JAL-1264 new unit tests

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
new file mode 100644 (file)
index 0000000..d9101cf
--- /dev/null
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -0,0 +1,106 @@
+package jalview.datamodel;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertSame;
+import static org.junit.Assert.assertTrue;
+
+import java.util.List;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class SequenceTest
+{
+  Sequence seq;
+
+  @Before
+  public void setUp()
+  {
+    seq = new Sequence("FER1", "AKPNGVL");
+  }
+  @Test
+  public void testGetAnnotation()
+  {
+    // initial state returns null not an empty array
+    assertNull(seq.getAnnotation());
+    AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
+            1f);
+    AlignmentAnnotation[] anns = seq.getAnnotation();
+    assertEquals(1, anns.length);
+    assertSame(ann, anns[0]);
+
+    // removing all annotations reverts array to null
+    seq.removeAlignmentAnnotation(ann);
+    assertNull(seq.getAnnotation());
+  }
+
+  @Test
+  public void testGetAnnotation_forLabel()
+  {
+    AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1", 1f);
+    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2", 1f);
+    AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3", 1f);
+    AlignmentAnnotation[] anns = seq.getAnnotation("label1");
+    assertEquals(2, anns.length);
+    assertSame(ann1, anns[0]);
+    assertSame(ann3, anns[1]);
+  }
+
+  private AlignmentAnnotation addAnnotation(String label,
+          String description, String calcId,
+          float value)
+  {
+    final AlignmentAnnotation annotation = new AlignmentAnnotation(label, description,
+            value);
+    annotation.setCalcId(calcId);
+    seq.addAlignmentAnnotation(annotation);
+    return annotation;
+  }
+
+  @Test
+  public void testGetAlignmentAnnotations_forCalcIdAndLabel()
+  {
+    AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
+            1f);
+    AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
+            1f);
+    AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
+            1f);
+    AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
+            1f);
+    AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null,
+            1f);
+    AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3",
+            1f);
+    List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
+            "label2");
+    assertEquals(2, anns.size());
+    assertSame(ann2, anns.get(0));
+    assertSame(ann4, anns.get(1));
+    
+    assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
+    assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
+    assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
+    assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
+    assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
+  }
+
+  /**
+   * Tests for addAlignmentAnnotation. Note this method has the side-effect of
+   * setting the sequenceRef on the annotation.
+   */
+  @Test
+  public void testAddAlignmentAnnotation()
+  {
+    assertNull(seq.annotation);
+    final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
+            "b", 2d);
+    assertNull(annotation.sequenceRef);
+    seq.addAlignmentAnnotation(annotation);
+    assertSame(seq, annotation.sequenceRef);
+    AlignmentAnnotation[] anns = seq.getAnnotation();
+    assertEquals(1, anns.length);
+    assertSame(annotation, anns[0]);
+  }
+}

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
new file mode 100644 (file)
index 0000000..ea1dfb0
--- /dev/null
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -0,0 +1,150 @@
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenuItem;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class PopupMenuTest
+{
+  // 4 sequences x 13 positions
+  final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+          + "TIETHKEAELVG-\n"
+          + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+          + "TIETHKEAELVG-\n"
+          + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+          + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+          + "TIETHKEEELTA-\n";
+
+  AlignmentI alignment;
+
+  AlignmentPanel parentPanel;
+
+  PopupMenu testee = null;
+
+  @Before
+  public void setUp() throws IOException
+  {
+    alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+            AppletFormatAdapter.PASTE, "FASTA");
+    AlignFrame af = new AlignFrame(alignment, 700, 500);
+    parentPanel = new AlignmentPanel(af, af.getViewport());
+    testee = new PopupMenu(parentPanel, null, null);
+    int i = 0;
+    for (SequenceI seq : alignment.getSequences())
+    {
+      final AlignmentAnnotation annotation = new AlignmentAnnotation("label" + i,
+              "desc" + i, i);
+      annotation.setCalcId("calcId" + i);
+      seq.addAlignmentAnnotation(annotation);
+      annotation.setSequenceRef(seq);
+    }
+  }
+
+  @Test
+  public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
+  {
+    JMenuItem menu = new JMenuItem();
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertFalse(menu.isEnabled());
+    assertEquals(
+            MessageManager.getString("label.add_reference_annotations"),
+            menu.getText());
+    // now try null list
+    menu.setEnabled(true);
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertFalse(menu.isEnabled());
+  }
+
+  /**
+   * Test building the 'add reference annotations' menu for the case where there
+   * are no reference annotations to add to the alignment. The menu item should
+   * be disabled.
+   */
+  @Test
+  public void testConfigureReferenceAnnotationsMenu_noReferenceAnnotations()
+  {
+    JMenuItem menu = new JMenuItem();
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+
+    /*
+     * Initial state is that sequences have annotations, and have dataset
+     * sequences, but the dataset sequences have no annotations. Hence nothing
+     * to add.
+     */
+    seqs = parentPanel.getAlignment().getSequences();
+
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertFalse(menu.isEnabled());
+  }
+
+  /**
+   * Test building the 'add reference annotations' menu for the case where all
+   * reference annotations are already on the alignment. The menu item should be
+   * disabled.
+   */
+  @Test
+  public void testConfigureReferenceAnnotationsMenu_alreadyAdded()
+  {
+    JMenuItem menu = new JMenuItem();
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+
+    seqs = parentPanel.getAlignment().getSequences();
+    // copy annotation from sequence to dataset
+    seqs.get(1).getDatasetSequence()
+            .addAlignmentAnnotation(seqs.get(1).getAnnotation()[0]);
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertFalse(menu.isEnabled());
+  }
+
+  /**
+   * Test building the 'add reference annotations' menu for the case where
+   * several reference annotations are on the dataset but not on the sequences.
+   * The menu item should be enabled, and acquire a tooltip which lists the
+   * annotation sources (calcIds) and type (labels).
+   */
+  @Test
+  public void testConfigureReferenceAnnotationsMenu()
+  {
+    JMenuItem menu = new JMenuItem();
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
+
+    seqs = parentPanel.getAlignment().getSequences();
+    // make up new annotations and add to dataset sequences
+
+    // PDB.secondary structure on Sequence0
+    AlignmentAnnotation annotation = new AlignmentAnnotation(
+            "secondary structure", "", 0);
+    annotation.setCalcId("PBD");
+    seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+
+    // PDB.Temp on Sequence1
+    annotation = new AlignmentAnnotation("Temp", "", 0);
+    annotation.setCalcId("PBD");
+    seqs.get(1).getDatasetSequence().addAlignmentAnnotation(annotation);
+
+    // JMOL.secondary structure on Sequence0
+    annotation = new AlignmentAnnotation("secondary structure", "", 0);
+    annotation.setCalcId("JMOL");
+    seqs.get(0).getDatasetSequence().addAlignmentAnnotation(annotation);
+
+    testee.configureReferenceAnnotationsMenu(menu, seqs);
+    assertTrue(menu.isEnabled());
+    String expected = "<html><table width=350 border=0><tr><td>Add annotations for<br/>JMOL/secondary structure<br/>PBD/Temp</td></tr></table></html>";
+    assertEquals(expected, menu.getToolTipText());
+  }
+}