package jalview.datamodel;
-import jalview.ws.params.InvalidArgumentException;
-
+import java.awt.Color;
+import java.math.BigInteger;
import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
import java.util.List;
+import java.util.Spliterator;
+import java.util.StringTokenizer;
+
+import jalview.bin.Console;
-public class ContactMatrix implements ContactMatrixI
+public abstract class ContactMatrix implements ContactMatrixI
{
/**
* are contacts reflexive ?
{
if (left < 0 || right < 0)
{
- throw new Error(new InvalidArgumentException(
+ throw new Error(new RuntimeException(
"Cannot have negative indices for contact left=" + left
+ " right=" + right + " strength=" + strength));
}
}
}
-
@Override
public ContactListI getContactList(final int column)
{
int p = column;
@Override
+ public int getPosition()
+ {
+ return p;
+ }
+
+ @Override
public int getContactHeight()
{
return width;
}
@Override
- public boolean hasReferenceSeq()
+ public String getAnnotLabel()
{
- // TODO Auto-generated method stub
- return false;
+ return "Contact Matrix";
}
@Override
- public SequenceI getReferenceSeq()
+ public String getAnnotDescr()
{
- // TODO Auto-generated method stub
- return null;
+ return "Contact Matrix";
+ }
+
+ GroupSet grps = new GroupSet();
+
+ @Override
+ public GroupSetI getGroupSet()
+ {
+ return grps;
+ }
+
+ @Override
+ public void setGroupSet(GroupSet makeGroups)
+ {
+ grps = makeGroups;
+ }
+
+ public static String contactToFloatString(ContactMatrixI cm)
+ {
+ StringBuilder sb = new StringBuilder();
+ for (int c = 0; c < cm.getWidth(); c++)
+ {
+ ContactListI cl = cm.getContactList(c);
+ if (cl != null)
+ {
+ for (int h = 0; h <= cl.getContactHeight(); h++)
+ {
+ if (sb.length() > 0)
+ {
+ 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');
+ 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;
}
}