/**
* Resolve a sequence of ties, using the configured {@link TiesStrategy}. The input <code>ranks
* </code> array is expected to take the same value for all indices in <code>tiesTrace</code>. The
* common value is recoded according to the tiesStrategy. For example, if ranks =
* <5,8,2,6,2,7,1,2>, tiesTrace = <2,4,7> and tiesStrategy is MINIMUM, ranks will be unchanged.
* The same array and trace with tiesStrategy AVERAGE will come out <5,8,3,6,3,7,1,3>.
*
* @param ranks array of ranks
* @param tiesTrace list of indices where <code>ranks</code> is constant -- that is, for any i and
* j in TiesTrace, <code> ranks[i] == ranks[j]
* </code>
*/
private void resolveTie(double[] ranks, List<Integer> tiesTrace) {
// constant value of ranks over tiesTrace
final double c = ranks[tiesTrace.get(0)];
// length of sequence of tied ranks
final int length = tiesTrace.size();
switch (tiesStrategy) {
case AVERAGE: // Replace ranks with average
fill(ranks, tiesTrace, (2 * c + length - 1) / 2d);
break;
case MAXIMUM: // Replace ranks with maximum values
fill(ranks, tiesTrace, c + length - 1);
break;
case MINIMUM: // Replace ties with minimum
fill(ranks, tiesTrace, c);
break;
case RANDOM: // Fill with random integral values in [c, c + length - 1]
Iterator<Integer> iterator = tiesTrace.iterator();
long f = FastMath.round(c);
while (iterator.hasNext()) {
// No advertised exception because args are guaranteed valid
ranks[iterator.next()] = randomData.nextLong(f, f + length - 1);
}
break;
case SEQUENTIAL: // Fill sequentially from c to c + length - 1
// walk and fill
iterator = tiesTrace.iterator();
f = FastMath.round(c);
int i = 0;
while (iterator.hasNext()) {
ranks[iterator.next()] = f + i++;
}
break;
default: // this should not happen unless TiesStrategy enum is changed
throw new MathInternalError();
}
}
/**
* Create the objects needed for linear transformation.
*
* <p>Each {@link org.orekit.propagation.semianalytical.dsst.utilities.hansenHansenTesseralLinear
* HansenTesseralLinear} uses a fixed value for s and j. Since j varies from -maxJ to +maxJ and s
* varies from -maxDegree to +maxDegree, a 2 * maxDegree + 1 x 2 * maxJ + 1 matrix of objects
* should be created. The size of this matrix can be reduced by taking into account the expression
* (2.7.3-2). This means that is enough to create the objects for positive values of j and all
* values of s.
*
* @param meanOnly create only the objects required for the mean contribution
*/
private void createHansenObjects(final boolean meanOnly) {
// Allocate the two dimensional array
this.hansenObjects = new HansenTesseralLinear[2 * maxDegree + 1][jMax + 1];
if (meanOnly) {
// loop through the resonant orders
for (int m : resOrders) {
// Compute the corresponding j term
final int j = FastMath.max(1, (int) FastMath.round(ratio * m));
// Compute the sMin and sMax values
final int sMin = FastMath.min(maxEccPow - j, maxDegree);
final int sMax = FastMath.min(maxEccPow + j, maxDegree);
// loop through the s values
for (int s = 0; s <= sMax; s++) {
// Compute the n0 value
final int n0 = FastMath.max(FastMath.max(2, m), s);
// Create the object for the pair j,s
this.hansenObjects[s + maxDegree][j] =
new HansenTesseralLinear(maxDegree, s, j, n0, maxHansen);
if (s > 0 && s <= sMin) {
// Also create the object for the pair j, -s
this.hansenObjects[maxDegree - s][j] =
new HansenTesseralLinear(maxDegree, -s, j, n0, maxHansen);
}
}
}
} else {
// create all objects
for (int j = 0; j <= jMax; j++) {
for (int s = -maxDegree; s <= maxDegree; s++) {
// Compute the n0 value
final int n0 = FastMath.max(2, FastMath.abs(s));
this.hansenObjects[s + maxDegree][j] =
new HansenTesseralLinear(maxDegree, s, j, n0, maxHansen);
}
}
}
}
/**
* Get the resonant and non-resonant tesseral terms in the central body spherical harmonic field.
*
* @param resonantOnly extract only resonant terms
*/
private void getResonantAndNonResonantTerms(final boolean resonantOnly) {
// Compute natural resonant terms
final double tolerance =
1. / FastMath.max(MIN_PERIOD_IN_SAT_REV, MIN_PERIOD_IN_SECONDS / orbitPeriod);
// Search the resonant orders in the tesseral harmonic field
resOrders.clear();
nonResOrders.clear();
for (int m = 1; m <= maxOrder; m++) {
final double resonance = ratio * m;
int jRes = 0;
final int jComputedRes = (int) FastMath.round(resonance);
if (jComputedRes > 0
&& jComputedRes <= jMax
&& FastMath.abs(resonance - jComputedRes) <= tolerance) {
// Store each resonant index and order
resOrders.add(m);
jRes = jComputedRes;
}
if (!resonantOnly && !mDailiesOnly && m <= maxOrderTesseralSP) {
// compute non resonant orders in the tesseral harmonic field
final List<Integer> listJofM = new ArrayList<Integer>();
// for the moment we take only the pairs (j,m) with |j| <= maxDegree + maxEccPow (from |s-j|
// <= maxEccPow and |s| <= maxDegree)
for (int j = -jMax; j <= jMax; j++) {
if (j != 0 && j != jRes) {
listJofM.add(j);
}
}
nonResOrders.put(m, listJofM);
}
}
}
/**
* Computes the potential U derivatives.
*
* <p>The following elements are computed from expression 3.3 - (4).
*
* <pre>
* dU / da
* dU / dh
* dU / dk
* dU / dλ
* dU / dα
* dU / dβ
* dU / dγ
* </pre>
*
* @param date current date
* @return potential derivatives
* @throws OrekitException if an error occurs
*/
private double[] computeUDerivatives(final AbsoluteDate date) throws OrekitException {
// Potential derivatives
double dUda = 0.;
double dUdh = 0.;
double dUdk = 0.;
double dUdl = 0.;
double dUdAl = 0.;
double dUdBe = 0.;
double dUdGa = 0.;
// Compute only if there is at least one resonant tesseral
if (!resOrders.isEmpty()) {
// Gmsj and Hmsj polynomials
final GHmsjPolynomials ghMSJ = new GHmsjPolynomials(k, h, alpha, beta, I);
// GAMMAmns function
final GammaMnsFunction gammaMNS = new GammaMnsFunction(fact, gamma, I);
// R / a up to power degree
final double[] roaPow = new double[maxDegree + 1];
roaPow[0] = 1.;
for (int i = 1; i <= maxDegree; i++) {
roaPow[i] = roa * roaPow[i - 1];
}
// SUM over resonant terms {j,m}
for (int m : resOrders) {
// Resonant index for the current resonant order
final int j = FastMath.max(1, (int) FastMath.round(ratio * m));
// Phase angle
final double jlMmt = j * lm - m * theta;
final double sinPhi = FastMath.sin(jlMmt);
final double cosPhi = FastMath.cos(jlMmt);
// Potential derivatives components for a given resonant pair {j,m}
double dUdaCos = 0.;
double dUdaSin = 0.;
double dUdhCos = 0.;
double dUdhSin = 0.;
double dUdkCos = 0.;
double dUdkSin = 0.;
double dUdlCos = 0.;
double dUdlSin = 0.;
double dUdAlCos = 0.;
double dUdAlSin = 0.;
double dUdBeCos = 0.;
double dUdBeSin = 0.;
double dUdGaCos = 0.;
double dUdGaSin = 0.;
// s-SUM from -sMin to sMax
final int sMin = FastMath.min(maxEccPow - j, maxDegree);
final int sMax = FastMath.min(maxEccPow + j, maxDegree);
for (int s = 0; s <= sMax; s++) {
// Compute the initial values for Hansen coefficients using newComb operators
this.hansenObjects[s + maxDegree][j].computeInitValues(e2, chi, chi2);
// n-SUM for s positive
final double[][] nSumSpos =
computeNSum(date, j, m, s, maxDegree, roaPow, ghMSJ, gammaMNS);
dUdaCos += nSumSpos[0][0];
dUdaSin += nSumSpos[0][1];
dUdhCos += nSumSpos[1][0];
dUdhSin += nSumSpos[1][1];
dUdkCos += nSumSpos[2][0];
dUdkSin += nSumSpos[2][1];
dUdlCos += nSumSpos[3][0];
dUdlSin += nSumSpos[3][1];
dUdAlCos += nSumSpos[4][0];
dUdAlSin += nSumSpos[4][1];
dUdBeCos += nSumSpos[5][0];
dUdBeSin += nSumSpos[5][1];
dUdGaCos += nSumSpos[6][0];
dUdGaSin += nSumSpos[6][1];
// n-SUM for s negative
if (s > 0 && s <= sMin) {
// Compute the initial values for Hansen coefficients using newComb operators
this.hansenObjects[maxDegree - s][j].computeInitValues(e2, chi, chi2);
final double[][] nSumSneg =
computeNSum(date, j, m, -s, maxDegree, roaPow, ghMSJ, gammaMNS);
dUdaCos += nSumSneg[0][0];
dUdaSin += nSumSneg[0][1];
dUdhCos += nSumSneg[1][0];
dUdhSin += nSumSneg[1][1];
dUdkCos += nSumSneg[2][0];
dUdkSin += nSumSneg[2][1];
dUdlCos += nSumSneg[3][0];
dUdlSin += nSumSneg[3][1];
dUdAlCos += nSumSneg[4][0];
dUdAlSin += nSumSneg[4][1];
dUdBeCos += nSumSneg[5][0];
dUdBeSin += nSumSneg[5][1];
dUdGaCos += nSumSneg[6][0];
dUdGaSin += nSumSneg[6][1];
}
}
// Assembly of potential derivatives componants
dUda += cosPhi * dUdaCos + sinPhi * dUdaSin;
dUdh += cosPhi * dUdhCos + sinPhi * dUdhSin;
dUdk += cosPhi * dUdkCos + sinPhi * dUdkSin;
dUdl += cosPhi * dUdlCos + sinPhi * dUdlSin;
dUdAl += cosPhi * dUdAlCos + sinPhi * dUdAlSin;
dUdBe += cosPhi * dUdBeCos + sinPhi * dUdBeSin;
dUdGa += cosPhi * dUdGaCos + sinPhi * dUdGaSin;
}
dUda *= -moa / a;
dUdh *= moa;
dUdk *= moa;
dUdl *= moa;
dUdAl *= moa;
dUdBe *= moa;
dUdGa *= moa;
}
return new double[] {dUda, dUdh, dUdk, dUdl, dUdAl, dUdBe, dUdGa};
}
public void process(String mgfFile, PeakProcessorChain<PeakAnnotation> aChain, double scoreLimit)
throws IOException {
MgfReader reader = new MgfReader(new File(mgfFile));
String core = FilePathUtil.removeExtension(mgfFile);
PrintWriter log = new PrintWriter(core + "_log.csv");
log.println("Scan1,Mz1,Charge1,Scan2,Mz2,Charge2,DeltaCount,NewMz,PeakCount,FilterPeakCount");
MgfWriter writer = new MgfWriter(new File(core + "_pair.mgf"));
List<MsnSpectrum> specList = loadMgf(reader, aChain);
PeakListExtractor extractor = new PeakListExtractor(iMs2Tol);
HashMap<Integer, SpectrumSpectrumMatch> map = new HashMap<>();
double labelDelta = iHeavyMod.getMolecularMass() - iLightMod.getMolecularMass();
double maxDelta = labelDelta * iMaxModCount;
for (int lId = 0; lId < specList.size(); lId++) {
MsnSpectrum lSpec = specList.get(lId);
Peak lPeak = lSpec.getPrecursor();
for (int hId = lId + 1; hId < specList.size(); hId++) {
MsnSpectrum hSpec = specList.get(hId);
Peak hPeak = hSpec.getPrecursor();
double delta = hPeak.getMass() - lPeak.getMass();
if (iMs1Tol.check(maxDelta, delta).equals(Location.LARGER)) break;
if (iMs1Tol.check(labelDelta, delta).equals(Location.SMALLER)) continue;
if (iChargeTol.isPresent()) {
int deltaE = iChargeTol.get();
int lightE = lPeak.getCharge();
int heavyE = hPeak.getCharge();
if (Math.abs(lightE - heavyE) > deltaE) break;
}
if (iIntensityTol.isPresent()) {
double deltaIn = iIntensityTol.get();
double lightI = lPeak.getIntensity();
double heavyI = hPeak.getIntensity();
if (Math.abs(Math.log(lightI / heavyI)) > Math.log(deltaIn)) break;
}
if (iTimeTol.isPresent()) {
double lightT = lSpec.getRetentionTimes().getFirst().getTime();
double heavyT = hSpec.getRetentionTimes().getFirst().getTime();
int deltaTime = iTimeTol.get();
if (Math.abs(lightT - heavyT) > deltaTime) break;
}
for (int mCount = iMaxModCount; mCount > 0; mCount--) {
if (!iMs1Tol.withinTolerance(mCount * labelDelta, delta)) continue;
double lBaseIn = lSpec.getBasePeakIntensity();
double hBaseIn = hSpec.getBasePeakIntensity();
MsnSpectrum lFilterSpec = lSpec.copy(new ThresholdFilter<>(lBaseIn * 0.01));
MsnSpectrum hFilterSpec = hSpec.copy(new ThresholdFilter<>(hBaseIn * 0.01));
HashMap<Integer, Integer> filterMatch =
extractor.getMatchPeaks(lFilterSpec, hFilterSpec, labelDelta, mCount);
if (filterMatch.size() < scoreLimit) break;
HashMap<Integer, Integer> pairPeaksIndex =
extractor.getMatchPeaks(lSpec, hSpec, labelDelta, mCount);
MsnSpectrum peaks = new MsnSpectrum();
for (Entry<Integer, Integer> entry : pairPeaksIndex.entrySet()) {
double lightMz = lSpec.getMz(entry.getKey());
double heavyMz = hSpec.getMz(entry.getValue());
double intensity = lSpec.getIntensity(entry.getKey());
int count = (int) (FastMath.round((heavyMz - lightMz) / labelDelta));
if (count != 0) {
lightMz = lightMz - count * iLightMod.getMolecularMass();
}
peaks.add(lightMz, intensity);
}
double newMz = lPeak.getMz() - mCount * iLightMod.getMolecularMass() / lPeak.getCharge();
Peak rPeak = Peak.noIntensity(newMz, lPeak.getCharge());
peaks.setPrecursor(rPeak);
log.print(lSpec.getScanNumbers().getFirst().getValue() + ",");
log.print(lPeak.getMz() + ",");
log.print(lPeak.getCharge() + ",");
log.print(hSpec.getScanNumbers().getFirst().getValue() + ",");
log.print(hPeak.getMz() + ",");
log.print(hPeak.getCharge() + ",");
log.print(mCount + ",");
log.print(newMz + ",");
log.print(pairPeaksIndex.size() + ",");
log.print(filterMatch.size() + "\n");
SpectrumSpectrumMatch aMatch =
new SpectrumSpectrumMatch(lSpec.getComment(), hSpec.getComment());
aMatch.setFirstPrecursorPeak(lPeak);
aMatch.setSecondPrecursorPeak(hPeak);
aMatch.setFirstRetentionTime(lSpec.getRetentionTimes().getFirst());
aMatch.setSecondRetentionTime(hSpec.getRetentionTimes().getFirst());
aMatch.setFirstScanNumber(lSpec.getScanNumbers().getFirst());
aMatch.setSecondScanNumber(hSpec.getScanNumbers().getFirst());
aMatch.setCommonPeaks(peaks);
aMatch.setLabelDelta(mCount);
aMatch.setMatchCount(peaks.size());
if (map.containsKey(lId)) {
SpectrumSpectrumMatch spectrumSpectrumMatch = map.get(lId);
if (spectrumSpectrumMatch.getMatchCount() < peaks.size()) {
map.put(lId, aMatch);
}
} else {
map.put(lId, aMatch);
}
break;
}
}
}
for (SpectrumSpectrumMatch match : map.values()) {
MsnSpectrum spec = match.getCommonPeaks();
spec.setComment(String.valueOf(match.getLabelDelta().get()));
spec.addScanNumber(match.getFirstScanNumber());
spec.addScanNumber(match.getSecondScanNumber());
spec.addRetentionTime(match.getFirstRetentionTime());
spec.addRetentionTime(match.getSecondRetentionTime());
writer.write(spec);
}
writer.close();
log.close();
}