X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSearchResultsTest.java;h=a08c57732e963cdc6f534a8d6927aff020b9e281;hb=bdc5ecb2b1d6021d235c633112990cbacd072c4a;hp=983bd3449be954829a20002481159ffe372c776e;hpb=0c37e7cea9a7028130b6f2164961af24c3c48ec2;p=jalview.git diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java index 983bd34..a08c577 100644 --- a/test/jalview/datamodel/SearchResultsTest.java +++ b/test/jalview/datamodel/SearchResultsTest.java @@ -1,19 +1,42 @@ +/* + * 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 . + * 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.testng.annotations.Test; public class SearchResultsTest { - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testToString() { SequenceI seq = new Sequence("", "abcdefghijklm"); - SearchResults sr = new SearchResults(); + SearchResultsI sr = new SearchResults(); sr.addResult(seq, 1, 1); assertEquals("0a", sr.toString()); sr.addResult(seq, 3, 5); @@ -25,11 +48,26 @@ public class SearchResultsTest } @Test(groups = { "Functional" }) + public void testGetCharacters() + { + SequenceI seq = new Sequence("", "abcdefghijklm"); + SearchResults sr = new SearchResults(); + sr.addResult(seq, 1, 1); + assertEquals("a", sr.getCharacters()); + sr.addResult(seq, 3, 5); + assertEquals("acde", sr.getCharacters()); + + seq = new Sequence("", "pqrstuvwxy"); + sr.addResult(seq, 6, 7); + assertEquals("acdeuv", sr.getCharacters()); + } + + @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 @@ -73,8 +111,8 @@ 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); @@ -89,8 +127,8 @@ 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); @@ -107,8 +145,8 @@ 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 @@ -131,4 +169,102 @@ 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 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(); + + sr.addResult(seq1, 1,1); + sr.addResult(seq2, 1,2); + + // 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(0)); + + /* + * 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()); + } }