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 jalview.api.AlignmentColsCollectionI;
25 import java.util.BitSet;
26 import java.util.Iterator;
28 public class AllColsCollection implements AlignmentColsCollectionI
36 public AllColsCollection(int s, int e, AlignmentI al)
40 hidden = al.getHiddenColumns();
44 public Iterator<Integer> iterator()
46 return new AllColsIterator(start, end, hidden);
50 public boolean isHidden(int c)
52 return !hidden.isVisible(c);
56 public boolean hasHidden()
58 return hidden.hasHiddenColumns();
61 private BitSet bsVisible;
64 public BitSet getHiddenBitSet()
66 return hidden.getBitset();
70 * Returns all columns, including any hidden in the alignment
73 public BitSet getShownBitSet()
75 if (bsVisible == null)
77 bsVisible = new BitSet(end + 1);
78 bsVisible.set(0, end + 1);