package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import java.util.List;
import java.util.Random;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
public class AnnotationSorterTest
{
/*
* Set up 6 sequences and 7 annotations.
*/
- @Before
+ @BeforeMethod
public void setUp()
{
al = buildAlignment(NUM_SEQS);
* sequence ref</li>
* </ul>
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortBySequenceAndType_autocalcLast()
{
// @formatter:off
/**
* Variant with autocalculated annotations sorting to front
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortBySequenceAndType_autocalcFirst()
{
// @formatter:off
* sequence ref</li>
* </ul>
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortByTypeAndSequence_autocalcLast()
{
// @formatter:off
/**
* Variant of test with autocalculated annotations sorted to front
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSortByTypeAndSequence_autocalcFirst()
{
// @formatter:off
* Variant of test with autocalculated annotations sorted to front but
* otherwise no change.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testNoSort_autocalcFirst()
{
// @formatter:off
assertEquals("Structure", anns[6].label);
}
- @Test
+ @Test(groups ={ "Functional" })
public void testSort_timingPresorted()
{
- final long targetTime = 100; // ms
- final int numSeqs = 10000;
- final int numAnns = 20000;
- al = buildAlignment(numSeqs);
- anns = buildAnnotations(numAnns);
+ testTiming_presorted(50, 100);
+ testTiming_presorted(500, 1000);
+ testTiming_presorted(5000, 10000);
+ }
+
+ /**
+ * Test timing to sort annotations already in the sort order.
+ *
+ * @param numSeqs
+ * @param numAnns
+ */
+ private void testTiming_presorted(final int numSeqs, final int numAnns)
+ {
+ Alignment alignment = buildAlignment(numSeqs);
+ AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
/*
* Set the annotations presorted by label
*/
Random r = new Random();
- final SequenceI[] sequences = al.getSequencesArray();
- for (int i = 0; i < anns.length; i++)
+ final SequenceI[] sequences = alignment.getSequencesArray();
+ for (int i = 0; i < annotations.length; i++)
{
SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
- anns[i].sequenceRef = randomSequenceRef;
- anns[i].label = "label" + i;
+ annotations[i].sequenceRef = randomSequenceRef;
+ annotations[i].label = "label" + i;
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(al, false);
- testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ AnnotationSorter testee = new AnnotationSorter(alignment, false);
+ testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
System.out.println("Timing test for presorted " + numSeqs
+ " sequences and "
+ numAnns + " annotations took " + elapsed + "ms");
- assertTrue("Sort took more than " + targetTime + "ms",
- elapsed <= targetTime);
}
/**
- * Timing test for sorting randomly sorted annotations
+ * Timing tests for sorting randomly sorted annotations for various sizes.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSort_timingUnsorted()
{
- final int numSeqs = 2000;
- final int numAnns = 4000;
- al = buildAlignment(numSeqs);
- anns = buildAnnotations(numAnns);
+ testTiming_unsorted(50, 100);
+ testTiming_unsorted(500, 1000);
+ testTiming_unsorted(5000, 10000);
+ }
+
+ /**
+ * Generate annotations randomly sorted with respect to sequences, and time
+ * sorting.
+ *
+ * @param numSeqs
+ * @param numAnns
+ */
+ private void testTiming_unsorted(final int numSeqs, final int numAnns)
+ {
+ Alignment alignment = buildAlignment(numSeqs);
+ AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
/*
* Set the annotations in random order with respect to the sequences
*/
Random r = new Random();
- final SequenceI[] sequences = al.getSequencesArray();
- for (int i = 0; i < anns.length; i++)
+ final SequenceI[] sequences = alignment.getSequencesArray();
+ for (int i = 0; i < annotations.length; i++)
{
SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
- anns[i].sequenceRef = randomSequenceRef;
- anns[i].label = "label" + i;
+ annotations[i].sequenceRef = randomSequenceRef;
+ annotations[i].label = "label" + i;
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(al, false);
- testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ AnnotationSorter testee = new AnnotationSorter(alignment, false);
+ testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
System.out.println("Timing test for unsorted " + numSeqs
/**
* Timing test for sorting annotations with a limited range of types (labels).
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSort_timingSemisorted()
{
- final int numSeqs = 2000;
- final int numAnns = 4000;
- al = buildAlignment(numSeqs);
- anns = buildAnnotations(numAnns);
+ testTiming_semiSorted(50, 100);
+ testTiming_semiSorted(500, 1000);
+ testTiming_semiSorted(5000, 10000);
+ }
+
+ /**
+ * Mimic 'semi-sorted' annotations:
+ * <ul>
+ * <li>set up in sequence order, with randomly assigned labels from a limited
+ * range</li>
+ * <li>sort by label and sequence order, report timing</li>
+ * <li>resort by sequence and label, report timing</li>
+ * <li>resort by label and sequence, report timing</li>
+ * </ul>
+ *
+ * @param numSeqs
+ * @param numAnns
+ */
+ private void testTiming_semiSorted(final int numSeqs, final int numAnns)
+ {
+ Alignment alignment = buildAlignment(numSeqs);
+ AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
String[] labels = new String[]
{ "label1", "label2", "label3", "label4", "label5", "label6" };
* Set the annotations in sequence order with randomly assigned labels.
*/
Random r = new Random();
- final SequenceI[] sequences = al.getSequencesArray();
- for (int i = 0; i < anns.length; i++)
+ final SequenceI[] sequences = alignment.getSequencesArray();
+ for (int i = 0; i < annotations.length; i++)
{
SequenceI sequenceRef = sequences[i % sequences.length];
- anns[i].sequenceRef = sequenceRef;
- anns[i].label = labels[r.nextInt(labels.length)];
+ annotations[i].sequenceRef = sequenceRef;
+ annotations[i].label = labels[r.nextInt(labels.length)];
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(al, false);
- testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ AnnotationSorter testee = new AnnotationSorter(alignment, false);
+ testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
long elapsed = endTime - startTime;
- System.out.println("Sort by type for semisorted " + numSeqs
+ System.out.println("Sort by label for semisorted " + numSeqs
+ " sequences and "
+ numAnns + " annotations took " + elapsed + "ms");
// now resort by sequence
startTime = System.currentTimeMillis();
- testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
endTime = System.currentTimeMillis();
elapsed = endTime - startTime;
System.out.println("Resort by sequence for semisorted " + numSeqs
+ " sequences and " + numAnns + " annotations took " + elapsed
+ "ms");
- // now resort by type
+ // now resort by label
startTime = System.currentTimeMillis();
- testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
endTime = System.currentTimeMillis();
elapsed = endTime - startTime;
- System.out.println("Resort by type for semisorted " + numSeqs
+ System.out.println("Resort by label for semisorted " + numSeqs
+ " sequences and " + numAnns + " annotations took " + elapsed
+ "ms");
}