/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import jalview.api.AlignmentColsCollectionI;
import java.util.BitSet;
import java.util.Iterator;
public class AllColsCollection implements AlignmentColsCollectionI
{
final int start;
final int end;
HiddenColumns hidden;
public AllColsCollection(int s, int e, AlignmentI al)
{
start = s;
end = e;
hidden = al.getHiddenColumns();
}
@Override
public Iterator iterator()
{
return new AllColsIterator(start, end, hidden);
}
@Override
public boolean isHidden(int c)
{
return !hidden.isVisible(c);
}
@Override
public boolean hasHidden()
{
return hidden.hasHiddenColumns();
}
private BitSet bsVisible;
@Override
public BitSet getHiddenBitSet()
{
return hidden.getBitset();
}
/**
* Returns all columns, including any hidden in the alignment
*/
@Override
public BitSet getShownBitSet()
{
if (bsVisible == null)
{
bsVisible = new BitSet(end + 1);
bsVisible.set(0, end + 1);
}
return bsVisible;
}
}