/*
* 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.util.ArrayList;
import java.util.List;
import java.util.StringTokenizer;
import jalview.bin.Console;
public abstract class ContactMatrix extends GroupSetHolder
implements ContactMatrixI
{
/**
* are contacts reflexive ?
*/
boolean symmetric = true;
public ContactMatrix(boolean symmetric)
{
this.symmetric = symmetric;
}
List> contacts = null;
int width = 0, numcontacts = 0;
float min = 0f, max = 0f;
public void addContact(int left, int right, float strength)
{
if (left < 0 || right < 0)
{
throw new Error(new RuntimeException(
"Cannot have negative indices for contact left=" + left
+ " right=" + right + " strength=" + strength));
}
if (symmetric)
{
if (left > right)
{
// swap
int r = right;
right = left;
left = r;
}
}
if (contacts == null)
{
// TODO: use sparse list for efficiency ?
contacts = new ArrayList>();
}
List clist = contacts.get(left);
if (clist == null)
{
clist = new ArrayList();
contacts.set(left, clist);
}
Float last = clist.set(right, strength);
// TODO: if last is non null, may need to recompute range
checkBounds(strength);
if (last == null)
{
numcontacts++;
}
}
private void checkBounds(float strength)
{
if (min > strength)
{
min = strength;
}
if (max < strength)
{
max = strength;
}
}
@Override
public ContactListI getContactList(final int column)
{
if (column < 0 || column >= width)
{
return null;
}
return new ContactListImpl(new ContactListProviderI()
{
int p = column;
@Override
public int getPosition()
{
return p;
}
@Override
public int getContactHeight()
{
return width;
}
@Override
public double getContactAt(int column)
{
Float cl = getFloatElementAt(column, p);
if (cl == null)
{
// return 0 not NaN ?
return Double.NaN;
}
return cl.doubleValue();
}
});
}
private Float getFloatElementAt(int column, int p)
{
List clist;
Float cl = null;
if (symmetric)
{
if (p < column)
{
clist = contacts.get(p);
cl = clist.get(column);
}
else
{
clist = contacts.get(column);
cl = clist.get(p);
}
}
else
{
clist = contacts.get(p);
cl = clist.get(column);
}
return cl;
}
@Override
public double getElementAt(int column, int row)
{
Float cl = getFloatElementAt(column, row);
if (cl != null)
{
return cl;
}
throw (new RuntimeException("Out of Bounds " + column + "," + row));
}
@Override
public float getMin()
{
return min;
}
@Override
public float getMax()
{
return max;
}
@Override
public String getAnnotLabel()
{
return "Contact Matrix";
}
@Override
public String getAnnotDescr()
{
return "Contact Matrix";
}
public static String contactToFloatString(ContactMatrixI cm)
{
StringBuilder sb = new StringBuilder();
for (int c = 0; c < cm.getWidth(); c++)
{
ContactListI cl = cm.getContactList(c);
long lastsb = -1;
if (cl != null)
{
for (int h = 0; h <= cl.getContactHeight(); h++)
{
if (sb.length() > 0)
{
if (sb.length() - lastsb > 320)
{
// newline
sb.append('\n');
lastsb = sb.length();
}
else
{
sb.append('\t');
}
}
sb.append(cl.getContactAt(h));
}
}
}
return sb.toString();
}
public static float[][] fromFloatStringToContacts(String values, int cols,
int rows)
{
float[][] vals = new float[cols][rows];
StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n');
int c = 0, r = 0;
while (tabsep.hasMoreTokens())
{
double elem = Double.valueOf(tabsep.nextToken());
vals[c][r++] = (float) elem;
if (r >= vals[c].length)
{
r = 0;
c++;
}
if (c >= vals.length)
{
break;
}
}
if (tabsep.hasMoreElements())
{
Console.warn(
"Ignoring additional elements for Float string to contact matrix parsing.");
}
return vals;
}
}