X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSearchResultsTest.java;h=838b259ea0c93e1df519cfc9768b9d35e75428a2;hb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;hp=3838ac84149725eb228a3f9f5df12d3302d4d8aa;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java index 3838ac8..838b259 100644 --- a/test/jalview/datamodel/SearchResultsTest.java +++ b/test/jalview/datamodel/SearchResultsTest.java @@ -22,49 +22,48 @@ 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(groups = { "Functional" }) - public void testToString() + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() { - SequenceI seq = new Sequence("", "abcdefghijklm"); - SearchResults sr = new SearchResults(); - sr.addResult(seq, 1, 1); - assertEquals("0a", sr.toString()); - sr.addResult(seq, 3, 5); - assertEquals("0a2cde", sr.toString()); - - seq = new Sequence("", "pqrstuvwxy"); - sr.addResult(seq, 6, 7); - assertEquals("0a2cde5uv", sr.toString()); + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @Test(groups = { "Functional" }) - public void testGetCharacters() + 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.getCharacters()); + assertEquals("[Seq1/1-1]", sr.toString()); sr.addResult(seq, 3, 5); - assertEquals("acde", sr.getCharacters()); + 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.getCharacters()); + assertEquals("[Seq1/1-1, Seq1/3-5, Seq2/6-7]", sr.toString()); } @Test(groups = { "Functional" }) public void testEquals() { SequenceI seq1 = new Sequence("", "abcdefghijklm"); - SearchResults sr1 = new SearchResults(); - SearchResults sr2 = new SearchResults(); + SearchResultsI sr1 = new SearchResults(); + SearchResultsI sr2 = new SearchResults(); assertFalse(sr1.equals(null)); // null object assertFalse(sr1.equals(seq1)); // wrong type @@ -73,7 +72,7 @@ public class SearchResultsTest assertTrue(sr2.equals(sr1)); // reflexive /* - * only one result is not empty + * if only one result is not empty */ sr1.addResult(seq1, 1, 1); assertTrue(sr1.equals(sr1)); @@ -108,8 +107,8 @@ public class SearchResultsTest { SequenceI seq1 = new Sequence("", "abcdefghijklm"); SequenceI seq2 = new Sequence("", "abcdefghijklm"); - SearchResults sr1 = new SearchResults(); - SearchResults sr2 = new SearchResults(); + SearchResultsI sr1 = new SearchResults(); + SearchResultsI sr2 = new SearchResults(); sr1.addResult(seq1, 1, 1); sr2.addResult(seq2, 1, 1); @@ -124,8 +123,8 @@ public class SearchResultsTest public void testEquals_orderDiffers() { SequenceI seq1 = new Sequence("", "abcdefghijklm"); - SearchResults sr1 = new SearchResults(); - SearchResults sr2 = new SearchResults(); + SearchResultsI sr1 = new SearchResults(); + SearchResultsI sr2 = new SearchResults(); sr1.addResult(seq1, 1, 1); sr1.addResult(seq1, 2, 2); @@ -142,8 +141,8 @@ public class SearchResultsTest public void testHashcode() { SequenceI seq1 = new Sequence("", "abcdefghijklm"); - SearchResults sr1 = new SearchResults(); - SearchResults sr2 = new SearchResults(); + SearchResultsI sr1 = new SearchResults(); + SearchResultsI sr2 = new SearchResults(); /* * both empty @@ -166,4 +165,206 @@ public class SearchResultsTest 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)); + } }