X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentAnnotationTests.java;h=7c1aa8136bd9a66b2734cc61f29abfcb484c4928;hb=fd9ed8df6a98c86228100aa4e9d6698c87a61c08;hp=f23b3d2ea38baf32af977a2aa0f8058ad890423e;hpb=898ef7e2238d8eade34829e9fc86b422f14f29d8;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index f23b3d2..7c1aa81 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -1,11 +1,13 @@
 package jalview.datamodel;
 
 import static org.junit.Assert.assertEquals;
-import jalview.analysis.AlignSeq;
-import jalview.io.AppletFormatAdapter;
+import static org.junit.Assert.assertNull;
 
 import org.junit.Test;
 
+import jalview.analysis.AlignSeq;
+import jalview.io.AppletFormatAdapter;
+
 public class AlignmentAnnotationTests
 {
   @Test
@@ -153,7 +155,48 @@ public class AlignmentAnnotationTests
                       : "Out of range");
       assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
     }
-    // new jalview.io.FormatAdapter().formatSequences("STOCKHOLM", n)
   }
 
+  @Test
+  public void testAdjustForAlignment()
+  {
+    SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
+    seq.createDatasetSequence();
+
+    /*
+     * Annotate positions 3/4/5 (CDE) with values 1/2/3
+     */
+    Annotation[] anns = new Annotation[]
+    { null, null, new Annotation(1), new Annotation(2), new Annotation(3) };
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", anns);
+    seq.addAlignmentAnnotation(ann);
+
+    /*
+     * Check annotation map before modifying aligned sequence
+     */
+    assertNull(ann.getAnnotationForPosition(1));
+    assertNull(ann.getAnnotationForPosition(2));
+    assertNull(ann.getAnnotationForPosition(6));
+    assertNull(ann.getAnnotationForPosition(7));
+    assertEquals(1, ann.getAnnotationForPosition(3).value, 0.001d);
+    assertEquals(2, ann.getAnnotationForPosition(4).value, 0.001d);
+    assertEquals(3, ann.getAnnotationForPosition(5).value, 0.001d);
+
+    /*
+     * Trim the displayed sequence to BCD and adjust annotations
+     */
+    seq.setSequence("BCD");
+    seq.setStart(2);
+    seq.setEnd(4);
+    ann.adjustForAlignment();
+
+    /*
+     * Should now have annotations for aligned positions 2, 3Q (CD) only
+     */
+    assertEquals(3, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertEquals(1, ann.annotations[1].value, 0.001);
+    assertEquals(2, ann.annotations[2].value, 0.001);
+  }
 }