import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.bin.Cache;
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.bin.Cache;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
- 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);
// should match seq2 efH only
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 1);
- 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);
// should match seq2 efH and seq3 EFH
sr = f.getSearchResults();
assertEquals(sr.getCount(), 2);
- f.findAll("M", false, false, false);
+ f.findAll("M", false, false, false, false);
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 5);
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 5);
- f.findNext("9", false, false, false);
+ f.findNext("9", false, false, false, false);
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 1);
List<SearchResultMatchI> matches = sr.getResults();
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 1);
List<SearchResultMatchI> matches = sr.getResults();
- f.findAll("9", false, false, false);
+ f.findAll("9", false, false, false, false);
sr = f.getSearchResults();
assertEquals(sr.getCount(), 2);
matches = sr.getResults();
sr = f.getSearchResults();
assertEquals(sr.getCount(), 2);
matches = sr.getResults();
- f.findNext(" 9", false, false, false);
+ f.findNext(" 9", false, false, false, false);
Finder f = new Finder(av);
PA.setValue(f, "sequenceIndex", 1);
PA.setValue(f, "residueIndex", -1);
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);
assertTrue(f.getSearchResults().isEmpty());
assertEquals(f.getIdMatches().size(), 1);
f = new Finder(av);
PA.setValue(f, "sequenceIndex", 1);
PA.setValue(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
+ f.findNext("e", false, false, false, false); // matches in sequence
assertTrue(f.getIdMatches().isEmpty());
assertEquals(f.getSearchResults().getCount(), 1);
List<SearchResultMatchI> matches = f.getSearchResults().getResults();
assertTrue(f.getIdMatches().isEmpty());
assertEquals(f.getSearchResults().getCount(), 1);
List<SearchResultMatchI> matches = f.getSearchResults().getResults();
f = new Finder(av);
PA.setValue(f, "sequenceIndex", 1);
PA.setValue(f, "residueIndex", 7);
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());
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
assertTrue(f.getSearchResults().isEmpty());
- 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());
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
- 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));
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
- 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());
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
- 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));
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
- 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();
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
SearchResultsI searchResults = f.getSearchResults();
- f.findAll("SEQ1", true, false, false);
+ f.findAll("SEQ1", true, false, false, false);
AlignViewportI av2 = new AlignViewport(al2);
al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
f = new Finder(av2);
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();
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
searchResults = f.getSearchResults();
- 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertEquals(match.getStart(), 16);
assertEquals(match.getEnd(), 16);
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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertEquals(match.getStart(), 18);
assertEquals(match.getEnd(), 18);
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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertEquals(match.getStart(), 8);
assertEquals(match.getEnd(), 8);
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
*/
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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
- 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
- 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 3);
match = searchResults.getResults().get(0);
- 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
assertEquals(match.getStart(), 1);
assertEquals(match.getEnd(), 2);
assertEquals(match.getStart(), 1);
assertEquals(match.getEnd(), 2);
- f.findAll("bC", true, false, false);
+ f.findAll("bC", true, false, false, false);
- 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);
assertTrue(f.getIdMatches().isEmpty());
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
- f.findNext("b", false, false, false);
+ f.findNext("b", false, false, false, false);
- f.findNext("d", false, false, false);
+ f.findNext("d", false, false, false, false);
assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 4);
assertEquals(match.getEnd(), 4);
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);
assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
- 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));
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
- 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));
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
- 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);
assertTrue(f.getIdMatches().isEmpty());
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
- 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
- f.findAll("AD", false, false, false);
+ f.findAll("AD", false, false, false, false);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
match = searchResults.getResults().get(0);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
match = searchResults.getResults().get(0);
- f.findAll("BE", false, false, false);
+ f.findAll("BE", false, false, false, false);
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
* should match seq2/1, seq2/7, not seq3/6
*/
Finder f = new Finder(av);
* 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
- f.findAll("abe", false, false, true); // true = ignore hidden
+ f.findAll("abe", false, false, false, true); // true = ignore hidden
- 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 2);
assertEquals(match.getStart(), 12); // E
assertEquals(match.getEnd(), 12);
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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 2);
* find all matching across two hidden column regions
* note one 'match' is returned as three contiguous matches
*/
* 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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 3);
selection.setEndRes(9);
al.getSequences().forEach(seq -> selection.addSequence(seq, false));
av.setSelectionGroup(selection);
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);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 3);