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JAL-2780 SequenceI.findFeatures takes column numbers in base 1…

2018-02-13 Jim ProcterJAL-2780 SequenceI.findFeatures takes column numbers...
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2018-02-13 Jim ProcterJAL-2780 JAL-2781 don’t create a mapping if sequence...
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2018-02-13 Jim ProcterJAL-2780 JAL-2781 only create a mapping entry or write...
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2018-02-13 Jim ProcterJAL-2781 JAL-2780 include sequence start number when...
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2018-02-13 Jim ProcterJAL-2781 ensure Trim is disabled before test starts
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2018-02-13 Jim ProcterJAL-2781 refactor ‘trim retrieved sequence’ preference...
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2018-02-13 Jim ProcterJAL-2781 null local siftsClient variable if exception...
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2018-02-13 Jim ProcterJAL-2781 refactor StructureSelectionManager.siftsClient...
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2018-02-13 Jim ProcterJAL-2781 FIXME: value of sourceType parameter always...
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2018-02-13 Jim ProcterJAL-2781 refactor possibly non-functional ‘extract...
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2018-02-13 Jim ProcterJAL-2781 tidy up comments on getMapping/computeMapping
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2018-02-13 Jim ProcterJAL-2781 report exactly which residues do not receive...
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2018-02-13 Jim ProcterJAL-2905 added additional jvmarg for testng task conditional...
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2018-02-12 Jim ProcterJAL-2780 JAL-2781 extra column in mapping array
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2018-02-12 Jim ProcterJAL-2904 JAL-2780 JAL-2781 update JmolCommandsTest...
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2018-02-12 Jim ProcterJAL-2780 JAL-2781 ahem - add a semicolon if there isn...
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2018-02-12 Jim ProcterJAL-2780 use value of ’UNASSIGNED’ constant in assert...
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2018-02-12 Jim ProcterJAL-2904 replaced assert for (getEnd()-getStart()+1...
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2018-02-11 Jim ProcterJAL-2781 use SIFTs mapping rather than maxChain AlignSeq...
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2018-02-11 Jim ProcterJAL-2780 JAL-2781 use PDBe numbering to map between...
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2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping...
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2018-02-11 Jim ProcterJAL-2780 JAL-2781 include a Mapping object in StructureMappi...
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2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Integer.Min
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2018-02-11 Jim ProcterJAL-2781 fix test data for full length annotation
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2018-02-09 Jim ProcterUse the “PDBe” or “PDB” numbering (starts from 1, correspond...
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2018-02-09 Jim ProcterJAL-2780 JAL-2781 should always ensure SIFTS mappings...
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2018-02-07 Jim ProcterJAL-2780 JAL-2781 run sequentially and ensure windows...
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2018-02-07 Jim ProcterJAL-2780 JAL-2891 clear all windows always beforeTest...
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2018-02-07 Jim ProcterJAL-2902 catch case where viewer is closed (therefore...
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2018-02-07 Jim ProcterJAL-2902 thread off dialog close op to avoid deadlock...
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2018-02-07 Jim ProcterJAL-2780 JAL-2781 first pass at failing test for incorrect...
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2018-02-07 Jim ProcterJAL-2780 JAL-2781 JAL-2902 refactored helper method...
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2018-02-07 Jim ProcterJAL-2902 - isBusy and hasMapping methods so client...
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2018-02-07 Jim ProcterJAL-2780 JAL-2781 fix javadoc in line with behaviour...
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2018-02-07 Jim ProcterJAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to...
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2018-02-07 Jim ProcterJAL-2780 JAL-2781 don’t assume contiguous mapping to...
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2018-02-05 Jim ProcterJAL-2780 JAL-2781 (failing) test comparing location...
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2018-02-05 Jim ProcterJAL-2780 JAL-2781 programmatically select structures...
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2018-02-05 Jim ProcterJAL-2780 JAL-2871 only look up current table view once
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2018-02-05 Jim ProcterJAL-2780 JAL-2781 test AlignmentI.findAnnotations locates...
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2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI...
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2018-01-26 Jim ProcterMerge branch 'releases/Release_2_10_3_Branch' into...
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2018-01-24 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2018-01-24 Jim ProcterJAL-2858 update release date and rejig what's new message
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2018-01-23 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2018-01-23 Jim ProcterJAL-2858 fix what's new
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2018-01-23 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2018-01-23 Jim ProcterJAL-2858 update latest release notes link in TOC
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2018-01-23 Jim ProcterJAL-2859 release notes
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2018-01-23 Jim ProcterJAL-2858 update release notes
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2018-01-22 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2018-01-22 Jim ProcterJAL-2858 release notes for 2.10.3b1 (including revision...
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2018-01-22 Jim ProcterJAL-2858 bump version number for 2.10.3b1
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2017-12-19 Jim ProcterJAL-2880 disabled non-functional test - Jmol parser...
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2017-12-01 Jim ProcterMerge branch 'develop' into bugs/JAL-2780_JAL-2781_pdbnegati...
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2017-11-30 Jim ProcterJAL-2858 tweak OSX specific jar resources in JNLP
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2017-11-30 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2017-11-30 Jim ProcterJAL-2849 release notes
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2017-11-30 Jim ProcterMerge branch 'bug/JAL-2849' into develop
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2017-11-30 Jim ProcterJAL-2849 JAL-2863 file format preferences TODO

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2017-11-30 Jim ProcterJAL-2849 fix
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2017-11-28 Jim ProcterMerge branch 'bug/JAL-2859_uniprottowrongpdbid' into...
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2017-11-28 Jim ProcterJAL-2740 release notes
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2017-11-28 Jim ProcterMerge branch 'bug/JAL-2740' into develop
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2017-11-28 Jim ProcterJAL-2827 release notes
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2017-11-28 Jim ProcterMerge branch 'bug/JAL-2827' into develop
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2017-11-28 Jim ProcterJAL-2842 release notes
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2017-11-28 Jim ProcterMerge branch 'bug/JAL-2842' into develop
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2017-11-27 Jim ProcterJAL-2859 disambiguate with PDB ID if no file path
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2017-11-27 Jim ProcterJAL-2859 failing test demonstrating sequences with...
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2017-11-27 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2017-11-27 Jim ProcterJAL-2851 JAL-2858 release notes for 2.10.3b1
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2017-11-27 Jim ProcterMerge branch 'develop' into releases/Release_2_10_3_Branch
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2017-11-27 Jim ProcterMerge branch 'bug/JAL-2851' into develop
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2017-11-20 Jim ProcterJAL-2698 only allow InstallAnywhere launches with version...
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2017-11-20 Jim ProcterJAL-2698 patch path for InstallAnywhere build. Webstart...
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2017-11-17 Jim ProcterJAL-2698 tidy release notes and whats new
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2017-11-17 Jim ProcterJAL-2698 source code licencing
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2017-11-17 Jim ProcterJAL-2698 tidy up release notes
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2017-11-17 Jim ProcterJAL-2698 Cached PDB Entries -> Cached Structures in...
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2017-11-17 Jim ProcterJAL-2466 revised help text for sort by PID
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2017-11-17 Jim ProcterJAL-2698 what’s new and release notes
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2017-11-17 Jim ProcterJAL-2822 known defect for 2.10.3
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2017-11-17 Jim ProcterMerge branch 'bug/JAL-2784' into develop
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2017-11-17 Jim ProcterJAL-2841 JAL-2791 new known defect


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2017-11-17 Jim ProcterJAL-2541 known defect
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2017-11-17 Jim ProcterJAL-2684 clarify release notes
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2017-11-17 Jim ProcterMerge branch 'bug/JAL-2821' into develop
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2017-11-17 Jim ProcterJAL-2840 release notes
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2017-11-17 Jim ProcterMerge branch 'bug/JAL-2837' into develop
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2017-11-17 Jim ProcterMerge branch 'doc/JAL-2494_JAL-2828_mergefindAnnotation...
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2017-11-17 Jim ProcterJAL-2811 release note
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2017-11-17 Jim ProcterJAL-2541 not in 2.10.3, JAL-2831 signed off.
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2017-11-17 Jim ProcterJAL-2698 11th hour release today
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2017-11-17 Jim ProcterMerge branch 'bug/JAL-2831' into develop
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2017-11-16 Jim ProcterJAL-2541 JAL-2829 JAL-2830 JAL-2822 catch all release...
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2017-11-16 Jim ProcterMerge branch 'bug/JAL-2829deleteCharsWithGaps' into...
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2017-11-14 Jim ProcterJAL-2758 update uniprot retrieval test
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2017-11-13 Jim ProcterJAL-2758 release notes
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2017-11-13 Jim ProcterJAL-2698 formatting
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