+ @Override
+ public float getMin()
+ {
+ return min;
+ }
+
+ @Override
+ public float getMax()
+ {
+ return max;
+ }
+
+ @Override
+ public boolean hasReferenceSeq()
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public SequenceI getReferenceSeq()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @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);
+ 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;
+ }