JAL-2780 JAL-2781 test AlignmentI.findAnnotations locates sequence associated annotat...

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index c5d09c1..74ac146 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -37,7 +37,6 @@ import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
@@ -620,6 +619,78 @@ public class AlignmentTest
     assertFalse(iter.hasNext());
   }
 
+  /**
+   * Test method that returns annotations that match on reference sequence,
+   * label, or calcId.
+   */
+  @Test(groups = { "Functional" })
+  public void testFindAnnotations_bySeqLabelandorCalcId()
+  {
+    // TODO: finish testFindAnnotations_bySeqLabelandorCalcId test
+    /* Note - this is an incomplete test - need to check null or
+     * non-null [ matches, not matches ] behaviour for each of the three
+     * parameters..*/
+
+    // search for a single, unique calcId with wildcards on other params
+    Iterable<AlignmentAnnotation> anns = al.findAnnotations(null,
+            "CalcIdForD.melanogaster.2", null);
+    Iterator<AlignmentAnnotation> iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    AlignmentAnnotation ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // save reference to test sequence reference parameter
+    SequenceI rseq = ann.sequenceRef;
+
+    // search for annotation associated with a single sequence
+    anns = al.findAnnotations(rseq, null, null);
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    ann = iter.next();
+    assertEquals("D.melanogaster.2", ann.sequenceRef.getName());
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a non-existant calcId
+    anns = al.findAnnotations(null, "CalcIdForD.melanogaster.?", null);
+    iter = anns.iterator();
+    assertFalse(iter.hasNext());
+
+    // search for annotation with a particular label - expect three
+    anns = al.findAnnotations(null, null, "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    assertTrue(iter.hasNext());
+    iter.next();
+    // third found.. so
+    assertFalse(iter.hasNext());
+
+    // search for annotation on one sequence with a particular label - expect
+    // one
+    SequenceI sqfound;
+    anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+            "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    // expect reference to sequence 1 in the alignment
+    assertTrue(sqfound == iter.next().sequenceRef);
+    assertFalse(iter.hasNext());
+
+    // null on all parameters == find all annotations
+    anns = al.findAnnotations(null, null, null);
+    iter = anns.iterator();
+    int n = al.getAlignmentAnnotation().length;
+    while (iter.hasNext())
+    {
+      n--;
+      iter.next();
+    }
+    assertTrue("Found " + n + " fewer annotations from search.", n == 0);
+  }
+
   @Test(groups = { "Functional" })
   public void testDeleteAllAnnotations_includingAutocalculated()
   {
@@ -1046,35 +1117,6 @@ public class AlignmentTest
             "addSequence broke dataset reference integrity");
   }
 
-  @Test(groups = "Functional")
-  public void getVisibleStartAndEndIndexTest()
-  {
-    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
-    AlignmentI align = new Alignment(new SequenceI[] { seq });
-    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-
-    int[] startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(0, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 0, 0 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(1, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 6, 9 });
-    hiddenCols.add(new int[] { 11, 12 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    assertEquals(1, startEnd[0]);
-    assertEquals(25, startEnd[1]);
-
-    hiddenCols.add(new int[] { 24, 25 });
-    startEnd = align.getVisibleStartAndEndIndex(hiddenCols);
-    System.out.println(startEnd[0] + " : " + startEnd[1]);
-    assertEquals(1, startEnd[0]);
-    assertEquals(23, startEnd[1]);
-  }
-
   /**
    * Tests that dbrefs with mappings to sequence get updated if the sequence
    * acquires a dataset sequence
@@ -1269,4 +1311,43 @@ public class AlignmentTest
     AlignmentI alignment = new Alignment(new SequenceI[] { seq });
     alignment.setDataset(alignment);
   }
+
+  @Test(groups = "Functional")
+  public void testAppend()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+    alignment.setGapCharacter('-');
+    SequenceI seq2 = new Sequence("seq1", "KP..L.FQII.");
+    AlignmentI alignment2 = new Alignment(new SequenceI[] { seq2 });
+    alignment2.setGapCharacter('.');
+
+    alignment.append(alignment2);
+
+    assertEquals('-', alignment.getGapCharacter());
+    assertSame(seq, alignment.getSequenceAt(0));
+    assertEquals("KP--L-FQII-", alignment.getSequenceAt(1)
+            .getSequenceAsString());
+
+    // todo test coverage for annotations, mappings, groups,
+    // hidden sequences, properties
+  }
+
+  /**
+   * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+   * an annotation with a null calcId
+   * 
+   */
+  @Test(groups = "Functional")
+  public void testFindOrCreateForNullCalcId()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+    AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+            "Temperature Factor", null, false, seq, null);
+    assertNotNull(ala);
+    assertEquals(seq, ala.sequenceRef);
+    assertEquals("", ala.calcId);
+  }
 }