X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSearchResultsTest.java;h=b1bb43c5bd7999c914d4c4c0348c81d953c9cc55;hb=31aca2e9990ff33e088faa41419bb60014a6fbcf;hp=349b5d1b0a941ef6be7122c2778020d76f40fba2;hpb=745806901cdcda04d9b5c496cb5249a03af19971;p=jalview.git diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java index 349b5d1..b1bb43c 100644 --- a/test/jalview/datamodel/SearchResultsTest.java +++ b/test/jalview/datamodel/SearchResultsTest.java @@ -25,14 +25,15 @@ 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 java.util.List; import org.junit.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import jalview.gui.JvOptionPane; + public class SearchResultsTest { @@ -214,15 +215,16 @@ public class SearchResultsTest int marked = 0; SequenceI seq1 = new Sequence("", "abcdefghijklm"); SequenceI seq2 = new Sequence("", "abcdefghijklm"); - SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup(); + 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); @@ -230,7 +232,7 @@ public class SearchResultsTest 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); @@ -250,11 +252,10 @@ public class SearchResultsTest 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, + "Didn't count number of bits marked for existing marked set", 0, sr.markColumns(s1g, bs)); bs.clear(); - + /* * just seq2 */ @@ -263,7 +264,7 @@ public class SearchResultsTest 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 @@ -281,8 +282,10 @@ public class SearchResultsTest 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("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()); @@ -297,10 +300,114 @@ public class SearchResultsTest SequenceI seq1 = new Sequence("", "abcdefghijklm"); SearchResultsI sr = new SearchResults(); sr.addResult(seq1, 3, 5); - assertEquals(1, sr.getSize()); + assertEquals(1, sr.getCount()); sr.addResult(seq1, 3, 5); - assertEquals(1, sr.getSize()); + assertEquals(1, sr.getCount()); sr.addResult(seq1, 3, 6); - assertEquals(2, sr.getSize()); + 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)); + } + + /** + * Test extraction of Sequence objects for matched ranges on a sequence + */ + @Test(groups = { "Functional" }) + public void testGetSequences() + { + SequenceI seq1 = new Sequence("", "abcdefghijklm"); + SequenceI seq2 = new Sequence("", "nopqrstuvwxyz"); + seq2.setStart(23); + seq2.setEnd(35); + List seqres = null; + + SearchResultsI sr = new SearchResults(); + seqres = sr.getMatchingSubSequences(); + assertEquals(0, seqres.size()); + + sr.addResult(seq1, 3, 5); + seqres = sr.getMatchingSubSequences(); + + assertEquals(1, seqres.size()); + assertEquals("cde", seqres.get(0).getSequenceAsString()); + assertEquals(3, seqres.get(0).getStart()); + assertEquals(seq1, seqres.get(0).getDatasetSequence()); + + sr.addResult(seq1, 3, 6); + seqres = sr.getMatchingSubSequences(); + + assertEquals(2, seqres.size()); + assertEquals("cdef", seqres.get(1).getSequenceAsString()); + assertEquals(3, seqres.get(1).getStart()); + + // this is a quirk - match on 26-29 yields subsequence 27-30 + sr.addResult(seq2, 26, 29); + seqres = sr.getMatchingSubSequences(); + assertEquals(3, seqres.size()); + assertEquals("qrst", seqres.get(2).getSequenceAsString()); + assertEquals(26, seqres.get(2).getStart()); + } + }