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CKronik.cpp
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CKronik.cpp
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/*
Copyright 2007-2015, Michael R. Hoopmann, University of Washington
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 "CKronik.h"
//-------------------------------------
// Constructors and Destructors
//-------------------------------------
CKronik::CKronik(){
bGaussFit = false;
dPPMTol = 10.0;
iGapTol = 1;
iMatchTol = 3;
}
CKronik::~CKronik(){
}
CKronik::CKronik(const CKronik& c){
bGaussFit=c.bGaussFit;
dPPMTol=c.dPPMTol;
iGapTol=c.iGapTol;
iMatchTol=c.iMatchTol;
iPercent=c.iPercent;
vPeps.clear();
for(unsigned int i=0;i<c.vPeps.size();i++) vPeps.push_back(c.vPeps[i]);
hkData.clear();
for(unsigned int i=0;i<c.hkData.size();i++) hkData.push_back(c.hkData[i]);
vFile.clear();
for(unsigned int i=0;i<c.vFile.size();i++) vFile.push_back(c.vFile[i]);
vMods.clear();
for(unsigned int i=0;i<c.vMods.size();i++) vMods.push_back(c.vMods[i]);
}
//-------------------------------------
// Operator Overloads
//-------------------------------------
CKronik& CKronik::operator=(const CKronik& c){
if(this!=&c){
bGaussFit=c.bGaussFit;
dPPMTol=c.dPPMTol;
iGapTol=c.iGapTol;
iMatchTol=c.iMatchTol;
iPercent=c.iPercent;
vPeps.clear();
for(unsigned int i=0;i<c.vPeps.size();i++) vPeps.push_back(c.vPeps[i]);
hkData.clear();
for(unsigned int i=0;i<c.hkData.size();i++) hkData.push_back(c.hkData[i]);
vFile.clear();
for(unsigned int i=0;i<c.vFile.size();i++) vFile.push_back(c.vFile[i]);
vMods.clear();
for(unsigned int i=0;i<c.vMods.size();i++) vMods.push_back(c.vMods[i]);
}
return *this;
}
sPepProfile& CKronik::operator[ ](const unsigned int& i){
return vPeps[i];
}
//-------------------------------------
// Data Manipulation
//-------------------------------------
void CKronik::add(sPepProfile &p){
vPeps.push_back(p);
}
sPepProfile& CKronik::at(unsigned int i){
return vPeps[i];
}
void CKronik::clear(){
vPeps.clear();
hkData.clear();
vFile.clear();
vMods.clear();
}
void CKronik::clearHK(){
hkData.clear();
}
void CKronik::erase(unsigned int i){
vPeps.erase(vPeps.begin()+i);
}
//------------------------------
// Automation
//------------------------------
int CKronik::getPercent(){
return iPercent;
}
bool CKronik::loadHK(const char* in){
FILE *hkr;
sScan scan;
sPep pep;
double td;
char tag;
bool firstScan;
char line[256];
char mods[256];
char* tok;
string str;
int i;
int pepCount=0;
sPepProfile s;
sProfileData p;
//Read in the Hardklor results
firstScan=true;
hkr = fopen(in,"rt");
if(hkr==NULL) {
cout << "Problem reading file." << endl;
return false;
}
vFile.clear();
hkData.clear();
while(!feof(hkr)){
tag=fgetc(hkr);
if(tag=='S') {
if(firstScan) firstScan=false;
else hkData.push_back(scan);
scan.clear();
fgets(line,256,hkr);
tok=strtok(line,"\t\n");
scan.scanNum=atoi(tok);
tok=strtok(NULL,"\t\n");
scan.rTime=(float)atof(tok);
tok=strtok(NULL,"\t\n");
for(i=0;i<(int)vFile.size();i++){
if(strcmp(&vFile[i][0],tok)==0) break;
}
if(i==(int)vFile.size()) {
str=tok;
vFile.push_back(str);
}
scan.file=(char)i;
//fscanf(hkr,"\t%d\t%f%s\n",&scan.scanNum,&scan.rTime,scan.file);
} else {
pepCount++;
fscanf(hkr,"\t%lf\t%d\t%f\t%lf\t%lf-%lf\t%lf\t%s\t%lf\n", &pep.monoMass,&i,&pep.intensity,&pep.basePeak,&td,&td,&td,mods,&pep.xCorr);
pep.charge=(char)i;
for(i=0;i<(int)vMods.size();i++){
if(strcmp(&vMods[i][0],mods)==0) break;
}
if(i==(int)vMods.size()) {
str=mods;
vMods.push_back(str);
}
pep.mods=(char)i;
scan.vPep->push_back(pep);
}
}
hkData.push_back(scan);
fclose(hkr);
cout << pepCount << " peptides from " << hkData.size() << " scans." << endl;
}
bool CKronik::processHK(const char* in, const char* out) {
FILE *hkr;
sScan scan;
sPep pep;
double td;
char tag;
bool firstScan;
int sIndex,pIndex;
int i,j,k,k1,k2;
string str;
char line[256];
char mods[256];
char* tok;
int pepCount=0;
vector<sScan> allScans;
double mass;
int charge;
int gap;
int matchCount;
bool bMatch;
sPepProfile s;
sProfileData p;
//for tracking which peptides
iTwo t;
vector<iTwo> vLeft;
vector<iTwo> vRight;
//for indexing peptides by intensity
intenIndex ii;
vector<intenIndex> vi;
//clear data
vFile.clear();
vMods.clear();
vPeps.clear();
//Read in the Hardklor results
firstScan=true;
hkr = fopen(in,"rt");
if(hkr==NULL) {
cout << "Problem reading file." << endl;
return false;
}
while(!feof(hkr)){
tag=fgetc(hkr);
if(tag=='S') {
if(firstScan) firstScan=false;
else allScans.push_back(scan);
scan.clear();
fgets(line,256,hkr);
tok=strtok(line,"\t\n");
scan.scanNum=atoi(tok);
tok=strtok(NULL,"\t\n");
scan.rTime=(float)atof(tok);
tok=strtok(NULL,"\t\n");
for(i=0;i<(int)vFile.size();i++){
if(strcmp(&vFile[i][0],tok)==0) break;
}
if(i==(int)vFile.size()) {
str=tok;
vFile.push_back(str);
}
scan.file=(char)i;
//fscanf(hkr,"\t%d\t%f%s\n",&scan.scanNum,&scan.rTime,scan.file);
} else {
pepCount++;
fscanf(hkr,"\t%lf\t%d\t%f\t%lf\t%lf-%lf\t%lf\t%s\t%lf\n", &pep.monoMass,&i,&pep.intensity,&pep.basePeak,&td,&td,&td,mods,&pep.xCorr);
pep.charge=(char)i;
for(i=0;i<(int)vMods.size();i++){
if(strcmp(&vMods[i][0],mods)==0) break;
}
if(i==(int)vMods.size()) {
str=mods;
vMods.push_back(str);
}
pep.mods=(char)i;
scan.vPep->push_back(pep);
}
}
allScans.push_back(scan);
fclose(hkr);
cout << pepCount << " peptides from " << allScans.size() << " scans." << endl;
//for(i=0;i<allScans.size();i++) allScans[i].sortIntRev();
for(i=0;i<allScans.size();i++) allScans[i].sortMonoMass();
cout << "Finding persistent peptide signals:" << endl;
int lastPercent=0;
int intIndex=0;
int totAnalyzed=0;
cout << lastPercent;
sScan tmpScan;
int flushMem[11];
int flushPos=0;
for(i=0;i<11;i++) flushMem[i]=i*10+10;
vector<int> pepCounter;
for(i=0;i<allScans.size();i++) pepCounter.push_back(0);
intenIndex topBuffer[51];
//Perform the Kronik analysis (in chunks of 75 per scan event)
while(true){
vi.clear();
//clear memory on the fly; every 10%
if(lastPercent>flushMem[flushPos]){
flushPos++;
for(i=0;i<allScans.size();i++){
tmpScan.clear();
for(j=0;j<allScans[i].vPep->size();j++){
if(allScans[i].vPep->at(j).intensity>0) tmpScan.vPep->push_back(allScans[i].vPep->at(j));
}
allScans[i].clear();
for(j=0;j<tmpScan.vPep->size();j++){
allScans[i].vPep->push_back(tmpScan.vPep->at(j));
}
}
}
for(i=0;i<allScans.size();i++){
pepCounter[i]=0;
//clear buffer
for(k=0;k<50;k++) topBuffer[k].intensity=0.0f;
for(j=0;j<allScans[i].vPep->size();j++){
if(allScans[i].vPep->at(j).intensity<0.0f) continue;
topBuffer[50].intensity=allScans[i].vPep->at(j).intensity;
topBuffer[50].pep=j;
topBuffer[50].scan=i;
k=49;
while(k>-1){
if(topBuffer[k].intensity<topBuffer[k+1].intensity){
ii=topBuffer[k];
topBuffer[k]=topBuffer[k+1];
topBuffer[k+1]=ii;
} else {
break;
}
k--;
}
}
for(k=0;k<50;k++){
if(topBuffer[k].intensity<0.1f) break;
vi.push_back(topBuffer[k]);
//cout << topBuffer[k].scan << "\t" << topBuffer[k].pep << "\t" << topBuffer[k].intensity << endl;
}
//if(k>0) exit(0);
}
if(vi.size()==0) break;
qsort(&vi[0],vi.size(),sizeof(intenIndex),compareIntRev3);
//Although we sorted much more, only process top 100 ions
intIndex=0;
//cout << "Processing: " << vi[intIndex].scan << ", " << vi[intIndex].pep << ", " << vi[intIndex].intensity << endl;
while(intIndex<vi.size()){
if(allScans[vi[intIndex].scan].vPep->at(vi[intIndex].pep).intensity<0) {
pepCounter[vi[intIndex].scan]++;
if(pepCounter[vi[intIndex].scan]==50) break;
intIndex++;
continue;
}
sIndex=vi[intIndex].scan;
pIndex=vi[intIndex].pep;
mass=allScans[sIndex].vPep->at(pIndex).monoMass;
charge=allScans[sIndex].vPep->at(pIndex).charge;
matchCount=1;
//cout << "Checking " << intIndex << "\t" << mass << " " << allScans[sIndex].vPep->at(pIndex).intensity << " +" << charge << " from " << sIndex << endl;
//look left
vLeft.clear();
gap=0;
i=sIndex-1;
while(i>-1 && gap<=iGapTol){
bMatch=false;
t.scan=i;
t.pep=binarySearch(allScans,i,mass,charge);
if(t.pep>-1){
matchCount++;
gap=0;
} else {
gap++;
}
vLeft.push_back(t);
i--;
}
//look right
vRight.clear();
gap=0;
i=sIndex+1;
while(i<allScans.size() && gap<=iGapTol){
bMatch=false;
t.scan=i;
t.pep=binarySearch(allScans,i,mass,charge);
if(t.pep>-1){
matchCount++;
gap=0;
} else {
gap++;
}
vRight.push_back(t);
i++;
}
//Only keep sufficient matches
if(matchCount>=iMatchTol){
//trim gaps
while(vLeft.size()>0 && vLeft[vLeft.size()-1].pep<0) vLeft.pop_back();
while(vRight.size()>0 && vRight[vRight.size()-1].pep<0) vRight.pop_back();
//apply basic information
s.rTime=allScans[sIndex].rTime;
s.basePeak=allScans[sIndex].vPep->at(pIndex).basePeak;
s.bestScan=allScans[sIndex].scanNum;
s.charge=allScans[sIndex].vPep->at(pIndex).charge;
s.intensity=allScans[sIndex].vPep->at(pIndex).intensity;
s.monoMass=allScans[sIndex].vPep->at(pIndex).monoMass;
s.mods=allScans[sIndex].vPep->at(pIndex).mods;
//strcpy(s.mods,allScans[sIndex].vPep->at(pIndex).mods);
s.xCorr=allScans[sIndex].vPep->at(pIndex).xCorr;
s.setPoints(vLeft.size()+vRight.size()+1);
if(vLeft.size()==0) {
s.lowScan=allScans[sIndex].scanNum;
s.firstRTime=allScans[sIndex].rTime;
} else {
s.lowScan=allScans[vLeft[vLeft.size()-1].scan].scanNum;
s.firstRTime=allScans[vLeft[vLeft.size()-1].scan].rTime;
}
if(vRight.size()==0) {
s.highScan=allScans[sIndex].scanNum;
s.lastRTime=allScans[sIndex].rTime;
} else {
s.highScan=allScans[vRight[vRight.size()-1].scan].scanNum;
s.lastRTime=allScans[vRight[vRight.size()-1].scan].rTime;
}
//apply datapoints
s.profile[0].intensity=allScans[sIndex].vPep->at(pIndex).intensity;
s.profile[0].interpolated=false;
s.profile[0].monoMass=allScans[sIndex].vPep->at(pIndex).monoMass;
s.profile[0].rTime=allScans[sIndex].rTime;
s.profile[0].scanNum=allScans[sIndex].scanNum;
s.profile[0].xCorr=allScans[sIndex].vPep->at(pIndex).xCorr;
i=1;
j=0;
while(j<vLeft.size()){
//Handle interpolated data
if(vLeft[j].pep<0) {
k=0;
while(vLeft[j+k].pep<0) k++;
k2=j+k;
if(j==0){
s.profile[i].intensity=(float)interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,(double)s.profile[0].intensity,(double)allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).intensity,allScans[vLeft[j].scan].scanNum);
s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,s.profile[0].monoMass, allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).monoMass, allScans[vLeft[j].scan].scanNum);
} else {
k=0;
while(j+k>=0 && vLeft[j+k].pep<0) k--;
k1=j+k;
if(k1<0){
s.profile[i].intensity=(float)interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,(double)s.profile[0].intensity,(double)allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).intensity,allScans[vLeft[j].scan].scanNum);
s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,s.profile[0].monoMass, allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).monoMass, allScans[vLeft[j].scan].scanNum);
} else {
s.profile[i].intensity=(float)interpolate(allScans[vLeft[k1].scan].scanNum,allScans[vLeft[k2].scan].scanNum,(double)allScans[vLeft[k1].scan].vPep->at(vLeft[k1].pep).intensity,(double)allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).intensity,allScans[vLeft[j].scan].scanNum);
s.profile[i].monoMass =interpolate(allScans[vLeft[k1].scan].scanNum,allScans[vLeft[k2].scan].scanNum,allScans[vLeft[k1].scan].vPep->at(vLeft[k1].pep).monoMass, allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).monoMass, allScans[vLeft[j].scan].scanNum);
}
}
s.profile[i].interpolated=true;
s.profile[i].rTime=allScans[vLeft[j].scan].rTime;
s.profile[i].scanNum=allScans[vLeft[j].scan].scanNum;
s.profile[i].xCorr=0.0;
} else {
s.profile[i].intensity=allScans[vLeft[j].scan].vPep->at(vLeft[j].pep).intensity;
s.profile[i].interpolated=false;
s.profile[i].monoMass=allScans[vLeft[j].scan].vPep->at(vLeft[j].pep).monoMass;
s.profile[i].rTime=allScans[vLeft[j].scan].rTime;
s.profile[i].scanNum=allScans[vLeft[j].scan].scanNum;
s.profile[i].xCorr=allScans[vLeft[j].scan].vPep->at(vLeft[j].pep).xCorr;
}
i++;
j++;
}
j=0;
while(j<vRight.size()){
//Handle interpolated data
if(vRight[j].pep<0) {
k=0;
while(vRight[j+k].pep<0)k++;
k2=j+k;
if(j==0){
s.profile[i].intensity=(float)interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].intensity,allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).intensity,allScans[vRight[j].scan].scanNum);
s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].monoMass, allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).monoMass, allScans[vRight[j].scan].scanNum);
} else {
k=0;
while((j+k>-1) && vRight[j+k].pep<0)k--;
k1=j+k;
if(k1<0){
s.profile[i].intensity=(float)interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].intensity,allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).intensity,allScans[vRight[j].scan].scanNum);
s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].monoMass, allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).monoMass, allScans[vRight[j].scan].scanNum);
} else {
s.profile[i].intensity=(float)interpolate(allScans[vRight[k1].scan].scanNum,allScans[vRight[k2].scan].scanNum,allScans[vRight[k1].scan].vPep->at(vRight[k1].pep).intensity,allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).intensity,allScans[vRight[j].scan].scanNum);
s.profile[i].monoMass =interpolate(allScans[vRight[k1].scan].scanNum,allScans[vRight[k2].scan].scanNum,allScans[vRight[k1].scan].vPep->at(vRight[k1].pep).monoMass, allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).monoMass, allScans[vRight[j].scan].scanNum);
}
}
s.profile[i].interpolated=true;
s.profile[i].rTime=allScans[vRight[j].scan].rTime;
s.profile[i].scanNum=allScans[vRight[j].scan].scanNum;
s.profile[i].xCorr=0.0;
} else {
s.profile[i].intensity=allScans[vRight[j].scan].vPep->at(vRight[j].pep).intensity;
s.profile[i].interpolated=false;
s.profile[i].monoMass=allScans[vRight[j].scan].vPep->at(vRight[j].pep).monoMass;
s.profile[i].rTime=allScans[vRight[j].scan].rTime;
s.profile[i].scanNum=allScans[vRight[j].scan].scanNum;
s.profile[i].xCorr=allScans[vRight[j].scan].vPep->at(vRight[j].pep).xCorr;
}
i++;
j++;
}
//Add this peptide
s.sortScanNum();
//summed intensity (including interpolation)
s.sumIntensity=0.0f;
for(i=0;i<s.datapoints;i++) s.sumIntensity+=s.profile[i].intensity;
vPeps.push_back(s);
//Erase datapoints already used
for(i=0;i<vLeft.size();i++){
if(vLeft[i].pep<0) continue;
allScans[vLeft[i].scan].vPep->at(vLeft[i].pep).intensity=-1.0;
totAnalyzed++;
}
for(i=0;i<vRight.size();i++){
if(vRight[i].pep<0) continue;
allScans[vRight[i].scan].vPep->at(vRight[i].pep).intensity=-1.0;
totAnalyzed++;
}
}
//erase the one we're looking at
allScans[sIndex].vPep->at(pIndex).intensity=-1.0;
totAnalyzed++;
//update percent
iPercent=(int)((float)totAnalyzed/(float)pepCount*100.0);
if(iPercent>lastPercent){
cout << "\b\b\b" << iPercent;
lastPercent=iPercent;
}
pepCounter[vi[intIndex].scan]++;
if(pepCounter[vi[intIndex].scan]==50) break;
intIndex++;
}
}
cout << endl;
if(bGaussFit){
cout << "Computing Gaussian chromatograms...";
for(i=0;i<vPeps.size();i++){
vPeps[i].gaussR2 = polynomialBestFit(vPeps[i].profile,vPeps[i].datapoints,vPeps[i].intensity,vPeps[i].gaussian);
}
cout << "Done." << endl;
}
if(out[0]!='\0'){
FILE* f;
f=fopen(out,"wt");
//Heading line
fprintf(f,"First Scan\tLast Scan\tNum of Scans\tCharge\tMonoisotopic Mass\tBase Isotope Peak\t");
fprintf(f,"Best Intensity\tSummed Intensity\tFirst RTime\tLast RTime\tBest RTime\tBest Correlation\tModifications");
if(bGaussFit) fprintf(f,"\tFWHM\t4sigma\tr2");
fprintf(f,"\n");
for(i=0;i<vPeps.size();i++){
fprintf(f,"%d\t%d\t%d\t%d\t%lf\t%lf\t%f\t%f\t%f\t%f\t%f\t%lf\t%s",
vPeps[i].lowScan,
vPeps[i].highScan,
vPeps[i].datapoints,
vPeps[i].charge,
vPeps[i].monoMass,
vPeps[i].basePeak,
vPeps[i].intensity,
vPeps[i].sumIntensity,
vPeps[i].firstRTime,
vPeps[i].lastRTime,
vPeps[i].rTime,
vPeps[i].xCorr,
&vMods[vPeps[i].mods][0]);
if(bGaussFit){
fprintf(f,"\t%lf\t%lf\t%.6lf",FWHMCONST*vPeps[i].gaussian[2],
4*vPeps[i].gaussian[2],
vPeps[i].gaussR2);
}
fprintf(f,"\n");
}
fclose(f);
}
return true;
}
int CKronik::binarySearch(vector<sScan>& v, int index, double mass, int charge){
int lower,mid,upper;
int sz=(int)v[index].vPep->size();
int i;
double lowMass=mass-(mass/1000000*dPPMTol);
double highMass=mass+(mass/1000000*dPPMTol);
if(sz<1) return -1;
//Find a mass within ppm tolerance. Use binary search to for speed.
//Stop searching when first mass is found (although a second may exist).
mid=sz/2;
lower=0;
upper=sz;
while(v[index].vPep->at(mid).monoMass<lowMass || v[index].vPep->at(mid).monoMass>highMass){
if(lower>=upper) break;
if(mass<v[index].vPep->at(mid).monoMass){
upper=mid-1;
mid=(lower+upper)/2;
} else {
lower=mid+1;
mid=(lower+upper)/2;
}
if(mid==sz) {
mid--;
break;
}
}
//Check that mass is correct
if(v[index].vPep->at(mid).monoMass<lowMass || v[index].vPep->at(mid).monoMass>highMass) return -1;
//Now that we have the right mass, check charge state. If incorrect, check neighbors
//until we exceed mass tolerance.
i=mid;
if(v[index].vPep->at(i).charge==charge && v[index].vPep->at(i).intensity>0.0) return i;
//check left - note the inherent bias of always looking left first before right
while(i>0){
i--;
if(v[index].vPep->at(i).monoMass<lowMass) break;
if(v[index].vPep->at(i).charge==charge && v[index].vPep->at(i).intensity>0.0) return i;
}
//check right
i=mid;
while(i<(sz-1)){
i++;
if(v[index].vPep->at(i).monoMass>highMass) break;
if(v[index].vPep->at(i).charge==charge && v[index].vPep->at(i).intensity>0.0) return i;
}
//if nothing has matched, return -1
return -1;
}
bool CKronik::findMax(vector<sScan>& v, int& s, int& p){
float max=0;
unsigned int i;
p=0;
for(i=0;i<v.size();i++){
if(v[i].vPep->size()==0) continue;
if(v[i].vPep->at(0).intensity>max){
max=v[i].vPep->at(0).intensity;
s=i;
}
}
return true;
}
//-----------------------------------------
// Tools
//-----------------------------------------
bool CKronik::getRT(int scanNum, float& rt){
unsigned int i;
for(i=0;i<hkData.size();i++){
if(hkData[i].scanNum==scanNum){
rt=hkData[i].rTime;
return true;
}
}
rt=0.0f;
return false;
}
//-----------------------------------------
// Filters
//-----------------------------------------
void CKronik::filterRT(float rt1, float rt2){
unsigned int i;
vector<sPepProfile> temp;
for(i=0;i<vPeps.size();i++){
if(vPeps[i].rTime>=rt1 && vPeps[i].rTime<=rt2){
temp.push_back(vPeps[i]);
}
}
vPeps.clear();
for(i=0;i<temp.size();i++) vPeps.push_back(temp[i]);
}
void CKronik::removeContaminants(float rt){
unsigned int i;
vector<sPepProfile> temp;
//while(vPeps.size()>0){
for(i=0;i<vPeps.size() /*&& i<1000 */;i++){
if((vPeps[i].lastRTime-vPeps[i].firstRTime)<rt){
temp.push_back(vPeps[i]);
}
}
//vPeps.erase(vPeps.begin(),vPeps.begin()+i);
//}
vPeps.clear();
for(i=0;i<temp.size();i++) vPeps.push_back(temp[i]);
}
void CKronik::removeMass(double m1, double m2){
unsigned int i;
vector<sPepProfile> temp;
for(i=0;i<vPeps.size();i++){
if( vPeps[i].monoMass>=m1 && vPeps[i].monoMass<=m2 ){
temp.push_back(vPeps[i]);
}
}
vPeps.clear();
for(i=0;i<temp.size();i++) vPeps.push_back(temp[i]);
}
//-----------------------------------------
// Parameter accessors and modifiers
//-----------------------------------------
void CKronik::setPPMTol(double d){
dPPMTol=d;
}
void CKronik::setMatchTol(int i){
iMatchTol=i;
}
void CKronik::setGapTol(int i){
iGapTol=i;
}
void CKronik::setGaussFit(bool b){
bGaussFit=b;
}
size_t CKronik::size(){
return vPeps.size();
}
//------------------------------------------------------
// STATISTICS FUNCTIONS (adapted from numerical recipes)
//------------------------------------------------------
bool CKronik::pearson(int i1, int i2, bool byScan, bool interpolate, double& rval, double& pval, double& slope, double& intercept, float& sum1, float& sum2){
int i,j;
double sxx=0.0,syy=0.0,sxy=0.0;
double ax=0.0,ay=0.0;
double sumx=0.0,sumy=0.0,sumxy=0.0,sumxx=0.0;
double yt,xt,t,df;
double TINY=1.0e-20;
double lrval;
pval=1.0;
rval=0.0;
vector<float> p1;
vector<float> p2;
/*
cout << "\n1: " << endl;
for(i=0;i<vPeps[i1].datapoints;i++){
cout << vPeps[i1].profile[i].scanNum << "\t" << vPeps[i1].profile[i].intensity << endl;
}
cout << "2: " << endl;
for(i=0;i<vPeps[i2].datapoints;i++){
cout << vPeps[i2].profile[i].scanNum << "\t" << vPeps[i2].profile[i].intensity << endl;
}
*/
if(byScan){
i=0;
j=0;
while(true){
if(i==vPeps[i1].datapoints) return false;
if(j==vPeps[i2].datapoints) return false;
if(vPeps[i1].profile[i].scanNum<vPeps[i2].profile[j].scanNum){
i++;
continue;
} else if(vPeps[i1].profile[i].scanNum>vPeps[i2].profile[j].scanNum){
j++;
continue;
} else {
break;
}
}
while(i<vPeps[i1].datapoints && j<vPeps[i2].datapoints){
//Build correlation vectors
p1.push_back(vPeps[i1].profile[i++].intensity);
p2.push_back(vPeps[i2].profile[j++].intensity);
//cout << "Add: " << i-1 << " " << p1[p1.size()-1] << "\t" << j-1 << " " << p2[p2.size()-1] << endl;
}
} else {
//Find center for each peptide
float max;
int max1, max2;
max=0.0f;
for(i=0;i<vPeps[i1].datapoints;i++){
if(vPeps[i1].profile[i].intensity>max){
max=vPeps[i1].profile[i].intensity;
max1=i;
}
}
max=0.0f;
for(i=0;i<vPeps[i2].datapoints;i++){
if(vPeps[i2].profile[i].intensity>max){
max=vPeps[i2].profile[i].intensity;
max2=i;
}
}
//Build correlation vectors
p1.push_back(vPeps[i1].profile[max1].intensity);
p2.push_back(vPeps[i2].profile[max2].intensity);
j=0;
while((max1-j)>0 && (max2-j)>0){
j++;
if(vPeps[i1].profile[max1-j].interpolated && !interpolate) p1.push_back(0.0f);
else p1.push_back(vPeps[i1].profile[max1-j].intensity);
if(vPeps[i2].profile[max2-j].interpolated && !interpolate) p2.push_back(0.0f);
else p2.push_back(vPeps[i2].profile[max2-j].intensity);
}
j=1;
while((max1+j)<vPeps[i1].datapoints && (max2+j)<vPeps[i2].datapoints ){
if(vPeps[i1].profile[max1+j].interpolated && !interpolate) p1.push_back(0.0f);
else p1.push_back(vPeps[i1].profile[max1+j].intensity);
if(vPeps[i2].profile[max2+j].interpolated && !interpolate) p2.push_back(0.0f);
else p2.push_back(vPeps[i2].profile[max2+j].intensity);
j++;
}
}
//Get totals
for(i=0;i<p1.size();i++){
//cout << p1[i] << "\t" << p2[i] << endl;
sumx+=p1[i];
sumy+=p2[i];
sumxy+=p1[i]*p2[i];
sumxx+=p1[i]*p1[i];
}
//Pearsons
ax=sumx/p1.size();
ay=sumy/p2.size();
for(i=0;i<p1.size();i++){
xt=p1[i]-ax;
yt=p2[i]-ay;
sxx+=xt*xt;
syy+=yt*yt;
sxy+=xt*yt;
}
rval=sxy/(sqrt(sxx*syy)+TINY);
if(rval<0.0) lrval=0.0; //negative correlations are false hits in this analysis
else lrval=rval;
df=(double)p1.size()-2;
if(df<1) {
pval=1.0;
} else {
t=lrval*sqrt(df/((1-lrval+TINY)*(1+lrval+TINY)));
pval=betai(0.5*df,0.5,df/(df+t*t));
}
//Line of best fit
slope = (sumx*sumy - p1.size()*sumxy) / (sumx*sumx - p1.size()*sumxx);
intercept = (sumx*sumxy - sumy*sumxx) / (sumx*sumx - p1.size()*sumxx);
sum1=(float)sumx;
sum2=(float)sumy;
return true;
}
double CKronik::polynomialBestFit(sProfileData* profile, size_t sz, float max, double* coeff, int degree){
if(degree>3){
cout << "High order polynomials not supported with this function. Max=3" << endl;
exit(1);
}
if(degree<2){
cout << "Polynomials need at least two degrees. Min=2" << endl;
exit(1);
}
int i,j,a;
int n;
float threshold=max*0.25f;
vector<double> x;
vector<double> y;
degree++;
for(i=0;i<sz;i++) {
if(profile[i].intensity>threshold){
x.push_back(profile[i].rTime);
y.push_back(log((double)profile[i].intensity));
}
}
if(x.size()<3) {
coeff[0]=coeff[1]=coeff[2]=coeff[3]=0.0;
return 0.0;
}
//This is an offset to be reapplied later; It improves coefficient accuracy using this polynomial method.
n=(int)x.size();
double sFactor=x[n/2];
//set X matrix
double** X = new double* [n];
for(i=0;i<n;i++){
X[i] = new double [degree];
X[i][0] = 1.0;
for(j=1;j<degree;j++) X[i][j]=X[i][j-1]*(x[i]-sFactor);
}
//make transpose of X
double** Xt = new double* [degree];
for(j=0;j<degree;j++) Xt[j] = new double [n];
for(i=0;i<n;i++){
for(j=0;j<degree;j++){
Xt[j][i] = X[i][j];
}
}
//matrix multiplication
double** XtX = new double* [degree];
for(i=0;i<degree;i++){
XtX[i] = new double [degree];
for(j=0;j<degree;j++){
XtX[i][j]=0;
for(a=0;a<n;a++) XtX[i][j]+=(Xt[i][a]*X[a][j]);
}
}
//inverse using Gauss-Jordan Elimination
double** XtXi = new double* [degree];
for(i=0;i<degree;i++){
XtXi[i] = new double [degree*2];
for(j=0;j<degree*2;j++){
if(j<degree) XtXi[i][j]=XtX[i][j];
else if(j-degree==i) XtXi[i][j]=1;
else XtXi[i][j]=0;
}
}
double d;
for(j=0;j<degree;j++){
for(i=0;i<degree;i++){
if(i==j) continue;
if(XtXi[i][j]==0) continue;
d=-XtXi[i][j]/XtXi[j][j];
for(a=0;a<degree*2;a++) XtXi[i][a]+=(d*XtXi[j][a]);
}
}
for(i=0;i<degree;i++){
d=1/XtXi[i][i];
for(j=0;j<degree*2;j++) XtXi[i][j]*=d;
}
//matrix multiplication
double* Xty = new double [degree];
for(i=0;i<degree;i++){
Xty[i]=0;
for(j=0;j<n;j++) Xty[i]+=Xt[i][j]*y[j];
}
//matrix multiplication
double* c = new double [degree];
for(i=0;i<degree;i++){
c[i]=0;