+
+ @Override
+ public String getAnnotLabel()
+ {
+ return "Contact Matrix";
+ }
+
+ @Override
+ public String getAnnotDescr()
+ {
+ 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;
+ }