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2018-03-21	Jim Procter	JAL-2754 remove duplicate java 8 classpath	commit \| commitdiff \| tree
2018-03-21	Jim Procter	Merge branch 'develop' into features/JAL-2909_bamImport2_11	commit \| commitdiff \| tree
2018-03-21	Jim Procter	Merge branch 'patch/JAL-2754_patch2104forJava8' into...	commit \| commitdiff \| tree
2018-03-21	Jim Procter	Merge branch 'patch/JAL-2754_patch2104forJava8' into...	commit \| commitdiff \| tree
2018-03-21	Jim Procter	JAL-2754 dont put '<>' in <echo> text!	commit \| commitdiff \| tree
2018-03-21	Jim Procter	Merge branch 'feature/JAL-2909bamfiles_features' into...	commit \| commitdiff \| tree
2018-03-21	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	commit \| commitdiff \| tree
2018-03-21	Jim Procter	Merge branch 'patch/JAL-2754_patch2104forJava8' into...	commit \| commitdiff \| tree
2018-03-21	Jim Procter	JAL-2754 clean up proguard path spec and config variables	commit \| commitdiff \| tree
2018-03-21	gmungoc	JAL-2754 renamed proguard.jar to include version number	commit \| commitdiff \| tree
2018-03-21	gmungoc	JAL-2754 5.3.3 update of proguard.jar	commit \| commitdiff \| tree
2018-03-21	gmungoc	JAL-2754 update to specify Java 1.8(+)	commit \| commitdiff \| tree
2018-03-21	gmungoc	JAL-2754 update to Java 1.8	commit \| commitdiff \| tree
2018-03-20	Jim Procter	JAL-2909 separate reverse and forward strand reads...	commit \| commitdiff \| tree
2018-03-20	Jim Procter	JAL-2909 recognise .bam extension in URL and allow...	commit \| commitdiff \| tree
2018-03-14	Jim Procter	JAL-2930 JAL-2924 JAL-2913 JAL-2926 JAL-2906 2.10.4...	commit \| commitdiff \| tree
2018-03-07	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	commit \| commitdiff \| tree
2018-03-03	Jim Procter	JAL-2909 soft clip and handclap features (should use...	commit \| commitdiff \| tree
2018-03-02	Jim Procter	JAL-2909 add sequence feature for quality	commit \| commitdiff \| tree
2018-03-02	Jim Procter	JAL-2909 add sequence feature for insertions	commit \| commitdiff \| tree
2018-02-28	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch_merged_JAL...	commit \| commitdiff \| tree
2018-02-27	Jim Procter	JAL-2759 release notes for 2.10.4	commit \| commitdiff \| tree
2018-02-27	Jim Procter	Merge branch 'feature/JAL-2759' into merge/JAL-2759_2104	commit \| commitdiff \| tree
2018-02-27	Jim Procter	fix for JAL-2922 - update states all at once and then...	commit \| commitdiff \| tree
2018-02-26	Jim Procter	Merge branch 'feature/JAL-984splitAdjuster' into releases...	commit \| commitdiff \| tree
2018-02-26	Jim Procter	JAL-984 remove all references to idwidth.gif - in build...	commit \| commitdiff \| tree
2018-02-23	Jim Procter	JAL-2885 release notes	commit \| commitdiff \| tree
2018-02-23	Jim Procter	Merge branch 'features/JAL-2885UniprotHttps' into releases...	commit \| commitdiff \| tree
2018-02-23	Jim Procter	JAL-2885 xfam https	commit \| commitdiff \| tree
2018-02-23	Jim Procter	JAL-2885 XFAM_DOMAIN->XFAM_BASEURL	commit \| commitdiff \| tree
2018-02-23	Jim Procter	JAL-2885 Ensembl* -> https	commit \| commitdiff \| tree
2018-02-23	Jim Procter	JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL	commit \| commitdiff \| tree
2018-02-23	Jim Procter	JAL-2885 renamed base URL getter from getDomain..	commit \| commitdiff \| tree
2018-02-22	Jim Procter	Merge branch 'feature/JAL-984splitAdjuster' into releases...	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-984 ID width adjuster needs to be white !	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-2666 release notes	commit \| commitdiff \| tree
2018-02-22	Jim Procter	Merge branch 'bug/JAL-2666' into releases/Release_2_10_4_Branch	commit \| commitdiff \| tree
2018-02-22	Jim Procter	Merge branch 'feature/JAL-984splitAdjuster' into releases...	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-984 remove all references to idwidth.gif and use...	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-2906 typo fixes	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-984 release notes	commit \| commitdiff \| tree
2018-02-22	Jim Procter	Merge branch 'feature/JAL-984splitAdjuster' into releases...	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-294 remove unneeded paint() method	commit \| commitdiff \| tree
2018-02-22	Jim Procter	JAL-984 remove commented/unnecessary if clause	commit \| commitdiff \| tree
2018-02-21	Jim Procter	JAL-2906 release notes for 2.10.4	commit \| commitdiff \| tree
2018-02-21	Jim Procter	Merge branch 'bug/JAL-2778again' into releases/Release_2_10_...	commit \| commitdiff \| tree
2018-02-21	Jim Procter	JAL-2778 reinstate transparent windows to avoid ugly...	commit \| commitdiff \| tree
2018-02-20	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	commit \| commitdiff \| tree
2018-02-20	Jim Procter	Merge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums...	commit \| commitdiff \| tree
2018-02-15	Jim Procter	Merge branch 'develop' into releases/Release_2_10_4_Branch	commit \| commitdiff \| tree
2018-02-15	Jim Procter	JAL-2906 bump release version and cut new release note...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2780 scan all test IDs before testing and reporting...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2780 SequenceI.findFeatures takes column numbers...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2780 JAL-2781 don’t create a mapping if sequence...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2780 JAL-2781 only create a mapping entry or write...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 JAL-2780 include sequence start number when...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 ensure Trim is disabled before test starts	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 refactor ‘trim retrieved sequence’ preference...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 null local siftsClient variable if exception...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 refactor StructureSelectionManager.siftsClient...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 FIXME: value of sourceType parameter always...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 refactor possibly non-functional ‘extract...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 tidy up comments on getMapping/computeMapping	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2781 report exactly which residues do not receive...	commit \| commitdiff \| tree
2018-02-13	Jim Procter	JAL-2905 added additional jvmarg for testng task conditional...	commit \| commitdiff \| tree
2018-02-12	Jim Procter	JAL-2780 JAL-2781 extra column in mapping array	commit \| commitdiff \| tree
2018-02-12	Jim Procter	JAL-2904 JAL-2780 JAL-2781 update JmolCommandsTest...	commit \| commitdiff \| tree
2018-02-12	Jim Procter	JAL-2780 JAL-2781 ahem - add a semicolon if there isn...	commit \| commitdiff \| tree
2018-02-12	Jim Procter	JAL-2780 use value of ’UNASSIGNED’ constant in assert...	commit \| commitdiff \| tree
2018-02-12	Jim Procter	JAL-2904 replaced assert for (getEnd()-getStart()+1...	commit \| commitdiff \| tree
2018-02-11	Jim Procter	JAL-2781 use SIFTs mapping rather than maxChain AlignSeq...	commit \| commitdiff \| tree
2018-02-11	Jim Procter	JAL-2780 JAL-2781 use PDBe numbering to map between...	commit \| commitdiff \| tree
2018-02-11	Jim Procter	JAL-2781 mark aligned positions via StructureMapping...	commit \| commitdiff \| tree
2018-02-11	Jim Procter	JAL-2780 JAL-2781 include a Mapping object in StructureMappi...	commit \| commitdiff \| tree
2018-02-11	Jim Procter	JAL-2780 JAL-2781 UNASSIGNED positions marked as Integer.Min	commit \| commitdiff \| tree
2018-02-11	Jim Procter	JAL-2781 fix test data for full length annotation	commit \| commitdiff \| tree
2018-02-09	Jim Procter	Use the “PDBe” or “PDB” numbering (starts from 1, correspond...	commit \| commitdiff \| tree
2018-02-09	Jim Procter	JAL-2780 JAL-2781 should always ensure SIFTS mappings...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2781 run sequentially and ensure windows...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2891 clear all windows always beforeTest...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2902 catch case where viewer is closed (therefore...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2902 thread off dialog close op to avoid deadlock...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2781 first pass at failing test for incorrect...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2781 JAL-2902 refactored helper method...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2902 - isBusy and hasMapping methods so client...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2781 fix javadoc in line with behaviour...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2781 JAL-2902 refactor ‘OK’ action to...	commit \| commitdiff \| tree
2018-02-07	Jim Procter	JAL-2780 JAL-2781 don’t assume contiguous mapping to...	commit \| commitdiff \| tree
2018-02-05	Jim Procter	JAL-2780 JAL-2781 (failing) test comparing location...	commit \| commitdiff \| tree
2018-02-05	Jim Procter	JAL-2780 JAL-2781 programmatically select structures...	commit \| commitdiff \| tree
2018-02-05	Jim Procter	JAL-2780 JAL-2871 only look up current table view once	commit \| commitdiff \| tree
2018-02-05	Jim Procter	JAL-2780 JAL-2781 test AlignmentI.findAnnotations locates...	commit \| commitdiff \| tree
2018-02-05	Jim Procter	JAL-2780 JAL-2781 - patch and first test for AlignmentI...	commit \| commitdiff \| tree
2018-01-26	Jim Procter	Merge branch 'releases/Release_2_10_3_Branch' into...	commit \| commitdiff \| tree
2018-01-24	Jim Procter	Merge branch 'develop' into releases/Release_2_10_3_Branch	commit \| commitdiff \| tree
2018-01-24	Jim Procter	JAL-2858 update release date and rejig what's new message	commit \| commitdiff \| tree
2018-01-23	Jim Procter	Merge branch 'develop' into releases/Release_2_10_3_Branch	commit \| commitdiff \| tree
2018-01-23	Jim Procter	JAL-2858 fix what's new	commit \| commitdiff \| tree
2018-01-23	Jim Procter	Merge branch 'develop' into releases/Release_2_10_3_Branch	commit \| commitdiff \| tree
2018-01-23	Jim Procter	JAL-2858 update latest release notes link in TOC	commit \| commitdiff \| tree
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