2154 keep track of incomplete sequences and report... tree | commitdiff
2016-07-24 Jim ProcterJAL-2154 systematic pattern for defining/resolving... tree | commitdiff
2016-07-23 Jim ProcterJAL-2154 patch the hack (Jalview2XML tests pass) tree | commitdiff
2016-07-20 gmungocJAL-2154 poke JSeq start/end into Vamsas sequence tree | commitdiff
2016-07-20 gmungocJAL-2023 stronger check for whether to start cdna consensus tree | commitdiff
2016-07-20 gmungocJAL-2023 avoid writing / loading empty mappings tree | commitdiff
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co... tree | commitdiff
2016-07-20 gmungocJAL-2068 AnnotationWorker create/update annotation... tree | commitdiff
2016-07-19 gmungocJAL-2068 small refactor to reuse shared method tree | commitdiff
2016-07-19 gmungocJAL-2068 update rather than recreate AlignmentAnnotatio... tree | commitdiff
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences tree | commitdiff
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... tree | commitdiff
2016-07-18 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... tree | commitdiff
2016-07-18 Jim ProcterJAL-666 patch JAL-1947 in applet where overview is... tree | commitdiff
2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response tree | commitdiff
2016-07-18 gmungocJAL-2099 ensure initial setting of scaleAbove reaches... tree | commitdiff
2016-07-18 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-07-18 gmungocJAL-2099 JAL-2100 port scale number / hidden column... tree | commitdiff
2016-07-18 Jim ProcterJAL-2068 scale annotation display character to width... tree | commitdiff
2016-07-18 Jim ProcterJAL-2121 cleanup TODO tree | commitdiff
2016-07-18 gmungocJAL-2015 restore check for null colour in paint() tree | commitdiff
2016-07-18 Jim ProcterMerge branch 'features/JAL-2068groovyAnnotationWorker... tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation... tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 documentation of getWidth() tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 JAL-1551 formatting tree | commitdiff
2016-07-18 Jim ProcterJAL-2145 fix: build alignments before building AlignFra... tree | commitdiff
2016-07-14 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-07-14 tcofoegbuJAL-1919 house-keeping tree | commitdiff
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
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