+ SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
+ + key, null, true, true, false, 0, width - 1);
+
+ groups[i++] = group;
+ }
+ gps.clear();
+ pgroup.clear();
+ return groups;
+ }
+
+ /**
+ * Divide the given sequences based on the equivalence of characters at
+ * selected columns If exgroups is provided, existing groups will be
+ * subdivided.
+ *
+ * @param sequences
+ * @param columnSelection
+ * @param list
+ * @return
+ */
+ public static SequenceGroup[] makeGroupsFromCols(SequenceI[] sequences,
+ ColumnSelection cs, List<SequenceGroup> list)
+ {
+ // TODO: determine how to get/recover input data for group generation
+ Map<String, List<SequenceI>> gps = new HashMap<String, List<SequenceI>>();
+ Map<String, SequenceGroup> pgroup = new HashMap<String, SequenceGroup>();
+ if (list != null)
+ {
+ for (SequenceGroup sg : list)
+ {
+ for (SequenceI sq : sg.getSequences(null))
+ {
+ pgroup.put(sq.toString(), sg);
+ }
+ }
+ }
+
+ /*
+ * get selected columns (in the order they were selected);
+ * note this could include right-to-left ranges
+ */
+ int[] spos = new int[cs.getSelected().size()];
+ int width = -1;
+ int i = 0;
+ for (Integer pos : cs.getSelected())
+ {
+ spos[i++] = pos.intValue();
+ }
+
+ for (i = 0; i < sequences.length; i++)
+ {
+ int slen = sequences[i].getLength();
+ if (width < slen)
+ {
+ width = slen;
+ }
+
+ SequenceGroup pgp = pgroup.get(((Object) sequences[i]).toString());
+ StringBuilder schar = new StringBuilder();
+ if (pgp != null)
+ {
+ schar.append(pgp.getName() + ":");
+ }
+ for (int p : spos)
+ {
+ if (p >= slen)
+ {
+ schar.append("~");
+ }
+ else
+ {
+ schar.append(sequences[i].getCharAt(p));
+ }
+ }
+ List<SequenceI> svec = gps.get(schar.toString());
+ if (svec == null)
+ {
+ svec = new ArrayList<SequenceI>();
+ gps.put(schar.toString(), svec);
+ }
+ svec.add(sequences[i]);
+ }
+ // make some groups
+ SequenceGroup[] groups = new SequenceGroup[gps.size()];
+ i = 0;
+ for (String key : gps.keySet())
+ {
+ SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
+ + key, null, true, true, false, 0, width - 1);