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JAL-1541 added Jsoup to the InstallAnywhere config
[jalview.git] / src /
2014-11-12 Charles OfoegbuModified biojs exporter/importer to preserve SequenceFe... tree | commitdiff
2014-11-07 Charles OfoegbuModified BioJsHTMLOutput.java to clean up and close... tree | commitdiff
2014-11-07 Charles OfoegbuModified BioJsHTMLOutput.java to use class loader while... tree | commitdiff
2014-11-06 Charles OfoegbuChanges from JAL-1541 patch tree | commitdiff
2014-11-06 Charles OfoegbuUpdated BioJs Html to be capable of launching jalivew tree | commitdiff
2014-11-06 Jim ProcterMerge branch 'features/JAL-1541_BioJsMSAViewer-export... tree | commitdiff
2014-11-03 Jim ProcterMerge branch 'bug/JAL-1250_redundance-removal' into... tree | commitdiff
2014-11-03 Jim ProcterJAL-795 JAL-674 tweaked logic to avoid black annotation... tree | commitdiff
2014-11-03 Jim Procterfix for JAL-1579 create threshold object for annotation... tree | commitdiff
2014-11-03 Jim ProcterJAL-1578 JAL-674 store/restore alignment annotation... tree | commitdiff
2014-11-03 Jim ProcterJAL-1578 formatting and imports tree | commitdiff
2014-11-03 Jim ProcterJAL-1551 formatting tree | commitdiff
2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor... tree | commitdiff
2014-11-03 Jim Procterjavadoc tree | commitdiff
2014-10-31 Jim ProcterJAL-674 JAL-961 pass row reference to handler to check... tree | commitdiff
2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional informat... tree | commitdiff
2014-10-31 Charles OfoegbuJAL-1541 upadated BioJs emmitter to store alignment... tree | commitdiff
2014-10-30 Jim ProcterMerge branch 'develop' into features/ssFromPDBEntry tree | commitdiff
2014-10-30 Jim ProcterJAL-674 hang on to sequences created by secondary parsi... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 propagate annotation onto mapped sequence and... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 register PDB IDs when ever they are resolved... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 use PDB ID<>File registry to look up correct... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method tree | commitdiff
2014-10-30 Jim ProcterJAL-674 flag and proxy method to distinguish setMapping... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 map on StructureSelectionManager to record... tree | commitdiff
2014-10-30 Jim Procterpatch for JAL-795 - use base secondary structure colour... tree | commitdiff
2014-10-30 Jim ProcterJAL-1551 format and tidy tree | commitdiff
2014-10-30 Charles OfoegbuJAL-353 updated patch for undo successive remove redund... tree | commitdiff
2014-10-30 Charles OfoegbuJAL-1541 BioJs MSA Viewer export option implementation tree | commitdiff
2014-10-29 Charles OfoegbuJAL-353 updated patch for undo successive remove redund... tree | commitdiff
2014-10-29 Jim ProcterJAL-1264 JAL-674 method to copy annotation on structure... tree | commitdiff
2014-10-29 Jim ProcterJAL-674 JAL-1264 remap method to allow annotation posit... tree | commitdiff
2014-10-28 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2014-10-28 gmungocJAL-1264 refactor to add menu options to _both_ sequenc... tree | commitdiff
2014-10-28 Charles Ofoegbu2_8_2_Branch merge tree | commitdiff
2014-10-28 Charles OfoegbuJAL-353 undo for successive removal of redundant sequen... tree | commitdiff
2014-10-28 Charles OfoegbuJAL-1250 Redundancy removal bug fix for Applet version tree | commitdiff
2014-10-27 Jim ProcterMerge branch 'Release_2_8_2_Branch' into merge_r282_dev tree | commitdiff
2014-10-27 Charles OfoegbuUpdated RedundancyPanel.java to referesh the tree view... tree | commitdiff
2014-10-27 Charles OfoegbuPatch for redundancy removal tree | commitdiff
2014-10-23 Jim ProcterMerge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch tree | commitdiff
2014-10-23 unknownJAL-1521 updated xerces to 2.11 along with xml-apis tree | commitdiff
2014-10-23 Jim Procterpatch fixes JAL-1558 tree | commitdiff
2014-10-23 gmungocJAL-1264 further refactoring and tests tree | commitdiff
2014-10-21 Jim ProcterJAL-674 check for null vector before ... tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 reinstate missing import tree | commitdiff
2014-10-21 Jim ProcterJAL-674 initial implementation - only need to extract... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge tree | commitdiff
2014-10-21 Jim ProcterJAL-674 remove any spurious PDBEntrys generated by... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 methods and test for PDB derived annotation... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 store ID in MCview.PDBfile calcId string, not... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 don't create multiple secondary structure lines... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 test for presence of annotation derived from... tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 formatting tree | commitdiff
2014-10-21 Jim ProcterJAL-674 patch for duplicate row bug tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 formatting tree | commitdiff
2014-10-21 Jim ProcterJAL-674 patch to ensure existing annotation is properly... tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 source formatting tree | commitdiff
2014-10-21 Jim ProcterJAL-674 JAL-207 getTers for aligned sequences in datase... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 refactor method to match and transfer annotatio... tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 formatting tree | commitdiff
2014-10-21 Jim ProcterMerge branch 'features/JAL-1264_showHideAnnotations... tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 crlf changes tree | commitdiff
2014-10-16 Jim ProcterMerge branch 'feature/JAL-674_dssp' into features/JAL... features/JAL-1264_showHideAnnotations tree | commitdiff
2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto tree | commitdiff
2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto tree | commitdiff
2014-10-15 Jim ProcterJAL-674 always try to extract secondary structure when... tree | commitdiff
2014-10-15 Jim ProcterJAL-674 support preservation of any annotation created... tree | commitdiff
2014-10-15 Jim ProcterJAL-674 make transferAnnotation method static tree | commitdiff
2014-10-15 Jim ProcterJAL-348 JAL-674 JAL-1564 TODO and implementation error... tree | commitdiff
2014-10-15 Jim ProcterJAL-674 patch logic to test whether old and new sequenc... tree | commitdiff
2014-10-15 Jim ProcterJAL-674 JAL-1305 JAL-348 new liftOver method and test... tree | commitdiff
2014-10-10 Jim ProcterJAL-674 disable secondary structure annotation when... tree | commitdiff
2014-10-10 Jim ProcterJAL-674 typo tree | commitdiff
2014-10-10 Jim ProcterJAL-674 new constructors to pass flags about annotating... tree | commitdiff
2014-10-10 Jim ProcterJAL-674 parser flag to control secondary structure... tree | commitdiff
2014-10-10 Jim ProcterJAL-674 change jalview.io.AlignFile to allow parsing... tree | commitdiff
2014-10-10 gmungocJAL-1481 wrap tooltip in html tree | commitdiff
2014-10-10 gmungocJAL-1264 added getAlignmentAnnotations(calcId, label) tree | commitdiff
2014-10-10 gmungocJAL-1264 reverted (removed added method) tree | commitdiff
2014-10-10 darolmarJAL-1420 tree | commitdiff
2014-10-10 darolmarJAL-1355 tree | commitdiff
2014-10-09 Jim Procterpatch fixes JAL-1558 tree | commitdiff
2014-10-08 gmungocMerge branch 'Release_2_8_2_Branch' into tree | commitdiff
2014-10-07 Jim ProcterJAL-1557 partial implementation - need to think about... tree | commitdiff
2014-10-07 Jim Procterpatch for JAL-1151 - select whole sequence when double... tree | commitdiff
2014-10-07 Jim ProcterJAL-1421 remove Vector and pass a list tree | commitdiff
2014-10-07 Jim ProcterJAL-1151 source tidy tree | commitdiff
2014-10-07 gmungocJAL-1264 wip tree | commitdiff
2014-10-07 gmungocJAL-1554 handle left-then-right click on sequence id tree | commitdiff
2014-10-06 Jim ProcterMerge branch 'Release_2_8_2_Branch' into JAL-429_phylip... tree | commitdiff
2014-10-06 Jim ProcterJAL-1500 JAL-1265 patch to parse PDB database refs... tree | commitdiff
2014-10-06 Jim ProcterJAL-654 remove any annotation rows for chain specific... tree | commitdiff
2014-10-06 Jim ProcterJAL-654 JAL-1264 sequence associated annotation is... tree | commitdiff
2014-10-06 Jim ProcterJAL-1115 TODO remove use of java.util.Vector tree | commitdiff
2014-10-06 Jim ProcterJAL-654 javadoc createDatasetSequence and transferAnnot... tree | commitdiff
2014-10-06 Jim ProcterJAL-654_dssp formatting and javadoc tree | commitdiff
2014-10-03 Charles OfoegbuIntegration of David Corsars Phylip File support tree | commitdiff
2014-10-03 Jim ProcterJAL-1355 removed all top level html tags from message... tree | commitdiff
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