JAL-3053

[jalview.git] / test / jalview / io / StockholmFileTest.java

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 2427167..a6ae630 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -624,13 +624,13 @@ public class StockholmFileTest
   {
     for (char ch : new char[] { '{', '}', '[', ']', '(', ')', '<', '>' })
     {
-      Assert.assertTrue(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0),
-              "Didn't recognise " + ch + " as a WUSS bracket");
+      Assert.assertTrue(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+              "Didn't recognise '" + ch + "' as a WUSS bracket");
     }
-    for (char ch : new char[] { '@', '!', 'V', 'Q', '*', ' ', '-', '.' })
+    for (char ch : new char[] { '@', '!', '*', ' ', '-', '.' })
     {
-      Assert.assertFalse(StockholmFile.DETECT_BRACKETS.matchAt("" + ch, 0),
-              "Shouldn't recognise " + ch + " as a WUSS bracket");
+      Assert.assertFalse(StockholmFile.RNASS_BRACKETS.indexOf(ch) >= 0,
+              "Shouldn't recognise '" + ch + "' as a WUSS bracket");
     }
   }
   private static void roundTripSSForRNA(String aliFile, String annFile)
@@ -655,4 +655,79 @@ public class StockholmFileTest
     testAlignmentEquivalence(al, newAl, true, true, true);
 
   }
+
+  // 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);
+  }
+
 }