--- /dev/null
+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());
+ }
+}