--- /dev/null
+package jalview.analysis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+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()
+ {
+ // @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);
+ testee.sortBySequenceAndType(anns);
+ 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
+ }
+
+ /**
+ * 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()
+ {
+ // @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);
+ testee.sortByTypeAndSequence(anns);
+ 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
+ }
+
+ @Test
+ public void testSortBySequenceAndType_timing()
+ {
+ final long targetTime = 300; // 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
+ */
+ 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;
+ }
+ long startTime = System.currentTimeMillis();
+ AnnotationSorter testee = new AnnotationSorter(al);
+ testee.sortByTypeAndSequence(anns);
+ long endTime = System.currentTimeMillis();
+ final long elapsed = endTime - startTime;
+ System.out.println("Timing test for " + numSeqs + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
+ assertTrue("Sort took more than " + targetTime + "ms",
+ elapsed <= targetTime);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff