JAL-1264 further refactoring and tests
[jalview.git] / test / jalview / analysis / AlignmentAnnotationUtilsTest.java
diff --git a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java
new file mode 100644 (file)
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+package jalview.analysis;
+
+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 java.io.IOException;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class AlignmentAnnotationUtilsTest
+{
+  // 4 sequences x 13 positions
+  final static String EOL = "\n";
+
+  // @formatter:off
+  final static String TEST_DATA = 
+          ">FER_CAPAA Ferredoxin" + EOL +
+          "TIETHKEAELVG-" + EOL +
+          ">FER_CAPAN Ferredoxin, chloroplast precursor" + EOL +
+          "TIETHKEAELVG-" + EOL +
+          ">FER1_SOLLC Ferredoxin-1, chloroplast precursor" + EOL +
+          "TIETHKEEELTA-" + EOL + 
+          ">Q93XJ9_SOLTU Ferredoxin I precursor" + EOL +
+          "TIETHKEEELTA-" + EOL;
+  // @formatter:on
+
+  private static final int SEQ_ANN_COUNT = 10;
+
+  private AlignmentI alignment;
+
+  /**
+   * Test method that converts a (possibly null) array to a list.
+   */
+  @Test
+  public void testAsList()
+  {
+    // null array
+    Collection<AlignmentAnnotation> c1 = AlignmentAnnotationUtils
+            .asList(null);
+    assertTrue(c1.isEmpty());
+    
+    // empty array
+    AlignmentAnnotation[] anns = new AlignmentAnnotation[0];
+    c1 = AlignmentAnnotationUtils.asList(anns);
+    assertTrue(c1.isEmpty());
+
+    // non-empty array
+    anns = new AlignmentAnnotation[2];
+    anns[0] = new AlignmentAnnotation("label0", "desc0", 0.0f);
+    anns[1] = new AlignmentAnnotation("label1", "desc1", 1.0f);
+    c1 = AlignmentAnnotationUtils.asList(anns);
+    assertEquals(2, c1.size());
+    assertTrue(c1.contains(anns[0]));
+    assertTrue(c1.contains(anns[1]));
+  }
+
+  /**
+   * This output is not part of the test but may help make sense of it...
+   * 
+   * @param shownTypes
+   * @param hiddenTypes
+   */
+  protected void consoleDebug(Map<String, List<List<String>>> shownTypes,
+          Map<String, List<List<String>>> hiddenTypes)
+  {
+    for (String calcId : shownTypes.keySet())
+    {
+      System.out.println("Visible annotation types for calcId=" + calcId);
+      for (List<String> type : shownTypes.get(calcId))
+      {
+        System.out.println("   " + type);
+      }
+    }
+    for (String calcId : hiddenTypes.keySet())
+    {
+      System.out.println("Hidden annotation types for calcId=" + calcId);
+      for (List<String> type : hiddenTypes.get(calcId))
+      {
+        System.out.println("   " + type);
+      }
+    }
+  }
+
+  /**
+   * Add a sequence group to the alignment with the specified sequences (base 0)
+   * in it
+   * 
+   * @param i
+   * @param more
+   */
+  private List<SequenceI> selectSequences(int... selected)
+  {
+    List<SequenceI> result = new ArrayList<SequenceI>();
+    SequenceI[] seqs = alignment.getSequencesArray();
+    for (int i : selected)
+    {
+      result.add(seqs[i]);
+    }
+    return result;
+  }
+
+  @Before
+  public void setUp() throws IOException
+  {
+    alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+            AppletFormatAdapter.PASTE, "FASTA");
+  
+    AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
+    for (int i = 0; i < anns.length; i++)
+    {
+      anns[i] = new AlignmentAnnotation("Label" + i, null, 0d);
+      anns[i].setCalcId("CalcId" + i);
+      anns[i].visible = true;
+      alignment.addAnnotation(anns[i]);
+    }
+  }
+
+  /**
+   * Test a mixture of show/hidden annotations in/outside selection group.
+   */
+  @Test
+  public void testGetShownHiddenTypes_forSelectionGroup()
+  {
+    Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
+    Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    SequenceI[] seqs = alignment.getSequencesArray();
+  
+    /*
+     * Configure annotation properties for test
+     */
+    // not in selection group (should be ignored):
+    // hidden annotation Label4 not in selection group
+    anns[4].sequenceRef = seqs[2];
+    anns[4].visible = false;
+    anns[7].sequenceRef = seqs[1];
+    anns[7].visible = true;
+  
+    /*
+     * in selection group, hidden:
+     */
+    anns[2].sequenceRef = seqs[3]; // CalcId2/Label2
+    anns[2].visible = false;
+    anns[3].sequenceRef = seqs[3]; // CalcId3/Label2
+    anns[3].visible = false;
+    anns[3].label = "Label2";
+    anns[4].sequenceRef = seqs[3]; // CalcId2/Label3
+    anns[4].visible = false;
+    anns[4].label = "Label3";
+    anns[4].setCalcId("CalcId2");
+    anns[8].sequenceRef = seqs[0]; // CalcId9/Label9
+    anns[8].visible = false;
+    anns[8].label = "Label9";
+    anns[8].setCalcId("CalcId9");
+    /*
+     * in selection group, visible
+     */
+    anns[6].sequenceRef = seqs[0]; // CalcId6/Label6
+    anns[6].visible = true;
+    anns[9].sequenceRef = seqs[3]; // CalcId9/Label9
+    anns[9].visible = true;
+  
+    List<SequenceI> selected = selectSequences(0, 3);
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(anns),
+            selected);
+  
+    // check results; note CalcId9/Label9 is both hidden and shown (for
+    // different sequences) so should be in both
+    // shown: CalcId6/Label6 and CalcId9/Label9
+    assertEquals(2, shownTypes.size());
+    assertEquals(1, shownTypes.get("CalcId6").size());
+    assertEquals(1, shownTypes.get("CalcId6").get(0).size());
+    assertEquals("Label6", shownTypes.get("CalcId6").get(0).get(0));
+    assertEquals(1, shownTypes.get("CalcId9").size());
+    assertEquals(1, shownTypes.get("CalcId9").get(0).size());
+    assertEquals("Label9", shownTypes.get("CalcId9").get(0).get(0));
+  
+    // hidden: CalcId2/Label2, CalcId2/Label3, CalcId3/Label2, CalcId9/Label9
+    assertEquals(3, hiddenTypes.size());
+    assertEquals(2, hiddenTypes.get("CalcId2").size());
+    assertEquals(1, hiddenTypes.get("CalcId2").get(0).size());
+    assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
+    assertEquals(1, hiddenTypes.get("CalcId2").get(1).size());
+    assertEquals("Label3", hiddenTypes.get("CalcId2").get(1).get(0));
+    assertEquals(1, hiddenTypes.get("CalcId3").size());
+    assertEquals(1, hiddenTypes.get("CalcId3").get(0).size());
+    assertEquals("Label2", hiddenTypes.get("CalcId3").get(0).get(0));
+    assertEquals(1, hiddenTypes.get("CalcId9").size());
+    assertEquals(1, hiddenTypes.get("CalcId9").get(0).size());
+    assertEquals("Label9", hiddenTypes.get("CalcId9").get(0).get(0));
+  
+    consoleDebug(shownTypes, hiddenTypes);
+  }
+
+  /**
+   * Test case where there are 'grouped' annotations, visible and hidden, within
+   * and without the selection group.
+   */
+  @Test
+  public void testGetShownHiddenTypes_withGraphGroups()
+  {
+    final int GROUP_4 = 4;
+    final int GROUP_5 = 5;
+    final int GROUP_6 = 6;
+  
+    Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
+    Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    SequenceI[] seqs = alignment.getSequencesArray();
+  
+    /*
+     * Configure annotation properties for test
+     */
+    // annotations for selection group and graph group
+    // hidden annotations Label2, Label3, in (hidden) group 5
+    anns[2].sequenceRef = seqs[3];
+    anns[2].visible = false;
+    anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[2].graphGroup = GROUP_5; // not a visible group
+    anns[3].sequenceRef = seqs[0];
+    anns[3].visible = false;
+    anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[3].graphGroup = GROUP_5;
+    // need to ensure annotations have the same calcId as well
+    anns[3].setCalcId("CalcId2");
+  
+    // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
+    anns[1].sequenceRef = seqs[3];
+    // being in a visible group should take precedence over this visibility
+    anns[1].visible = false;
+    anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[1].graphGroup = GROUP_6;
+    anns[5].sequenceRef = seqs[0];
+    anns[5].visible = true;
+    anns[5].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[5].graphGroup = GROUP_6;
+    anns[5].setCalcId("CalcId1");
+  
+    // annotations outwith selection group - should be ignored
+    // hidden grouped annotations
+    anns[6].sequenceRef = seqs[2];
+    anns[6].visible = false;
+    anns[6].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[6].graphGroup = GROUP_4;
+    anns[8].sequenceRef = seqs[1];
+    anns[8].visible = false;
+    anns[8].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[8].graphGroup = GROUP_4;
+    // visible grouped annotations Label7, Label9
+    anns[7].sequenceRef = seqs[2];
+    anns[7].visible = true;
+    anns[7].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[7].graphGroup = GROUP_4;
+    anns[9].sequenceRef = seqs[1];
+    anns[9].visible = true;
+    anns[9].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[9].graphGroup = GROUP_4;
+  
+    List<SequenceI> selected = selectSequences(0, 3);
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(anns),
+            selected);
+  
+    consoleDebug(shownTypes, hiddenTypes);
+  
+    // CalcId1 / Label1, Label5 (only) should be 'shown', as a compound type
+    assertEquals(1, shownTypes.get("CalcId1").size());
+    assertEquals(2, shownTypes.get("CalcId1").get(0).size());
+    assertEquals("Label1", shownTypes.get("CalcId1").get(0).get(0));
+    assertEquals("Label5", shownTypes.get("CalcId1").get(0).get(1));
+  
+    // CalcId2 / Label2, Label3 (only) should be 'hidden'
+    assertEquals(1, hiddenTypes.get("CalcId2").size());
+    assertEquals(2, hiddenTypes.get("CalcId2").get(0).size());
+    assertEquals("Label2", hiddenTypes.get("CalcId2").get(0).get(0));
+    assertEquals("Label3", hiddenTypes.get("CalcId2").get(0).get(1));
+  }
+
+  /**
+   * Test method that determines visible graph groups.
+   */
+  @Test
+  public void testGetVisibleGraphGroups()
+  {
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    /*
+     * a bar graph group is not included
+     */
+    anns[0].graph = AlignmentAnnotation.BAR_GRAPH;
+    anns[0].graphGroup = 1;
+    anns[0].visible = true;
+  
+    /*
+     * a line graph group is included as long as one of its members is visible
+     */
+    anns[1].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[1].graphGroup = 5;
+    anns[1].visible = false;
+    anns[2].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[2].graphGroup = 5;
+    anns[2].visible = true;
+  
+    /*
+     * a line graph group with no visible rows is not included
+     */
+    anns[3].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[3].graphGroup = 3;
+    anns[3].visible = false;
+  
+    // a visible line graph with no graph group is not included
+    anns[4].graph = AlignmentAnnotation.LINE_GRAPH;
+    anns[4].graphGroup = -1;
+    anns[4].visible = true;
+  
+    BitSet result = AlignmentAnnotationUtils
+            .getVisibleLineGraphGroups(AlignmentAnnotationUtils
+                    .asList(anns));
+    assertTrue(result.get(5));
+    assertFalse(result.get(0));
+    assertFalse(result.get(1));
+    assertFalse(result.get(2));
+    assertFalse(result.get(3));
+  }
+
+  /**
+   * Test for case where no sequence is selected. Shouldn't normally arise but
+   * check it handles it gracefully.
+   */
+  @Test
+  public void testGetShownHiddenTypes_noSequenceSelected()
+  {
+    Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
+    Map<String, List<List<String>>> hiddenTypes = new HashMap<String, List<List<String>>>();
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    // selected sequences null
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(anns), null);
+    assertTrue(shownTypes.isEmpty());
+    assertTrue(hiddenTypes.isEmpty());
+
+    List<SequenceI> sequences = new ArrayList<SequenceI>();
+    // selected sequences empty list
+    AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+            AlignmentAnnotationUtils.asList(anns), sequences);
+    assertTrue(shownTypes.isEmpty());
+    assertTrue(hiddenTypes.isEmpty());
+  }
+}