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jalview.git
2018-03-21 Jim ProcterJAL-2909 update tests for stranded insert map and write... features/JAL-2909_bamImport2_11 spikes/kira commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'develop' into features/JAL-2909_bamImport2_11 commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 reinstate PA import from bad conflict merge commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 remove duplicate classpath entry again commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'develop' into features/JAL-2909_bamImport2_11 commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'patch/JAL-2754_patch2104forJava8' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 don’t use deprecated api for getting font... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 fix eclipse compilation error about referencin... commit | commitdiff | tree | snapshot
2018-03-21 gmungocJAL-2929 use configure Overview gap colour instead... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 remove duplicate java 8 classpath commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'develop' into features/JAL-2909_bamImport2_11 commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'patch/JAL-2754_patch2104forJava8' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'patch/JAL-2754_patch2104forJava8' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'patch/JAL-2754_patch2104forJava8' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 dont put '<>' in <echo> text! commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'feature/JAL-2909bamfiles_features' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterMerge branch 'patch/JAL-2754_patch2104forJava8' into... commit | commitdiff | tree | snapshot
2018-03-21 Jim ProcterJAL-2754 clean up proguard path spec and config variables commit | commitdiff | tree | snapshot
2018-03-21 gmungocJAL-2754 renamed proguard.jar to include version number commit | commitdiff | tree | snapshot
2018-03-21 gmungocJAL-2754 5.3.3 update of proguard.jar commit | commitdiff | tree | snapshot
2018-03-21 gmungocJAL-2754 update to specify Java 1.8(+) commit | commitdiff | tree | snapshot
2018-03-21 gmungocJAL-2754 update to Java 1.8 commit | commitdiff | tree | snapshot
2018-03-20 Jim ProcterJAL-2909 separate reverse and forward strand reads... feature/JAL-2909bamfiles_features commit | commitdiff | tree | snapshot
2018-03-20 Jim ProcterJAL-2909 recognise .bam extension in URL and allow... commit | commitdiff | tree | snapshot
2018-03-16 gmungocJAL-2679 getGeneId() now uses the same pattern as getGe... commit | commitdiff | tree | snapshot
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2... commit | commitdiff | tree | snapshot
2018-03-16 gmungocJAL-2922 update FeatureRenderer and repaint feature... commit | commitdiff | tree | snapshot
2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop commit | commitdiff | tree | snapshot
2018-03-15 gmungocJAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES commit | commitdiff | tree | snapshot
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db... commit | commitdiff | tree | snapshot
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge commit | commitdiff | tree | snapshot
2018-03-14 gmungocJAL-2679 reinstating changes lost in VCF merge commit | commitdiff | tree | snapshot
2018-03-14 Jim ProcterJAL-2930 JAL-2924 JAL-2913 JAL-2926 JAL-2906 2.10.4... commit | commitdiff | tree | snapshot
2018-03-13 gmungocJAL-2913 use FIGURE_FIXEDIDWIDTH (not FIGURE_USERIDWIDTH) commit | commitdiff | tree | snapshot
2018-03-08 gmungocMerge remote-tracking branch 'origin/releases/Release_2... merges/JAL-2906_update2_11_from_2_10_4 commit | commitdiff | tree | snapshot
2018-03-08 gmungocJAL-2885 tests updated for code changes commit | commitdiff | tree | snapshot
2018-03-08 gmungocJAL-2930 use MouseWheelEvent.getPreciseWheelRotation... commit | commitdiff | tree | snapshot
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff | tree | snapshot
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2922 [2] not [1] for Boolean column of table bugs/JAL-2922 commit | commitdiff | tree | snapshot
2018-03-07 gmungocMerge branch 'bugs/JAL-2922' into releases/Release_2_10... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2922 i18n and bespoke handler for Invert Selection commit | commitdiff | tree | snapshot
2018-03-07 gmungocMerge branch 'bug/JAL-2924nullTooltip' into releases... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2926 fix copy group consensus (and paste sequence... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group... commit | commitdiff | tree | snapshot
2018-03-07 gmungocJAL-2913 use FIGURE_USERIDWIDTH for fixed id width... commit | commitdiff | tree | snapshot
2018-03-03 Jim ProcterJAL-2909 soft clip and handclap features (should use... commit | commitdiff | tree | snapshot
2018-03-02 Jim ProcterJAL-2909 add sequence feature for quality commit | commitdiff | tree | snapshot
2018-03-02 Jim ProcterJAL-2909 add sequence feature for insertions commit | commitdiff | tree | snapshot
2018-03-01 kiramtJAL-2909 Updated tests feature/JAL-2909bamfiles commit | commitdiff | tree | snapshot
2018-03-01 kiramtJAL-2909 fixed another insertions bug commit | commitdiff | tree | snapshot
2018-02-28 kiramtJAL-2909 Fixed a bug in the insertions code commit | commitdiff | tree | snapshot
2018-02-28 gmungocJAL-2924 no tooltip over null annotation positions bug/JAL-2924nullTooltip commit | commitdiff | tree | snapshot
2018-02-28 kiramtJAL-2909 Gaps at start of reads only from start of... commit | commitdiff | tree | snapshot
2018-02-28 kiramtJAL-2909 Wire up coordinates dialog with bam file reader commit | commitdiff | tree | snapshot
2018-02-28 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch_merged_JAL... commit | commitdiff | tree | snapshot
2018-02-27 Jim ProcterJAL-2759 release notes for 2.10.4 commit | commitdiff | tree | snapshot
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 commit | commitdiff | tree | snapshot
2018-02-27 Jim Procterfix for JAL-2922 - update states all at once and then... commit | commitdiff | tree | snapshot
2018-02-27 kiramtJAL-2909 Tidy up bam file cigar code commit | commitdiff | tree | snapshot
2018-02-26 kiramtJAL-2909 Bam file parsing with insertions, first pass commit | commitdiff | tree | snapshot
2018-02-26 kiramtJAL-2909 Changes to htsjdk import control commit | commitdiff | tree | snapshot
2018-02-26 kiramtJAL-2909 Cigar parsing tests commit | commitdiff | tree | snapshot
2018-02-26 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-26 Jim ProcterJAL-984 remove all references to idwidth.gif - in build... feature/JAL-984splitAdjuster commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 release notes commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 Ensembl* -> https commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL commit | commitdiff | tree | snapshot
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain.. commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 ID width adjuster needs to be white ! commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-2666 release notes commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'bug/JAL-2666' into releases/Release_2_10_... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 remove all references to idwidth.gif and use... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-2906 typo fixes commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 release notes commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterMerge branch 'feature/JAL-984splitAdjuster' into releas... commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-294 remove unneeded paint() method commit | commitdiff | tree | snapshot
2018-02-22 Jim ProcterJAL-984 remove commented/unnecessary if clause commit | commitdiff | tree | snapshot
2018-02-21 Jim ProcterJAL-2906 release notes for 2.10.4 commit | commitdiff | tree | snapshot
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_... commit | commitdiff | tree | snapshot
2018-02-21 Jim ProcterJAL-2778 reinstate transparent windows to avoid ugly... bug/JAL-2778again commit | commitdiff | tree | snapshot
2018-02-21 kiramtJAL-2909 Partial insertions commit | commitdiff | tree | snapshot
2018-02-21 kiramtJAL-2778 Adjust cursor changes in overview panel commit | commitdiff | tree | snapshot
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation commit | commitdiff | tree | snapshot
2018-02-20 kiramtJAL-2909 Modified classpath commit | commitdiff | tree | snapshot
2018-02-20 kiramtJAL-2909 Insertions almost commit | commitdiff | tree | snapshot
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... commit | commitdiff | tree | snapshot
2018-02-20 gmungocJAL-2897 updated unit test for code change features/JAL-1793VCF commit | commitdiff | tree | snapshot
2018-02-20 gmungocMerge branch 'develop' into features/JAL-1793VCF commit | commitdiff | tree | snapshot
2018-02-20 Jim ProcterMerge branch 'bugs/JAL-2780_JAL-2781_pdbnegativenums... commit | commitdiff | tree | snapshot
2018-02-19 kiramtJAL-2909 Read in a bam file - but strand/location unaware commit | commitdiff | tree | snapshot
2018-02-19 kiramtJAL-2909 Removed buggy CIGAR parsing code which was... commit | commitdiff | tree | snapshot
2018-02-15 Jim ProcterMerge branch 'develop' into releases/Release_2_10_4_Branch commit | commitdiff | tree | snapshot
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