public CachedProbe(AffyProbe ap, Vector<AffyExperiment> expts) {
probe = ap;
min = max = 0.0;
color = Color.lightGray;
stroke = new BasicStroke((float) 2.0);
values = new Vector<Double>();
for (AffyExperiment e : expts) {
AffyMeasurement am = e.getMeasurement(probe);
if (am != null) {
values.add(am.getValue());
min = Math.min(am.getValue(), min);
max = Math.max(am.getValue(), max);
} else {
values.add(null);
}
}
}
public void paintProbe(Graphics2D g2, int x1, int y1, int x2, int y2, double tmin, double tmax) {
g2.setStroke(stroke);
g2.setColor(color);
int ppx = -1, ppy = -1;
for (int i = 0; i < values.size(); i++) {
Double v = values.get(i);
if (v != null && tmax - tmin > 0.0) {
double frac = (v - tmin) / (tmax - tmin);
int pixY = y2 - (int) Math.round(frac * (y2 - y1));
int pixX = x1 + (int) Math.floor((double) (i + 1) / (double) (values.size() + 2));
if (ppx != -1) {
g2.drawLine(ppx, ppy, pixX, pixY);
}
ppx = pixX;
ppy = pixY;
} else {
ppx = ppy = -1;
}
}
}
public WeightMatrix getRepresentative(Cluster<WeightMatrix> cluster) {
Set<WeightMatrix> matrices = cluster.getElements();
WeightMatrix bestwm = null;
double bestdist = Double.MAX_VALUE;
for (WeightMatrix i : matrices) {
double sum = 0;
for (WeightMatrix j : matrices) {
sum += Math.pow(comp.compare(i, j), 2);
}
// System.err.println(" " + i + " : " + sum + " <? " + bestdist);
sum = sum / matrices.size();
if (sum < bestdist) {
bestwm = i;
bestdist = sum;
}
}
if (bestwm == null) {
System.err.println("OOPS!" + bestdist);
System.err.println(matrices.toString());
}
return bestwm;
}