+++ /dev/null
-/*
- * 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.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.datamodel.Alignment;
-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;
-
- private static final String SS = "secondary structure";
-
- AlignmentAnnotation[] anns = new AlignmentAnnotation[0];
-
- Alignment al = null;
-
- /*
- * Set up 6 sequences and 7 annotations.
- */
- @BeforeMethod(alwaysRun = true)
- 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(groups = { "Functional" })
- 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].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
-
- 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); // autocalc annotations
- assertEquals("Consensus", anns[6].label); // retain ordering
- }
-
- /**
- * Variant with autocalculated annotations sorting to front
- */
- @Test(groups = { "Functional" })
- 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].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
-
- AnnotationSorter testee = new AnnotationSorter(al, true);
- testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
- assertEquals("Quality", anns[0].label); // autocalc 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(groups = { "Functional" })
- 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].autoCalculated = true; anns[3].label = "Quality";
- anns[4].autoCalculated = true; 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); // autocalc annotations
- assertEquals("Consensus", anns[6].label); // retain ordering
- }
-
- /**
- * Variant of test with autocalculated annotations sorted to front
- */
- @Test(groups = { "Functional" })
- 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].autoCalculated = true; anns[3].label = "Quality";
- anns[4].autoCalculated = true; 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); // autocalc 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(groups = { "Functional" })
- 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].autoCalculated = true; anns[3].label = "Quality";
- anns[4].autoCalculated = true; 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); // autocalc 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(groups = { "Functional" })
- 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)
- {
- Alignment alignment = buildAlignment(numSeqs);
- AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
-
- /*
- * Set the annotations presorted by label
- */
- Random r = new Random();
- final SequenceI[] sequences = alignment.getSequencesArray();
- for (int i = 0; i < annotations.length; i++)
- {
- SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
- annotations[i].sequenceRef = randomSequenceRef;
- annotations[i].label = "label" + i;
- }
- long startTime = System.currentTimeMillis();
- 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");
- }
-
- /**
- * Timing tests for sorting randomly sorted annotations for various sizes.
- */
- @Test(groups = { "Functional" })
- 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)
- {
- 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 = alignment.getSequencesArray();
- for (int i = 0; i < annotations.length; i++)
- {
- SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
- annotations[i].sequenceRef = randomSequenceRef;
- annotations[i].label = "label" + i;
- }
- long startTime = System.currentTimeMillis();
- 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
- + " sequences and " + numAnns + " annotations took " + elapsed
- + "ms");
- }
-
- /**
- * Timing test for sorting annotations with a limited range of types (labels).
- */
- @Test(groups = { "Functional" })
- 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)
- {
- 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 = alignment.getSequencesArray();
- for (int i = 0; i < annotations.length; i++)
- {
- SequenceI sequenceRef = sequences[i % sequences.length];
- annotations[i].sequenceRef = sequenceRef;
- annotations[i].label = labels[r.nextInt(labels.length)];
- }
- long startTime = System.currentTimeMillis();
- 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 label for semisorted " + numSeqs
- + " sequences and " + numAnns + " annotations took " + elapsed
- + "ms");
-
- // now resort by sequence
- startTime = System.currentTimeMillis();
- 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 label
- startTime = System.currentTimeMillis();
- testee.sort(annotations, 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