JAL-1499 Gene and Domain parsed to AlignmentAnnotation (currently as

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

diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index bdae11a..40a7c6e 100644 (file)
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -685,6 +685,60 @@ public class MegaFileTest
       verifySequenceFeature(sfs[7], "MEF2A", "Gene", 31, 36);
       verifySequenceFeature(sfs[8], "BindingSite", "Domain", 37, 42);
     }
+
+    /*
+     * verify gene and domain alignment annotations
+     */
+    assertEquals(2, testee.annotations.size());
+    AlignmentAnnotation ann = testee.annotations.get(0);
+    assertEquals("MEGA Gene", ann.label);
+    assertEquals(42, ann.annotations.length);
+    verifyAnnotation(ann, 0, 6, null);
+    verifyAnnotation(ann, 6, 24, "Adh");
+    verifyAnnotation(ann, 24, 30, "Opsin");
+    verifyAnnotation(ann, 30, 36, "MEF2A");
+    verifyAnnotation(ann, 37, 42, null);
+
+    ann = testee.annotations.get(1);
+    assertEquals("MEGA Domain", ann.label);
+    assertEquals(42, ann.annotations.length);
+    verifyAnnotation(ann, 0, 6, null);
+    verifyAnnotation(ann, 6, 12, "Exon1 (Adh Coding)");
+    verifyAnnotation(ann, 12, 18, "Intron1 (Adh Noncoding)");
+    verifyAnnotation(ann, 19, 24, "Exon2 (Adh Coding)");
+    verifyAnnotation(ann, 25, 30, "Intron1 (Opsin Noncoding)");
+    verifyAnnotation(ann, 31, 36, "Exon1 (MEF2A Coding)");
+    verifyAnnotation(ann, 37, 42, "BindingSite");
+
+  }
+
+  /**
+   * Helper method to verify a range of annotation positions all have the given
+   * description
+   * 
+   * @param ann
+   *          array of annotations to check
+   * @param from
+   *          start index to check
+   * @param to
+   *          end index to check (exclusive)
+   * @param description
+   *          value to assert
+   */
+  protected void verifyAnnotation(AlignmentAnnotation ann, int from,
+          int to, String description)
+  {
+    for (int pos = from; pos < to; pos++)
+    {
+      if (description == null)
+      {
+        assertNull(ann.annotations[pos]);
+      }
+      else
+      {
+        assertEquals(description, ann.annotations[pos].description);
+      }
+    }
   }
 
   /**