--- /dev/null
+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.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
+import java.io.IOException;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Unit tests for PopupMenu
+ *
+ * @author gmcarstairs
+ *
+ */
+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";
+
+ private static final int SEQ_ANN_COUNT = 10;
+
+ private static final int AUTO_ANNS = 3;
+
+ AlignmentI alignment;
+
+ AlignmentPanel parentPanel;
+
+ @Before
+ public void setUp() throws IOException
+ {
+ AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+ AppletFormatAdapter.PASTE, "FASTA");
+ AlignFrame af = new AlignFrame(al, 700, 500);
+ parentPanel = new AlignmentPanel(af, af.getViewport());
+ alignment = parentPanel.getAlignment();
+
+ 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 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 = PopupMenu.getVisibleLineGraphGroups(anns);
+ assertTrue(result.get(5));
+ assertFalse(result.get(0));
+ assertFalse(result.get(1));
+ assertFalse(result.get(2));
+ assertFalse(result.get(3));
+ }
+
+ /**
+ * Test a mixture of show/hidden annotations in/outside selection group.
+ */
+ @Test
+ public void testGetAnnotationTypesForShowHide_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();
+ BitSet visibleGraphGroups = new BitSet();
+ selectSequences(0, 3);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+
+ /*
+ * Configure annotation properties for test (offsetting for auto-calculated
+ * rows).
+ */
+ // not in selection group (should be ignored):
+ // hidden annotation Label4 not in selection group
+ anns[AUTO_ANNS + 4].sequenceRef = seqs[2];
+ anns[AUTO_ANNS + 4].visible = false;
+ anns[AUTO_ANNS + 7].sequenceRef = seqs[1];
+ anns[AUTO_ANNS + 7].visible = true;
+
+ /*
+ * in selection group, hidden:
+ */
+ anns[AUTO_ANNS + 2].sequenceRef = seqs[3]; // CalcId2/Label2
+ anns[AUTO_ANNS + 2].visible = false;
+ anns[AUTO_ANNS + 3].sequenceRef = seqs[3]; // CalcId3/Label2
+ anns[AUTO_ANNS + 3].visible = false;
+ anns[AUTO_ANNS + 3].label = "Label2";
+ anns[AUTO_ANNS + 4].sequenceRef = seqs[3]; // CalcId2/Label3
+ anns[AUTO_ANNS + 4].visible = false;
+ anns[AUTO_ANNS + 4].label = "Label3";
+ anns[AUTO_ANNS + 4].setCalcId("CalcId2");
+ anns[AUTO_ANNS + 8].sequenceRef = seqs[0]; // CalcId9/Label9
+ anns[AUTO_ANNS + 8].visible = false;
+ anns[AUTO_ANNS + 8].label = "Label9";
+ anns[AUTO_ANNS + 8].setCalcId("CalcId9");
+ /*
+ * in selection group, visible
+ */
+ anns[AUTO_ANNS + 6].sequenceRef = seqs[0]; // CalcId6/Label6
+ anns[AUTO_ANNS + 6].visible = true;
+ anns[AUTO_ANNS + 9].sequenceRef = seqs[3]; // CalcId9/Label9
+ anns[AUTO_ANNS + 9].visible = true;
+
+ PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
+ visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
+
+ // 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);
+ }
+
+ /**
+ * 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);
+ }
+ }
+ }
+
+ /**
+ * Test case where there are 'grouped' annotations, visible and hidden, within
+ * and without the selection group.
+ */
+ @Test
+ public void testGetAnnotationTypesForShowHide_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();
+ BitSet visibleGraphGroups = new BitSet();
+ visibleGraphGroups.set(GROUP_4);
+ visibleGraphGroups.set(GROUP_6);
+ selectSequences(0, 3);
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+
+ /*
+ * Configure annotation properties for test (offsetting for auto-calculated
+ * rows).
+ */
+ // annotations for selection group and graph group
+ // hidden annotations Label2, Label3, in (hidden) group 5
+ anns[AUTO_ANNS + 2].sequenceRef = seqs[3];
+ anns[AUTO_ANNS + 2].visible = false;
+ anns[AUTO_ANNS + 2].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 2].graphGroup = GROUP_5; // not a visible group
+ anns[AUTO_ANNS + 3].sequenceRef = seqs[0];
+ anns[AUTO_ANNS + 3].visible = false;
+ anns[AUTO_ANNS + 3].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 3].graphGroup = GROUP_5;
+ // need to ensure annotations have the same calcId as well
+ anns[AUTO_ANNS + 3].setCalcId("CalcId2");
+
+ // annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
+ anns[AUTO_ANNS + 1].sequenceRef = seqs[3];
+ // being in a visible group should take precedence over this visibility
+ anns[AUTO_ANNS + 1].visible = false;
+ anns[AUTO_ANNS + 1].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 1].graphGroup = GROUP_6;
+ anns[AUTO_ANNS + 5].sequenceRef = seqs[0];
+ anns[AUTO_ANNS + 5].visible = true; // visibleGraphGroups overrides this
+ anns[AUTO_ANNS + 5].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 5].graphGroup = GROUP_6;
+ anns[AUTO_ANNS + 5].setCalcId("CalcId1");
+
+ // annotations outwith selection group - should be ignored
+ // hidden grouped annotations
+ anns[AUTO_ANNS + 6].sequenceRef = seqs[2];
+ anns[AUTO_ANNS + 6].visible = false;
+ anns[AUTO_ANNS + 6].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 6].graphGroup = GROUP_4;
+ anns[AUTO_ANNS + 8].sequenceRef = seqs[1];
+ anns[AUTO_ANNS + 8].visible = false;
+ anns[AUTO_ANNS + 8].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 8].graphGroup = GROUP_4;
+ // visible grouped annotations Label7, Label9
+ anns[AUTO_ANNS + 7].sequenceRef = seqs[2];
+ anns[AUTO_ANNS + 7].visible = true;
+ anns[AUTO_ANNS + 7].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 7].graphGroup = GROUP_4;
+ anns[AUTO_ANNS + 9].sequenceRef = seqs[1];
+ anns[AUTO_ANNS + 9].visible = true;
+ anns[AUTO_ANNS + 9].graph = AlignmentAnnotation.LINE_GRAPH;
+ anns[AUTO_ANNS + 9].graphGroup = GROUP_4;
+
+ PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
+ visibleGraphGroups, anns, parentPanel.av.getSelectionGroup());
+
+ 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));
+ }
+
+ /**
+ * Add a sequence group to the alignment with the specified sequences (base 0)
+ * in it
+ *
+ * @param i
+ * @param more
+ */
+ private void selectSequences(int... selected)
+ {
+ SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+ SequenceGroup sg = new SequenceGroup();
+ for (int i : selected)
+ {
+ sg.addSequence(seqs[i], false);
+ }
+ parentPanel.av.setSelectionGroup(sg);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff