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jalview.git
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 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 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
2014-10-29 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
2014-10-28 gmungocJAL-1264 refactor to add menu options to _both_ sequenc... commit | commitdiff | tree | snapshot
2014-10-27 Jim ProcterMerge branch 'Release_2_8_2_Branch' into merge_r282_dev commit | commitdiff | tree | snapshot
2014-10-23 Jim ProcterMerge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch commit | commitdiff | tree | snapshot
2014-10-23 Jim ProcterMerge branch 'hotfix/JAL-1521' into develop commit | commitdiff | tree | snapshot
2014-10-23 unknownJAL-1521 updated xerces to 2.11 along with xml-apis commit | commitdiff | tree | snapshot
2014-10-23 Jim ProcterJAL-1521 patch is to remove xerces from classpath.... commit | commitdiff | tree | snapshot
2014-10-23 Jim ProcterJAL-1521 test to check registry is returning sources commit | commitdiff | tree | snapshot
2014-10-23 Jim Procterpatch fixes JAL-1558 commit | commitdiff | tree | snapshot
2014-10-23 Jim ProcterJAL-1503 tag 2.8.1b1 hotfix - last in 2.8.1 line commit | commitdiff | tree | snapshot
2014-10-23 gmungocJAL-1264 new unit tests commit | commitdiff | tree | snapshot
2014-10-23 gmungocJAL-1264 further refactoring and tests commit | commitdiff | tree | snapshot
2014-10-22 gmungocJAL-1304 repositioned tab to correct example commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterMerge branch 'forpush/JAL-674_dssp' into develop commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 check for null vector before ... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterMerge branch 'patch_sjf4j_typo' into develop commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1216 update varna dependency string in jalviewLite... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterMerge branch 'patch_sjf4j_typo' into develop commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJWS-59 JAL-1216 patch broken InstallAnywhere build commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterMerge branch 'forpush/JAL-674_dssp' into develop commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 reinstate missing import commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 initial implementation - only need to extract... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 crlf commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1216 update to VARNA 3.91 commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 remove any spurious PDBEntrys generated by... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 methods and test for PDB derived annotation... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 store ID in MCview.PDBfile calcId string, not... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 don't create multiple secondary structure lines... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 test for the test for presence of annotation... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 test for presence of annotation derived from... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 patch for duplicate row bug commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 test for duplicate alignment annotation rows... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 patch to ensure existing annotation is properly... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 test to ensure sequence and annotation on seque... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 source formatting commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 JAL-207 getTers for aligned sequences in datase... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-674 refactor method to match and transfer annotatio... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 formatting commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterMerge branch 'features/JAL-1264_showHideAnnotations... commit | commitdiff | tree | snapshot
2014-10-21 Jim ProcterJAL-1551 crlf changes commit | commitdiff | tree | snapshot
2014-10-16 Jim ProcterMerge branch 'feature/JAL-674_dssp' into features/JAL... features/JAL-1264_showHideAnnotations commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterMerge branch 'jims_crlf_hell_JAL-1551' of https://sourc... commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-674 always try to extract secondary structure when... commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-674 support preservation of any annotation created... commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-674 make transferAnnotation method static commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-348 JAL-674 JAL-1564 TODO and implementation error... commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-674 patch logic to test whether old and new sequenc... commit | commitdiff | tree | snapshot
2014-10-15 Jim ProcterJAL-674 JAL-1305 JAL-348 new liftOver method and test... commit | commitdiff | tree | snapshot
2014-10-14 gmungocJAL-1551 CRLF handling commit | commitdiff | tree | snapshot
2014-10-13 gmungocJAL-1264 unneeded setup removed commit | commitdiff | tree | snapshot
2014-10-13 gmungocJAL-1264 unit test corrected commit | commitdiff | tree | snapshot
2014-10-12 gmungocJAL-1544 SEQENCE -> SEQUENCE commit | commitdiff | tree | snapshot
2014-10-12 gmungocJAL-1264 help updates for show/hide annotations on commit | commitdiff | tree | snapshot
2014-10-10 Jim ProcterJAL-674 employ new signature in Annotate3D service... commit | commitdiff | tree | snapshot
2014-10-10 Jim ProcterJAL-674 disable secondary structure annotation when... commit | commitdiff | tree | snapshot
2014-10-10 Jim ProcterJAL-674 typo commit | commitdiff | tree | snapshot
2014-10-10 Jim ProcterJAL-674 new constructors to pass flags about annotating... commit | commitdiff | tree | snapshot
2014-10-10 Jim ProcterJAL-674 parser flag to control secondary structure... commit | commitdiff | tree | snapshot
2014-10-10 Jim ProcterJAL-674 change jalview.io.AlignFile to allow parsing... commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1551 project-specific settings commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1551 proposed project settings for code cleanup... commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1264 unit tests commit | commitdiff | tree | snapshot
2014-10-10 gmungocSuppressed test that needs user interaction to allow... commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1551 CRLF handling commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1264 show/hide annotations, plus merged changes commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1481 wrap tooltip in html commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1264 added getAlignmentAnnotations(calcId, label) commit | commitdiff | tree | snapshot
2014-10-10 gmungocJAL-1264 reverted (removed added method) commit | commitdiff | tree | snapshot
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