/**
* Compares two realisations
*
* @throws TopologyException
* @throws NewickIOException
* @params realisation
* @params Vertices-Realisation Points Map returns the populated map
*/
public static void verticesDistribution(
String real, LinkedHashMap<Integer, List<Double>> vrMap, RBTreeArcDiscretiser dtimes)
throws NewickIOException, TopologyException {
boolean flag = true;
Realisation r = UnparsedRealisation.parseRealisation(real);
RootedBifurcatingTree t = r.getTree();
int noofvertices = t.getNoOfVertices();
for (int i = 0; i < noofvertices; i++) {
if (vrMap.get(i) != null) {
List<Double> list = vrMap.get(i);
String meta = r.getPlacements().get(i);
int[] point = {0, 0};
point[0] = Integer.parseInt(meta.substring(meta.indexOf("(") + 1, meta.lastIndexOf(",")));
point[1] = Integer.parseInt(meta.substring(meta.indexOf(",") + 1, meta.lastIndexOf(")")));
Double time = dtimes.getDiscretisationTime(point[0], point[1]);
list.add(time);
vrMap.put(i, list);
} else {
List<Double> list = new ArrayList<Double>();
String meta = r.getPlacements().get(i);
int[] point = {0, 0};
point[0] = Integer.parseInt(meta.substring(meta.indexOf("(") + 1, meta.lastIndexOf(",")));
point[1] = Integer.parseInt(meta.substring(meta.indexOf(",") + 1, meta.lastIndexOf(")")));
Double time = dtimes.getDiscretisationTime(point[0], point[1]);
list.add(time);
vrMap.put(i, list);
}
}
}
/**
* Compares two realisations
*
* @throws TopologyException
* @throws NewickIOException
* @params realisation1
* @params realisation2 returns true if similar or false otherwise
*/
public static boolean compareRealisation(String real1, String real2)
throws NewickIOException, TopologyException {
boolean flag = true;
Realisation r1 = UnparsedRealisation.parseRealisation(real1);
Realisation r2 = UnparsedRealisation.parseRealisation(real2);
RootedBifurcatingTree t1 = r1.getTree();
RootedBifurcatingTree t2 = r2.getTree();
assert (t1
== t2); // Assumes the realisations have same gene tree otherwise comparing realisation
// makes no sense
int noofvertices = r1.getTree().getNoOfVertices();
for (int i = 0; i < noofvertices; i++) {
if (Integer.parseInt(
r1.getPlacements()
.get(i)
.substring(
r1.getPlacements().get(i).indexOf("(") + 1,
r1.getPlacements().get(i).indexOf(",")))
!= Integer.parseInt(
r2.getPlacements()
.get(i)
.substring(
r2.getPlacements().get(i).indexOf("(") + 1,
r2.getPlacements().get(i).indexOf(",")))
|| (Integer.parseInt(
r1.getPlacements()
.get(i)
.substring(
r1.getPlacements().get(i).indexOf(",") + 1,
r1.getPlacements().get(i).indexOf(")")))
!= Integer.parseInt(
r2.getPlacements()
.get(i)
.substring(
r2.getPlacements().get(i).indexOf(",") + 1,
r2.getPlacements().get(i).indexOf(")"))))) return false;
}
return flag;
}