X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=0220c36effdc8f951b2c3f6e7d20368731cd3127;hb=404d5b51a7a7781ad6924df6a7ce63c754370f16;hp=1f45f70d597d334b57db6ed92771bb2338537a00;hpb=4bd3d60110787a65e53b5c1b9d4f10ddb7025090;p=jalview.git diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java index 1f45f70..0220c36 100644 --- a/test/jalview/analysis/FinderTest.java +++ b/test/jalview/analysis/FinderTest.java @@ -24,6 +24,12 @@ import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import java.util.List; + +import org.testng.annotations.AfterMethod; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.api.AlignViewportI; import jalview.api.FinderI; import jalview.bin.Cache; @@ -34,19 +40,14 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; 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 @@ -82,6 +83,12 @@ public class FinderTest DataSourceType.PASTE); av = af.getViewport(); al = av.getAlignment(); + al.getSequenceAt(0).addSequenceFeature( + new SequenceFeature("BBBB", "FeatureB", 9, 11, "")); + al.getSequenceAt(3).addSequenceFeature( + new SequenceFeature("BBAB", "FeatureA", 1, 3, "")); + al.getSequenceAt(3).addSequenceFeature( + new SequenceFeature("AAAA", "FeatureA", 9, 11, "")); } @AfterMethod(alwaysRun = true) @@ -100,7 +107,7 @@ public class FinderTest * find next match only */ Finder f = new Finder(av); - f.findNext("E.H", false, false, false); // 'E, any character, H' + f.findNext("E.H", false, false, false, false); // 'E, any character, H' // should match seq2 efH only SearchResultsI sr = f.getSearchResults(); assertEquals(sr.getCount(), 1); @@ -110,7 +117,7 @@ public class FinderTest assertEquals(matches.get(0).getEnd(), 7); f = new Finder(av); - f.findAll("E.H", false, false, false); // 'E, any character, H' + f.findAll("E.H", false, false, false, false); // 'E, any character, H' // should match seq2 efH and seq3 EFH sr = f.getSearchResults(); assertEquals(sr.getCount(), 2); @@ -131,11 +138,12 @@ public class FinderTest * single symbol should find *all* matching symbols */ Finder f = new Finder(av); - f.findAll("M", false,false,false); + f.findAll("M", false, false, false, false); SearchResultsI sr = f.getSearchResults(); - assertEquals(sr.getCount(),5); - + assertEquals(sr.getCount(), 5); + } + /** * Test for (undocumented) find residue by position */ @@ -147,7 +155,7 @@ public class FinderTest /* * find first match should return seq1 residue 9 */ - f.findNext("9", false, false, false); + f.findNext("9", false, false, false, false); SearchResultsI sr = f.getSearchResults(); assertEquals(sr.getCount(), 1); List matches = sr.getResults(); @@ -162,7 +170,7 @@ public class FinderTest f = new Finder(av); String name = al.getSequenceAt(0).getName(); al.getSequenceAt(0).setName("Q9XA0"); - f.findAll("9", false, false, false); + f.findAll("9", false, false, false, false); sr = f.getSearchResults(); assertEquals(sr.getCount(), 2); matches = sr.getResults(); @@ -178,7 +186,7 @@ public class FinderTest * parsing of search string as integer is strict */ f = new Finder(av); - f.findNext(" 9", false, false, false); + f.findNext(" 9", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -195,7 +203,7 @@ public class FinderTest Finder f = new Finder(av); PA.setValue(f, "sequenceIndex", 1); PA.setValue(f, "residueIndex", -1); - f.findNext("e", false, false, false); // matches id + f.findNext("e", false, false, false, false); // matches id assertTrue(f.getSearchResults().isEmpty()); assertEquals(f.getIdMatches().size(), 1); @@ -207,7 +215,7 @@ public class FinderTest f = new Finder(av); PA.setValue(f, "sequenceIndex", 1); PA.setValue(f, "residueIndex", 0); - f.findNext("e", false, false, false); // matches in sequence + f.findNext("e", false, false, false, false); // matches in sequence assertTrue(f.getIdMatches().isEmpty()); assertEquals(f.getSearchResults().getCount(), 1); List matches = f.getSearchResults().getResults(); @@ -223,7 +231,7 @@ public class FinderTest f = new Finder(av); PA.setValue(f, "sequenceIndex", 1); PA.setValue(f, "residueIndex", 7); - f.findNext("e", false, false, false); + f.findNext("e", false, false, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al.getSequenceAt(2)); assertTrue(f.getSearchResults().isEmpty()); @@ -245,7 +253,7 @@ public class FinderTest * find first match only */ Finder f = new Finder(av2); - f.findNext("rAF", false, true, false); + f.findNext("rAF", false, true, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); @@ -254,7 +262,7 @@ public class FinderTest * find all matches */ f = new Finder(av2); - f.findAll("rAF", false, true, false); + f.findAll("rAF", false, true, false, false); assertEquals(f.getIdMatches().size(), 2); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); @@ -264,7 +272,7 @@ public class FinderTest * case sensitive */ f = new Finder(av2); - f.findAll("RAF", true, true, false); + f.findAll("RAF", true, true, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertTrue(f.getSearchResults().isEmpty()); @@ -280,7 +288,7 @@ public class FinderTest /* * sequence matches should have no duplicates */ - f.findAll("EFH", false, true, false); + f.findAll("EFH", false, true, false, false); assertEquals(f.getIdMatches().size(), 2); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); @@ -308,7 +316,7 @@ public class FinderTest * case insensitive; seq1 occurs twice in sequence id but * only one match should be returned */ - f.findAll("SEQ1", false, false, false); + f.findAll("SEQ1", false, false, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al.getSequenceAt(0)); SearchResultsI searchResults = f.getSearchResults(); @@ -318,7 +326,7 @@ public class FinderTest * case sensitive */ f = new Finder(av); - f.findAll("SEQ1", true, false, false); + f.findAll("SEQ1", true, false, false, false); searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); @@ -329,7 +337,7 @@ public class FinderTest AlignViewportI av2 = new AlignViewport(al2); al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ")); f = new Finder(av2); - f.findAll("ABZ", false, false, false); + f.findAll("ABZ", false, false, false, false); assertEquals(f.getIdMatches().size(), 1); assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4)); searchResults = f.getSearchResults(); @@ -358,7 +366,7 @@ public class FinderTest * efh should be matched in seq2 only */ FinderI f = new Finder(av); - f.findNext("EfH", false, false, false); + f.findNext("EfH", false, false, false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -370,7 +378,7 @@ public class FinderTest * I should be found in seq1 (twice) and seq2 (once) */ f = new Finder(av); - f.findNext("I", false, false, false); // find next: seq1/16 + f.findNext("I", false, false, false, false); // find next: seq1/16 searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -378,7 +386,7 @@ public class FinderTest assertEquals(match.getStart(), 16); assertEquals(match.getEnd(), 16); - f.findNext("I", false, false, false); // find next: seq1/18 + f.findNext("I", false, false, false, false); // find next: seq1/18 searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -386,7 +394,7 @@ public class FinderTest assertEquals(match.getStart(), 18); assertEquals(match.getEnd(), 18); - f.findNext("I", false, false, false); // find next: seq2/8 + f.findNext("I", false, false, false, false); // find next: seq2/8 searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -394,13 +402,13 @@ public class FinderTest assertEquals(match.getStart(), 8); assertEquals(match.getEnd(), 8); - f.findNext("I", false, false, false); + f.findNext("I", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); /* * find should reset to start of alignment after a failed search */ - f.findNext("I", false, false, false); // find next: seq1/16 + f.findNext("I", false, false, false, false); // find next: seq1/16 searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -417,7 +425,7 @@ public class FinderTest public void testFindAll_maximalResultOnly() { Finder f = new Finder(av); - f.findAll("M+", false, false, false); + f.findAll("M+", false, false, false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); SearchResultMatchI match = searchResults.getResults().get(0); @@ -433,7 +441,7 @@ public class FinderTest public void testFindAll() { Finder f = new Finder(av); - f.findAll("EfH", false, false, false); + f.findAll("EfH", false, false, false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -448,7 +456,7 @@ public class FinderTest /* * find all I should find 2 positions in seq1, 1 in seq2 */ - f.findAll("I", false, false, false); + f.findAll("I", false, false, false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 3); match = searchResults.getResults().get(0); @@ -476,7 +484,7 @@ public class FinderTest /* * BC should match seq1/9-10 and seq2/2-3 */ - f.findAll("BC", true, false, false); + f.findAll("BC", true, false, false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -492,7 +500,7 @@ public class FinderTest * bc should match seq3/1-2 */ f = new Finder(av); - f.findAll("bc", true, false, false); + f.findAll("bc", true, false, false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -500,7 +508,7 @@ public class FinderTest assertEquals(match.getStart(), 1); assertEquals(match.getEnd(), 2); - f.findAll("bC", true, false, false); + f.findAll("bC", true, false, false, false); assertTrue(f.getSearchResults().isEmpty()); } @@ -523,7 +531,7 @@ public class FinderTest av.setSelectionGroup(sg); FinderI f = new Finder(av); - f.findNext("b", false, false, false); + f.findNext("b", false, false, false, false); assertTrue(f.getIdMatches().isEmpty()); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); @@ -535,12 +543,12 @@ public class FinderTest /* * a second Find should not return the 'b' in seq3 as outside the selection */ - f.findNext("b", false, false, false); + f.findNext("b", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); assertTrue(f.getIdMatches().isEmpty()); f = new Finder(av); - f.findNext("d", false, false, false); + f.findNext("d", false, false, false, false); assertTrue(f.getIdMatches().isEmpty()); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); @@ -548,7 +556,7 @@ public class FinderTest assertSame(match.getSequence(), al.getSequenceAt(1)); assertEquals(match.getStart(), 4); assertEquals(match.getEnd(), 4); - f.findNext("d", false, false, false); + f.findNext("d", false, false, false, false); assertTrue(f.getIdMatches().isEmpty()); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); @@ -575,12 +583,12 @@ public class FinderTest 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(av); - f.findAll("e", false, false, false); + f.findAll("e", false, false, false, false); assertEquals(f.getIdMatches().size(), 2); assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); @@ -595,7 +603,7 @@ public class FinderTest * search for 'Q' should match two sequence ids only */ f = new Finder(av); - f.findAll("Q", false, false, false); + f.findAll("Q", false, false, false, false); assertEquals(f.getIdMatches().size(), 2); assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); @@ -626,7 +634,7 @@ public class FinderTest * search for 'I' should match two sequence positions */ Finder f = new Finder(av); - f.findAll("I", false, false, false); + f.findAll("I", false, false, false, false); assertTrue(f.getIdMatches().isEmpty()); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); @@ -641,8 +649,8 @@ public class FinderTest } /** - * Test that find does not report hidden positions, but does report matches that - * span hidden gaps + * Test that find does not report hidden positions, but does report matches + * that span hidden gaps */ @Test(groups = "Functional") public void testFind_withHiddenColumns() @@ -663,7 +671,7 @@ public class FinderTest hc.hideColumns(3, 3); al.setHiddenColumns(hc); Finder f = new Finder(av); - f.findAll("aaa", false, false, false); + f.findAll("aaa", false, false, false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -685,7 +693,7 @@ public class FinderTest * find the visible D in seq2 */ f = new Finder(av); - f.findAll("D", false, false, false); + f.findAll("D", false, false, false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -698,7 +706,7 @@ public class FinderTest * consecutive in the visible columns */ f = new Finder(av); - f.findAll("AD", false, false, false); + f.findAll("AD", false, false, false, false); searchResults = f.getSearchResults(); assertTrue(searchResults.isEmpty()); @@ -707,7 +715,7 @@ public class FinderTest * (first run includes hidden gaps) */ f = new Finder(av); - f.findAll("aaa", false, false, false); + f.findAll("aaa", false, false, false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); match = searchResults.getResults().get(0); @@ -726,7 +734,7 @@ public class FinderTest */ hc.hideColumns(2, 5); f = new Finder(av); - f.findAll("aaa", false, false, false); + f.findAll("aaa", false, false, false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); match = searchResults.getResults().get(0); @@ -741,7 +749,7 @@ public class FinderTest /* * find all 'BE' should not match across hidden columns in seq1 */ - f.findAll("BE", false, false, false); + f.findAll("BE", false, false, false, false); assertTrue(f.getSearchResults().isEmpty()); /* @@ -751,7 +759,7 @@ public class FinderTest hc.revealAllHiddenColumns(new ColumnSelection()); hc.hideColumns(8, 13); f = new Finder(av); - f.findNext("H", false, false, false); + f.findNext("H", false, false, false, false); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); match = searchResults.getResults().get(0); @@ -770,7 +778,7 @@ public class FinderTest * --bcdEFH * aa---aMMMMMaaa */ - + /* * hide columns 2-4 and 6-7 */ @@ -778,7 +786,7 @@ public class FinderTest hc.hideColumns(2, 4); hc.hideColumns(6, 7); al.setHiddenColumns(hc); - + /* * select rows 2-3 */ @@ -794,7 +802,7 @@ public class FinderTest * should match seq2/1, seq2/7, not seq3/6 */ Finder f = new Finder(av); - f.findAll("[AH]", false, false, false); + f.findAll("[AH]", false, false, false, false); SearchResultsI searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 2); SearchResultMatchI match = searchResults.getResults().get(0); @@ -831,7 +839,7 @@ public class FinderTest * aaaMMMMaaa */ Finder f = new Finder(av); - f.findAll("abe", false, false, true); // true = ignore hidden + f.findAll("abe", false, false, false, true); // true = ignore hidden SearchResultsI searchResults = f.getSearchResults(); /* @@ -850,7 +858,7 @@ public class FinderTest assertEquals(match.getEnd(), 12); f = new Finder(av); - f.findNext("a.E", false, false, true); + f.findNext("a.E", false, false, false, true); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); assertEquals(searchResults.getResults().size(), 2); @@ -863,7 +871,7 @@ public class FinderTest assertEquals(match.getStart(), 12); // E assertEquals(match.getEnd(), 12); - f.findNext("a.E", false, false, true); + f.findNext("a.E", false, false, false, true); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); assertEquals(searchResults.getResults().size(), 2); @@ -880,7 +888,7 @@ public class FinderTest * find all matching across two hidden column regions * note one 'match' is returned as three contiguous matches */ - f.findAll("BEG", false, false, true); + f.findAll("BEG", false, false, false, true); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); assertEquals(searchResults.getResults().size(), 3); @@ -907,7 +915,7 @@ public class FinderTest selection.setEndRes(9); al.getSequences().forEach(seq -> selection.addSequence(seq, false)); av.setSelectionGroup(selection); - f.findAll("A.*H", false, false, true); + f.findAll("A.*H", false, false, false, true); searchResults = f.getSearchResults(); assertEquals(searchResults.getCount(), 1); assertEquals(searchResults.getResults().size(), 3); @@ -925,4 +933,60 @@ public class FinderTest assertEquals(match.getStart(), 7); // H (there is no G) assertEquals(match.getEnd(), 7); } + + @Test(groups = "Functional") + public void testFind_featuresOnly() + { + Finder f = new Finder(av); + // no match when not searching feature descriptions + f.findAll("Feature", false, false, false, true); + assertEquals(f.getSearchResults().getCount(), 0); + + // no match when case sensitive on feature descriptions + f.findAll("feature", true, false, true, true); + assertEquals(f.getSearchResults().getCount(), 0); + + // search feature descriptions - all match + f.findAll("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 3); + + List seqs = f.getSearchResults().getMatchingSubSequences(); + // assume order is preserved in results + assertEquals(al.getSequenceAt(0).getDatasetSequence(), + seqs.get(0).getDatasetSequence()); + assertEquals(seqs.get(0).getStart(), 9); + assertEquals(seqs.get(0).getEnd(), 11); + assertEquals(al.getSequenceAt(3).getDatasetSequence(), + seqs.get(1).getDatasetSequence()); + assertEquals(seqs.get(1).getStart(), 9); + assertEquals(seqs.get(1).getEnd(), 11); + assertEquals(al.getSequenceAt(3).getDatasetSequence(), + seqs.get(2).getDatasetSequence()); + assertEquals(seqs.get(2).getStart(), 1); + assertEquals(seqs.get(2).getEnd(), 3); + + SequenceI sq = null; + // search feature descriptions incrementally + // assume same order as before + f.findNext("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 1); + sq = f.getSearchResults().getMatchingSubSequences().get(0); + assertEquals(sq.getSequenceAsString(), + seqs.get(0).getSequenceAsString()); + + // .. + f.findNext("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 1); + sq = f.getSearchResults().getMatchingSubSequences().get(0); + assertEquals(sq.getSequenceAsString(), + seqs.get(1).getSequenceAsString()); + + // .. + f.findNext("Feature", false, false, true, true); + assertEquals(f.getSearchResults().getCount(), 1); + sq = f.getSearchResults().getMatchingSubSequences().get(0); + assertEquals(sq.getSequenceAsString(), + seqs.get(2).getSequenceAsString()); + + } }