+/*
+ * 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.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AnnotationSorterTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final int NUM_SEQS = 6;
private static final int NUM_ANNS = 7;
*/
protected AlignmentAnnotation[] buildAnnotations(int numAnns)
{
- List<AlignmentAnnotation> annlist = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> annlist = new ArrayList<>();
for (int i = 0; i < numAnns; i++)
{
AlignmentAnnotation ann = new AlignmentAnnotation(SS + i, "", 0);
* </ul>
*/
@Test(groups = { "Functional" })
- public void testSortBySequenceAndType_autocalcLast()
+ public void testSortBySequenceAndLabel_autocalcLast()
{
// @formatter:off
anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
// @formatter:on
- AnnotationSorter testee = new AnnotationSorter(al, false);
+ AnnotationSorter testee = new AnnotationSorter(al, false, false);
testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
assertEquals("label5", anns[0].label); // for sequence 0
assertEquals("label0", anns[1].label); // for sequence 1
* Variant with autocalculated annotations sorting to front
*/
@Test(groups = { "Functional" })
- public void testSortBySequenceAndType_autocalcFirst()
+ public void testSortBySequenceAndLabel_autocalcFirst()
{
// @formatter:off
anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
// @formatter:on
- AnnotationSorter testee = new AnnotationSorter(al, true);
+ AnnotationSorter testee = new AnnotationSorter(al, true, false);
testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
assertEquals("Quality", anns[0].label); // autocalc annotations
assertEquals("Consensus", anns[1].label); // retain ordering
* </ul>
*/
@Test(groups = { "Functional" })
- public void testSortByTypeAndSequence_autocalcLast()
+ public void testSortByLabelAndSequence_autocalcLast()
{
// @formatter:off
anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
// @formatter:on
- AnnotationSorter testee = new AnnotationSorter(al, false);
+ AnnotationSorter testee = new AnnotationSorter(al, false, false);
testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
assertEquals("IRON", anns[0].label); // IRON / sequence 0
assertEquals("iron", anns[1].label); // iron / sequence 3
* Variant of test with autocalculated annotations sorted to front
*/
@Test(groups = { "Functional" })
- public void testSortByTypeAndSequence_autocalcFirst()
+ public void testSortByLabelAndSequence_autocalcFirst()
{
// @formatter:off
anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
// @formatter:on
- AnnotationSorter testee = new AnnotationSorter(al, true);
+ AnnotationSorter testee = new AnnotationSorter(al, true, false);
testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
assertEquals("Quality", anns[0].label); // autocalc annotations
assertEquals("Consensus", anns[1].label); // retain ordering
anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
// @formatter:on
- AnnotationSorter testee = new AnnotationSorter(al, true);
+ AnnotationSorter testee = new AnnotationSorter(al, true, false);
testee.sort(anns, SequenceAnnotationOrder.NONE);
assertEquals("Quality", anns[0].label); // autocalc annotations
assertEquals("Consensus", anns[1].label); // retain ordering
annotations[i].label = "label" + i;
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(alignment, false);
+ AnnotationSorter testee = new AnnotationSorter(alignment, false, false);
testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
annotations[i].label = "label" + i;
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(alignment, false);
+ AnnotationSorter testee = new AnnotationSorter(alignment, false, false);
testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
annotations[i].label = labels[r.nextInt(labels.length)];
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(alignment, false);
+ AnnotationSorter testee = new AnnotationSorter(alignment, false, false);
testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
long elapsed = endTime - startTime;
+ " sequences and " + numAnns + " annotations took " + elapsed
+ "ms");
}
+
+ /**
+ * Test that sort does nothing if sort order is CUSTOM (manually ordered
+ * annotations)
+ */
+ @Test(groups = { "Functional" })
+ public void testSort_custom()
+ {
+ // @formatter:off
+ anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
+ anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
+ anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
+ anns[3].autoCalculated = true; anns[3].label = "Quality";
+ anns[4].autoCalculated = true; anns[4].label = "Consensus";
+ anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "label5";
+ anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
+ // @formatter:on
+
+ /*
+ * showAutocalcAbove=true ignored if CUSTOM ordering
+ */
+ AnnotationSorter testee = new AnnotationSorter(al, true, false);
+ testee.sort(anns, SequenceAnnotationOrder.CUSTOM);
+ assertEquals("label0", anns[0].label); // all unchanged
+ assertEquals("structure", anns[1].label);
+ assertEquals("iron", anns[2].label);
+ assertEquals("Quality", anns[3].label);
+ assertEquals("Consensus", anns[4].label);
+ assertEquals("label5", anns[5].label);
+ assertEquals("IRP", anns[6].label);
+ }
+
+ /**
+ * Test of sorting only autocalculated annotations
+ */
+ @Test(groups = { "Functional" })
+ public void testSort_autocalcOnly()
+ {
+ // @formatter:off
+ anns[0].sequenceRef = al.getSequenceAt(1); anns[0].label = "label0";
+ anns[1].sequenceRef = al.getSequenceAt(3); anns[1].label = "structure";
+ anns[2].sequenceRef = al.getSequenceAt(3); anns[2].label = "iron";
+ anns[3].autoCalculated = true; anns[3].label = "Quality";
+ anns[4].autoCalculated = true; anns[4].label = "Consensus";
+ anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "label5";
+ anns[6].sequenceRef = al.getSequenceAt(3); anns[6].label = "IRP";
+ // @formatter:on
+
+ /*
+ * showAutocalcAbove=true, autocalcOnly=true
+ */
+ AnnotationSorter testee = new AnnotationSorter(al, true, true);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ assertEquals("Quality", anns[0].label); // moved to top
+ assertEquals("Consensus", anns[1].label); // moved to top
+ assertEquals("label0", anns[2].label); // the rest unchanged
+ assertEquals("structure", anns[3].label);
+ assertEquals("iron", anns[4].label);
+ assertEquals("label5", anns[5].label);
+ assertEquals("IRP", anns[6].label);
+
+ /*
+ * showAutocalcAbove=false, autocalcOnly=true
+ */
+ testee = new AnnotationSorter(al, false, true);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ assertEquals("label0", anns[0].label); // unchanged
+ assertEquals("structure", anns[1].label);
+ assertEquals("iron", anns[2].label);
+ assertEquals("label5", anns[3].label);
+ assertEquals("IRP", anns[4].label);
+ assertEquals("Quality", anns[5].label); // moved to bottom
+ assertEquals("Consensus", anns[6].label); // moved to bottom
+ }
}
git://source.jalview.org / jalview.git / blobdiff