import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
* </ul>
*/
@Test
- public void testSortBySequenceAndType()
+ public void testSortBySequenceAndType_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);
- testee.sortBySequenceAndType(anns);
+ AnnotationSorter testee = new AnnotationSorter(al, false);
+ testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
assertEquals("label5", anns[0].label); // for sequence 0
assertEquals("label0", anns[1].label); // for sequence 1
assertEquals("iron", anns[2].label); // sequence 3 /iron
}
/**
+ * Variant with autocalculated annotations sorting to front
+ */
+ @Test
+ public void testSortBySequenceAndType_autocalcFirst()
+ {
+ // @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].sequenceRef = null; anns[3].label = "Quality";
+ anns[4].sequenceRef = null; 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
+
+ AnnotationSorter testee = new AnnotationSorter(al, true);
+ testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ assertEquals("Quality", anns[0].label); // non-sequence annotations
+ assertEquals("Consensus", anns[1].label); // retain ordering
+ assertEquals("label5", anns[2].label); // for sequence 0
+ assertEquals("label0", anns[3].label); // for sequence 1
+ assertEquals("iron", anns[4].label); // sequence 3 /iron
+ assertEquals("IRP", anns[5].label); // sequence 3/IRP
+ assertEquals("structure", anns[6].label); // sequence 3/structure
+ }
+
+ /**
* Test sorting by annotation type (label) within sequence order, including
* <ul>
* <li>annotations with no sequence reference - sort to end keeping mutual
* </ul>
*/
@Test
- public void testSortByTypeAndSequence()
+ public void testSortByTypeAndSequence_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);
- testee.sortByTypeAndSequence(anns);
+ AnnotationSorter testee = new AnnotationSorter(al, false);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
assertEquals("IRON", anns[0].label); // IRON / sequence 0
assertEquals("iron", anns[1].label); // iron / sequence 3
assertEquals("label0", anns[2].label); // label0 / sequence 1
assertEquals("Consensus", anns[6].label); // retain ordering
}
+ /**
+ * Variant of test with autocalculated annotations sorted to front
+ */
+ @Test
+ public void testSortByTypeAndSequence_autocalcFirst()
+ {
+ // @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].sequenceRef = null; anns[3].label = "Quality";
+ anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
+ anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
+ // @formatter:on
+
+ AnnotationSorter testee = new AnnotationSorter(al, true);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ assertEquals("Quality", anns[0].label); // non-sequence annotations
+ assertEquals("Consensus", anns[1].label); // retain ordering
+ assertEquals("IRON", anns[2].label); // IRON / sequence 0
+ assertEquals("iron", anns[3].label); // iron / sequence 3
+ assertEquals("label0", anns[4].label); // label0 / sequence 1
+ assertEquals("Structure", anns[5].label); // Structure / sequence 2
+ assertEquals("structure", anns[6].label); // structure / sequence 3
+ }
+
+ /**
+ * Variant of test with autocalculated annotations sorted to front but
+ * otherwise no change.
+ */
+ @Test
+ public void testNoSort_autocalcFirst()
+ {
+ // @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].sequenceRef = null; anns[3].label = "Quality";
+ anns[4].sequenceRef = null; anns[4].label = "Consensus";
+ anns[5].sequenceRef = al.getSequenceAt(0); anns[5].label = "IRON";
+ anns[6].sequenceRef = al.getSequenceAt(2); anns[6].label = "Structure";
+ // @formatter:on
+
+ AnnotationSorter testee = new AnnotationSorter(al, true);
+ testee.sort(anns, SequenceAnnotationOrder.NONE);
+ assertEquals("Quality", anns[0].label); // non-sequence annotations
+ assertEquals("Consensus", anns[1].label); // retain ordering
+ assertEquals("label0", anns[2].label);
+ assertEquals("structure", anns[3].label);
+ assertEquals("iron", anns[4].label);
+ assertEquals("IRON", anns[5].label);
+ assertEquals("Structure", anns[6].label);
+ }
+
@Test
- public void testSortBySequenceAndType_timing()
+ public void testSort_timingPresorted()
{
- final long targetTime = 300; // ms
+ final long targetTime = 100; // ms
final int numSeqs = 10000;
final int numAnns = 20000;
al = buildAlignment(numSeqs);
anns = buildAnnotations(numAnns);
/*
- * Set the annotations in random order with respect to the sequences
+ * Set the annotations presorted by label
*/
Random r = new Random();
final SequenceI[] sequences = al.getSequencesArray();
{
SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
anns[i].sequenceRef = randomSequenceRef;
+ anns[i].label = "label" + i;
}
long startTime = System.currentTimeMillis();
- AnnotationSorter testee = new AnnotationSorter(al);
- testee.sortByTypeAndSequence(anns);
+ AnnotationSorter testee = new AnnotationSorter(al, false);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
- System.out.println("Timing test for " + numSeqs + " sequences and "
+ 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
+ */
+ @Test
+ public void testSort_timingUnsorted()
+ {
+ final int numSeqs = 2000;
+ final int numAnns = 4000;
+ al = buildAlignment(numSeqs);
+ anns = 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++)
+ {
+ SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
+ anns[i].sequenceRef = randomSequenceRef;
+ anns[i].label = "label" + i;
+ }
+ long startTime = System.currentTimeMillis();
+ AnnotationSorter testee = new AnnotationSorter(al, false);
+ testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ long endTime = System.currentTimeMillis();
+ final long elapsed = endTime - startTime;
+ System.out.println("Timing test for unsorted " + numSeqs
+ + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
+ }
+
+ /**
+ * Timing test for sorting annotations with a limited range of types (labels).
+ */
+ @Test
+ public void testSort_timingSemisorted()
+ {
+ final int numSeqs = 2000;
+ final int numAnns = 4000;
+ al = buildAlignment(numSeqs);
+ anns = 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++)
+ {
+ SequenceI sequenceRef = sequences[i % sequences.length];
+ anns[i].sequenceRef = sequenceRef;
+ anns[i].label = labels[r.nextInt(labels.length)];
+ }
+ long startTime = System.currentTimeMillis();
+ AnnotationSorter testee = new AnnotationSorter(al, false);
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ long endTime = System.currentTimeMillis();
+ long elapsed = endTime - startTime;
+ System.out.println("Sort by type for semisorted " + numSeqs
+ + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
+
+ // now resort by sequence
+ startTime = System.currentTimeMillis();
+ testee.sort(anns, 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
+ startTime = System.currentTimeMillis();
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ endTime = System.currentTimeMillis();
+ elapsed = endTime - startTime;
+ System.out.println("Resort by type for semisorted " + numSeqs
+ + " sequences and " + numAnns + " annotations took " + elapsed
+ + "ms");
+ }
}
git://source.jalview.org / jalview.git / blobdiff