private void makeFullMap(ArrayList QTL, double[][] map) {
ArrayList chromosomes = new ArrayList();
for (int i = 0; i < map.length; i++) {
ArrayList chromosome = new ArrayList();
for (int j = 0; j < map[i].length; j++) {
chromosome.add(new Double(map[i][j]));
}
chromosomes.add(chromosome);
}
for (Iterator e = QTL.iterator(); e.hasNext(); ) {
AbstractLoci al = (AbstractLoci) e.next();
int chr = al.getChr()[0];
double loc = al.getLocation()[0];
ArrayList chromosome = (ArrayList) chromosomes.get(chr);
for (int j = 0; j < chromosome.size(); j++) {
double loc_map = ((Double) chromosome.get(j)).doubleValue();
if (loc < loc_map) {
chromosome.add(j, new Double(loc));
al.setLoci(j);
break;
}
}
}
distance = new double[chromosomes.size()][];
for (int i = 0; i < chromosomes.size(); i++) {
ArrayList chromosome = (ArrayList) chromosomes.get(i);
distance[i] = new double[chromosome.size()];
for (int j = 0; j < chromosome.size(); j++) {
distance[i][j] = ((Double) chromosome.get(j)).doubleValue();
}
}
}
private void setup(ArrayList QTL, double[][] map, Parameter1 p) {
int[][] pointIndex = new int[QTL.size()][3];
pointPowerF = new Hashtable();
pointPowerWald = new Hashtable();
pointPowerLOD = new Hashtable();
pointPowerAT = new Hashtable();
pointPowerDT = new Hashtable();
pointPowerAPvalue = new Hashtable();
pointPowerDPvalue = new Hashtable();
pointPowerEmpiricalAPvalue = new Hashtable();
pointPowerEmpiricalDPvalue = new Hashtable();
for (int i = 0; i < QTL.size(); i++) {
AbstractLoci al = (AbstractLoci) QTL.get(i);
pointIndex[i][0] = al.getChr()[0];
double location = al.getLocation()[0];
for (int j = 0; j < map[al.getChr()[0]].length - 1; j++) {
if (location < map[al.getChr()[0]][j + 1]) {
pointIndex[i][1] = j;
pointIndex[i][2] =
(new Double((location - map[al.getChr()[0]][j]) / p.step)).intValue() + 1;
break;
}
}
pointPowerF.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerWald.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerLOD.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerAT.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerDT.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerAPvalue.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerDPvalue.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerEmpiricalAPvalue.put(Utils.makeKey(pointIndex[i]), new Integer(0));
pointPowerEmpiricalDPvalue.put(Utils.makeKey(pointIndex[i]), new Integer(0));
}
}