package jalview.datamodel;
+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;
-public class ContactMatrix implements ContactMatrixI
+import jalview.bin.Console;
+
+public abstract class ContactMatrix implements ContactMatrixI
{
/**
* are contacts reflexive ?
}
@Override
- public boolean hasReferenceSeq()
+ public String getAnnotLabel()
{
- // TODO Auto-generated method stub
- return false;
+ return "Contact Matrix";
}
@Override
- public SequenceI getReferenceSeq()
+ public String getAnnotDescr()
+ {
+ return "Contact Matrix";
+ }
+ List<BitSet> groups=null;
+ @Override
+ public void updateGroups(List<BitSet> colGroups)
+ {
+ groups = colGroups;
+ colorMap=new HashMap<>();
+ }
+ @Override
+ public boolean hasGroups()
+ {
+ return groups!=null && groups.size()>0;
+ }
+ @Override
+ public List<BitSet> getGroups()
+ {
+ return groups;
+ }
+ @Override
+ public BitSet getGroupsFor(int column)
+ {
+ for (BitSet gp:groups) {
+ if (gp.get(column))
+ {
+ return gp;
+ }
+ }
+ return ContactMatrixI.super.getGroupsFor(column);
+ }
+ HashMap<BitSet,Color> colorMap = new HashMap<>();
+ @Override
+ public Color getColourForGroup(BitSet bs)
+ {
+ if (bs==null) {
+ return Color.white;
+ }
+ Color groupCol=colorMap.get(bs);
+ if (groupCol==null)
+ {
+ return Color.white;
+ }
+ return groupCol;
+ }
+ @Override
+ public void setColorForGroup(BitSet bs,Color color)
+ {
+ colorMap.put(bs,color);
+ }
+ public static String contactToFloatString(ContactMatrixI cm)
{
- // TODO Auto-generated method stub
- return null;
+ 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;
}
}