X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=5f64b280e9074acdce85fcb868cc8c5f10212c4c;hb=73e00bb837f941b45364d920ef0300bae95f91d0;hp=e959e6272bb45f42c2b30a47e07208faaa1e659a;hpb=3ba65b98445f192453664357a1df25128fe07c84;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index e959e62..5f64b28 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -24,6 +24,8 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import jalview.api.AlignViewportI; +import jalview.api.FinderI; import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; @@ -34,15 +36,19 @@ import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; import jalview.gui.JvOptionPane; import jalview.io.DataSourceType; import jalview.io.FileLoader; import java.util.List; +import org.testng.annotations.AfterMethod; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import junit.extensions.PA; + public class FinderTest { @BeforeClass(alwaysRun = true) @@ -56,6 +62,8 @@ public class FinderTest private AlignmentI al; + private AlignViewportI av; + @BeforeClass(groups = "Functional") public void setUp() { @@ -67,7 +75,14 @@ public class FinderTest + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n"; af = new FileLoader().LoadFileWaitTillLoaded(seqData, DataSourceType.PASTE); - al = af.getViewport().getAlignment(); + av = af.getViewport(); + al = av.getAlignment(); + } + + @AfterMethod(alwaysRun = true) + public void tearDownAfterTest() + { + av.setSelectionGroup(null); } /** @@ -79,8 +94,8 @@ public class FinderTest /* * find next match only */ - Finder f = new Finder(al, null); - f.find("E.H"); // 'E, any character, H' + Finder f = new Finder(av); + f.findNext("E.H", false, false); // 'E, any character, H' // should match seq2 efH only SearchResultsI sr = f.getSearchResults(); assertEquals(sr.getSize(), 1); @@ -89,9 +104,8 @@ public class FinderTest assertEquals(matches.get(0).getStart(), 5); assertEquals(matches.get(0).getEnd(), 7); - f = new Finder(al, null); - f.setFindAll(true); - f.find("E.H"); // 'E, any character, H' + f = new Finder(av); + f.findAll("E.H", false, false); // 'E, any character, H' // should match seq2 efH and seq3 EFH sr = f.getSearchResults(); assertEquals(sr.getSize(), 2); @@ -110,12 +124,12 @@ public class FinderTest @Test(groups = "Functional") public void testFind_residueNumber() { - Finder f = new Finder(al, null); + Finder f = new Finder(av); /* * find first match should return seq1 residue 9 */ - f.find("9"); + f.findNext("9", false, false); SearchResultsI sr = f.getSearchResults(); assertEquals(sr.getSize(), 1); List matches = sr.getResults(); @@ -126,9 +140,8 @@ public class FinderTest /* * find all matches should return seq1 and seq4 (others are too short) */ - f = new Finder(al, null); - f.setFindAll(true); - f.find("9"); + f = new Finder(av); + f.findAll("9", false, false); sr = f.getSearchResults(); assertEquals(sr.getSize(), 2); matches = sr.getResults(); @@ -142,8 +155,8 @@ public class FinderTest /* * parsing of search string as integer is strict */ - f = new Finder(al, null); - f.find(" 9"); + f = new Finder(av); + f.findNext(" 9", false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -157,34 +170,40 @@ public class FinderTest * start at second sequence; colIndex of -1 * means sequence id / description is searched */ - Finder f = new Finder(al, null, 1, -1); - f.find("e"); // matches id + Finder f = new Finder(av); + PA.setValue(f, "sequenceIndex", 1); + PA.setValue(f, "columnIndex", -1); + f.findNext("e", false, false); // matches id assertTrue(f.getSearchResults().isEmpty()); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); // colIndex is now 0 - for use in next find next // searching A--BCDefHI - assertEquals(f.getColumnIndex(), 0); - f = new Finder(al, null, 1, 0); - f.find("e"); // matches in sequence - assertTrue(f.getIdMatch().isEmpty()); + assertEquals(PA.getValue(f, "columnIndex"), 0); + f = new Finder(av); + PA.setValue(f, "sequenceIndex", 1); + PA.setValue(f, "columnIndex", 0); + f.findNext("e", false, false); // matches in sequence + assertTrue(f.getIdMatches().isEmpty()); assertEquals(f.getSearchResults().getSize(), 1); List matches = f.getSearchResults().getResults(); assertEquals(matches.get(0).getStart(), 5); assertEquals(matches.get(0).getEnd(), 5); assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); // still in the second sequence - assertEquals(f.getSequenceIndex(), 1); + assertEquals(PA.getValue(f, "sequenceIndex"), 1); // next column position to search from is 7 - assertEquals(f.getColumnIndex(), 7); + assertEquals(PA.getValue(f, "columnIndex"), 7); // find next from end of sequence - finds next sequence id - f = new Finder(al, null, 1, 7); - f.find("e"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(2)); + f = new Finder(av); + PA.setValue(f, "sequenceIndex", 1); + PA.setValue(f, "columnIndex", 7); + f.findNext("e", false, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(2)); assertTrue(f.getSearchResults().isEmpty()); } @@ -198,39 +217,34 @@ public class FinderTest al2.getSequenceAt(0).setDescription("BRAF"); al2.getSequenceAt(1).setDescription("braf"); + AlignViewportI av2 = new AlignViewport(al2); + /* * find first match only */ - Finder f = new Finder(al2, null); - f.setIncludeDescription(true); - f.find("rAF"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + Finder f = new Finder(av2); + f.findNext("rAF", false, true); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); /* * find all matches */ - f = new Finder(al2, null); - f.setFindAll(true); - f.setIncludeDescription(true); - f.find("rAF"); - assertEquals(f.getIdMatch().size(), 2); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); - assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1)); + f = new Finder(av2); + f.findAll("rAF", false, true); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); + assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); assertTrue(f.getSearchResults().isEmpty()); /* * case sensitive */ - f = new Finder(al2, null); - f.setFindAll(true); - f.setCaseSensitive(true); - f.setIncludeDescription(true); - - f.find("RAF"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); + f = new Finder(av2); + f.findAll("RAF", true, true); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); /* @@ -239,17 +253,15 @@ public class FinderTest al2.getSequenceAt(0).setDescription("the efh sequence"); al2.getSequenceAt(0).setName("mouseEFHkinase"); al2.getSequenceAt(1).setName("humanEFHkinase"); - f = new Finder(al2, null); - f.setFindAll(true); - f.setIncludeDescription(true); + f = new Finder(av2); /* * sequence matches should have no duplicates */ - f.find("EFH"); - assertEquals(f.getIdMatch().size(), 2); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0)); - assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1)); + f.findAll("EFH", false, true); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); + assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); assertEquals(f.getSearchResults().getSize(), 2); SearchResultMatchI match = f.getSearchResults().getResults().get(0); @@ -268,26 +280,23 @@ public class FinderTest @Test(groups = "Functional") public void testFindAll_sequenceIds() { - Finder f = new Finder(al, null); - f.setFindAll(true); + Finder f = new Finder(av); /* * case insensitive; seq1 occurs twice in sequence id but * only one match should be returned */ - f.find("SEQ1"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(0)); + f.findAll("SEQ1", false, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(0)); SearchResultsI searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); /* * case sensitive */ - f = new Finder(al, null); - f.setFindAll(true); - f.setCaseSensitive(true); - f.find("SEQ1"); + f = new Finder(av); + f.findAll("SEQ1", true, false); searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); @@ -295,12 +304,12 @@ public class FinderTest * match both sequence id and sequence */ AlignmentI al2 = new Alignment(al); + AlignViewportI av2 = new AlignViewport(al2); al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ")); - f = new Finder(al2, null); - f.setFindAll(true); - f.find("ABZ"); - assertEquals(f.getIdMatch().size(), 1); - assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4)); + f = new Finder(av2); + f.findAll("ABZ", false, false); + assertEquals(f.getIdMatches().size(), 1); + assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4)); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -322,8 +331,8 @@ public class FinderTest /* * efh should be matched in seq2 only */ - Finder f = new Finder(al, null); - f.find("EfH"); + FinderI f = new Finder(av); + f.findNext("EfH", false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -334,8 +343,8 @@ public class FinderTest /* * I should be found in seq1 (twice) and seq2 (once) */ - f = new Finder(al, null); - f.find("I"); // find next: seq1/16 + f = new Finder(av); + f.findNext("I", false, false); // find next: seq1/16 searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -343,7 +352,7 @@ public class FinderTest assertEquals(match.getStart(), 16); assertEquals(match.getEnd(), 16); - f.find("I"); // find next: seq1/18 + f.findNext("I", false, false); // find next: seq1/18 searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -351,7 +360,7 @@ public class FinderTest assertEquals(match.getStart(), 18); assertEquals(match.getEnd(), 18); - f.find("I"); // find next: seq2/8 + f.findNext("I", false, false); // find next: seq2/8 searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -359,8 +368,19 @@ public class FinderTest assertEquals(match.getStart(), 8); assertEquals(match.getEnd(), 8); - f.find("I"); + f.findNext("I", false, false); assertTrue(f.getSearchResults().isEmpty()); + + /* + * find should reset to start of alignment after a failed search + */ + f.findNext("I", false, false); // find next: seq1/16 + searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 1); + match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(0)); + assertEquals(match.getStart(), 16); + assertEquals(match.getEnd(), 16); } /** @@ -370,9 +390,8 @@ public class FinderTest @Test(groups = "Functional") public void testFind_maximalResultOnly() { - Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("M+"); + Finder f = new Finder(av); + f.findAll("M+", false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -387,9 +406,8 @@ public class FinderTest @Test(groups = "Functional") public void testFind_findAll() { - Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("EfH"); + Finder f = new Finder(av); + f.findAll("EfH", false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -404,7 +422,7 @@ public class FinderTest /* * find all I should find 2 positions in seq1, 1 in seq2 */ - f.find("I"); + f.findAll("I", false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 3); match = searchResults.getResults().get(0); @@ -427,14 +445,12 @@ public class FinderTest @Test(groups = "Functional") public void testFind_findAllCaseSensitive() { - Finder f = new Finder(al, null); - f.setCaseSensitive(true); - f.setFindAll(true); + Finder f = new Finder(av); /* * BC should match seq1/9-10 and seq2/2-3 */ - f.find("BC"); + f.findAll("BC", true, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -449,10 +465,8 @@ public class FinderTest /* * bc should match seq3/1-2 */ - f = new Finder(al, null); - f.setCaseSensitive(true); - f.setFindAll(true); - f.find("bc"); + f = new Finder(av); + f.findAll("bc", true, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -460,7 +474,7 @@ public class FinderTest assertEquals(match.getStart(), 1); assertEquals(match.getEnd(), 2); - f.find("bC"); + f.findAll("bC", true, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -480,10 +494,11 @@ public class FinderTest sg.setEndRes(5); sg.addSequence(al.getSequenceAt(1), false); sg.addSequence(al.getSequenceAt(2), false); + av.setSelectionGroup(sg); - Finder f = new Finder(al, sg); - f.find("b"); - assertTrue(f.getIdMatch().isEmpty()); + FinderI f = new Finder(av); + f.findNext("b", false, false); + assertTrue(f.getIdMatches().isEmpty()); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -494,21 +509,21 @@ public class FinderTest /* * a second Find should not return the 'b' in seq3 as outside the selection */ - f.find("b"); + f.findNext("b", false, false); assertTrue(f.getSearchResults().isEmpty()); - assertTrue(f.getIdMatch().isEmpty()); + assertTrue(f.getIdMatches().isEmpty()); - f = new Finder(al, sg); - f.find("d"); - assertTrue(f.getIdMatch().isEmpty()); + f = new Finder(av); + f.findNext("d", false, false); + assertTrue(f.getIdMatches().isEmpty()); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 4); assertEquals(match.getEnd(), 4); - f.find("d"); - assertTrue(f.getIdMatch().isEmpty()); + f.findNext("d", false, false); + assertTrue(f.getIdMatches().isEmpty()); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -533,16 +548,16 @@ public class FinderTest sg.setEndRes(5); sg.addSequence(al.getSequenceAt(1), false); sg.addSequence(al.getSequenceAt(2), false); + av.setSelectionGroup(sg); /* * search for 'e' should match two sequence ids and one residue */ - Finder f = new Finder(al, sg); - f.setFindAll(true); - f.find("e"); - assertEquals(f.getIdMatch().size(), 2); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); - assertSame(f.getIdMatch().get(1), al.getSequenceAt(2)); + Finder f = new Finder(av); + f.findAll("e", false, false); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); + assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -553,12 +568,11 @@ public class FinderTest /* * search for 'Q' should match two sequence ids only */ - f = new Finder(al, sg); - f.setFindAll(true); - f.find("Q"); - assertEquals(f.getIdMatch().size(), 2); - assertSame(f.getIdMatch().get(0), al.getSequenceAt(1)); - assertSame(f.getIdMatch().get(1), al.getSequenceAt(2)); + f = new Finder(av); + f.findAll("Q", false, false); + assertEquals(f.getIdMatches().size(), 2); + assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); + assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); assertTrue(f.getSearchResults().isEmpty()); } @@ -580,14 +594,14 @@ public class FinderTest sg.addSequence(al.getSequenceAt(1), false); sg.addSequence(al.getSequenceAt(2), false); sg.addSequence(al.getSequenceAt(3), false); - + av.setSelectionGroup(sg); + /* * search for 'I' should match two sequence positions */ - Finder f = new Finder(al, sg); - f.setFindAll(true); - f.find("I"); - assertTrue(f.getIdMatch().isEmpty()); + Finder f = new Finder(av); + f.findAll("I", false, false); + assertTrue(f.getIdMatches().isEmpty()); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -625,9 +639,8 @@ public class FinderTest * find all search for D should ignore hidden positions in seq1 and seq3, * find the visible D in seq2 */ - Finder f = new Finder(al, null); - f.setFindAll(true); - f.find("D"); + Finder f = new Finder(av); + f.findAll("D", false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -640,8 +653,8 @@ public class FinderTest * find all 'aaa' should find end of seq4 only */ hc.hideColumns(2, 5); - f = new Finder(al, null); - f.find("aaa"); + f = new Finder(av); + f.findAll("aaa", false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -652,7 +665,7 @@ public class FinderTest /* * find all 'BE' should not match across hidden columns in seq1 */ - f.find("BE"); + f.findAll("BE", false, false); assertTrue(f.getSearchResults().isEmpty()); /* @@ -661,8 +674,8 @@ public class FinderTest */ hc.revealAllHiddenColumns(new ColumnSelection()); hc.hideColumns(8, 13); - f = new Finder(al, null); - f.find("H"); + f = new Finder(av); + f.findNext("H", false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getSize(), 1); match = searchResults.getResults().get(0); @@ -670,4 +683,51 @@ public class FinderTest assertEquals(match.getStart(), 6); assertEquals(match.getEnd(), 6); } + + @Test(groups = "Functional") + public void testFind_withHiddenColumnsAndSelection() + { + /* + * 0 5 9 + * ABCD--EF-GHI + * A--BCDefHI + * --bcdEFH + * aa---aMMMMMaaa + */ + + /* + * hide columns 2-4 and 6-7 + */ + HiddenColumns hc = new HiddenColumns(); + hc.hideColumns(2, 4); + hc.hideColumns(6, 7); + al.setHiddenColumns(hc); + + /* + * select rows 2-3 + */ + SequenceGroup sg = new SequenceGroup(); + sg.addSequence(al.getSequenceAt(1), false); + sg.addSequence(al.getSequenceAt(2), false); + sg.setStartRes(0); + sg.setEndRes(13); + av.setSelectionGroup(sg); + + /* + * find all search for A or H + * should match seq2/1, seq2/7, not seq3/6 + */ + Finder f = new Finder(av); + f.findAll("[AH]", false, false); + SearchResultsI searchResults = f.getSearchResults(); + assertEquals(searchResults.getSize(), 2); + SearchResultMatchI match = searchResults.getResults().get(0); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 1); + assertEquals(match.getEnd(), 1); + match = searchResults.getResults().get(1); + assertSame(match.getSequence(), al.getSequenceAt(1)); + assertEquals(match.getStart(), 7); + assertEquals(match.getEnd(), 7); + } }