se[1])
- se[1]=p;
+ // TODO: refactor to sequenceGroup for efficiency -
+ // getAlignmentRowInterval(AlignmentI al)
+ int[] se = null;
+ for (SequenceI sq : sg.getSequencesInOrder(al))
+ {
+ p = al.findIndex(sq);
+ if (lowest>p)
+ {
+ lowest=p;
+ }
+ if (highest se[1])
+ se[1] = p;
+ }
}
+ if (se != null)
+ {
+ gl.add(se);
+ }
+ }
+ }
+ // are there any more sequences ungrouped that should be added as a single
+ // remaining group ? - these might be at the start or the end
+ if (gl.size() > 0)
+ {
+ if (lowest-1>minsize)
+ {
+ gl.add(0, new int[]
+ { 0, lowest-2});
}
- if (se!=null)
+ if ((al.getHeight()-1-highest)>minsize)
{
- gl.add(se);
+ gl.add(new int[] { highest+1, al.getHeight()-1});
}
}
+ else
+ {
+ gl.add(new int[]
+ { 0, al.getHeight() - 1 });
+ }
+ if (min >= 0 && gl.size() < min)
+ {
+ throw new NoValidInputDataException(
+ "Not enough sequence groups for input. Need at least " + min
+ + " groups (including ungrouped regions).");
+ }
+ if (max > 0 && gl.size() > max)
+ {
+ throw new NoValidInputDataException(
+ "Too many sequence groups for input. Need at most " + max
+ + " groups (including ungrouped regions).");
+ }
int[][] vals = gl.toArray(new int[gl.size()][]);
int[] srt = new int[gl.size()];
- for (int i=0;i last)
{
- idvector.append(sep);
+ if (list)
+ {
+ idvector.append(sep);
+ }
+ idvector.append(range[1] - last);
+ last = range[1];
+ list = true;
}
- idvector.append(range[1]-range[0]+1);
- list=true;
}
return new StringBody(idvector.toString());
}
-
-}
\ No newline at end of file
+
+ /**
+ * set minimum number of sequences allowed in a partition. Default is 1
+ * sequence.
+ *
+ * @param i
+ * (number greater than 1)
+ */
+ public void setMinsize(int i)
+ {
+ if (minsize >= 1)
+ {
+ minsize = i;
+ }
+ else
+ {
+ minsize = 1;
+ }
+ }
+
+ @Override
+ public List getURLEncodedParameter()
+ {
+ ArrayList prms = new ArrayList();
+ super.addBaseParams(prms);
+ prms.add("minsize='" + minsize + "'");
+ prms.add("sep='" + sep + "'");
+ if (type != null)
+ {
+ prms.add("type='" + type + "'");
+ }
+ return prms;
+ }
+
+ @Override
+ public String getURLtokenPrefix()
+ {
+ return "PARTITION";
+ }
+
+ @Override
+ public boolean configureProperty(String tok, String val,
+ StringBuffer warnings)
+ {
+
+ if (tok.startsWith("sep"))
+ {
+ sep = val;
+ return true;
+ }
+ if (tok.startsWith("minsize"))
+ {
+ try
+ {
+ minsize = Integer.valueOf(val);
+ if (minsize >= 0)
+ return true;
+ } catch (Exception x)
+ {
+
+ }
+ warnings.append("Invalid minsize value '" + val
+ + "'. Must be a positive integer.\n");
+ }
+ if (tok.startsWith("type"))
+ {
+ try
+ {
+ type = molType.valueOf(val);
+ return true;
+ } catch (Exception x)
+ {
+ warnings.append("Invalid molecule type '" + val
+ + "'. Must be one of (");
+ for (molType v : molType.values())
+ {
+ warnings.append(" " + v);
+ }
+ warnings.append(")\n");
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public List getOptions()
+ {
+ List lst = getBaseOptions();
+ lst.add(new Option("sep",
+ "Separator character between elements of vector", true, ",",
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
+ lst.add(new IntegerParameter("minsize",
+ "Minimum size of partition allowed by service", true, 1,
+ minsize, 1, 0));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
+ molType.MIX));
+ return lst;
+ }
+
+}