X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignmentTest.java;h=63f8e93d83f1e12ab27ac5209d7b99bcc915107e;hb=a4143dac9ce4bbf4e3c60496c5818d30fc75e759;hp=ddba94991a40f1a7927abc7131410e36cbb91e2f;hpb=53ef0b8b1f5cad886db96520528e367aadec2712;p=jalview.git

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index ddba949..63f8e93 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -28,7 +28,6 @@ import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -248,7 +247,9 @@ public class AlignmentTest
                   if (raiseAssert)
                   {
                     Assert.fail(message
-                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                            + " DBRefEntry " + dbr + " for sequence "
+                            + seqds
+                            + " in alignment has map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -262,7 +263,7 @@ public class AlignmentTest
       {
         for (AlignedCodonFrame alc : alignment.getCodonFrames())
         {
-          for (SequenceToSequenceMapping ssm : alc.getMappings())
+          for (SequenceMapping ssm : alc.getMappings())
           {
             if (ssm.getFromSeq().getDatasetSequence() != null)
             {
@@ -669,6 +670,17 @@ public class AlignmentTest
     // 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();
@@ -1323,6 +1335,24 @@ public class AlignmentTest
     // 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);
+  }
+
   @Test(groups = "Functional")
   public void testPropagateInsertions()
   {
@@ -1453,4 +1483,82 @@ public class AlignmentTest
     assertEquals(".JKLMNO", seq2.getSequenceAsString());
     assertEquals(".PQR...", seq3.getSequenceAsString());
   }
+
+  /**
+   * Test for setHiddenColumns, to check it returns true if the hidden columns
+   * have changed, else false
+   */
+  @Test(groups = { "Functional" })
+  public void testSetHiddenColumns()
+  {
+    AlignmentI al = new Alignment(new SequenceI[] {});
+    assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+    HiddenColumns hc = new HiddenColumns();
+    assertFalse(al.setHiddenColumns(hc)); // no change
+    assertSame(hc, al.getHiddenColumns());
+
+    hc.hideColumns(2, 4);
+    assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+    /*
+     * set a different object but with the same columns hidden
+     */
+    HiddenColumns hc2 = new HiddenColumns();
+    hc2.hideColumns(2, 4);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+    assertSame(hc2, al.getHiddenColumns());
+
+    assertTrue(al.setHiddenColumns(null));
+    assertNull(al.getHiddenColumns());
+    assertTrue(al.setHiddenColumns(hc));
+    assertSame(hc, al.getHiddenColumns());
+
+    al.getHiddenColumns().hideColumns(10, 12);
+    hc2.hideColumns(10, 12);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+
+    /*
+     * hide columns 15-16 then 17-18 in hc
+     * hide columns 15-18 in hc2
+     * these are not now 'equal' objects even though they
+     * represent the same set of columns
+     */
+    assertSame(hc2, al.getHiddenColumns());
+    hc.hideColumns(15, 16);
+    hc.hideColumns(17, 18);
+    hc2.hideColumns(15, 18);
+    assertFalse(hc.equals(hc2));
+    assertTrue(al.setHiddenColumns(hc)); // 'changed'
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getWidth());
+
+    // width includes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(9, a.getWidth());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getVisibleWidth());
+
+    // width excludes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(5, a.getVisibleWidth());
+  }
 }