+++ /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.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 jalview.gui.JvOptionPane;
-
-import java.util.BitSet;
-
-import org.junit.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class SearchResultsTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testToString()
- {
- SequenceI seq = new Sequence("Seq1", "abcdefghijklm");
- SearchResultsI sr = new SearchResults();
- sr.addResult(seq, 1, 1);
- assertEquals("[Seq1/1-1]", sr.toString());
- sr.addResult(seq, 3, 5);
- assertEquals("[Seq1/1-1, Seq1/3-5]", sr.toString());
-
- seq = new Sequence("Seq2", "pqrstuvwxy");
- sr.addResult(seq, 6, 7);
- 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.getSize());
- sr.addResult(seq1, 3, 5);
- assertEquals(1, sr.getSize());
- sr.addResult(seq1, 3, 6);
- assertEquals(2, sr.getSize());
- }
-}
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