/**
* Main method.
*
* @param args the command-line arguments
*/
public static void main(String[] args) {
try {
System.out.println("FOP ExampleAWTViewer\n");
System.out.println("Preparing...");
// Setup directories
File baseDir = new File(".");
File outDir = new File(baseDir, "out");
outDir.mkdirs();
// Setup input and output files
File fofile = new File(baseDir, "xml/fo/helloworld.fo");
System.out.println("Input: XSL-FO (" + fofile + ")");
System.out.println("Output: AWT Viewer");
System.out.println();
System.out.println("Starting AWT Viewer...");
ExampleAWTViewer app = new ExampleAWTViewer();
app.viewFO(fofile);
System.out.println("Success!");
} catch (Exception e) {
System.err.println(ExceptionUtil.printStackTrace(e));
System.exit(-1);
}
}
@Override
public void run() {
float lowrt = peakA.ApexRT - parameter.ApexDelta;
float highrt = peakA.ApexRT + parameter.ApexDelta;
float lowmz = InstrumentParameter.GetMzByPPM(peakA.TargetMz, 1, parameter.MS1PPM);
float highmz =
InstrumentParameter.GetMzByPPM(
(peakA.TargetMz + ((float) this.MaxNoOfClusters / this.StartCharge)),
1,
-parameter.MS1PPM);
Object[] found = null;
try {
found = PeakCurveSearchTree.range(new double[] {lowrt, lowmz}, new double[] {highrt, highmz});
} catch (KeySizeException ex) {
Logger.getRootLogger().error(ExceptionUtil.printStackTrace(ex));
}
if (found == null || found.length == 0) {
return;
}
SortedCurveCollectionMZ PeakCurveListMZ = new SortedCurveCollectionMZ();
for (Object peakCurve : found) {
PeakCurveListMZ.add((PeakCurve) peakCurve);
}
float Arange = peakA.EndRT() - peakA.StartRT();
for (int charge = EndCharge; charge >= StartCharge; charge--) {
float mass = charge * (peakA.TargetMz - (float) ElementaryIon.proton.getTheoreticMass());
if (mass < parameter.MinPrecursorMass
|| mass > parameter.MaxPrecursorMass
|| (parameter.MassDefectFilter
&& !MD.InMassDefectRange(mass, parameter.MassDefectOffset))) {
continue;
}
PeakCluster peakCluster = new PeakCluster(MaxNoOfClusters, charge);
peakCluster.IsoPeaksCurves[0] = peakA;
peakCluster.MonoIsotopePeak = peakA;
XYData[] Ranges = new XYData[MaxNoOfClusters - 1];
for (int i = 0; i < MaxNoOfClusters - 1; i++) {
Entry range = IsotopePatternMap[i].ceilingEntry(peakCluster.NeutralMass());
if (range == null) {
range = IsotopePatternMap[i].lastEntry();
}
Ranges[i] = (XYData) range.getValue();
}
for (int pkidx = 1; pkidx < MaxNoOfClusters; pkidx++) {
float ppmthreshold = parameter.MS1PPM + (parameter.MS1PPM * pkidx * 0.5f);
float lowtheomz =
InstrumentParameter.GetMzByPPM(
peakA.TargetMz
+ (pkidx * ((float) ElementaryIon.proton.getTheoreticMass() / charge)),
charge,
ppmthreshold);
float uptheomz =
InstrumentParameter.GetMzByPPM(
peakA.TargetMz
+ (pkidx * ((float) ElementaryIon.proton.getTheoreticMass() / charge)),
charge,
-ppmthreshold);
int startmzidx = PeakCurveListMZ.BinarySearchLower(lowtheomz);
float theomz =
peakA.TargetMz + (pkidx * ((float) ElementaryIon.proton.getTheoreticMass() / charge));
float maxscore = 0f;
float maxcorr = 0f;
float maxoverlap = 0f;
PeakCurve closestPeak = null;
for (int mzidx = startmzidx; mzidx < PeakCurveListMZ.size(); mzidx++) {
PeakCurve peakB = PeakCurveListMZ.get(mzidx);
if (peakB.TargetMz <= peakA.TargetMz) {
continue;
}
if (peakB.TargetMz > uptheomz) {
break;
}
float Brange = peakB.EndRT() - peakB.StartRT();
float OverlapP = 0f;
if (peakA.StartRT() >= peakB.StartRT()
&& peakA.StartRT() <= peakB.EndRT()
&& peakA.EndRT() >= peakB.EndRT()) {
OverlapP = (peakB.EndRT() - peakA.StartRT()) / Brange;
} else if (peakA.EndRT() >= peakB.StartRT()
&& peakA.EndRT() <= peakB.EndRT()
&& peakA.StartRT() <= peakB.StartRT()) {
OverlapP = (peakA.EndRT() - peakB.StartRT()) / Brange;
} else if (peakA.StartRT() <= peakB.StartRT() && peakA.EndRT() >= peakB.EndRT()) {
OverlapP = 1;
} else if (peakA.StartRT() >= peakB.StartRT() && peakA.EndRT() <= peakB.EndRT()) {
OverlapP = Arange / Brange;
}
if (parameter.TargetIDOnly
|| (OverlapP > parameter.MiniOverlapP
&& (!parameter.CheckMonoIsotopicApex
|| (peakA.ApexRT >= peakB.StartRT()
&& peakA.ApexRT <= peakB.EndRT()
&& peakB.ApexRT >= peakA.StartRT()
&& peakB.ApexRT <= peakA.EndRT())))) {
float ppm = InstrumentParameter.CalcPPM(theomz, peakB.TargetMz);
if (ppm < ppmthreshold) {
float corr = 0f;
try {
corr = PeakCurveCorrCalc.CalPeakCorr(peakA, peakB, parameter.NoPeakPerMin);
} catch (IOException ex) {
Logger.getRootLogger().error(ExceptionUtil.printStackTrace(ex));
}
if (Float.isNaN(corr)) {
corr = 0f;
// System.out.print("Corr=NAN\n");
}
float PeakIntA = peakA.ApexInt;
float PeakIntB =
peakB.GetMaxIntensityByRegionRange(
Math.max(peakA.StartRT(), peakB.StartRT()),
Math.min(peakB.EndRT(), peakA.EndRT()));
if ((parameter.TargetIDOnly && corr > 0.2f) || corr > parameter.IsoCorrThreshold) {
// if (corr > parameter.IsoCorrThreshold || (PeakIntA > PeakIntB*1.5f &&
// PeakIntB>0.1f * PeakIntA && (peakA.EndScan-peakA.StartScan)>4 &&
// (peakB.EndScan-peakB.StartScan)>4)) {
float intscore = 0f;
float IntRatio = PeakIntB / PeakIntA;
if (IntRatio > Ranges[pkidx - 1].getY() && IntRatio <= Ranges[pkidx - 1].getX()) {
intscore = 1f;
} else {
if (Math.abs(IntRatio - Ranges[pkidx - 1].getY())
> Math.abs(IntRatio - Ranges[pkidx - 1].getX())) {
intscore = 1 - Math.abs(IntRatio - Ranges[pkidx - 1].getX());
} else {
intscore = 1 - Math.abs(IntRatio - Ranges[pkidx - 1].getY());
}
}
if (intscore < 0f) {
intscore = 0f;
}
float score = ((ppmthreshold - ppm) / ppmthreshold) + corr + intscore;
if (maxscore < score) {
maxscore = score;
closestPeak = peakB;
maxcorr = corr;
maxoverlap = OverlapP;
}
}
}
}
}
if (closestPeak != null) {
peakCluster.Corrs[pkidx - 1] = maxcorr;
peakCluster.IsoPeaksCurves[pkidx] = closestPeak;
peakCluster.OverlapRT[pkidx - 1] = maxoverlap;
peakCluster.GetSNR(pkidx - 1);
if (pkidx == 1) {
peakCluster.OverlapP = maxoverlap;
}
}
if (closestPeak == null) {
break;
}
}
if (peakCluster.IsotopeComplete(MinNoOfClusters)) {
peakCluster.CalcPeakArea_V2();
peakCluster.UpdateIsoMapProb(IsotopePatternMap);
peakCluster.AssignConfilictCorr();
peakCluster.LeftInt = peakA.GetSmoothedList().Data.get(0).getY();
peakCluster.RightInt =
peakA.GetSmoothedList().Data.get(peakA.GetSmoothedList().PointCount() - 1).getY();
if (parameter.TargetIDOnly || peakCluster.IsoMapProb > parameter.IsoPattern) {
ResultClusters.add(peakCluster);
if (!parameter.TargetIDOnly
|| (parameter.RemoveGroupedPeaks
&& peakCluster.Corrs[0] > parameter.RemoveGroupedPeaksCorr
&& peakCluster.OverlapP > parameter.RemoveGroupedPeaksRTOverlap)) {
for (int i = 1; i < peakCluster.IsoPeaksCurves.length; i++) {
PeakCurve peak = peakCluster.IsoPeaksCurves[i];
if (peak != null
&& peakCluster.Corrs[i - 1] > parameter.RemoveGroupedPeaksCorr
&& peakCluster.OverlapRT[i - 1] > parameter.RemoveGroupedPeaksRTOverlap) {
peak.ChargeGrouped.add(charge);
}
}
}
}
}
}
PeakCurveListMZ = null;
// System.out.print("....done\n");
}
