-package jalview.gui;
+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.SequenceGroup;
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;
-/**
- * Unit tests for PopupMenu
- *
- * @author gmcarstairs
- *
- */
-public class PopupMenuTest
+public class AlignmentAnnotationUtilsTest
{
// 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";
+ 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 static final int AUTO_ANNS = 3;
+ private AlignmentI alignment;
- 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]));
+ }
- AlignmentPanel parentPanel;
+ /**
+ * 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
{
- AlignmentI al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
+ alignment = 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++)
{
}
/**
- * 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()
+ 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();
- BitSet visibleGraphGroups = new BitSet();
- selectSequences(0, 3);
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
-
+ SequenceI[] seqs = alignment.getSequencesArray();
+
/*
- * Configure annotation properties for test (offsetting for auto-calculated
- * rows).
+ * Configure annotation properties for test
*/
// 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;
-
+ anns[4].sequenceRef = seqs[2];
+ anns[4].visible = false;
+ anns[7].sequenceRef = seqs[1];
+ 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");
+ 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[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());
-
+ 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(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("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()
+ 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();
- BitSet visibleGraphGroups = new BitSet();
- visibleGraphGroups.set(GROUP_4);
- visibleGraphGroups.set(GROUP_6);
- selectSequences(0, 3);
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
-
+ SequenceI[] seqs = alignment.getSequencesArray();
+
/*
- * Configure annotation properties for test (offsetting for auto-calculated
- * rows).
+ * Configure annotation properties for test
*/
// 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;
+ 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[AUTO_ANNS + 3].setCalcId("CalcId2");
-
+ anns[3].setCalcId("CalcId2");
+
// annotations Label1 (hidden), Label5 (visible) in group 6 (visible)
- anns[AUTO_ANNS + 1].sequenceRef = seqs[3];
+ 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");
-
+ 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[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;
+ 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[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());
-
+ 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());
}
/**
- * Add a sequence group to the alignment with the specified sequences (base 0)
- * in it
- *
- * @param i
- * @param more
+ * Test method that determines visible graph groups.
*/
- private void selectSequences(int... selected)
+ @Test
+ public void testGetVisibleGraphGroups()
{
- SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
- SequenceGroup sg = new SequenceGroup();
- for (int i : selected)
- {
- sg.addSequence(seqs[i], false);
- }
- parentPanel.av.setSelectionGroup(sg);
+ 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());
}
}
git://source.jalview.org / jalview.git / blobdiff