/*
* 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 java.awt.Color;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import jalview.util.MapList;
import jalview.ws.datamodel.alphafold.MappableContactMatrix;
/**
* Dummy contact matrix based on sequence distance
*
* @author jprocter
*
*/
public class SeqDistanceContactMatrix
extends MappableContactMatrix
implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
private int width = 0;
public SeqDistanceContactMatrix(int width)
{
this.width = width;
}
@Override
public float getMin()
{
return 0f;
}
@Override
public float getMax()
{
return width;
}
@Override
public ContactListI getContactList(final int column)
{
if (column < 0 || column >= width)
{
return null;
}
return new ContactListImpl(new ContactListProviderI()
{
int p = column;
// @Override
// public Color getColorForScore(int column)
// {
// return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
// 0, Color.white, width, Color.magenta);
// }
// @Override
// public Color getColorForRange(int from_column, int to_column)
// {
// return jalview.util.ColorUtils.getGraduatedColour(
// Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
// Color.magenta);
// }
@Override
public int getContactHeight()
{
return width;
}
@Override
public int getPosition()
{
return p;
}
@Override
public double getContactAt(int column)
{
return Math.abs(column - p);
}
});
}
@Override
public String getAnnotDescr()
{
return "Sequence distance matrix";
}
@Override
public String getAnnotLabel()
{
return "Sequence Distance";
}
@Override
public String getType()
{
return SEQUENCE_DISTANCE;
}
@Override
public int getWidth()
{
return width;
}
@Override
public int getHeight()
{
return width;
}
@Override
public double getElementAt(int _column, int i)
{
return Math.abs(_column - i);
}
@Override
protected SeqDistanceContactMatrix newMappableContactMatrix(
SequenceI newRefSeq, MapList newFromMapList)
{
return new SeqDistanceContactMatrix(width);
}
}