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2014-11-24 Jim ProcterJAL-1595 update annotation sort on opening of the ... commit | commitdiff | tree | snapshot
2014-11-24 Jim ProcterJAL-1595 annotation score is total number of rna helices commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 interactive editing of secondary structure... commit | commitdiff | tree | snapshot
2014-11-23 Jim Procteremploy test and secondary structure character for deter... commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 formatting commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1593 allow per-sequence shading of RNA helix (store... commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 test for open/close RNA parenthesis character commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 formatting commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 refactoring of stockholm test commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 consistent handling of sequence and alignment... commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 revise tests to count number and type of annot... commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 formatting commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 preserve input ordering for stockholm files... commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1569 remove stdout on parsing RNA commit | commitdiff | tree | snapshot
2014-11-23 Jim ProcterJAL-1152 avoid NPE on null alignment annotation vector commit | commitdiff | tree | snapshot
2014-11-21 Jim ProcterJAL-674 add RNA sequence associated annotation to align... commit | commitdiff | tree | snapshot
2014-11-21 Jim ProcterJAL-1569 formatting commit | commitdiff | tree | snapshot
2014-11-21 Jim ProcterJAL-1140 sensible name for seuqences in RNAML files... commit | commitdiff | tree | snapshot
2014-11-21 Jim ProcterJAL-1489 change initial value to distinguish non-rna... commit | commitdiff | tree | snapshot
2014-11-21 Jim ProcterJAL-1592 JAL-1489 avoid invalid RNA structure and disti... commit | commitdiff | tree | snapshot
2014-11-20 Jim ProcterJAL-1569 rna pair code in secondary structure character... commit | commitdiff | tree | snapshot
2014-11-20 Jim ProcterJAL-674 JAL-1569 mark RNA helix number in the value... commit | commitdiff | tree | snapshot
2014-11-20 Jim ProcterJAL-1569 remove log output during RNA secondary structu... commit | commitdiff | tree | snapshot
2014-11-17 Jim ProcterJAL-1469 help documentation commit | commitdiff | tree | snapshot
2014-11-17 Jim ProcterJAL-1469 help documentation commit | commitdiff | tree | snapshot
2014-11-17 Jim ProcterMerge branch 'mrg_dev_282' into Release_2_8_2_Branch commit | commitdiff | tree | snapshot
2014-11-17 Jim ProcterMerge branch 'Release_2_8_2_Branch' into mrg_dev_282 commit | commitdiff | tree | snapshot
2014-11-17 Charles Ofoegbucomand line support for svg generation commit | commitdiff | tree | snapshot
2014-11-17 gmungocJAL-1580 size parameters dialog to height of Desktop commit | commitdiff | tree | snapshot
2014-11-17 Charles OfoegbuMerge branch 'bug/JAL-1570_unable-to-add-JABAWS-Server... commit | commitdiff | tree | snapshot
2014-11-17 Charles OfoegbuJAL-1570 patch to enable adding a webservice which... commit | commitdiff | tree | snapshot
2014-11-17 Jim ProcterMerge branch 'mrg_dev_282' into Release_2_8_2_Branch commit | commitdiff | tree | snapshot
2014-11-17 gmungocJAL-1528 Chimera Help doc + fixes to setting colours commit | commitdiff | tree | snapshot
2014-11-17 gmungocJAL-1528 new Preference CHIMERA_PATH (Preferences ... commit | commitdiff | tree | snapshot
2014-11-17 gmungocJAL-1528 Chimera tidy errors, focus after align, close... commit | commitdiff | tree | snapshot
2014-11-17 gmungocJAL-1528 bug fixes and adjustments to Chimera interface commit | commitdiff | tree | snapshot
2014-11-17 Jim ProcterMerge commit '1d9e1c80fb6c0e32313a976ae0065fd32639f2bc... commit | commitdiff | tree | snapshot
2014-11-13 Jim ProcterMerge branch 'features/JAL-1469_svg-output-for-figure... commit | commitdiff | tree | snapshot
2014-11-13 Jim ProcterJAL-1469 added jfreesvg to desktop dependencies commit | commitdiff | tree | snapshot
2014-11-12 Charles Ofoegbuhouse-keeping commit | commitdiff | tree | snapshot
2014-11-12 Charles OfoegbuAdded support for SVG Export commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into... commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-974 fix class contamination for jalviewLite build commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into... commit | commitdiff | tree | snapshot
2014-11-12 Jim Procterjavadoc commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-674 use the getMapping/transfer to transfer annotat... commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-674 patch broken getMapping function commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-674 switch from .transfer to .liftOver for transfer... commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-674 note about broken .transfer method (expect... commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-674 javadoc commit | commitdiff | tree | snapshot
2014-11-12 Jim ProcterJAL-674 new tests and deprecated tests for PDB mapping... commit | commitdiff | tree | snapshot
2014-11-11 gmungocJAL-1527 opening a project saved with JMol should use... commit | commitdiff | tree | snapshot
2014-11-06 Jim ProcterMerge branch 'features/JAL-1152annotationSorting' into... commit | commitdiff | tree | snapshot
2014-11-06 gmungocJAL-1152 use a proper RadioButton not a faked one commit | commitdiff | tree | snapshot
2014-11-05 gmungocJAL-674 Prefences tweaks incl help documentation for... commit | commitdiff | tree | snapshot
2014-11-05 gmungocJAL-1152 new Structure tab on Preferences for SS deriva... commit | commitdiff | tree | snapshot
2014-11-04 gmungocJAL-1152 help updates for Preferences commit | commitdiff | tree | snapshot
2014-11-04 gmungocJAL-1152 annotation sort algorithm optimisation commit | commitdiff | tree | snapshot
2014-11-04 Jim ProcterJAL-1213 normalise sequence extracted from Jmol in... commit | commitdiff | tree | snapshot
2014-11-04 Jim ProcterJAL-1213 test to ensure JMol extracted sequences are... commit | commitdiff | tree | snapshot
2014-11-03 gmungocMerge branch 'features/JAL-1152annotationSorting' of... commit | commitdiff | tree | snapshot
2014-11-03 gmungocJAL-1152 annotation sorting preferences and help docume... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotation... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterMerge branch 'bug/JAL-1250_redundance-removal' into... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotation... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterMerge branch 'features/ssFromPDBEntry' into develop commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-795 JAL-674 tweaked logic to avoid black annotation... commit | commitdiff | tree | snapshot
2014-11-03 Jim Procterfix for JAL-1579 create threshold object for annotation... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-1578 test property accessors/copy constructor commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-1578 JAL-674 store/restore alignment annotation... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-1578 formatting and imports commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-674 peptide structure input so test is not dependen... commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor... commit | commitdiff | tree | snapshot
2014-11-03 Jim Procterjavadoc commit | commitdiff | tree | snapshot
2014-10-31 gmungocJAL-1152 bug fix for 'no sort' case + tests for autocal... commit | commitdiff | tree | snapshot
2014-10-31 gmungocJAL-1152 menu tweaks plus new option to put Autocalc... commit | commitdiff | tree | snapshot
2014-10-31 Jim ProcterJAL-674 JAL-961 pass row reference to handler to check... commit | commitdiff | tree | snapshot
2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional informat... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterMerge branch 'develop' into features/ssFromPDBEntry commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 hang on to sequences created by secondary parsi... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 count number of annotation transferred in test commit | commitdiff | tree | snapshot
2014-10-30 gmungocJAL-1152 with sticky annotation sort order that updates... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 propagate annotation onto mapped sequence and... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 register PDB IDs when ever they are resolved... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 use PDB ID<>File registry to look up correct... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 flag and proxy method to distinguish setMapping... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 map on StructureSelectionManager to record... commit | commitdiff | tree | snapshot
2014-10-30 Jim Procterpatch for JAL-795 - use base secondary structure colour... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-674 patch test to verify presence of annotation... commit | commitdiff | tree | snapshot
2014-10-30 Jim ProcterJAL-1551 format and tidy commit | commitdiff | tree | snapshot
2014-10-30 gmungocJAL-1152 prototype of new Annotations menu with sort... commit | commitdiff | tree | snapshot
2014-10-30 Charles OfoegbuJAL-353 updated patch for undo successive remove redund... commit | commitdiff | tree | snapshot
2014-10-29 Charles OfoegbuJAL-353 updated patch for undo successive remove redund... commit | commitdiff | tree | snapshot
2014-10-29 Jim ProcterJAL-1264 JAL-674 test to exercise the AlignmentAnnotati... commit | commitdiff | tree | snapshot
2014-10-29 Jim ProcterJAL-1264 JAL-674 method to copy annotation on structure... commit | commitdiff | tree | snapshot
2014-10-29 Jim ProcterJAL-674 JAL-1264 remap method to allow annotation posit... commit | commitdiff | tree | snapshot
2014-10-28 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
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