+
+ @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);
+ }