2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import java.util.Iterator;
24 import java.util.NoSuchElementException;
27 * An iterator which iterates over all visible rows in an alignment
32 public class VisibleRowsIterator implements Iterator<Integer>
40 private HiddenSequences hidden;
42 private AlignmentI al;
45 * Create an iterator for all visible rows in the alignment
48 * absolute row index to start from
50 * absolute row index to end at
52 * alignment to work with
54 public VisibleRowsIterator(int firstrow, int lastrow, AlignmentI alignment)
59 hidden = al.getHiddenSequences();
60 while (last > current && hidden.isHidden(last))
65 while (current < last && hidden.isHidden(current))
73 public boolean hasNext()
83 throw new NoSuchElementException();
89 } while (next <= last && hidden.isHidden(next));
96 throw new UnsupportedOperationException();