+
+ // this is the single sequence alignment and the SS annotations equivalent to
+ // the ones in file RnaSSTestFile
+ String aliFileRnaSSAlphaChars = ">Test.sequence/1-14\n"
+ + "GUACAAAAAAAAAA";
+ String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|E,E|H,H|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+ String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ + "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ + "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|H,H|E,E|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ + "\n"
+ + "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ + "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+ @Test(groups = { "Functional" })
+ public void stockholmFileRnaSSAlphaChars() throws Exception
+ {
+ AppletFormatAdapter af = new AppletFormatAdapter();
+ AlignmentI al = af.readFile(RnaSSTestFile, DataSourceType.FILE,
+ jalview.io.FileFormat.Stockholm);
+ Iterable<AlignmentAnnotation> aai = al.findAnnotations(null, null,
+ "Secondary Structure");
+ AlignmentAnnotation aa = aai.iterator().next();
+ Assert.assertTrue(aa.isRNA(),
+ "'" + RnaSSTestFile + "' not recognised as RNA SS");
+ Assert.assertTrue(aa.isValidStruc(),
+ "'" + RnaSSTestFile + "' not recognised as valid structure");
+ Annotation[] as = aa.annotations;
+ char[] As = new char[as.length];
+ for (int i = 0; i < as.length; i++)
+ {
+ As[i] = as[i].secondaryStructure;
+ }
+ char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E',
+ ')', 'e', ')', '>' };
+ Assert.assertTrue(
+ Arrays.equals(As, shouldBe),
+ "Annotation is " + new String(As) + " but should be "
+ + new String(shouldBe));
+
+ // this should result in the same RNA SS Annotations
+ AlignmentI newAl = new AppletFormatAdapter().readFile(
+ aliFileRnaSSAlphaChars,
+ DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+ AnnotationFile aaf = new AnnotationFile();
+ aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars,
+ DataSourceType.PASTE);
+
+ Assert.assertTrue(
+ testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
+ newAl.getAlignmentAnnotation()[0]));
+
+ // this should NOT result in the same RNA SS Annotations
+ newAl = new AppletFormatAdapter().readFile(
+ aliFileRnaSSAlphaChars, DataSourceType.PASTE,
+ jalview.io.FileFormat.Fasta);
+ aaf = new AnnotationFile();
+ aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars,
+ DataSourceType.PASTE);
+
+ boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
+ newAl.getAlignmentAnnotation()[0]);
+ Assert.assertFalse( mismatch );
+ }
+
+ private static boolean testRnaSSAnnotationsEquivalent(
+ AlignmentAnnotation a1,
+ AlignmentAnnotation a2)
+ {
+ return a1.rnaSecondaryStructureEquivalent(a2);
+ }
+