public void paintItem(Graphics2D g, int x1, int y1, int x2, int y2) {
if (!canPaint()) {
return;
}
Iterator<ScoredRegion> regions = model.getResults();
while (regions.hasNext()) {
ScoredRegion r = regions.next();
int minx = getXPos(r.getStart(), getRegion().getStart(), getRegion().getEnd(), x1, x2);
int maxx = getXPos(r.getEnd(), getRegion().getStart(), getRegion().getEnd(), x1, x2);
float percent = (float) (1.0 - r.getScore() / maxScore);
g.setColor(new Color(percent, percent, percent, (float) 1.0));
g.fillRect(minx, y1, maxx - minx, (y2 - y1));
}
if (props.DrawTrackLabel) {
g.setColor(new Color((float) 0.0, (float) 0.0, (float) 0.0, (float) 0.5));
g.drawString(getLabel(), x1, y2);
}
}
public static void main(String args[]) throws Exception {
Genome genome = Args.parseGenome(args).cdr();
ChipChipDataset dataset = new ChipChipDataset(genome);
List<Region> regions = Args.parseRegionsOrDefault(args);
double means[] = new double[CGHCallExpander.numStates],
stddevs[] = new double[CGHCallExpander.numStates];
String[] pieces =
Args.parseString(
args,
"low",
String.format(
"%f;%f",
CGHCallExpander.defaultParams[0][0],
Math.sqrt(CGHCallExpander.defaultParams[0][1])))
.split(";");
means[CGHCallExpander.LOW] = Double.parseDouble(pieces[0]);
stddevs[CGHCallExpander.LOW] = Math.pow(Double.parseDouble(pieces[1]), 2);
pieces =
Args.parseString(
args,
"middle",
String.format(
"%f;%f",
CGHCallExpander.defaultParams[0][0],
Math.sqrt(CGHCallExpander.defaultParams[0][1])))
.split(";");
means[CGHCallExpander.ONE] = Double.parseDouble(pieces[0]);
stddevs[CGHCallExpander.ONE] = Math.pow(Double.parseDouble(pieces[1]), 2);
pieces =
Args.parseString(
args,
"high",
String.format(
"%f;%f",
CGHCallExpander.defaultParams[0][0],
Math.sqrt(CGHCallExpander.defaultParams[0][1])))
.split(";");
means[CGHCallExpander.HIGH] = Double.parseDouble(pieces[0]);
stddevs[CGHCallExpander.HIGH] = Math.pow(Double.parseDouble(pieces[1]), 2);
for (ExptNameVersion env : Args.parseENV(args)) {
ChipChipData ccd = dataset.getData(env);
CGHCallExpander cgh = new CGHCallExpander(ccd);
cgh.setStateParameters(
CGHCallExpander.LOW, means[CGHCallExpander.LOW], stddevs[CGHCallExpander.LOW]);
cgh.setStateParameters(
CGHCallExpander.ONE, means[CGHCallExpander.ONE], stddevs[CGHCallExpander.ONE]);
cgh.setStateParameters(
CGHCallExpander.HIGH, means[CGHCallExpander.HIGH], stddevs[CGHCallExpander.HIGH]);
cgh.resetHMM();
for (Region r : regions) {
List<ScoredRegion> calls = cgh.executeList(r);
for (ScoredRegion call : calls) {
System.out.println(call.getScore() + "\t" + call.regionString());
}
}
}
}