X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FAlignmentAnnotationTests.java;h=1aff519120f7793fba27fbc469028cf075f30f7b;hb=d4b4cffe60c2fc80b7f9a56aa9c497f8077d6bed;hp=d5e9d036f3cb808136798610d7f09deb1025e220;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index d5e9d03..1aff519 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -219,4 +219,65 @@ public class AlignmentAnnotationTests
     assertEquals(1, ann.annotations[1].value, 0.001);
     assertEquals(2, ann.annotations[2].value, 0.001);
   }
-}
+
+  /**
+   * Test the method that defaults rna symbol to the one matching the preceding
+   * unmatched opening bracket (if any)
+   */
+  @Test(groups = { "Functional" })
+  public void testGetDefaultRnaHelixSymbol()
+  {
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", null);
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
+
+    Annotation[] anns = new Annotation[20];
+    ann.annotations = anns;
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(4));
+
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(0));
+    assertEquals("(", ann.getDefaultRnaHelixSymbol(1));
+    assertEquals(")", ann.getDefaultRnaHelixSymbol(2));
+    assertEquals(")", ann.getDefaultRnaHelixSymbol(3));
+
+    /*
+     * .(.[.{.<.}.>.).].
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[5] = new Annotation("{", "S", '{', 0f);
+    anns[7] = new Annotation("<", "S", '<', 0f);
+    anns[9] = new Annotation("}", "S", '}', 0f);
+    anns[11] = new Annotation(">", "S", '>', 0f);
+    anns[13] = new Annotation(")", "S", ')', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+
+    String expected = "(())]]}}>>>>]]]](";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+
+    /*
+     * .(.[.(.).{.}.<.].D.
+     */
+    anns[1] = new Annotation("(", "S", '(', 0f);
+    anns[3] = new Annotation("[", "S", '[', 0f);
+    anns[5] = new Annotation("(", "S", '(', 0f);
+    anns[7] = new Annotation(")", "S", ')', 0f);
+    anns[9] = new Annotation("{", "S", '{', 0f);
+    anns[11] = new Annotation("}", "S", '}', 0f);
+    anns[13] = new Annotation("<", "S", '>', 0f);
+    anns[15] = new Annotation("]", "S", ']', 0f);
+    anns[17] = new Annotation("D", "S", 'D', 0f);
+
+    expected = "(())]]))]]}}]]>>>>dd";
+    for (int i = 0; i < expected.length(); i++)
+    {
+      assertEquals("column " + i, String.valueOf(expected.charAt(i)),
+              ann.getDefaultRnaHelixSymbol(i));
+    }
+  }
+}
\ No newline at end of file