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.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()
{
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";
+ //@formatter:off
+ String seqData =
+ "seq1/8-18 ABCD--EF-GHIJI\n" +
+ "seq2 A--BCDefHI\n" +
+ "seq3 --bcdEFH\n" +
+ "seq4 aa---aMMMMMaaa\n";
+ //@formatter:on
af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
- al = af.getViewport().getAlignment();
+ av = af.getViewport();
+ al = av.getAlignment();
+
+ // JAL-3765 bug test data
+ String longSeqData =
+ ">O80429_MAIZE/2-140 Ferredoxin\n" +
+ "AAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGEV\n" +
+ "ELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVV\n" +
+ "IETHKEDDLL--\n" ;
+ af_oneseq=new FileLoader().LoadFileWaitTillLoaded(longSeqData, DataSourceType.PASTE);
+ av_oneseq = af_oneseq.getViewport();
+ al_oneseq = av_oneseq.getAlignment();
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDownAfterTest()
+ {
+ av.setSelectionGroup(null);
}
/**
/*
* 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, false); // 'E, any character, H'
// should match seq2 efH only
SearchResultsI sr = f.getSearchResults();
- assertEquals(sr.getSize(), 1);
+ assertEquals(sr.getCount(), 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(al, null);
- f.setFindAll(true);
- f.find("E.H"); // 'E, any character, H'
+ f = new Finder(av);
+ f.findAll("E.H", false, false, false); // 'E, any character, H'
// should match seq2 efH and seq3 EFH
sr = f.getSearchResults();
- assertEquals(sr.getSize(), 2);
+ assertEquals(sr.getCount(), 2);
matches = sr.getResults();
assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
assertSame(matches.get(1).getSequence(), al.getSequenceAt(2));
@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, false);
SearchResultsI sr = f.getSearchResults();
- assertEquals(sr.getSize(), 1);
+ assertEquals(sr.getCount(), 1);
List<SearchResultMatchI> matches = sr.getResults();
assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
assertEquals(matches.get(0).getStart(), 9);
/*
* find all matches should return seq1 and seq4 (others are too short)
+ * (and not matches in sequence ids)
*/
- f = new Finder(al, null);
- f.setFindAll(true);
- f.find("9");
+ f = new Finder(av);
+ String name = al.getSequenceAt(0).getName();
+ al.getSequenceAt(0).setName("Q9XA0");
+ f.findAll("9", false, false, false);
sr = f.getSearchResults();
- assertEquals(sr.getSize(), 2);
+ assertEquals(sr.getCount(), 2);
matches = sr.getResults();
assertSame(matches.get(0).getSequence(), al.getSequenceAt(0));
assertSame(matches.get(1).getSequence(), al.getSequenceAt(3));
assertEquals(matches.get(0).getEnd(), 9);
assertEquals(matches.get(1).getStart(), 9);
assertEquals(matches.get(1).getEnd(), 9);
+ al.getSequenceAt(0).setName(name);
/*
* 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, false);
assertTrue(f.getSearchResults().isEmpty());
}
public void testFindNext()
{
/*
- * start at second sequence; colIndex of -1
+ * start at second sequence; residueIndex 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, "residueIndex", -1);
+ f.findNext("e", false, 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
+ // residueIndex 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(f.getSearchResults().getSize(), 1);
+ assertEquals(PA.getValue(f, "residueIndex"), 0);
+ f = new Finder(av);
+ PA.setValue(f, "sequenceIndex", 1);
+ PA.setValue(f, "residueIndex", 0);
+ f.findNext("e", false, false, false); // matches in sequence
+ assertTrue(f.getIdMatches().isEmpty());
+ assertEquals(f.getSearchResults().getCount(), 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.getSequenceIndex(), 1);
- // next column position to search from is 7
- assertEquals(f.getColumnIndex(), 7);
+ assertEquals(PA.getValue(f, "sequenceIndex"), 1);
+ // next residue offset to search from is 5
+ assertEquals(PA.getValue(f, "residueIndex"), 5);
// 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, "residueIndex", 7);
+ f.findNext("e", false, false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
assertTrue(f.getSearchResults().isEmpty());
}
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, false);
+ 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, false);
+ 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, false);
+ 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, false);
+ 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);
+ assertEquals(f.getSearchResults().getCount(), 2);
SearchResultMatchI match = f.getSearchResults().getResults().get(0);
assertSame(match.getSequence(), al2.getSequenceAt(1));
assertEquals(match.getStart(), 5);
@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, 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, 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));
+ f = new Finder(av2);
+ f.findAll("ABZ", false, false, false);
+ assertEquals(f.getIdMatches().size(), 1);
+ assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 2);
+ assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al2.getSequenceAt(4));
assertEquals(match.getStart(), 4);
@Test(groups = "Functional")
public void testFind_findNext()
{
+ // "seq1/8-18 ABCD--EF-GHIJI\n" +
+ // "seq2 A--BCDefHI\n" +
+ // "seq3 --bcdEFH\n" +
+ // "seq4 aa---aMMMMMaaa\n";
/*
* 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, false);
SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 5);
/*
* 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, false); // find next: seq1/16
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(0));
assertEquals(match.getStart(), 16);
assertEquals(match.getEnd(), 16);
- f.find("I"); // find next: seq1/18
+ f.findNext("I", false, false, false); // find next: seq1/18
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(0));
assertEquals(match.getStart(), 18);
assertEquals(match.getEnd(), 18);
- f.find("I"); // find next: seq2/8
+ f.findNext("I", false, false, false); // find next: seq2/8
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 8);
assertEquals(match.getEnd(), 8);
- f.find("I");
+ f.findNext("I", 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
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 1);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 16);
+ assertEquals(match.getEnd(), 16);
}
/**
* result
*/
@Test(groups = "Functional")
- public void testFind_maximalResultOnly()
+ public void testFindAll_maximalResultOnly()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("M+");
+ Finder f = new Finder(av);
+ f.findAll("M+", false, false, false);
SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(3));
assertEquals(match.getStart(), 4); // dataset sequence positions
* Test finding all matches of a sequence pattern in an alignment
*/
@Test(groups = "Functional")
- public void testFind_findAll()
+ public void testFindAll()
{
- Finder f = new Finder(al, null);
- f.setFindAll(true);
- f.find("EfH");
+ Finder f = new Finder(av);
+ f.findAll("EfH", false, false, false);
SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 2);
+ assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 5);
/*
* find all I should find 2 positions in seq1, 1 in seq2
*/
- f.find("I");
+ f.findAll("I", false, false, false);
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 3);
+ assertEquals(searchResults.getCount(), 3);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(0));
assertEquals(match.getStart(), 16);
* Test finding all matches, case-sensitive
*/
@Test(groups = "Functional")
- public void testFind_findAllCaseSensitive()
+ public void testFindAll_caseSensitive()
{
- 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, false);
SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 2);
+ assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(0));
assertEquals(match.getStart(), 9);
/*
* 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, false);
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(2));
assertEquals(match.getStart(), 1);
assertEquals(match.getEnd(), 2);
- f.find("bC");
+ f.findAll("bC", true, false, false);
assertTrue(f.getSearchResults().isEmpty());
}
* Test finding next match of a sequence pattern in a selection group
*/
@Test(groups = "Functional")
- public void testFind_inSelection()
+ public void testFindNext_inSelection()
{
/*
* select sequences 2 and 3, columns 4-6 which contains
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, false);
+ assertTrue(f.getIdMatches().isEmpty());
SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 2);
/*
* a second Find should not return the 'b' in seq3 as outside the selection
*/
- f.find("b");
+ f.findNext("b", false, 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, false);
+ assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 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, false);
+ assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(2));
assertEquals(match.getStart(), 3);
* Test finding all matches of a search pattern in a selection group
*/
@Test(groups = "Functional")
- public void testFind_findAllInSelection()
+ public void testFindAll_inSelection()
{
/*
* select sequences 2 and 3, columns 4-6 which contains
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, 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);
+ assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(2));
assertEquals(match.getStart(), 4);
/*
* 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, 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());
}
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, false);
+ assertTrue(f.getIdMatches().isEmpty());
SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 2);
+ assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(0));
assertEquals(match.getStart(), 16);
}
/**
- * Test that find does not report hidden positions
+ * Test that find does not report hidden positions, but does report matches that
+ * span hidden gaps
*/
@Test(groups = "Functional")
public void testFind_withHiddenColumns()
*/
/*
- * hide 2-4 (CD- -BC bcd ---)
+ * hide column 3 only, search for aaa
+ * should find two matches: aa-[-]-aa and trailing aaa
*/
HiddenColumns hc = new HiddenColumns();
- hc.hideColumns(2, 4);
+ hc.hideColumns(3, 3);
al.setHiddenColumns(hc);
+ Finder f = new Finder(av);
+ f.findAll("aaa", false, false, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 3);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 11);
+
+ /*
+ * hide 2-4 (CD- -BC bcd ---)
+ */
+ hc.hideColumns(2, 4);
/*
* 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");
- SearchResultsI searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
- SearchResultMatchI match = searchResults.getResults().get(0);
+ f = new Finder(av);
+ f.findAll("D", false, false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 1);
+ match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 4);
assertEquals(match.getEnd(), 4);
/*
+ * search for AD should fail although these are now
+ * consecutive in the visible columns
+ */
+ f = new Finder(av);
+ f.findAll("AD", false, false, false);
+ searchResults = f.getSearchResults();
+ assertTrue(searchResults.isEmpty());
+
+ /*
+ * find all 'aaa' should find both start and end of seq4
+ * (first run includes hidden gaps)
+ */
+ f = new Finder(av);
+ f.findAll("aaa", false, false, false);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 2);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 3);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 9);
+ assertEquals(match.getEnd(), 11);
+
+ /*
* hide columns 2-5:
- * find all 'aaa' should find end of seq4 only
+ * find all 'aaa' should match twice in seq4
+ * (first match partly hidden, second all visible)
*/
hc.hideColumns(2, 5);
- f = new Finder(al, null);
- f.find("aaa");
+ f = new Finder(av);
+ f.findAll("aaa", false, false, false);
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 2);
match = searchResults.getResults().get(0);
assertSame(match.getSequence(), al.getSequenceAt(3));
+ assertEquals(match.getStart(), 1);
+ assertEquals(match.getEnd(), 3);
+ match = searchResults.getResults().get(1);
+ 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.find("BE");
+ f.findAll("BE", false, false, false);
assertTrue(f.getSearchResults().isEmpty());
/*
*/
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, false);
searchResults = f.getSearchResults();
- assertEquals(searchResults.getSize(), 1);
+ assertEquals(searchResults.getCount(), 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, false);
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 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);
+ }
+
+ @Test(groups = "Functional")
+ public void testFind_ignoreHiddenColumns()
+ {
+ /*
+ * 0 5 9
+ * ABCD--EF-GHI
+ * A--BCDefHI
+ * --bcdEFH
+ * aa---aMMMMMaaa
+ */
+ HiddenColumns hc = new HiddenColumns();
+ hc.hideColumns(2, 4);
+ hc.hideColumns(7, 7);
+ al.setHiddenColumns(hc);
+
+ /*
+ * now have
+ * 015689
+ * AB-E-GHI
+ * A-DeHI
+ * --EF
+ * aaaMMMMaaa
+ */
+ Finder f = new Finder(av);
+ f.findAll("abe", false, false, true); // true = ignore hidden
+ SearchResultsI searchResults = f.getSearchResults();
+
+ /*
+ * match of seq1 ABE made up of AB and E
+ * note only one match is counted
+ */
+ assertEquals(searchResults.getCount(), 1);
+ assertEquals(searchResults.getResults().size(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 8); // A
+ assertEquals(match.getEnd(), 9); // B
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 12); // E
+ assertEquals(match.getEnd(), 12);
+
+ f = new Finder(av);
+ f.findNext("a.E", false, false, true);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 1);
+ assertEquals(searchResults.getResults().size(), 2);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 8); // A
+ assertEquals(match.getEnd(), 9); // B
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 12); // E
+ assertEquals(match.getEnd(), 12);
+
+ f.findNext("a.E", false, false, true);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 1);
+ assertEquals(searchResults.getResults().size(), 2);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 1); // a
+ assertEquals(match.getEnd(), 1);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4); // D
+ assertEquals(match.getEnd(), 5); // e
+
+ /*
+ * find all matching across two hidden column regions
+ * note one 'match' is returned as three contiguous matches
+ */
+ f.findAll("BEG", false, false, true);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 1);
+ assertEquals(searchResults.getResults().size(), 3);
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 9); // B
+ assertEquals(match.getEnd(), 9);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 12); // E
+ assertEquals(match.getEnd(), 12);
+ match = searchResults.getResults().get(2);
+ assertSame(match.getSequence(), al.getSequenceAt(0));
+ assertEquals(match.getStart(), 14); // G
+ assertEquals(match.getEnd(), 14);
+
+ /*
+ * now select columns 0-9 and search for A.*H
+ * this should match in the second sequence (split as 3 matches)
+ * but not the first (as H is outside the selection)
+ */
+ SequenceGroup selection = new SequenceGroup();
+ selection.setStartRes(0);
+ selection.setEndRes(9);
+ al.getSequences().forEach(seq -> selection.addSequence(seq, false));
+ av.setSelectionGroup(selection);
+ f.findAll("A.*H", false, false, true);
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getCount(), 1);
+ assertEquals(searchResults.getResults().size(), 3);
+ // match made of contiguous matches A, DE, H
+ match = searchResults.getResults().get(0);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 1); // A
+ assertEquals(match.getEnd(), 1);
+ match = searchResults.getResults().get(1);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 4); // D
+ assertEquals(match.getEnd(), 5); // E
+ match = searchResults.getResults().get(2);
+ assertSame(match.getSequence(), al.getSequenceAt(1));
+ assertEquals(match.getStart(), 7); // H (there is no G)
+ assertEquals(match.getEnd(), 7);
+ }
}
git://source.jalview.org / jalview.git / blobdiff