From: gmungoc Date: Mon, 5 Feb 2018 09:54:10 +0000 (+0000) Subject: Merge branch 'spikes/mungo' into trialMerge X-Git-Tag: Release_2_11_0~62 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=241bd0223b016b5ad5ec78520310a8de32842722;p=jalview.git Merge branch 'spikes/mungo' into trialMerge Conflicts: src/jalview/analysis/AlignmentUtils.java test/jalview/analysis/AlignmentUtilsTests.java --- 241bd0223b016b5ad5ec78520310a8de32842722 diff --cc test/jalview/analysis/AlignmentUtilsTests.java index be6ba60,37b93fd..2b45eee --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@@ -2208,13 -2208,13 +2208,28 @@@ public class AlignmentUtilsTest assertEquals(1, sf.getBegin()); assertEquals(1, sf.getEnd()); assertEquals("synonymous_variant", sf.getType()); - assertEquals("aaA/aaG", sf.getDescription()); + assertEquals("AAG", sf.getDescription()); + assertEquals("var4", sf.getValue("ID")); + assertEquals("None", sf.getValue("clinical_significance")); + assertEquals("ID=var4;clinical_significance=None", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( - "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", ++ "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", ++ sf.links.get(0)); ++ assertEquals(cosmic, sf.getFeatureGroup()); ++ ++ // AAA -> AAG synonymous ++ sf = sfs.get(4); ++ assertEquals(1, sf.getBegin()); ++ assertEquals(1, sf.getEnd()); ++ assertEquals("synonymous_variant", sf.getType()); ++ assertEquals("AAG", sf.getDescription()); + assertEquals("var4", sf.getValue("ID")); + assertEquals("None", sf.getValue("clinical_significance")); + assertEquals("ID=var4;clinical_significance=None", sf.getAttributes()); + assertEquals(1, sf.links.size()); + assertEquals( + "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", sf.links.get(0)); assertEquals(cosmic, sf.getFeatureGroup());