private boolean spectrumHasPeaks(double mass, Edge[] edges, double direction) {
Envelope envelope = spectrum.getClosest(mass);
if (MassUtil.compare(envelope.getMass(), mass, MassUtil.ERROR_THRESHOLD * 4) != 0) {
return false;
}
for (Edge edge : edges) {
mass += edge.getMass() * direction;
envelope = spectrum.getClosest(mass);
if (MassUtil.compare(mass, envelope.getMass(), MassUtil.ERROR_THRESHOLD * 4) != 0) {
return false;
}
mass = envelope.getMass();
}
return true;
}
public Path getReversed() {
return new Path(
getReversedEdges(),
score,
MassUtil.convertIonsType(beginMass + getMass(), spectrum.parentMass),
spectrum,
!reversed);
}
public boolean isMonoTag() {
if (isMonoTag != null) {
return isMonoTag;
}
Edge[] edges = getEdges();
Edge[] reversedEdges = getReversedEdges();
isMonoTag =
spectrumHasPeaks(beginMass, edges, 1.)
|| spectrumHasPeaks(
MassUtil.convertIonsType(beginMass + getMass(), spectrum.parentMass), edges, -1.);
isMonoTag |=
spectrumHasPeaks(beginMass, reversedEdges, 1.)
|| spectrumHasPeaks(
MassUtil.convertIonsType(beginMass + getMass(), spectrum.parentMass),
reversedEdges,
-1.);
return isMonoTag;
}
private boolean checkDirection(Spectrum spectrum, double mass, Edge[] edges, double direction) {
for (Edge edge : edges) {
double needMass = mass + edge.getMass() * direction;
Envelope nextEnvelope = spectrum.getClosest(needMass);
if (MassUtil.compare(needMass, nextEnvelope.getMass(), 40e-6 * needMass) != 0) {
return false;
}
mass = nextEnvelope.getMass();
}
return true;
}