+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AlignmentAnnotationUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// 4 sequences x 13 positions
final static String EOL = "\n";
/**
* Test method that converts a (possibly null) array to a list.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
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);
*
* @throws IOException
*/
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws IOException
{
alignment = new jalview.io.FormatAdapter().readFile(TEST_DATA,
- AppletFormatAdapter.PASTE, "FASTA");
-
+ DataSourceType.PASTE, FileFormat.Fasta);
+
AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT];
for (int i = 0; i < anns.length; i++)
{
* array)
*/
anns[i] = new AlignmentAnnotation("Label" + i, "Desc " + i,
- new Annotation[]
- {});
+ new Annotation[] {});
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(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
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
*/
anns[4].visible = false;
anns[7].sequenceRef = seqs[1];
anns[7].visible = true;
-
+
/*
* in selection group, hidden:
*/
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);
-
+ 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);
}
* Test case where there are 'grouped' annotations, visible and hidden, within
* and without the selection group.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetShownHiddenTypes_withGraphGroups()
{
final int GROUP_3 = 3;
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();
-
+
/*
* Annotations for selection group and graph group
*
anns[11].graphGroup = GROUP_3;
anns[11].label = "Label2";
anns[11].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[0].graphGroup = GROUP_4;
anns[0].label = "Label5";
anns[0].setCalcId("CalcId1");
-
+
/*
* Annotations outwith selection group - should be ignored.
*/
anns[9].visible = true;
anns[9].graph = AlignmentAnnotation.LINE_GRAPH;
anns[9].graphGroup = GROUP_4;
-
+
/*
* Generate annotations[] arrays to match aligned columns
*/
List<SequenceI> selected = selectSequences(0, 3);
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
- AlignmentAnnotationUtils.asList(anns),
- selected);
-
+ AlignmentAnnotationUtils.asList(anns), selected);
+
consoleDebug(shownTypes, hiddenTypes);
-
+
// CalcId1 / Label1, Label5 (only) should be 'shown', once, as a compound
// type
assertEquals(1, shownTypes.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.size());
assertEquals(1, hiddenTypes.get("CalcId2").size());
/**
* Test method that determines visible graph groups.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetVisibleGraphGroups()
{
AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
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[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));
+
+ BitSet result = AlignmentAnnotationUtils.getVisibleLineGraphGroups(
+ AlignmentAnnotationUtils.asList(anns));
assertTrue(result.get(5));
assertFalse(result.get(0));
assertFalse(result.get(1));
* Test for case where no sequence is selected. Shouldn't normally arise but
* check it handles it gracefully.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGetShownHiddenTypes_noSequenceSelected()
{
Map<String, List<List<String>>> shownTypes = new HashMap<String, List<List<String>>>();
git://source.jalview.org / jalview.git / blobdiff