--- /dev/null
+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class AnnotationSorterTest
+{
+ private static final int NUM_SEQS = 6;
+
+ private static final int NUM_ANNS = 7;
+
+ private static final String SS = "secondary structure";
+
+ AlignmentAnnotation[] anns = new AlignmentAnnotation[0];
+
+ Alignment al = null;
+
+ /*
+ * Set up 6 sequences and 7 annotations.
+ */
+ @Before
+ public void setUp()
+ {
+ al = buildAlignment(NUM_SEQS);
+ anns = buildAnnotations(NUM_ANNS);
+ }
+
+ /**
+ * Construct an array of numAnns annotations
+ *
+ * @param numAnns
+ *
+ * @return
+ */
+ protected AlignmentAnnotation[] buildAnnotations(int numAnns)
+ {
+ List<AlignmentAnnotation> annlist = new ArrayList<AlignmentAnnotation>();
+ for (int i = 0; i < numAnns; i++)
+ {
+ AlignmentAnnotation ann = new AlignmentAnnotation(SS + i, "", 0);
+ annlist.add(ann);
+ }
+ return annlist.toArray(anns);
+ }
+
+ /**
+ * Make an alignment with numSeqs sequences in it.
+ *
+ * @param numSeqs
+ *
+ * @return
+ */
+ private Alignment buildAlignment(int numSeqs)
+ {
+ SequenceI[] seqs = new Sequence[numSeqs];
+ for (int i = 0; i < numSeqs; i++)
+ {
+ seqs[i] = new Sequence("Sequence" + i, "axrdkfp");
+ }
+ return new Alignment(seqs);
+ }
+
+ /**
+ * Test sorting by annotation type (label) within sequence order, including
+ * <ul>
+ * <li>annotations with no sequence reference - sort to end keeping mutual
+ * ordering</li>
+ * <li>annotations with sequence ref = sort in sequence order</li>
+ * <li>multiple annotations for same sequence ref - sort by label
+ * non-case-specific</li>
+ * <li>annotations with reference to sequence not in alignment - treat like no
+ * sequence ref</li>
+ * </ul>
+ */
+ @Test
+ public void testSortBySequenceAndType_autocalcLast()
+ {
+ // @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, 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
+ assertEquals("IRP", anns[3].label); // sequence 3/IRP
+ assertEquals("structure", anns[4].label); // sequence 3/structure
+ assertEquals("Quality", anns[5].label); // non-sequence annotations
+ assertEquals("Consensus", anns[6].label); // retain ordering
+ }
+
+ /**
+ * 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
+ * ordering</li>
+ * <li>annotations with sequence ref = sort in sequence order</li>
+ * <li>multiple annotations for same sequence ref - sort by label
+ * non-case-specific</li>
+ * <li>annotations with reference to sequence not in alignment - treat like no
+ * sequence ref</li>
+ * </ul>
+ */
+ @Test
+ public void testSortByTypeAndSequence_autocalcLast()
+ {
+ // @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, 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("Structure", anns[3].label); // Structure / sequence 2
+ assertEquals("structure", anns[4].label); // structure / sequence 3
+ assertEquals("Quality", anns[5].label); // non-sequence annotations
+ 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 testSort_timingPresorted()
+ {
+ 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)
+ {
+ al = buildAlignment(numSeqs);
+ anns = 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++)
+ {
+ 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.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");
+ }
+
+ /**
+ * Timing tests for sorting randomly sorted annotations for various sizes.
+ */
+ @Test
+ public void testSort_timingUnsorted()
+ {
+ 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)
+ {
+ 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()
+ {
+ 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)
+ {
+ 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 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);
+ 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 label
+ startTime = System.currentTimeMillis();
+ testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ endTime = System.currentTimeMillis();
+ elapsed = endTime - startTime;
+ System.out.println("Resort by label for semisorted " + numSeqs
+ + " sequences and " + numAnns + " annotations took " + elapsed
+ + "ms");
+ }
+}
git://source.jalview.org / jalview.git / blobdiff