+/*
+ * 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.datamodel;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.BitSet;
+
+import org.junit.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+
public class SearchResultsTest
{
- @Test
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
public void testToString()
{
- SequenceI seq = new Sequence("", "abcdefghijklm");
- SearchResults sr = new SearchResults();
+ SequenceI seq = new Sequence("Seq1", "abcdefghijklm");
+ SearchResultsI sr = new SearchResults();
sr.addResult(seq, 1, 1);
- assertEquals("a", sr.toString());
+ assertEquals("[Seq1/1-1]", sr.toString());
sr.addResult(seq, 3, 5);
- assertEquals("acde", sr.toString());
+ assertEquals("[Seq1/1-1, Seq1/3-5]", sr.toString());
- seq = new Sequence("", "pqrstuvwxy");
+ seq = new Sequence("Seq2", "pqrstuvwxy");
sr.addResult(seq, 6, 7);
- assertEquals("acdeuv", sr.toString());
+ assertEquals("[Seq1/1-1, Seq1/3-5, Seq2/6-7]", sr.toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testEquals()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr1 = new SearchResults();
+ SearchResultsI sr2 = new SearchResults();
+
+ assertFalse(sr1.equals(null)); // null object
+ assertFalse(sr1.equals(seq1)); // wrong type
+ assertTrue(sr1.equals(sr1)); // self
+ assertTrue(sr1.equals(sr2)); // empty
+ assertTrue(sr2.equals(sr1)); // reflexive
+
+ /*
+ * if only one result is not empty
+ */
+ sr1.addResult(seq1, 1, 1);
+ assertTrue(sr1.equals(sr1));
+ assertFalse(sr1.equals(sr2));
+ assertFalse(sr2.equals(sr1));
+
+ /*
+ * both the same
+ */
+ sr2.addResult(seq1, 1, 1);
+ assertTrue(sr1.equals(sr2));
+ assertTrue(sr2.equals(sr1));
+
+ /*
+ * both have three matches
+ */
+ sr1.addResult(seq1, 3, 4);
+ sr1.addResult(seq1, 6, 8);
+ sr2.addResult(seq1, 3, 4);
+ sr2.addResult(seq1, 6, 8);
+ assertTrue(sr1.equals(sr1));
+ assertTrue(sr2.equals(sr2));
+ assertTrue(sr1.equals(sr2));
+ assertTrue(sr2.equals(sr1));
+ }
+
+ /**
+ * Matches that are similar but for distinct sequences are not equal
+ */
+ @Test(groups = { "Functional" })
+ public void testEquals_distinctSequences()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr1 = new SearchResults();
+ SearchResultsI sr2 = new SearchResults();
+
+ sr1.addResult(seq1, 1, 1);
+ sr2.addResult(seq2, 1, 1);
+ assertFalse(sr1.equals(sr2));
+ assertFalse(sr2.equals(sr1));
+ }
+
+ /**
+ * Matches that are the same except for ordering are not equal
+ */
+ @Test(groups = { "Functional" })
+ public void testEquals_orderDiffers()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr1 = new SearchResults();
+ SearchResultsI sr2 = new SearchResults();
+
+ sr1.addResult(seq1, 1, 1);
+ sr1.addResult(seq1, 2, 2);
+ sr2.addResult(seq1, 2, 2);
+ sr2.addResult(seq1, 1, 1);
+ assertFalse(sr1.equals(sr2));
+ assertFalse(sr2.equals(sr1));
+ }
+
+ /**
+ * Verify that hashCode matches for equal objects
+ */
+ @Test(groups = { "Functional" })
+ public void testHashcode()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr1 = new SearchResults();
+ SearchResultsI sr2 = new SearchResults();
+
+ /*
+ * both empty
+ */
+ assertEquals(sr1.hashCode(), sr2.hashCode());
+
+ /*
+ * both one match
+ */
+ sr1.addResult(seq1, 1, 1);
+ sr2.addResult(seq1, 1, 1);
+ assertEquals(sr1.hashCode(), sr2.hashCode());
+
+ /*
+ * both three matches
+ */
+ sr1.addResult(seq1, 3, 4);
+ sr1.addResult(seq1, 6, 8);
+ sr2.addResult(seq1, 3, 4);
+ sr2.addResult(seq1, 6, 8);
+ assertEquals(sr1.hashCode(), sr2.hashCode());
+ }
+
+ /**
+ * Verify that SearchResults$Match constructor normalises start/end to the
+ * 'forwards' direction
+ */
+ @Test(groups = { "Functional" })
+ public void testMatchConstructor()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5);
+ assertSame(seq1, m.getSequence());
+ assertEquals(2, m.getStart());
+ assertEquals(5, m.getEnd());
+
+ // now a reverse mapping:
+ m = new SearchResults().new Match(seq1, 5, 2);
+ assertSame(seq1, m.getSequence());
+ assertEquals(2, m.getStart());
+ assertEquals(5, m.getEnd());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMatchContains()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "abcdefghijklm");
+ SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5);
+
+ assertTrue(m.contains(seq1, 2, 5));
+ assertTrue(m.contains(seq1, 3, 5));
+ assertTrue(m.contains(seq1, 2, 4));
+ assertTrue(m.contains(seq1, 3, 3));
+
+ assertFalse(m.contains(seq1, 2, 6));
+ assertFalse(m.contains(seq1, 1, 5));
+ assertFalse(m.contains(seq1, 1, 8));
+ assertFalse(m.contains(seq2, 3, 3));
+ assertFalse(m.contains(null, 3, 3));
+ }
+
+ /**
+ * test markColumns for creating column selections
+ */
+ @Test(groups = { "Functional" })
+ public void testMarkColumns()
+ {
+ int marked = 0;
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "abcdefghijklm");
+ SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup();
+ s1g.addSequence(seq1, false);
+ s2g.addSequence(seq2, false);
+ sallg.addSequence(seq1, false);
+ sallg.addSequence(seq2, false);
+
+ SearchResultsI sr = new SearchResults();
+ BitSet bs = new BitSet();
+
+ SearchResultMatchI srm = null;
+ srm = sr.addResult(seq1, 1, 1);
+ Assert.assertNotNull("addResult didn't return Match", srm);
+ srm = sr.addResult(seq2, 1, 2);
+ assertEquals("Sequence reference not set", seq2, srm.getSequence());
+ assertEquals("match start incorrect", 1, srm.getStart());
+ assertEquals("match end incorrect", 2, srm.getEnd());
+
+ // set start/end range for groups to cover matches
+
+ s1g.setStartRes(0);
+ s1g.setEndRes(5);
+ s2g.setStartRes(0);
+ s2g.setEndRes(5);
+ sallg.setStartRes(0);
+ sallg.setEndRes(5);
+
+ /*
+ * just seq1
+ */
+ marked = sr.markColumns(s1g, bs);
+ // check the bitset cardinality before checking the return value
+ assertEquals("Didn't mark expected number", 1, bs.cardinality());
+ assertEquals("Didn't return count of number of bits marked", 1, marked);
+ assertTrue("Didn't mark expected position", bs.get(0));
+ // now check return value for marking the same again
+ assertEquals(
+ "Didn't count number of bits marked for existing marked set",
+ 0,
+ sr.markColumns(s1g, bs));
+ bs.clear();
+
+ /*
+ * just seq2
+ */
+ marked = sr.markColumns(s2g, bs);
+ assertEquals("Didn't mark expected number", 2, bs.cardinality());
+ assertEquals("Didn't return count of number of bits marked", 2, marked);
+ assertTrue("Didn't mark expected position (1)", bs.get(0));
+ assertTrue("Didn't mark expected position (2)", bs.get(1));
+
+ /*
+ * both seq1 and seq2
+ * should be same as seq2
+ */
+ BitSet allbs = new BitSet();
+ assertEquals(2, sr.markColumns(sallg, allbs));
+ assertEquals(bs, allbs);
+
+ // now check range selection
+
+ /*
+ * limit s2g to just the second column, sallg to the first column
+ */
+ s2g.setStartRes(1);
+ s2g.setEndRes(1);
+ sallg.setEndRes(0);
+ BitSet tbs = new BitSet();
+ assertEquals("Group start/end didn't select columns to mark",1, sr.markColumns(s2g, tbs));
+ assertEquals("Group start/end didn't select columns to mark", 1, sr.markColumns(sallg, tbs));
+ assertEquals(
+ "Didn't set expected number of columns in total for two successive marks",
+ 2, tbs.cardinality());
+ }
+
+ /**
+ * Test to verify adding doesn't create duplicate results
+ */
+ @Test(groups = { "Functional" })
+ public void testAddResult()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResultsI sr = new SearchResults();
+ sr.addResult(seq1, 3, 5);
+ assertEquals(1, sr.getCount());
+ sr.addResult(seq1, 3, 5);
+ assertEquals(1, sr.getCount());
+ sr.addResult(seq1, 3, 6);
+ assertEquals(2, sr.getCount());
+ }
+
+ /**
+ * Test for method that checks if search results matches a sequence region
+ */
+ @Test(groups = { "Functional" })
+ public void testInvolvesSequence()
+ {
+ SequenceI dataset = new Sequence("genome", "ATGGCCCTTTAAGCAACATTT");
+ // first 'exon':
+ SequenceI cds1 = new Sequence("cds1/1-12", "ATGGCCCTTTAA");
+ cds1.setDatasetSequence(dataset);
+ // overlapping second 'exon':
+ SequenceI cds2 = new Sequence("cds2/7-18", "CTTTAAGCAACA");
+ cds2.setDatasetSequence(dataset);
+ // unrelated sequence
+ SequenceI cds3 = new Sequence("cds3", "ATGGCCCTTTAAGCAACA");
+
+ SearchResults sr = new SearchResults();
+ assertFalse(sr.involvesSequence(cds1));
+
+ /*
+ * cds1 and cds2 share the same dataset sequence, but
+ * only cds1 overlaps match 4:6 (fixes bug JAL-3613)
+ */
+ sr.addResult(dataset, 4, 6);
+ assertTrue(sr.involvesSequence(cds1));
+ assertFalse(sr.involvesSequence(cds2));
+ assertFalse(sr.involvesSequence(cds3));
+
+ /*
+ * search results overlap cds2 only
+ */
+ sr = new SearchResults();
+ sr.addResult(dataset, 18, 18);
+ assertFalse(sr.involvesSequence(cds1));
+ assertTrue(sr.involvesSequence(cds2));
+
+ /*
+ * add a search result overlapping cds1
+ */
+ sr.addResult(dataset, 1, 1);
+ assertTrue(sr.involvesSequence(cds1));
+ assertTrue(sr.involvesSequence(cds2));
+
+ /*
+ * single search result overlapping both
+ */
+ sr = new SearchResults();
+ sr.addResult(dataset, 10, 12);
+ assertTrue(sr.involvesSequence(cds1));
+ assertTrue(sr.involvesSequence(cds2));
+
+ /*
+ * search results matching aligned sequence
+ */
+ sr = new SearchResults();
+ sr.addResult(cds1, 10, 12);
+ assertTrue(sr.involvesSequence(cds1));
+ assertFalse(sr.involvesSequence(cds2));
+ sr.addResult(cds2, 1, 3); // no start-end overlap
+ assertFalse(sr.involvesSequence(cds2));
+ sr.addResult(cds2, 7, 9); // start-end overlap
+ assertTrue(sr.involvesSequence(cds2));
}
}
git://source.jalview.org / jalview.git / blobdiff