X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAlignmentUtilsTests.java;h=02955f179d20a484af033b16a8f47a0d7cf9c552;hb=0f26441e26325c728a3e9a108ac425d4d60dde1c;hp=9ef1b9abbe5e2f0b80b01525708e81f139e52ed8;hpb=5088f3a5830a92aca7db379a3b1d43a891611061;p=jalview.git

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 9ef1b9a..02955f1 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -22,6 +22,7 @@ package jalview.analysis;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
@@ -89,13 +90,16 @@ public class AlignmentUtilsTests
           "GGGTCAGGCAGT\n";
   // @formatter:on
 
-  public static Sequence ts=new Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
+  // public static Sequence ts=new
+  // Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
+  public static Sequence ts = new Sequence("short",
+          "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
 
   @Test
-  public void testExpandFlanks()
+  public void testExpandContext()
   {
     AlignmentI al = new Alignment(new Sequence[] {});
-    for (int i=4;i<14;i+=3)
+    for (int i = 4; i < 14; i += 2)
     {
       SequenceI s1=ts.deriveSequence().getSubSequence(i, i+7);
       al.addSequence(s1);
@@ -103,18 +107,132 @@ public class AlignmentUtilsTests
     System.out.println(new AppletFormatAdapter().formatSequences("Clustal", al, true));
     for (int flnk=-1;flnk<25; flnk++)
     {
-      AlignmentI exp;
-      System.out.println("\nFlank size: "+flnk);
-      System.out.println(new AppletFormatAdapter().formatSequences("Clustal", exp=AlignmentUtils.expandContext(al, flnk), true));
-      if (flnk==-1) {
-        for (SequenceI sq:exp.getSequences())
+      AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
+      System.out.println("\nFlank size: " + flnk);
+      System.out.println(new AppletFormatAdapter().formatSequences(
+              "Clustal", exp, true));
+      if (flnk == -1)
       {
+        /*
+         * Full expansion to complete sequences
+         */
+        for (SequenceI sq : exp.getSequences())
+        {
           String ung = sq.getSequenceAsString().replaceAll("-+", "");
-          assertTrue("Flanking sequence not the same as original dataset sequence.\n"+ung+"\n"+sq.getDatasetSequence().getSequenceAsString(),ung.equalsIgnoreCase(sq.getDatasetSequence().getSequenceAsString()));
+          final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
+                  + ung
+                  + "\n"
+                  + sq.getDatasetSequence().getSequenceAsString();
+          assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
+                  .getSequenceAsString()));
+        }
       }
+      else if (flnk == 24)
+      {
+        /*
+         * Last sequence is fully expanded, others have leading gaps to match
+         */
+        assertTrue(exp.getSequenceAt(4).getSequenceAsString()
+                .startsWith("abc"));
+        assertTrue(exp.getSequenceAt(3).getSequenceAsString()
+                .startsWith("--abc"));
+        assertTrue(exp.getSequenceAt(2).getSequenceAsString()
+                .startsWith("----abc"));
+        assertTrue(exp.getSequenceAt(1).getSequenceAsString()
+                .startsWith("------abc"));
+        assertTrue(exp.getSequenceAt(0).getSequenceAsString()
+                .startsWith("--------abc"));
       }
     }
-    }    
+  }
+
+  /**
+   * Test that annotations are correctly adjusted by expandContext
+   */
+  @Test
+  public void testExpandContext_annotation()
+  {
+    AlignmentI al = new Alignment(new Sequence[]
+    {});
+    SequenceI ds = new Sequence("Seq1", "ABCDEFGHI");
+    // subsequence DEF:
+    SequenceI seq1 = ds.deriveSequence().getSubSequence(3, 6);
+    al.addSequence(seq1);
+
+    /*
+     * Annotate DEF with 4/5/6 respectively
+     */
+    Annotation[] anns = new Annotation[]
+    { new Annotation(4), new Annotation(5), new Annotation(6) };
+    AlignmentAnnotation ann = new AlignmentAnnotation("SS",
+            "secondary structure", anns);
+    seq1.addAlignmentAnnotation(ann);
+
+    /*
+     * The annotations array should match aligned positions
+     */
+    assertEquals(3, ann.annotations.length);
+    assertEquals(4, ann.annotations[0].value, 0.001);
+    assertEquals(5, ann.annotations[1].value, 0.001);
+    assertEquals(6, ann.annotations[2].value, 0.001);
+
+    /*
+     * Check annotation to sequence position mappings before expanding the
+     * sequence; these are set up in Sequence.addAlignmentAnnotation ->
+     * Annotation.setSequenceRef -> createSequenceMappings
+     */
+    assertNull(ann.getAnnotationForPosition(1));
+    assertNull(ann.getAnnotationForPosition(2));
+    assertNull(ann.getAnnotationForPosition(3));
+    assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
+    assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
+    assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
+    assertNull(ann.getAnnotationForPosition(7));
+    assertNull(ann.getAnnotationForPosition(8));
+    assertNull(ann.getAnnotationForPosition(9));
+
+    /*
+     * Expand the subsequence to the full sequence abcDEFghi
+     */
+    AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
+    assertEquals("abcDEFghi", expanded.getSequenceAt(0)
+            .getSequenceAsString());
+
+    /*
+     * Confirm the alignment and sequence have the same SS annotation,
+     * referencing the expanded sequence
+     */
+    ann = expanded.getSequenceAt(0).getAnnotation()[0];
+    assertSame(ann, expanded.getAlignmentAnnotation()[0]);
+    assertSame(expanded.getSequenceAt(0), ann.sequenceRef);
+
+    /*
+     * The annotations array should have null values except for annotated
+     * positions
+     */
+    assertNull(ann.annotations[0]);
+    assertNull(ann.annotations[1]);
+    assertNull(ann.annotations[2]);
+    assertEquals(4, ann.annotations[3].value, 0.001);
+    assertEquals(5, ann.annotations[4].value, 0.001);
+    assertEquals(6, ann.annotations[5].value, 0.001);
+    assertNull(ann.annotations[6]);
+    assertNull(ann.annotations[7]);
+    assertNull(ann.annotations[8]);
+
+    /*
+     * sequence position mappings should be unchanged
+     */
+    assertNull(ann.getAnnotationForPosition(1));
+    assertNull(ann.getAnnotationForPosition(2));
+    assertNull(ann.getAnnotationForPosition(3));
+    assertEquals(4, ann.getAnnotationForPosition(4).value, 0.001);
+    assertEquals(5, ann.getAnnotationForPosition(5).value, 0.001);
+    assertEquals(6, ann.getAnnotationForPosition(6).value, 0.001);
+    assertNull(ann.getAnnotationForPosition(7));
+    assertNull(ann.getAnnotationForPosition(8));
+    assertNull(ann.getAnnotationForPosition(9));
+  }
 
   /**
    * Test method that returns a map of lists of sequences by sequence name.