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MSpectrum.cpp
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/*
Copyright 2018, Michael R. Hoopmann, Institute for Systems Biology
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
#include "MSpectrum.h"
#include <iostream>
using namespace std;
/*============================
Constructors & Destructors
============================*/
//MSpectrum::MSpectrum(const int& i, const double& bs, const double& os, const int& th){
// binOffset=os;
// binSize=bs;
// instrumentPrecursor=false;
// invBinSize=1.0/binSize;
// charge = 0;
// maxIntensity=0;
// mz = 0;
// precursor = new vector<mPrecursor>;
// singlets = new vector<MTopPeps>;
// spec = new vector<mSpecPoint>;
// scanNumber = 0;
// rTime = 0;
// xCorrArraySize=0;
// xCorrSparseArraySize=0;
// xCorrSparseArray=NULL;
// bigMonoMass=0;
// bigZ=0;
//
// singletCount=0;
// singletFirst=NULL;
// singletLast=NULL;
// singletMax=i;
//
// kojakSparseArray=NULL;
// kojakBins=0;
//
// //singletList=NULL;
// //singletBins=0;
//
// lowScore=0;
//
// hpSize=th;
// hp=new sHistoPep[hpSize];
// for(int j=0;j<hpSize;j++){
// hp[j].pepIndex=-1;
// hp[j].topScore=0;
// }
// for(int j=0;j<HISTOSZ;j++) histogram[j]=0;
// histogramCount=0;
// histoMaxIndex=0;
//
// //** temporary
// //for(int a=0;a<60;a++){
// // for (int j = 0; j<HISTOSZ; j++) hX[a][j] = 0;
// // hXCount[a] = 0;
// //}
// //**
//
// cc=0;
// sc=0;
//
// peakCounts=0;
//}
MSpectrum::MSpectrum(mParams& p){
//params->topCount, params->binSize, params->binOffset, params->threads
binOffset = p.binOffset;
binSize = p.binSize;
instrumentPrecursor = false;
invBinSize = 1.0 / binSize;
charge = 0;
maxIntensity = 0;
mz = 0;
precursor = new vector<mPrecursor>;
singlets = new vector<MTopPeps>;
spec = new vector<mSpecPoint>;
scanNumber = 0;
rTime = 0;
xCorrArraySize = 0;
xCorrSparseArraySize = 0;
xCorrSparseArray = NULL;
bigMonoMass=0;
bigZ=0;
singletCount = 0;
singletFirst = NULL;
singletLast = NULL;
singletMax = p.topCount;
kojakSparseArray = NULL;
kojakBins = 0;
lowScore = 0;
maxHistogramCount=3000;
minAdductMass=p.minAdductMass;
maxPepLen=p.maxPepLen;
mHisto=new MHistogram*[maxPepLen+1];
for(int j=0;j<p.maxPepLen+1;j++)mHisto[j]=NULL;
for(int j=0;j<6;j++) ionSeries[j]=p.ionSeries[j];
hpSize = p.threads;
hp = new sHistoPep[hpSize];
for (int j = 0; j<hpSize; j++){
hp[j].pepIndex = -1;
hp[j].topScore = 0;
}
for (int j = 0; j<HISTOSZ; j++) histogram[j] = 0;
histogramCount = 0;
histoMaxIndex = 0;
//** temporary
//for (int a = 0; a<60; a++){
// for (int j = 0; j<HISTOSZ; j++) hX[a][j] = 0;
// hXCount[a] = 0;
//}
//**
cc = 0;
sc = 0;
peakCounts=0;
maxX = (int)((p.maxPepMass + p.maxAdductMass + 100.0) / p.binSize);
}
MSpectrum::MSpectrum(const MSpectrum& p){
unsigned int i;
int j;
spec = new vector<mSpecPoint>(*p.spec);
for(i=0;i<20;i++) topHit[i]=p.topHit[i];
precursor = new vector<mPrecursor>(*p.precursor);
singlets = new vector<MTopPeps>(*p.singlets);
binOffset = p.binOffset;
binSize = p.binSize;
instrumentPrecursor = p.instrumentPrecursor;
invBinSize = p.invBinSize;
charge= p.charge;
maxIntensity = p.maxIntensity;
mz = p.mz;
scanNumber = p.scanNumber;
rTime = p.rTime;
xCorrArraySize = p.xCorrArraySize;
xCorrSparseArraySize = p.xCorrSparseArraySize;
lowScore=p.lowScore;
for(i = 0; i<HISTOSZ; i++) histogram[i] = p.histogram[i];
histogramCount = p.histogramCount;
histoMaxIndex = p.histoMaxIndex;
bigMonoMass=p.bigMonoMass;
bigZ=p.bigZ;
decoys=p.decoys;
maxHistogramCount = p.maxHistogramCount;
minAdductMass = p.minAdductMass;
maxPepLen = p.maxPepLen;
mHisto = new MHistogram*[maxPepLen+1];
for (int j = 0; j<p.maxPepLen+1; j++)mHisto[j] = NULL;
for (int j = 0; j<6; j++) ionSeries[j] = p.ionSeries[j];
cc=p.cc;
sc=p.sc;
peakCounts=p.peakCounts;
hpSize=p.hpSize;
hp=new sHistoPep[hpSize];
for(j=0;j<hpSize;j++)hp[j]=p.hp[j];
singletCount=p.singletCount;
singletMax=p.singletMax;
singletFirst=NULL;
singletLast=NULL;
mScoreCard* sc=NULL;
mScoreCard* tmp=p.singletFirst;
if(tmp!=NULL) {
singletFirst=new mScoreCard(*tmp);
sc=singletFirst;
tmp=tmp->next;
while(tmp!=NULL){
sc->next=new mScoreCard(*tmp);
sc->next->prev=sc;
sc=sc->next;
tmp=tmp->next;
}
singletLast=sc;
}
if(p.xCorrSparseArray==NULL){
xCorrSparseArray=NULL;
} else {
xCorrSparseArray = (mSparseMatrix *)calloc((size_t)xCorrSparseArraySize, (size_t)sizeof(mSparseMatrix));
for(j=0;j<xCorrSparseArraySize;j++) xCorrSparseArray[j]=p.xCorrSparseArray[j];
}
kojakBins=p.kojakBins;
if(p.kojakSparseArray==NULL){
kojakSparseArray=NULL;
} else {
for(j=0;j<kojakBins;j++){
if(p.kojakSparseArray[j]==NULL){
kojakSparseArray[j]=NULL;
} else {
kojakSparseArray[j] = new char[(int)invBinSize+1];
for(i=0;i<(unsigned int)invBinSize+1;i++) kojakSparseArray[j][i]=p.kojakSparseArray[j][i];
}
}
}
//** temporary
//for (int a = 0; a<60; a++){
// for (int j = 0; j<HISTOSZ; j++) hX[a][j] = p.hX[a][j];
// hXCount[a] = p.hXCount[a];
//}
//**
maxX=p.maxX;
}
MSpectrum::~MSpectrum(){
delete spec;
delete precursor;
delete singlets;
if(xCorrSparseArray!=NULL) free(xCorrSparseArray);
while(singletFirst!=NULL){
mScoreCard* tmp=singletFirst;
singletFirst=singletFirst->next;
delete tmp;
}
singletLast=NULL;
int j;
if(kojakSparseArray!=NULL){
for(j=0;j<kojakBins;j++){
if(kojakSparseArray[j]!=NULL) delete [] kojakSparseArray[j];
}
delete [] kojakSparseArray;
}
delete [] hp;
for (j = 0; j<maxPepLen+1; j++){
if (mHisto[j] != NULL) delete mHisto[j];
}
delete[] mHisto;
decoys=NULL;
}
/*============================
Operators
============================*/
MSpectrum& MSpectrum::operator=(const MSpectrum& p){
if(this!=&p){
delete spec;
spec = new vector<mSpecPoint>(*p.spec);
for(int i=0;i<20;i++) topHit[i]=p.topHit[i];
delete precursor;
precursor = new vector<mPrecursor>(*p.precursor);
delete singlets;
singlets = new vector<MTopPeps>(*p.singlets);
binOffset = p.binOffset;
binSize = p.binSize;
instrumentPrecursor = p.instrumentPrecursor;
invBinSize = p.invBinSize;
charge = p.charge;
maxIntensity = p.maxIntensity;
mz = p.mz;
scanNumber = p.scanNumber;
rTime = p.rTime;
xCorrArraySize = p.xCorrArraySize;
xCorrSparseArraySize = p.xCorrSparseArraySize;
lowScore = p.lowScore;
bigMonoMass = p.bigMonoMass;
bigZ=p.bigZ;
for (int i = 0; i<HISTOSZ; i++) histogram[i] = p.histogram[i];
histogramCount = p.histogramCount;
histoMaxIndex = p.histoMaxIndex;
for(int i=0;i<maxPepLen+1;i++){
if(mHisto[i]!=NULL) delete mHisto[i];
}
delete [] mHisto;
decoys = p.decoys;
maxHistogramCount = p.maxHistogramCount;
minAdductMass = p.minAdductMass;
maxPepLen = p.maxPepLen;
mHisto = new MHistogram*[maxPepLen+1];
for (int j = 0; j<p.maxPepLen+1; j++)mHisto[j] = NULL;
for (int j = 0; j<6; j++) ionSeries[j] = p.ionSeries[j];
cc = p.cc;
sc = p.sc;
peakCounts=p.peakCounts;
maxX=p.maxX;
delete [] hp;
hpSize = p.hpSize;
hp = new sHistoPep[hpSize];
for (int j = 0; j<hpSize; j++)hp[j] = p.hp[j];
singletCount=p.singletCount;
singletMax=p.singletMax;
singletFirst=NULL;
singletLast=NULL;
mScoreCard* sc=NULL;
mScoreCard* tmp=p.singletFirst;
if(tmp!=NULL) {
singletFirst=new mScoreCard(*tmp);
sc=singletFirst;
tmp=tmp->next;
while(tmp!=NULL){
sc->next=new mScoreCard(*tmp);
sc->next->prev=sc;
sc=sc->next;
tmp=tmp->next;
}
singletLast=sc;
}
if(xCorrSparseArray!=NULL) free(xCorrSparseArray);
if(p.xCorrSparseArray==NULL){
xCorrSparseArray=NULL;
} else {
xCorrSparseArray = (mSparseMatrix *)calloc((size_t)xCorrSparseArraySize, (size_t)sizeof(mSparseMatrix));
for(int j=0;j<xCorrSparseArraySize;j++) xCorrSparseArray[j]=p.xCorrSparseArray[j];
}
if(kojakSparseArray!=NULL){
for(int j=0;j<kojakBins;j++){
if(kojakSparseArray[j]!=NULL) delete [] kojakSparseArray[j];
}
delete [] kojakSparseArray;
}
kojakBins=p.kojakBins;
if(p.kojakSparseArray==NULL){
kojakSparseArray=NULL;
} else {
for(int j=0;j<kojakBins;j++){
if(p.kojakSparseArray[j]==NULL){
kojakSparseArray[j]=NULL;
} else {
kojakSparseArray[j] = new char[(int)invBinSize+1];
for(int i=0;i<(int)invBinSize+1;i++) kojakSparseArray[j][i]=p.kojakSparseArray[j][i];
}
}
}
}
return *this;
}
mSpecPoint& MSpectrum::operator [](const int &i){
return spec->at(i);
}
/*============================
Accessors
============================*/
double MSpectrum::getBinOffset(){
return binOffset;
}
int MSpectrum::getCharge(){
return charge;
}
bool MSpectrum::getInstrumentPrecursor(){
return instrumentPrecursor;
}
double MSpectrum::getInvBinSize(){
return invBinSize;
}
float MSpectrum::getMaxIntensity(){
return maxIntensity;
}
double MSpectrum::getMZ(){
return mz;
}
mPrecursor& MSpectrum::getPrecursor(int i){
return precursor->at(i);
}
mPrecursor* MSpectrum::getPrecursor2(int i){
return &precursor->at(i);
}
float MSpectrum::getRTime(){
return rTime;
}
int MSpectrum::getScanNumber(){
return scanNumber;
}
mScoreCard& MSpectrum::getScoreCard(int i){
return topHit[i];
}
int MSpectrum::getSingletCount(){
return singletCount;
}
mScoreCard& MSpectrum::getSingletScoreCard(int i){
if(i>=singletCount) return *singletLast;
mScoreCard* sc=singletFirst;
int j=0;
while(j<i){
if(sc->next==NULL) break;
sc=sc->next;
j++;
}
return *sc;
}
MTopPeps* MSpectrum::getTopPeps(int i){
return &singlets->at(i);
}
int MSpectrum::size(){
return (int)spec->size();
}
int MSpectrum::sizePrecursor(){
return (int)precursor->size();
}
/*============================
Modifiers
============================*/
void MSpectrum::addPoint(mSpecPoint& s){
spec->push_back(s);
}
void MSpectrum::addPrecursor(mPrecursor& p, int sz){
precursor->push_back(p);
MTopPeps tp;
tp.peptideMax=sz;
//tp.resetSingletList(p.monoMass);
singlets->push_back(tp);
if(p.monoMass>bigMonoMass) {
bigMonoMass=p.monoMass;
bigZ=p.charge;
}
}
void MSpectrum::clear(){
spec->clear();
precursor->clear();
singlets->clear();
bigMonoMass=0;
bigZ=0;
}
void MSpectrum::clearPrecursors(){
precursor->clear();
singlets->clear();
}
void MSpectrum::erasePrecursor(int i){
precursor->erase(precursor->begin()+i);
singlets->erase(singlets->begin()+i);
}
void MSpectrum::setCharge(int i){
charge=i;
}
void MSpectrum::setInstrumentPrecursor(bool b){
instrumentPrecursor=b;
}
void MSpectrum::setMaxIntensity(float f){
maxIntensity=f;
}
void MSpectrum::setMZ(double d){
mz=d;
}
void MSpectrum::setNativeID(string s){
nativeID = s;
}
void MSpectrum::setRTime(float f){
rTime=f;
}
void MSpectrum::setScanNumber(int i){
scanNumber=i;
}
/*============================
Functions
============================*/
bool MSpectrum::checkReporterIon(double mz, mParams* params){
int key = (int)mz;
if (key >= kojakBins) return false;
if (kojakSparseArray[key] == NULL) return false;
int pos = (int)((mz - key)*invBinSize);
if(kojakSparseArray[key][pos]>params->rIonThreshold) return true;
return false;
}
void MSpectrum::checkScore(mScoreCard& s, int th){
unsigned int i;
unsigned int j;
//edge case for "reversible" cross-links: check if already matches top hit identically
//note that such duplications still occur below the top score, but shouldn't influence the final result to the user
int k=0;
while(k<20 && s.eVal==topHit[k].eVal){
if(s.pep==topHit[k].pep && s.site==topHit[k].site){
if(s.mods->size()==topHit[k].mods->size()){
for(i=0;i<s.mods->size();i++){
if(s.mods->at(i).mass!=topHit[k].mods->at(i).mass || s.mods->at(i).pos!=topHit[k].mods->at(i).pos) break;
}
if(i==s.mods->size()) return;
}
}
k++;
}
for(i=0;i<20;i++){
if(s.eVal < topHit[i].eVal) {
for(j=19;j>i;j--) {
topHit[j]=topHit[j-1];
}
topHit[i] = s;
lowScore=topHit[19].eVal;
return;
}
}
}
//void MSpectrum::checkSingletScore(mScoreCard& s){
//
// mScoreCard* sc;
// mScoreCard* cur;
//
// //If list is empty, add the score card
// if(singletCount==0){
// singletFirst=new mScoreCard(s);
// singletLast=singletFirst;
// singletCount++;
// return;
// }
//
// //check if we can just add to the end
// if(s.simpleScore<singletLast->simpleScore){
// //check if we need to store the singlet
// if(singletCount==singletMax) return;
//
// singletLast->next=new mScoreCard(s);
// singletLast->next->prev=singletLast;
// singletLast=singletLast->next;
// singletCount++;
// return;
// }
//
// //check if it goes in the front
// if(s.simpleScore>=singletFirst->simpleScore){
//
// singletFirst->prev=new mScoreCard(s);
// singletFirst->prev->next=singletFirst;
// singletFirst=singletFirst->prev;
//
// //add to singlet list
// if(singletCount<singletMax) {
// singletCount++;
// } else {
// cur=singletLast;
// singletLast=singletLast->prev;
// singletLast->next=NULL;
// delete cur;
// }
// return;
// }
//
//
// //scan to find insertion point
// cur = singletFirst->next;
// int i=1;
// while(s.simpleScore < cur->simpleScore){
// i++;
// cur=cur->next;
// }
//
// sc=new mScoreCard(s);
// sc->prev=cur->prev;
// sc->next=cur;
// cur->prev->next=sc;
// cur->prev=sc;
// if(sc->prev==NULL) singletFirst=sc;
//
// if(singletCount<singletMax) {
// singletCount++;
// } else {
// cur=singletLast;
// singletLast=singletLast->prev;
// singletLast->next=NULL;
// delete cur;
// }
//
//}
double MSpectrum::computeE(double score, int len){
//if we haven't computed a histogram yet, do it now
if(mHisto[len]==NULL){
//cout << "Compute Histo: " << scanNumber << "\t" << len << endl;
//Clear histogram
for (int j = 0; j<HISTOSZ; j++) histogram[j] = 0;
histogramCount = 0;
if (!generateXcorrDecoys2(len)) {
//handle failure
cout << "Fail genXCorr2: " << scanNumber << "\t" << len << endl;
exit(1);
}
mHisto[len]=new MHistogram();
linearRegression3(mHisto[len]->slope, mHisto[len]->intercept, mHisto[len]->rSq);
//cout << "linReg3 success" << endl;
mHisto[len]->slope*=10;
//** temporary
//cout << "\nDecoy Histogram: " << len << "\t" << histogramCount << endl;
//for(int i=0;i<HISTOSZ;i++) cout << i << "\t" << histogram[i] << endl;
//cout << mHisto[len]->slope << "\t" << mHisto[len]->intercept << "\t" << mHisto[len]->rSq << endl;
//**
}
if (mHisto[len]->slope>=0){
//handle bad slopes
//cout << "Fail regression: " << scanNumber << "\t" << len << endl;
//cout << histogramCount << endl;
//for (int j = 0; j<HISTOSZ; j++) cout << j << "\t" << histogram[j] << endl;
//cout << score << "\t" << len << "\tslope=" << mHisto[len]->slope << endl;
return 1000;
//exit(1);
}
//cout << "Compute E: " << scanNumber << "\t" << len << endl;
return pow(10.0, mHisto[len]->slope * score + mHisto[len]->intercept);
}
void MSpectrum::resetSingletList(){
/*
size_t j;
double max;
if (singletList != NULL){
for (j = 0; j<singletBins; j++){
if (singletList[j] != NULL) delete singletList[j];
}
delete[] singletList;
}
max=precursor->at(0).monoMass;
for(j=1;j<precursor->size();j++){
if (precursor->at(j).monoMass>max) max = precursor->at(j).monoMass;
}
singletBins=(int)(max/10+1);
singletList = new list<mSingletScoreCard*>*[singletBins];
for (j = 0; j<singletBins; j++) singletList[j] = NULL;
*/
}
void MSpectrum::sortMZ(){
qsort(&spec->at(0),spec->size(),sizeof(mSpecPoint),compareMZ);
}
//void MSpectrum::xCorrScore(){
// kojakXCorr();
//}
/*============================
Private Functions
============================*/
void MSpectrum::kojakXCorr(double* pdTempRawData, double* pdTmpFastXcorrData, float* pfFastXcorrData, mPreprocessStruct*& pPre){
int i;
int j;
int iTmp;
double dTmp;
double dSum;
pPre->iHighestIon = 0;
pPre->dHighestIntensity = 0;
BinIons(pPre);
memset(pdTempRawData, 0, xCorrArraySize*sizeof(double));
memset(pdTmpFastXcorrData, 0, xCorrArraySize*sizeof(double));
memset(pfFastXcorrData, 0, xCorrArraySize*sizeof(float));
kojakSparseArray = new char*[kojakBins];
for (i = 0; i<kojakBins; i++) kojakSparseArray[i] = NULL;
// Create data for correlation analysis.
MakeCorrData(pdTempRawData, pPre, 50.0);
// Make fast xcorr spectrum.
mSpecPoint *pdCorrelationData = pPre->pdCorrelationData;
dSum = 0.0;
for (i = 0; i<75; i++) dSum += pdCorrelationData[i].intensity;
for (i = 75; i < xCorrArraySize + 75; i++) {
if (i<xCorrArraySize && pdCorrelationData[i].intensity>0) dSum += pdCorrelationData[i].intensity;
if (i >= 151 && pdCorrelationData[i - 151].intensity>0) dSum -= pdCorrelationData[i - 151].intensity;
pdTmpFastXcorrData[i - 75] = (dSum - pdCorrelationData[i - 75].intensity)* 0.0066666667;
}
xCorrSparseArraySize = 1;
double dTmp0 = pdCorrelationData[0].intensity - pdTmpFastXcorrData[0];
double dTmp1 = pdCorrelationData[1].intensity - pdTmpFastXcorrData[1];
double dTmp2 = pdCorrelationData[2].intensity - pdTmpFastXcorrData[2];
pfFastXcorrData[0] = (float)(dTmp0 + dTmp1*0.5);
pfFastXcorrData[1] = (float)(dTmp1 + (dTmp0 + dTmp2)*0.5);
for (i = 2; i<xCorrArraySize - 1; i++){
dTmp0 = dTmp1;
dTmp1 = dTmp2;
dTmp2 = pdCorrelationData[i + 1].intensity - pdTmpFastXcorrData[i + 1];
pfFastXcorrData[i] = (float)(dTmp1 + (dTmp0 + dTmp2)*0.5);
}
pfFastXcorrData[xCorrArraySize - 1] = (float)(dTmp2 + dTmp1*0.5);
//MH: Fill sparse matrix
for (i = 0; i<xCorrArraySize; i++){
if (pfFastXcorrData[i]>0.5 || pfFastXcorrData[i]<-0.5){
dTmp = binSize*i;
iTmp = (int)dTmp;
if (kojakSparseArray[iTmp] == NULL) {
kojakSparseArray[iTmp] = new char[(int)invBinSize + 1];
for (j = 0; j<(int)invBinSize + 1; j++) kojakSparseArray[iTmp][j] = 0;
}
j = (int)((dTmp - iTmp)*invBinSize/*+0.5*/);
if (pfFastXcorrData[i]>127) kojakSparseArray[iTmp][j] = 127;
else if (pfFastXcorrData[i]<-128) kojakSparseArray[iTmp][j] = -128;
else if (pfFastXcorrData[i]>0) kojakSparseArray[iTmp][j] = (char)(pfFastXcorrData[i] + 0.5);
else kojakSparseArray[iTmp][j] = (char)(pfFastXcorrData[i] - 0.5);
}
}
}
void MSpectrum::BinIons(mPreprocessStruct *pPre) {
int i;
unsigned int j;
double dPrecursor;
double dIon;
double dIntensity;
mSpecPoint *pdCorrelationData = pPre->pdCorrelationData;
// Just need to pad iArraySize by 75.
dPrecursor=0;
for(j=0;j<precursor->size();j++){
if(precursor->at(j).monoMass>dPrecursor) dPrecursor=precursor->at(j).monoMass;
}
xCorrArraySize = (int)((dPrecursor + 100.0) / binSize);
if(xCorrArraySize>pPre->iMaxXCorrArraySize) xCorrArraySize=pPre->iMaxXCorrArraySize;
kojakBins = (int)(spec->at(spec->size()-1).mass+100.0);
memset(pdCorrelationData, 0, xCorrArraySize*sizeof(mSpecPoint));
i = 0;
while(true) {
if (i >= (int)spec->size()) break;
dIon = spec->at(i).mass;
dIntensity = spec->at(i).intensity;
i++;
if (dIntensity > 0.0) {
if (dIon < (dPrecursor + 50.0)) {
//#define BIN(dMass) (int)(dMass*invBinSize + binOffset)
int iBinIon = (int)(dIon*invBinSize+binOffset);
dIntensity = sqrt(dIntensity);
if (iBinIon > pPre->iHighestIon) pPre->iHighestIon = iBinIon;
if ((iBinIon < xCorrArraySize) && (dIntensity > pPre->pdCorrelationData[iBinIon].intensity)) {
if (dIntensity > pPre->pdCorrelationData[iBinIon].intensity) {
pPre->pdCorrelationData[iBinIon].intensity = (float)dIntensity;
pPre->pdCorrelationData[iBinIon].mass = dIon;
}
if (pPre->pdCorrelationData[iBinIon].intensity > pPre->dHighestIntensity) pPre->dHighestIntensity = pPre->pdCorrelationData[iBinIon].intensity;
}
}
}
}
//Clear spectrum data that we no longer need
spec->clear();
}
// pdTempRawData now holds raw data, pdCorrelationData is windowed data.
void MSpectrum::MakeCorrData(double *pdTempRawData, mPreprocessStruct *pPre, double scale){
int i;
int ii;
int iBin;
int iWindowSize;
int iNumWindows=10;
double dMaxWindowInten;
double dMaxOverallInten;
double dTmp1;
double dTmp2;
dMaxOverallInten = 0.0;
// Normalize maximum intensity to 100.
dTmp1 = 1.0;
if (pPre->dHighestIntensity > 0.000001) dTmp1 = 100.0 / pPre->dHighestIntensity;
for (i=0; i < xCorrArraySize; i++) {
pdTempRawData[i] = pPre->pdCorrelationData[i].intensity*dTmp1;
pPre->pdCorrelationData[i].intensity=0.0;
if (dMaxOverallInten < pdTempRawData[i]) dMaxOverallInten = pdTempRawData[i];
}
iWindowSize = (int) ceil( (double)(pPre->iHighestIon)/iNumWindows);
for (i=0; i<iNumWindows; i++){
dMaxWindowInten = 0.0;
for (ii=0; ii<iWindowSize; ii++) { // Find max inten. in window.
iBin = i*iWindowSize+ii;
if (iBin < xCorrArraySize) {
if (pdTempRawData[iBin] > dMaxWindowInten)dMaxWindowInten = pdTempRawData[iBin];
}
}
if (dMaxWindowInten > 0.0) {
dTmp1 = scale / dMaxWindowInten;
dTmp2 = 0.05 * dMaxOverallInten;
for (ii=0; ii<iWindowSize; ii++){ // Normalize to max inten. in window.
iBin = i*iWindowSize+ii;
if (iBin < xCorrArraySize){
if (pdTempRawData[iBin] > dTmp2) pPre->pdCorrelationData[iBin].intensity = (float)(pdTempRawData[iBin]*dTmp1);
}
}
}
}
}
//from Comet
bool MSpectrum::calcEValue(mParams* params, MDecoys& decoys) {
int i;
int iLoopCount;
int iMaxCorr;
int iStartCorr;
int iNextCorr;
double dSlope;
double dIntercept;
double dRSq;
if(topHit[0].simpleScore==0) return true;
if (histogramCount < DECOY_SIZE) {
if (!generateXcorrDecoys(params,decoys)) return false;
}
//linearRegression(dSlope, dIntercept, iMaxCorr, iStartCorr, iNextCorr);
linearRegression2(dSlope, dIntercept, iMaxCorr, iStartCorr, iNextCorr,dRSq);
histoMaxIndex = iMaxCorr;
dSlope *= 10.0;
iLoopCount=20; //score all e-values among top hits?
for (i = 0; i<iLoopCount; i++) {
if(topHit[i].simpleScore==0) break; //score all e-values among top hits?
if (dSlope >= 0.0) {
topHit[i].eVal=1e12;
} else {
topHit[i].eVal = pow(10.0, dSlope * topHit[i].simpleScore + dIntercept);
}
}
return true;
}
//from Comet
// Make synthetic decoy spectra to fill out correlation histogram by going
// through each candidate peptide and rotating spectra in m/z space.
bool MSpectrum::generateXcorrDecoys(mParams* params, MDecoys& decoys) {
int i;
int n;
int j;
int k;
int maxZ;
int z;
size_t r=0;
int key;
int pos;
double dBion;
double dYion;
double dXcorr;
double dFragmentIonMass = 0.0;
// DECOY_SIZE is the minimum # of decoys required or else this function isn't
// called. So need to generate iLoopMax more xcorr scores for the histogram.
int iLoopMax = DECOY_SIZE - histogramCount;
int seed = (scanNumber*histogramCount);
if (seed<0) seed = -seed;
seed = seed % DECOY_SIZE; //don't always start at the top, but not random either; remains reproducible across threads
int decoyIndex;
j = 0;
for (i = 0; i<iLoopMax; i++) { // iterate through required # decoys
dXcorr = 0.0;
decoyIndex = (seed + i) % DECOY_SIZE;
//iterate over precursors
r++;
if (r >= precursor->size()) r = 0;
maxZ = precursor->at(r).charge;
if (maxZ>4) maxZ = 4;
for (j = 0; j<MAX_DECOY_PEP_LEN; j++) { // iterate through decoy fragment ions
dBion = decoys.decoyIons[decoyIndex].pdIonsN[j];
dYion = decoys.decoyIons[decoyIndex].pdIonsC[j];
if(dBion>precursor->at(r).monoMass && dYion>precursor->at(r).monoMass) break; //stop when fragment ion masses exceed precursor mass
for (n = 0; n<6; n++) {
if(!params->ionSeries[n]) continue;
switch (n) {
case 0: dFragmentIonMass = dBion - 27.9949141; break;
case 1: dFragmentIonMass = dBion; break;
case 2: dFragmentIonMass = dBion + 17.026547; break;
case 3: dFragmentIonMass = dYion + 25.9792649; break;
case 4: dFragmentIonMass = dYion; break;
case 5: dFragmentIonMass = dYion - 16.0187224; break;
}
if(dFragmentIonMass>precursor->at(r).monoMass) continue;
for (z=1;z<maxZ;z++) {
mz = (dFragmentIonMass + (z - 1)*1.007276466) / z;
mz = params->binSize * (int)(mz*invBinSize + params->binOffset);
key = (int)mz;
if(key>=kojakBins) break;
if(kojakSparseArray[key]==NULL) continue;
pos = (int)((mz - key)*invBinSize);
dXcorr += kojakSparseArray[key][pos];
}
}
}
if(dXcorr<=0.0) dXcorr=0.0;
k = (int)(dXcorr*0.05 + 0.5); // 0.05=0.005*10; see MAnalysis::mangnumScoring
if (k < 0) k = 0;
else if (k >= HISTOSZ) k = HISTOSZ - 1;
histogram[k] += 1;
histogramCount++;
}
return true;
}
//from Comet
// Make synthetic decoy spectra to fill out correlation histogram by going
// through each candidate peptide and rotating spectra in m/z space.
bool MSpectrum::generateXcorrDecoys2(int maxPepLen) {
int i;
int n;
int j;
int k;
int maxZ;
int z;
size_t r = 0;
int key;
int pos;
double dBion[3]; //0=N-term, 1=C-term, 2=center
double dYion[3];
double dXcorr[3];
double dFragmentIonMass = 0.0;
double oMass;