private Pair<Region, Region> findProbePair(
String primerName, Map<String, Set<Region>> primerHits) {
String leftName = String.format("%s_left", primerName);
String rightName = String.format("%s_right", primerName);
if (!primerHits.containsKey(leftName) || !primerHits.containsKey(rightName)) {
return null;
}
if (primerHits.get(leftName).size() != 1 || primerHits.get(rightName).size() != 1) {
return null;
}
Iterator<Region> leftitr = primerHits.get(leftName).iterator();
Iterator<Region> rightitr = primerHits.get(rightName).iterator();
Region left = leftitr.next();
Region right = rightitr.next();
if (!left.getChrom().equals(right.getChrom())) {
return null;
}
return new Pair<Region, Region>(left, right);
}
public Iterator<SimpleDomain> execute(Region a) {
try {
LinkedList<SimpleDomain> doms = new LinkedList<SimpleDomain>();
data.window(a.getChrom(), a.getStart(), a.getEnd());
int np = data.getCount();
for (int pi = 0; pi < np - 1; pi++) {
int f = findNextDomainIndex(pi, a);
if (f != -1) {
SimpleDomain dom = buildDomain(pi, f, a);
doms.addLast(dom);
pi = f;
}
}
return doms.iterator();
} catch (NotFoundException e) {
e.printStackTrace();
return new EmptyIterator<SimpleDomain>();
}
}
public Collection<NamedRegion> parseProbes() throws IOException {
double ethreshold = 1.0e-3;
Parser<BlastTabEntry> parser =
new Parser<BlastTabEntry>(blasttab, new BlastTabEntry.ParsingMapper());
Iterator<BlastTabEntry> itr =
new FilterIterator<BlastTabEntry, BlastTabEntry>(
new BlastTabEntry.ExpectedScoreFilter(ethreshold), parser);
Map<String, Set<Region>> primerHits = new TreeMap<String, Set<Region>>();
Set<String> primerNames = new TreeSet<String>();
while (itr.hasNext()) {
BlastTabEntry entry = itr.next();
NamedRegion r = createNamedRegion(entry);
if (!primerHits.containsKey(entry.getQuery())) {
primerHits.put(entry.getQuery(), new HashSet<Region>());
}
primerHits.get(entry.getQuery()).add(r);
primerNames.add(removePrimerLR(entry.getQuery()));
}
LinkedList<NamedRegion> probes = new LinkedList<NamedRegion>();
for (String primerName : primerNames) {
Pair<Region, Region> hits = findProbePair(primerName, primerHits);
if (hits != null) {
Region left = hits.getFirst(), right = hits.getLast();
int start = Math.min(left.getStart(), right.getStart());
int end = Math.max(left.getEnd(), right.getEnd());
NamedRegion probe = new NamedRegion(genome, left.getChrom(), start, end, primerName);
probes.addLast(probe);
}
}
return probes;
}
private SimpleDomain buildDomain(int pi, int farthest, Region w) {
int left = getLeftBound(pi, w);
int right = getRightBound(farthest, w);
return new SimpleDomain(w.getGenome(), w.getChrom(), left, right);
}
public void paintItem(Graphics2D g, int x1, int y1, int x2, int y2) {
if (!model.isReady()) {
return;
}
Set<Genome> genomes = model.getGenomes();
if (genomes == null) {
g.drawString("No Genomes Yet", x1 + 40, y1 + 40);
return;
}
Genome currentGenome = model.getCurrentGenome();
if (currentGenome == null) {
g.drawString("Haven't moved", x1 + 40, y1 + 40);
return;
}
genomes.remove(currentGenome);
if (genomes.size() == 0) {
g.drawString("Single genome isn't very interesting", x1 + 40, y1 + 40);
return;
}
cs.reset();
int h = y2 - y1;
int midY = y1 + h / 2;
int rstart = getRegion().getStart();
int rend = getRegion().getEnd();
Stroke old = g.getStroke();
Stroke thin = new BasicStroke(1);
Stroke medium = new BasicStroke(3);
Stroke thick = new BasicStroke(6);
for (Genome genome : genomes) {
Region best = model.getBestRegion(genome);
if (best == null) {
continue;
}
String bestc = best.getChrom();
int ostart = best.getStart();
int oend = best.getEnd();
java.util.List<MultiZAlignRegion> alignedRegions = model.getAlignedRegions(genome);
for (MultiZAlignRegion align : alignedRegions) {
if (align.getOtherChrom().equals(bestc)) {
g.setColor(
cs.colorAt(
hashPosPair(
align.getStart(),
align.getEnd(),
align.getOtherStart(),
align.getOtherEnd(),
cs.colorCount())));
int rsx = getXPos(align.getStart(), rstart, rend, x1, x2);
int osx = getXPos(align.getOtherStart(), ostart, oend, x1, x2);
int rex = getXPos(align.getEnd(), rstart, rend, x1, x2);
int oex = getXPos(align.getOtherEnd(), ostart, oend, x1, x2);
g.setStroke(medium);
if (myGenome == currentGenome) {
g.drawLine(rsx, midY, rex, midY);
g.drawLine(rsx, y1, rsx, y2);
g.drawLine(rex, y1, rex, y2);
addLabel(rsx, y1, rex - rsx, y2, align.toString());
} else {
g.drawLine(osx, midY, oex, midY);
g.drawLine(osx, y1, osx, y2);
g.drawLine(oex, y1, oex, y2);
addLabel(osx, y1, oex - osx, y2, align.toString());
}
}
}
}
g.setStroke(old);
g.setColor(Color.BLACK);
g.drawString(model.getAlignment(), x1 + 5, y2);
}