X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAnnotationSorterTest.java;fp=test%2Fjalview%2Fanalysis%2FAnnotationSorterTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=1c5a7f9dffa445c3db50c8ebb8c39da87dd66097;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java
deleted file mode 100644
index 1c5a7f9..0000000
--- a/test/jalview/analysis/AnnotationSorterTest.java
+++ /dev/null
@@ -1,413 +0,0 @@
-/*
- * 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");
-  }
-}