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2016-08-01 Jim ProcterJAL-2164 TODO: make test pass for JMOL_PARSER commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterJAL-2164 JAL-1919 JAL-1270 use structure import setting... commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-08-01 tcofoegbuJAL-2164 bugfix to convert insCodes of '\000' to '... commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterMerge branch 'bug/JAL-2154projectMappings' into develop commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterMerge branch 'task/JAL-2164_mcviewforoldjalviewprojects... commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterJAL-2164 prevent jalview news from opening task/JAL-2164_mcviewforoldjalviewprojects commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterJAL-2164 clear the desktop before testStoreAndRecoverEx... commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterMerge branch 'task/JAL-2164_mcviewforoldjalviewprojects... commit | commitdiff | tree | snapshot
2016-08-01 Jim ProcterJAL-1772 make sure we actually return reference to... commit | commitdiff | tree | snapshot
2016-07-29 Jim ProcterJAL-1772 JAL-2164 make expanded view save/restore test... commit | commitdiff | tree | snapshot
2016-07-29 Jim ProcterJAL-2164 JAL-1772 explodeViews can be static, so make... commit | commitdiff | tree | snapshot
2016-07-29 tcofoegbuJAL-1957 JAL-1479 updated SIFTS user docs commit | commitdiff | tree | snapshot
2016-07-29 Jim ProcterJAL-2164 revert tests depending on import of legacy... commit | commitdiff | tree | snapshot
2016-07-29 Jim ProcterJAL-2154 disable visual delay only after completed... commit | commitdiff | tree | snapshot
2016-07-29 Jim ProcterJAL-2154 register any new dataset codon frames only... commit | commitdiff | tree | snapshot
2016-07-29 Jim ProcterJAL-2154 only include mappings in dbref/alcodon in... commit | commitdiff | tree | snapshot
2016-07-29 tcofoegbuJAL-2157 fixed Jalview2xmlTest commit | commitdiff | tree | snapshot
2016-07-27 Jim ProcterJAL-2154 toString for forward references commit | commitdiff | tree | snapshot
2016-07-27 Jim ProcterMerge branch 'patch/JAL-2156_JAL-2163_saveSplitFrameFro... commit | commitdiff | tree | snapshot
2016-07-27 Jim ProcterJAL-2163 set title for the alignframe from restored... patch/JAL-2156_JAL-2163_saveSplitFrameFromSaveAs_restoreTitles commit | commitdiff | tree | snapshot
2016-07-27 Jim ProcterJAL-2156 resolve and add complementary views for saveAl... commit | commitdiff | tree | snapshot
2016-07-27 Jim ProcterJAL-2156 refactor saveState & saveAlignment to common... commit | commitdiff | tree | snapshot
2016-07-27 Jim ProcterJAL-2156 getter for AlignFrame(s) held in a splitframe commit | commitdiff | tree | snapshot
2016-07-27 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-27 tcofoegbuJAL-1919 added codes for End-2-End scan for sequence... commit | commitdiff | tree | snapshot
2016-07-26 Jim ProcterJAL-2157 todo: verify parser/file format enums and... commit | commitdiff | tree | snapshot
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring commit | commitdiff | tree | snapshot
2016-07-25 tcofoegbuJAL-2157 bugfix for regression from commit 82a6c8e2e25b... commit | commitdiff | tree | snapshot
2016-07-24 Jim ProcterJAL-2154 formatting commit | commitdiff | tree | snapshot
2016-07-24 Jim ProcterJAL-2154 keep track of incomplete sequences and report... commit | commitdiff | tree | snapshot
2016-07-24 Jim ProcterJAL-2154 systematic pattern for defining/resolving... commit | commitdiff | tree | snapshot
2016-07-23 Jim ProcterJAL-2154 patch the hack (Jalview2XML tests pass) commit | commitdiff | tree | snapshot
2016-07-22 tcofoegbuJAL-2148 Bugfix in structureImportSettings string-to... commit | commitdiff | tree | snapshot
2016-07-21 tcofoegbuResolve merge conflict for StructureImportSettings commit | commitdiff | tree | snapshot
2016-07-21 tcofoegbuJAL-2148 fix to heuristically determine chain terminati... commit | commitdiff | tree | snapshot
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop commit | commitdiff | tree | snapshot
2016-07-20 gmungocJAL-2154 poke JSeq start/end into Vamsas sequence commit | commitdiff | tree | snapshot
2016-07-20 Jim ProcterJAL-1926 JAL-2106 fix name for flag controlling additio... commit | commitdiff | tree | snapshot
2016-07-20 Jim ProcterJAL-1926 JAL-2106 don’t use PDB database constant as... commit | commitdiff | tree | snapshot
2016-07-20 Jim ProcterJAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMA... commit | commitdiff | tree | snapshot
2016-07-20 Jim ProcterJAL-1926 JAL-2106 remove startRes/endRes fields - not... commit | commitdiff | tree | snapshot
2016-07-20 gmungocJAL-2023 stronger check for whether to start cdna consensus commit | commitdiff | tree | snapshot
2016-07-20 gmungocJAL-2023 avoid writing / loading empty mappings commit | commitdiff | tree | snapshot
2016-07-20 gmungocJAL-2023 JAL-1681 fixed bug in computing '+' for co... commit | commitdiff | tree | snapshot
2016-07-20 gmungocJAL-2068 AnnotationWorker create/update annotation... commit | commitdiff | tree | snapshot
2016-07-19 gmungocJAL-2068 small refactor to reuse shared method commit | commitdiff | tree | snapshot
2016-07-19 gmungocJAL-2068 update rather than recreate AlignmentAnnotatio... commit | commitdiff | tree | snapshot
2016-07-19 gmungocJAL-391 corrected handling of gapped sequences commit | commitdiff | tree | snapshot
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-666 patch JAL-1947 in applet where overview is... commit | commitdiff | tree | snapshot
2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response commit | commitdiff | tree | snapshot
2016-07-18 gmungocJAL-2099 ensure initial setting of scaleAbove reaches... commit | commitdiff | tree | snapshot
2016-07-18 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-18 gmungocJAL-2099 JAL-2100 port scale number / hidden column... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2068 clearer instructions on how to use script... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2068 clarify comments commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2068 scale annotation display character to width... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2121 cleanup TODO commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2110 JAL-2145 fix out of date test for 2baee069f9ed... commit | commitdiff | tree | snapshot
2016-07-18 gmungocJAL-1976 Spanish version of new message commit | commitdiff | tree | snapshot
2016-07-18 gmungocJAL-2015 restore check for null colour in paint() commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterMerge branch 'features/JAL-2068groovyAnnotationWorker... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2145 improvement: ensure conservation calculation... commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2145 documentation of getWidth() commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2145 JAL-1551 formatting commit | commitdiff | tree | snapshot
2016-07-18 Jim ProcterJAL-2145 fix: build alignments before building AlignFra... commit | commitdiff | tree | snapshot
2016-07-14 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-14 tcofoegbuJAL-1919 house-keeping commit | commitdiff | tree | snapshot
2016-07-14 Jim Procterfix for JAL-2147 commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-2147 findMappingsBetweenSequenceAndOthers for scopi... commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-1115 change implementation to avoid possibility... commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-1270 test coverage TODO Alignment.append(AlignmentI) commit | commitdiff | tree | snapshot
2016-07-14 Jim ProcterJAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr... commit | commitdiff | tree | snapshot
2016-07-13 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications... commit | commitdiff | tree | snapshot
2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD... commit | commitdiff | tree | snapshot
2016-07-13 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-07-13 tcofoegbuJAL-2135 minor house-keeping commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2144 TODO - new methods for canonicalisation and... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 avoid potential race condition where user... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 TODO for JAL-2131 commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 note about use case for when alignAsSameSequen... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 test demonstrating limitation of current imple... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 javadoc and TODO re shortcomings of implementation commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 javadoc commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-2110 scalability todo commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-1381 JAL-2110 efficiency TODO commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... commit | commitdiff | tree | snapshot
2016-07-12 Jim ProcterJAL-1369 release notes for patch of save/restore repres... commit | commitdiff | tree | snapshot
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with... commit | commitdiff | tree | snapshot
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications commit | commitdiff | tree | snapshot
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... commit | commitdiff | tree | snapshot
2016-07-07 gmungocJAL-2110 added alignAsSameSequences to handle 'direct... commit | commitdiff | tree | snapshot
2016-07-07 gmungocJAL-2110 field 'cf' moved to stack commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 generic rather than specific check for gap... commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 AlignmentUtils.alignCdsAsProtein implemented commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds commit | commitdiff | tree | snapshot
2016-07-06 gmungocJAL-2110 add 'mapFromId' to Mapping (for e.g. EMBL... commit | commitdiff | tree | snapshot
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