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Merge branch 'features/typed_annotations_calcId' into develop
2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into...
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2014-11-12 Jim Procterjavadoc
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2014-11-12 Jim ProcterJAL-674 use the getMapping/transfer to transfer annotation...
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2014-11-12 Jim ProcterJAL-674 patch broken getMapping function
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2014-11-12 Jim ProcterJAL-674 switch from .transfer to .liftOver for transfer...
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2014-11-12 Jim ProcterJAL-674 note about broken .transfer method (expect...
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2014-11-12 Jim ProcterJAL-674 javadoc
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2014-11-12 Jim ProcterJAL-674 new tests and deprecated tests for PDB mapping...
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-06 Jim ProcterMerge branch 'features/JAL-1152annotationSorting' into...
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2014-11-06 Jim ProcterMerge branch 'features/JAL-1541_BioJsMSAViewer-export...
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2014-11-04 Jim ProcterJAL-1213 normalise sequence extracted from Jmol in...
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2014-11-04 Jim ProcterJAL-1213 test to ensure JMol extracted sequences are...
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2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotationSorting
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2014-11-03 Jim ProcterMerge branch 'bug/JAL-1250_redundance-removal' into...
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2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotationSorting
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2014-11-03 Jim ProcterMerge branch 'features/ssFromPDBEntry' into develop
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2014-11-03 Jim ProcterJAL-795 JAL-674 tweaked logic to avoid black annotation...
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2014-11-03 Jim Procterfix for JAL-1579 create threshold object for annotation...
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2014-11-03 Jim ProcterJAL-1578 test property accessors/copy constructor
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2014-11-03 Jim ProcterJAL-1578 JAL-674 store/restore alignment annotation...
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2014-11-03 Jim ProcterJAL-1578 formatting and imports
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2014-11-03 Jim ProcterJAL-674 peptide structure input so test is not dependent...
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2014-11-03 Jim ProcterJAL-1551 formatting
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2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor...
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2014-11-03 Jim Procterjavadoc
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2014-10-31 Jim ProcterJAL-674 JAL-961 pass row reference to handler to check...
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2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional information...
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2014-10-30 Jim ProcterMerge branch 'develop' into features/ssFromPDBEntry
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2014-10-30 Jim ProcterJAL-674 hang on to sequences created by secondary parsiing...
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2014-10-30 Jim ProcterJAL-674 count number of annotation transferred in test
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2014-10-30 Jim ProcterJAL-674 propagate annotation onto mapped sequence and...
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2014-10-30 Jim ProcterJAL-674 register PDB IDs when ever they are resolved...
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2014-10-30 Jim ProcterJAL-674 use PDB ID<>File registry to look up correct...
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2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and...
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2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method
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2014-10-30 Jim ProcterJAL-674 flag and proxy method to distinguish setMapping...
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2014-10-30 Jim ProcterJAL-674 map on StructureSelectionManager to record...
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2014-10-30 Jim Procterpatch for JAL-795 - use base secondary structure colour...
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2014-10-30 Jim ProcterJAL-674 patch test to verify presence of annotation...
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2014-10-30 Jim ProcterJAL-1551 format and tidy
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2014-10-29 Jim ProcterJAL-1264 JAL-674 test to exercise the AlignmentAnnotation...
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2014-10-29 Jim ProcterJAL-1264 JAL-674 method to copy annotation on structure...
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2014-10-29 Jim ProcterJAL-674 JAL-1264 remap method to allow annotation positions...
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2014-10-27 Jim ProcterMerge branch 'develop' into Release_2_8_2_Branch
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2014-10-27 Jim ProcterMerge branch 'Release_2_8_2_Branch' into merge_r282_dev
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2014-10-23 Jim ProcterMerge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch
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2014-10-23 Jim ProcterMerge branch 'hotfix/JAL-1521' into develop
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2014-10-23 Jim ProcterJAL-1521 patch is to remove xerces from classpath....
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2014-10-23 Jim ProcterJAL-1521 test to check registry is returning sources
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2014-10-23 Jim Procterpatch fixes JAL-1558
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2014-10-23 Jim ProcterJAL-1503 tag 2.8.1b1 hotfix - last in 2.8.1 line
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2014-10-21 Jim ProcterMerge branch 'forpush/JAL-674_dssp' into develop
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2014-10-21 Jim ProcterJAL-674 check for null vector before ...
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2014-10-21 Jim ProcterMerge branch 'patch_sjf4j_typo' into develop
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2014-10-21 Jim ProcterJAL-1216 update varna dependency string in jalviewLite...
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2014-10-21 Jim ProcterMerge branch 'patch_sjf4j_typo' into develop
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2014-10-21 Jim ProcterJWS-59 JAL-1216 patch broken InstallAnywhere build
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2014-10-21 Jim ProcterMerge branch 'forpush/JAL-674_dssp' into develop
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2014-10-21 Jim ProcterJAL-1551 reinstate missing import
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2014-10-21 Jim ProcterJAL-674 initial implementation - only need to extract...
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2014-10-21 Jim ProcterJAL-1551 crlf
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2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge
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2014-10-21 Jim ProcterJAL-1216 update to VARNA 3.91
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2014-10-21 Jim ProcterJAL-674 remove any spurious PDBEntrys generated by...
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2014-10-21 Jim ProcterJAL-674 methods and test for PDB derived annotation...
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2014-10-21 Jim ProcterJAL-674 store ID in MCview.PDBfile calcId string, not...
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2014-10-21 Jim ProcterJAL-674 don't create multiple secondary structure lines...
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2014-10-21 Jim ProcterJAL-674 test for the test for presence of annotation...
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2014-10-21 Jim ProcterJAL-674 test for presence of annotation derived from...
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2014-10-21 Jim ProcterJAL-1551 formatting
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2014-10-21 Jim ProcterJAL-1551 formatting
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2014-10-21 Jim ProcterJAL-674 patch for duplicate row bug
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2014-10-21 Jim ProcterJAL-674 test for duplicate alignment annotation rows...
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2014-10-21 Jim ProcterJAL-1551 formatting
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2014-10-21 Jim ProcterJAL-674 patch to ensure existing annotation is properly...
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2014-10-21 Jim ProcterJAL-674 test to ensure sequence and annotation on sequence...
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2014-10-21 Jim ProcterJAL-1551 source formatting
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2014-10-21 Jim ProcterJAL-674 JAL-207 getTers for aligned sequences in dataset...
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2014-10-21 Jim ProcterJAL-674 refactor method to match and transfer annotation...
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2014-10-21 Jim ProcterJAL-1551 formatting
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2014-10-21 Jim ProcterMerge branch 'features/JAL-1264_showHideAnnotations...
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2014-10-21 Jim ProcterJAL-1551 crlf changes
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2014-10-16 Jim ProcterMerge branch 'feature/JAL-674_dssp' into features/JAL...
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2014-10-15 Jim ProcterMerge branch 'jims_crlf_hell_JAL-1551' of https://source...
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2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto
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2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto
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2014-10-15 Jim ProcterJAL-674 always try to extract secondary structure when...
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2014-10-15 Jim ProcterJAL-674 support preservation of any annotation created...
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2014-10-15 Jim ProcterJAL-674 make transferAnnotation method static
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2014-10-15 Jim ProcterJAL-348 JAL-674 JAL-1564 TODO and implementation error...
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2014-10-15 Jim ProcterJAL-674 patch logic to test whether old and new sequence...
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2014-10-15 Jim ProcterJAL-674 JAL-1305 JAL-348 new liftOver method and test...
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2014-10-10 Jim ProcterJAL-674 employ new signature in Annotate3D service...
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2014-10-10 Jim ProcterJAL-674 disable secondary structure annotation when...
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2014-10-10 Jim ProcterJAL-674 typo
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2014-10-10 Jim ProcterJAL-674 new constructors to pass flags about annotating...
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