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;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultMatchI;
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)
private AlignmentI al;
+ private AlignViewportI av;
+
@BeforeClass(groups = "Functional")
public void setUp()
{
- String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.applicationProperties.setProperty("PAD_GAPS",
+ Boolean.FALSE.toString());
+
+ String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n"
+ "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);
}
/**
- * Test for find all matches of a regular expression
+ * Test for find matches of a regular expression
*/
@Test(groups = "Functional")
- public void testFindAll_regex()
+ public void testFind_regex()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("E.H"); // 'E, any character, H'
+ /*
+ * find next match only
+ */
+ 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);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 7);
+ f = new Finder(av);
+ f.findAll("E.H", false, false); // 'E, any character, H'
// should match seq2 efH and seq3 EFH
- SearchResultsI sr = f.getSearchResults();
+ sr = f.getSearchResults();
assertEquals(sr.getSize(), 2);
- List<SearchResultMatchI> matches = sr.getResults();
- assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
- assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+ matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
+ assertSame(matches.get(1).getSequence(), al.getSequenceAt(2));
assertEquals(matches.get(0).getStart(), 5);
assertEquals(matches.get(0).getEnd(), 7);
assertEquals(matches.get(1).getStart(), 4);
@Test(groups = "Functional")
public void testFind_residueNumber()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("9");
+ Finder f = new Finder(av);
- // seq1 and seq4 have 9 residues; no match in other sequences
+ /*
+ * find first match should return seq1 residue 9
+ */
+ f.findNext("9", false, false);
SearchResultsI sr = f.getSearchResults();
- assertEquals(sr.getSize(), 2);
+ assertEquals(sr.getSize(), 1);
List<SearchResultMatchI> matches = sr.getResults();
- assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
- assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
+ assertEquals(matches.get(0).getStart(), 9);
+ assertEquals(matches.get(0).getEnd(), 9);
+
+ /*
+ * find all matches should return seq1 and seq4 (others are too short)
+ */
+ f = new Finder(av);
+ f.findAll("9", false, false);
+ sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ matches = sr.getResults();
+ assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
+ assertSame(matches.get(1).getSequence(), al.getSequenceAt(3));
assertEquals(matches.get(0).getStart(), 9);
assertEquals(matches.get(0).getEnd(), 9);
assertEquals(matches.get(1).getStart(), 9);
assertEquals(matches.get(1).getEnd(), 9);
+
+ /*
+ * parsing of search string as integer is strict
+ */
+ f = new Finder(av);
+ f.findNext(" 9", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
}
/**
public void testFindNext()
{
/*
- * start at second sequence; resIndex of -1
+ * 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));
-
- // resIndex is now 0 - for use in next find next
- assertEquals(f.getResIndex(), 0);
- f = new Finder(al, null, 1, 0);
- f.find("e"); // matches in sequence
- assertTrue(f.getIdMatch().isEmpty());
+ 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(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<SearchResultMatchI> 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.getSeqIndex(), 1);
- // next residue position to search from is 5
- // (used as base 0 by RegEx so the same as 6 if base 1)
- assertEquals(f.getResIndex(), 5);
+ assertEquals(PA.getValue(f, "sequenceIndex"), 1);
+ // next column position to search from is 7
+ assertEquals(PA.getValue(f, "columnIndex"), 7);
// find next from end of sequence - finds next sequence id
- f = new Finder(al, null, 1, 5);
- 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());
}
/**
* Test for matching within sequence descriptions
*/
@Test(groups = "Functional")
- public void testFindAll_inDescription()
+ public void testFind_inDescription()
{
AlignmentI al2 = new Alignment(al);
al2.getSequenceAt(0).setDescription("BRAF");
al2.getSequenceAt(1).setDescription("braf");
- Finder 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));
+
+ AlignViewportI av2 = new AlignViewport(al2);
+
+ /*
+ * find first match only
+ */
+ 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());
/*
- * case sensitive
+ * find all matches
*/
- f = new Finder(al2, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.setIncludeDescription(true);
+ 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());
- f.find("RAF");
- assertEquals(f.getIdMatch().size(), 1);
- assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+ /*
+ * case sensitive
+ */
+ 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());
/*
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);
- assertSame(al2.getSequenceAt(1), match.getSequence());
- assertEquals(5, match.getStart());
- assertEquals(7, match.getEnd());
+ assertSame(match.getSequence(), al2.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
match = f.getSearchResults().getResults().get(1);
- assertSame(al2.getSequenceAt(2), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
+ assertSame(match.getSequence(), al2.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
}
/**
@Test(groups = "Functional")
public void testFindAll_sequenceIds()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
+ Finder f = new Finder(av);
/*
- * case insensitive
+ * 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));
- assertTrue(f.getSearchResults().isEmpty());
+ 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");
- assertTrue(f.getSearchResults().isEmpty());
+ f = new Finder(av);
+ f.findAll("SEQ1", true, false);
+ searchResults = f.getSearchResults();
+ assertTrue(searchResults.isEmpty());
/*
* 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));
- assertEquals(f.getSearchResults().getSize(), 2);
- SearchResultMatchI match = f.getSearchResults().getResults().get(0);
- assertSame(al2.getSequenceAt(4), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
- match = f.getSearchResults().getResults().get(1);
- assertSame(al2.getSequenceAt(4), match.getSequence());
- assertEquals(10, match.getStart());
- assertEquals(12, match.getEnd());
+ 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);
+ assertSame(match.getSequence(), al2.getSequenceAt(4));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al2.getSequenceAt(4));
+ assertEquals(match.getStart(), 10);
+ assertEquals(match.getEnd(), 12);
}
/**
- * Test finding all matches of a sequence pattern in an alignment
+ * Test finding next match of a sequence pattern in an alignment
*/
@Test(groups = "Functional")
- public void testFindAll_simpleMatch()
+ public void testFind_findNext()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
+ /*
+ * efh should be matched in seq2 only
+ */
+ FinderI f = new Finder(av);
+ f.findNext("EfH", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
/*
- * case insensitive first
+ * I should be found in seq1 (twice) and seq2 (once)
*/
- f.find("EfH");
+ 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);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+
+ f.findNext("I", false, false); // find next: seq1/18
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 18);
+ assertEquals(match.getEnd(), 18);
+
+ f.findNext("I", false, false); // find next: seq2/8
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
+
+ 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);
+ }
+
+ /**
+ * Test for JAL-2302 to verify that sub-matches are not included in a find all
+ * result
+ */
+ @Test(groups = "Functional")
+ public void testFind_maximalResultOnly()
+ {
+ Finder f = new Finder(av);
+ f.findAll("M+", false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 4); // dataset sequence positions
+ assertEquals(match.getEnd(), 8); // base 1
+ }
+
+ /**
+ * Test finding all matches of a sequence pattern in an alignment
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAll()
+ {
+ Finder f = new Finder(av);
+ f.findAll("EfH", false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(1), match.getSequence());
- assertEquals(5, match.getStart());
- assertEquals(7, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 5);
+ assertEquals(match.getEnd(), 7);
match = searchResults.getResults().get(1);
- assertSame(al.getSequenceAt(2), match.getSequence());
- assertEquals(4, match.getStart());
- assertEquals(6, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 6);
/*
- * case sensitive
+ * find all I should find 2 positions in seq1, 1 in seq2
*/
- f = new Finder(al, null);
- f.setFindAll(true);
- f.setCaseSensitive(true);
- f.find("BC");
+ f.findAll("I", false, false);
searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 3);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 18);
+ assertEquals(match.getEnd(), 18);
+ match = searchResults.getResults().get(2);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
+ }
+
+ /**
+ * Test finding all matches, case-sensitive
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllCaseSensitive()
+ {
+ Finder f = new Finder(av);
+
+ /*
+ * BC should match seq1/9-10 and seq2/2-3
+ */
+ f.findAll("BC", true, false);
+ SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 10);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 2);
+ assertEquals(match.getEnd(), 3);
+
+ /*
+ * bc should match seq3/1-2
+ */
+ f = new Finder(av);
+ f.findAll("bc", true, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 2);
+
+ f.findAll("bC", true, false);
+ assertTrue(f.getSearchResults().isEmpty());
+ }
+
+ /**
+ * Test finding next match of a sequence pattern in a selection group
+ */
+ @Test(groups = "Functional")
+ public void testFind_inSelection()
+ {
+ /*
+ * select sequences 2 and 3, columns 4-6 which contains
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(3);
+ sg.setEndRes(5);
+ sg.addSequence(al.getSequenceAt(1), false);
+ sg.addSequence(al.getSequenceAt(2), false);
+ av.setSelectionGroup(sg);
+
+ 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);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 2);
+ assertEquals(match.getEnd(), 2);
+
+ /*
+ * a second Find should not return the 'b' in seq3 as outside the selection
+ */
+ f.findNext("b", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+ assertTrue(f.getIdMatches().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(al.getSequenceAt(0), match.getSequence());
- assertEquals(2, match.getStart());
- assertEquals(3, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+ 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(2));
+ assertEquals(match.getStart(), 3);
+ assertEquals(match.getEnd(), 3);
+ }
+
+ /**
+ * Test finding all matches of a search pattern in a selection group
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllInSelection()
+ {
+ /*
+ * select sequences 2 and 3, columns 4-6 which contains
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(3);
+ 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(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);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+
+ /*
+ * search for 'Q' should match two sequence ids only
+ */
+ 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());
+ }
+
+ /**
+ * Test finding in selection with a sequence too short to reach it
+ */
+ @Test(groups = "Functional")
+ public void testFind_findAllInSelectionWithShortSequence()
+ {
+ /*
+ * select all sequences, columns 10-12
+ * BCD
+ * cdE
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(9);
+ sg.setEndRes(11);
+ sg.addSequence(al.getSequenceAt(0), false);
+ 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(av);
+ f.findAll("I", false, false);
+ assertTrue(f.getIdMatches().isEmpty());
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
match = searchResults.getResults().get(1);
- assertSame(al.getSequenceAt(1), match.getSequence());
- assertEquals(2, match.getStart());
- assertEquals(3, match.getEnd());
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 8);
+ assertEquals(match.getEnd(), 8);
}
/**
- * Test for JAL-2302 to verify that sub-matches are not included in a find all
- * result
+ * Test that find does not report hidden positions
*/
@Test(groups = "Functional")
- public void testFind_maximalResultOnly()
+ public void testFind_withHiddenColumns()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("M+");
+ /*
+ * 0 5 9
+ * ABCD--EF-GHI
+ * A--BCDefHI
+ * --bcdEFH
+ * aa---aMMMMMaaa
+ */
+
+ /*
+ * hide 2-4 (CD- -BC bcd ---)
+ */
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(2, 4);
+ al.setHiddenColumns(hc);
+
+ /*
+ * find all search for D should ignore hidden positions in seq1 and seq3,
+ * find the visible D in seq2
+ */
+ Finder f = new Finder(av);
+ f.findAll("D", false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
- assertSame(al.getSequenceAt(3), match.getSequence());
- assertEquals(4, match.getStart()); // dataset sequence positions
- assertEquals(8, match.getEnd()); // base 1
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4);
+ assertEquals(match.getEnd(), 4);
+
+ /*
+ * hide columns 2-5:
+ * find all 'aaa' should find end of seq4 only
+ */
+ hc.hideColumns(2, 5);
+ f = new Finder(av);
+ f.findAll("aaa", false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 11);
+
+ /*
+ * find all 'BE' should not match across hidden columns in seq1
+ */
+ f.findAll("BE", false, false);
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * boundary case: hide columns at end of alignment
+ * search for H should match seq3/6 only
+ */
+ hc.revealAllHiddenColumns(new ColumnSelection());
+ hc.hideColumns(8, 13);
+ f = new Finder(av);
+ f.findNext("H", false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(2));
+ 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);
}
}
git://source.jalview.org / jalview.git / blobdiff