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KData.cpp
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KData.cpp
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/*
Copyright 2014, 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 "KData.h"
using namespace std;
using namespace MSToolkit;
Mutex KData::mutexMemoryPool;
bool* KData::memoryPool;
double** KData::tempRawData;
double** KData::tmpFastXcorrData;
float** KData::fastXcorrData;
kPreprocessStruct** KData::preProcess;
kParams* KData::params;
KLog* KData::klog;
deque<Spectrum*> KData::dMS1;
vector<Spectrum*> KData::vMS1Buffer;
Mutex KData::mutexLockMS1;
CHardklor2** KData::h;
CHardklor** KData::hO;
CAveragine** KData::averagine;
CMercury8** KData::mercury;
CModelLibrary* KData::models;
Mutex* KData::mutexHardklor;
CHardklorSetting KData::hs;
CHardklorSetting KData::hs2;
CHardklorSetting KData::hs4;
bool* KData::bHardklor;
int KData::maxPrecursorMass;
/*============================
Constructors
============================*/
KData::KData(){
int i,j,k;
bScans=NULL;
params=NULL;
klog=NULL;
xlTable = new char*[128];
for (i = 0; i<128; i++) xlTable[i] = new char[20];
for(i=0;i<128;i++){
for(j=0;j<5;j++){
for(k=0;k<128;k++){
xlTargets[i][j].target[k]=false;
}
}
}
}
KData::KData(kParams* p){
bScans=NULL;
klog=NULL;
params=p;
size_t i;
int j,k;
for(i=0;i<p->fMods->size();i++) aa.addFixedMod((char)p->fMods->at(i).index,p->fMods->at(i).mass);
xlTable = new char*[128];
for (j = 0; j<128; j++) xlTable[j] = new char[20];
for (i = 0; i<128; i++){
for (j = 0; j<5; j++){
for (k = 0; k<128; k++){
xlTargets[i][j].target[k] = false;
}
}
}
}
KData::~KData(){
params=NULL;
klog=NULL;
if(bScans!=NULL) delete[] bScans;
for (int i = 0; i<128; i++) delete[] xlTable[i];
delete[] xlTable;
for(size_t a=0;a<spec.size();a++) delete spec[a];
}
/*============================
Operators
============================*/
KSpectrum& KData::operator [](const int& i){
return *spec[i];
}
/*============================
Functions
============================*/
void KData::addProteins(void* sh, KDatabase& db, int pIndex, bool xl, int linkA, int linkB) {
char c;
char n;
kPeptide pep = db.getPeptide(pIndex);
if(!xl) (*(CnpxSearchHit*)sh).num_tot_proteins = (int)pep.map->size();
else (*(CnpxLinkedPeptide*)sh).num_tot_proteins = (int)pep.map->size();
for (size_t j = 0; j<pep.map->size(); j++){
if (pep.n15 && db[pep.map->at(j).index].name.find(params->n15Label) == string::npos) {
if (!xl) (*(CnpxSearchHit*)sh).num_tot_proteins--;
else (*(CnpxLinkedPeptide*)sh).num_tot_proteins--;
continue;
}
if (!pep.n15 && strlen(params->n15Label)>0 && db[pep.map->at(j).index].name.find(params->n15Label) != string::npos) {
if (!xl) (*(CnpxSearchHit*)sh).num_tot_proteins--;
else (*(CnpxLinkedPeptide*)sh).num_tot_proteins--;
continue;
}
string protein = "";
for (size_t i = 0; i<db[pep.map->at(j).index].name.size(); i++){
if (params->truncate>0 && i == params->truncate) break;
if (db[pep.map->at(j).index].name[i]==' ') break;
protein += db[pep.map->at(j).index].name[i];
}
if (pep.map->at(j).start<1) n = '-';
else n = db[pep.map->at(j).index].sequence[pep.map->at(j).start - 1];
if (pep.map->at(j).stop + 1 == db[pep.map->at(j).index].sequence.size()) c = '-';
else c = db[pep.map->at(j).index].sequence[pep.map->at(j).stop + 1];
if(j==0){
if (!xl) {
(*(CnpxSearchHit*)sh).protein=protein;
(*(CnpxSearchHit*)sh).peptide_prev_aa=n;
(*(CnpxSearchHit*)sh).peptide_next_aa=c;
(*(CnpxSearchHit*)sh).peptide_start_pos = (int)pep.map->at(j).start + 1;
if (linkA>0) (*(CnpxSearchHit*)sh).protein_link_pos_a = pep.map->at(j).start + linkA;
if (linkB>0) (*(CnpxSearchHit*)sh).protein_link_pos_b = pep.map->at(j).start + linkB;
} else {
(*(CnpxLinkedPeptide*)sh).protein=protein;
(*(CnpxLinkedPeptide*)sh).peptide_next_aa=c;
(*(CnpxLinkedPeptide*)sh).peptide_prev_aa=n;
(*(CnpxLinkedPeptide*)sh).peptide_start_pos = (int)pep.map->at(j).start + 1;
(*(CnpxLinkedPeptide*)sh).protein_link_pos_a = pep.map->at(j).start + linkA;
}
} else {
CnpxAlternativeProtein ap;
ap.protein = protein;
ap.peptide_prev_aa = n;
ap.peptide_next_aa = c;
ap.peptide_start_pos = (int)pep.map->at(j).start + 1;
if (linkA>0) ap.protein_link_pos_a = pep.map->at(j).start + linkA;
if (linkB>0) ap.protein_link_pos_b = pep.map->at(j).start + linkB;
if (!xl) (*(CnpxSearchHit*)sh).alternative_protein.push_back(ap);
else (*(CnpxLinkedPeptide*)sh).alternative_protein.push_back(ap);
}
}
}
void KData::addSearchScore(CnpxSearchHit& sh, string name, double value, string fmt){
char score[32];
sprintf(score, fmt.c_str(), value);
CnpxSearchScore ss;
ss.name = name;
ss.value = score;
sh.search_score.push_back(ss);
}
void KData::addSearchScore(CnpxSearchHit& sh, string name, int value){
char score[32];
sprintf(score, "%d", value);
CnpxSearchScore ss;
ss.name = name;
ss.value = score;
sh.search_score.push_back(ss);
}
void KData::addXlinkScore(CnpxLinkedPeptide& lp, string name, double value, string fmt){
char score[32];
sprintf(score, fmt.c_str(), value);
CnpxXLinkScore xls;
xls.name=name;
xls.value=score;
lp.xlink_score.push_back(xls);
}
void KData::addXlinkScore(CnpxLinkedPeptide& lp, string name, int value){
char score[32];
sprintf(score, "%d", value);
CnpxXLinkScore xls;
xls.name = name;
xls.value = score;
lp.xlink_score.push_back(xls);
}
void KData::addXlinkScore(CnpxXLink& xl, string name, double value, string fmt){
char score[32];
sprintf(score, fmt.c_str(), value);
CnpxXLinkScore xls;
xls.name = name;
xls.value = score;
xl.xlink_score.push_back(xls);
}
void KData::addXlinkScore(CnpxXLink& xl, string name, int value){
char score[32];
sprintf(score, "%d", value);
CnpxXLinkScore xls;
xls.name = name;
xls.value = score;
xl.xlink_score.push_back(xls);
}
void KData::buildXLTable(){
int i, j;
int xlA, xlB;
size_t k;
//initialize/clear values
motifCount=0;
for (i = 0; i < 20; i++){
motifs[i].motif.clear();
for (int j = 0; j<10; j++){
motifs[i].xlIndex[j] = -1;
motifs[i].counterMotif[j] = -1;
}
}
for (i = 0; i < 128; i++){
for (j = 0; j<20; j++) xlTable[i][j] = -1;
}
//Iterate over all cross-linkers
for (k = 0; k<link.size(); k++){
//Add motifA, if needed
for (i = 0; i < motifCount; i++){
if (motifs[i].motif.compare(link[k].motifA) == 0) break;
}
if (i == motifCount) {
motifs[i].motif = link[k].motifA;
motifCount++;
}
link[k].motifAIndex = i;
//set index to cross-linker
for (j = 0; j < 10; j++){
if (motifs[link[k].motifAIndex].xlIndex[j] == (int)k) break;
if (motifs[link[k].motifAIndex].xlIndex[j] == -1) {
motifs[link[k].motifAIndex].xlIndex[j] = (int)k;
break;
}
}
xlA = j;
//Add motifB, if needed
for (i = 0; i < motifCount; i++){
if (motifs[i].motif.compare(link[k].motifB) == 0) break;
}
if (i == motifCount) { //Add new motif
motifs[i].motif = link[k].motifB;
motifCount++;
}
link[k].motifBIndex = i;
//set index
for (j = 0; j < 10; j++){
if (motifs[link[k].motifBIndex].xlIndex[j] == (int)k) break;
if (motifs[link[k].motifBIndex].xlIndex[j] == -1) {
motifs[link[k].motifBIndex].xlIndex[j] = (int)k;
break;
}
}
xlB = j;
//set counter motifs
motifs[link[k].motifAIndex].counterMotif[xlA] = link[k].motifBIndex;
motifs[link[k].motifBIndex].counterMotif[xlB] = link[k].motifAIndex;
}
//Build table of linked amino acids
for (i = 0; i < motifCount; i++){
//This lookup table is for fast referencing partner link sites when given a site
for(j=0;j<5;j++){
if(motifs[i].xlIndex[j]<0) break;
for (k = 0; k < motifs[motifs[i].counterMotif[j]].motif.size(); k++){
for(size_t n=0;n<motifs[i].motif.size();n++){
xlTargets[motifs[i].motif[n]][motifs[i].xlIndex[j]].target[motifs[motifs[i].counterMotif[j]].motif[k]] = true;
}
}
}
for (k = 0; k < motifs[i].motif.size(); k++){
for (j = 0; j < 20; j++){
if (xlTable[motifs[i].motif[k]][j] == -1){
xlTable[motifs[i].motif[k]][j] = i;
break;
}
}
}
}
////Output for diagnostic purposes
//for (i = 0; i < motifCount; i++){
// cout << "Motif " << i << ": " << &motifs[i].motif[0] << endl;
// for(k=0;k<10;k++){
// if(motifs[i].counterMotif[k]<0) break;
// cout << " XLink index: " << (int)motifs[i].xlIndex[k] << "\tCounter Motif: " << (int)motifs[i].counterMotif[k] << endl;
// }
//}
//bool bShow;
//char cStr[256];
//string str;
//for(i=0;i<128;i++){
// for(j=0;j<link.size();j++){
// bShow=false;
// sprintf(cStr,"%c: %s",(char)i,link[j].label);
// str=cStr;
// for(k=0;k<128;k++){
// if(xlTargets[i][j].target[k]) {
// str+=" ";
// str+=(char)k;
// bShow=true;
// }
// }
// if(bShow) cout << str << endl;
// }
//}
}
bool KData::checkLink(char p1Site, char p2Site, int linkIndex){
return xlTargets[p1Site][linkIndex].target[p2Site];
}
void KData::convertToDiag(kScoreCard& sc, kDiag& d, KDatabase& db){
size_t i, x;
char strs[256];
char st[32];
string pep1, pep2, tmp;
kPeptide pep;
pep = db.getPeptide(sc.pep1);
db.getPeptideSeq(pep.map->at(0).index, pep.map->at(0).start, pep.map->at(0).stop, strs);
pep1.clear();
if (pep.nTerm && aa.getFixedModMass('$') != 0) {
sprintf(st, "[%.2lf]", aa.getFixedModMass('$'));
pep1 += st;
}
for (i = 0; i < strlen(strs); i++) {
pep1 += strs[i];
for (x = 0; x < sc.mods1.size(); x++) {
if (sc.mods1[x].pos == (char)i) {
sprintf(st, "[%.2lf]", sc.mods1[x].mass);
pep1 += st;
}
}
if ((int)i == sc.k1 || (sc.pep2 < 0 && (int)i == sc.k2)) pep1 += "[x]";
}
if (pep.cTerm && aa.getFixedModMass('%') != 0) {
sprintf(st, "[%.2lf]", aa.getFixedModMass('%'));
pep1 += st;
}
pep2.clear();
if (sc.pep2 > -1) {
pep = db.getPeptide(sc.pep2);
db.getPeptideSeq(pep.map->at(0).index, pep.map->at(0).start, pep.map->at(0).stop, strs);
if (pep.nTerm && aa.getFixedModMass('$') != 0) {
sprintf(st, "[%.2lf]", aa.getFixedModMass('$'));
pep2 += st;
}
for (i = 0; i < strlen(strs); i++) {
pep2 += strs[i];
for (x = 0; x < sc.mods2.size(); x++) {
if (sc.mods2[x].pos == (char)i) {
sprintf(st, "[%.2lf]", sc.mods2[x].mass);
pep2 += st;
}
}
if ((int)i == sc.k2) pep2 += "[x]";
}
if (pep.cTerm && aa.getFixedModMass('%') != 0) {
sprintf(st, "[%.2lf]", aa.getFixedModMass('%'));
pep2 += st;
}
} else {
//fprintf(f2, "\t(%d)", spec[i].getScoreCard(j).k2);
}
if (pep2.size() > 0 && pep1.compare(pep2) > 0) {
tmp = pep1;
pep1 = pep2;
pep2 = tmp;
}
if (sc.link == -2) pep1 += "+";
else if (pep2.size() > 0) pep1 += "--";
pep1 += pep2;
d.sequence=pep1;
d.simpleScore= sc.simpleScore;
d.cpScore= sc.cpScore1 + sc.cpScore2;
d.evalue= sc.eVal;
d.mass= sc.mass;
if (sc.link < 0) d.xlMass=0;
else d.xlMass=link[sc.link].mass;
}
//Returns closet mz value to desired point
int KData::findPeak(Spectrum* s, double mass){
int sz = s->size();
int lower = 0;
int mid = sz / 2;
int upper = sz;
//binary search to closest mass
while (s->at(mid).mz != mass){
if (lower >= upper) break;
if (mass<s->at(mid).mz){
upper = mid - 1;
mid = (lower + upper) / 2;
} else {
lower = mid + 1;
mid = (lower + upper) / 2;
}
if (mid == sz) {
mid--;
break;
}
}
//Check that mass is closest
if (mid>0 && fabs(s->at(mid - 1).mz - mass)<fabs(s->at(mid).mz - mass)) return mid - 1;
if (mid<s->size() - 1 && fabs(s->at(mid + 1).mz - mass)<fabs(s->at(mid).mz - mass)) return mid + 1;
return mid;
}
//Returns point within precision or -1 if doesn't exist
int KData::findPeak(Spectrum* s, double mass, double prec){
int sz = s->size();
int lower = 0;
int mid = sz / 2;
int upper = sz;
double minMass = mass - (mass / 1000000 * prec);
double maxMass = mass + (mass / 1000000 * prec);
//binary search to closest mass
while (s->at(mid).mz<minMass || s->at(mid).mz>maxMass){
if (lower >= upper) break;
if (mass<s->at(mid).mz){
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 (s->at(mid).mz>minMass && s->at(mid).mz<maxMass) return mid;
return -1;
}
void KData::formatMS2(MSToolkit::Spectrum* s, KSpectrum* pls){
char nStr[256];
string sStr;
pls->setRTime(s->getRTime());
pls->setScanNumber(s->getScanNumber());
s->getNativeID(nStr,256);
sStr=nStr;
pls->setNativeID(sStr);
bool doCentroid=false;
switch(s->getCentroidStatus()){
case 0:
if(params->ms2Centroid) {
char tmpStr[256];
sprintf(tmpStr,"Kojak parameter indicates MS/MS data are centroid, but spectrum %d labeled as profile.",s->getScanNumber());
klog->addError(string(tmpStr));
} else doCentroid=true;
break;
case 1:
if (!params->ms2Centroid) {
klog->addWarning(0, "Spectrum is labeled as centroid, but Kojak parameter indicates data are profile. Ignoring Kojak parameter.");
}
break;
default:
if(!params->ms2Centroid) doCentroid=true;
break;
}
//If not centroided, do so now.
int totalPeaks=0;
if(doCentroid){
centroid(s, pls, params->ms2Resolution, params->instrument);
totalPeaks += pls->size();
} else {
kSpecPoint sp;
for(int i=0;i<s->size();i++){
sp.mass=s->at(i).mz;
sp.intensity=s->at(i).intensity;
pls->addPoint(sp);
}
}
//remove precursor if requested
if(params->removePrecursor>0){
double pMin=s->getMZ()-params->removePrecursor;
double pMax=s->getMZ()+params->removePrecursor;
for(int i=0;i<pls->size();i++){
if((*pls)[i].mass>pMin && (*pls)[i].mass<pMax) (*pls)[i].intensity=0;
}
}
//Collapse the isotope peaks
int collapsedPeaks=0;
if (params->specProcess == 1 && pls->size()>1) {
collapseSpectrum(*pls);
collapsedPeaks += pls->size();
}
//If user limits number of peaks to analyze, sort by intensity and take top N
if (params->maxPeaks>0 && pls->size()>params->maxPeaks){
if (pls->size()>1) pls->sortIntensityRev();
vector<kSpecPoint> v;
for (int i = 0; i<params->maxPeaks; i++) v.push_back((*pls)[i]);
pls->clear();
for (int i = 0; i<params->maxPeaks; i++) pls->addPoint(v[i]);
pls->sortMZ();
pls->setMaxIntensity(v[0].intensity);
} else {
float max=0;
for (int i = 0; i<pls->size(); i++){
if((*pls)[i].intensity>max) max=(*pls)[i].intensity;
}
pls->setMaxIntensity(max);
}
//Get any additional information user requested
pls->setCharge(s->getCharge());
pls->setMZ(s->getMZ());
if(params->preferPrecursor>0){
if(s->getMonoMZ()>0 && s->getCharge()>0){
kPrecursor pre;
pre.monoMass=s->getMonoMZ()*s->getCharge()-s->getCharge()*1.007276466;
pre.charge=s->getCharge();
pre.corr=0;
pls->addPrecursor(pre,params->topCount);
for(int px=1;px<=params->isotopeError;px++){
if(px==4) break;
pre.monoMass -= 1.00335483;
pre.corr -= 0.1;
pls->addPrecursor(pre, params->topCount);
}
pls->setInstrumentPrecursor(true);
}
}
}
KSpectrum* KData::getSpectrum(const int& i){
return spec[i];
}
char** KData::getXLTable(){
return xlTable;
}
KSpectrum& KData::at(const int& i){
return *spec[i];
}
//Places centroided peaks in bins, then finds average. Has potential for error when accuracy drifts into neighboring bins.
void KData::averageScansCentroid(vector<Spectrum*>& s, Spectrum& avg, double min, double max){
unsigned int i;
int j, k;
double binWidth;
double offset = -1.0;
float* bin;
float intensity;
int binCount;
int* pos;
double lowMZ = -1.0;
kScanBin sb;
vector<kScanBin> topList;
avg.clear();
//if vector is just one scan, then simply copy the peaks
if (s.size() == 1){
int index = findPeak(s[0], min);
if (s[0]->at(index).mz<min) index++;
while (index<s[0]->size() && s[0]->at(index).mz<max){
avg.add(s[0]->at(index++));
}
return;
}
pos = new int[s.size()];
//Set some really small bin width related to the mz region being summed.
binWidth = 0.0001;
binCount = (int)((max - min) / binWidth + 1);
bin = new float[binCount];
for (j = 0; j<binCount; j++) bin[j] = 0;
//align all spectra to point closest to min and set offset
for (i = 0; i<s.size(); i++) {
pos[i] = findPeak(s[i], min);
if (s[i]->at(pos[i]).mz<min) pos[i]++;
if (offset<0) offset = s[i]->at(pos[i]).mz;
else if (s[i]->at(pos[i]).mz<offset) offset = s[i]->at(pos[i]).mz;
}
//Iterate all spectra and add peaks to bins
for (i = 0; i<s.size(); i++) {
while (pos[i]<s[i]->size() && s[i]->at(pos[i]).mz<max){
j = (int)((s[i]->at(pos[i]).mz - offset) / binWidth);
if (j<0){
pos[i]++;
continue;
}
if (j >= binCount) break;
bin[j] += s[i]->at(pos[i]).intensity;
pos[i]++;
}
}
//Unsure of current efficiency. Finds bin of tallest peak, then combines with neighboring bins
//to produce an average. Thus summing of neighboring bins allows flexibility when dealing with mass accuracy drift.
//Using larger bins has the same effect, but perhaps fewer significant digits in the final result.
for (j = 0; j<binCount; j++){
if (bin[j]>0) {
sb.index = j;
sb.intensity = bin[j];
topList.push_back(sb);
}
}
if (topList.size()>0) {
qsort(&topList[0], topList.size(), sizeof(kScanBin), compareScanBinRev2);
for (i = 0; i<topList.size(); i++){
if (bin[topList[i].index] == 0) continue;
intensity = 0;
j = topList[i].index - 50; //This will sum bins within 0.05 m/z... might be too wide...
k = topList[i].index + 51;
if (j<0) j = 0;
if (k>binCount) k = binCount;
for (j = j; j<k; j++){
intensity += bin[j];
bin[j] = 0;
}
intensity /= s.size();
avg.add(offset + topList[i].index*binWidth, intensity);
}
avg.sortMZ();
}
//clean up memory
delete[] bin;
delete[] pos;
}
void KData::diagSinglet(){
int oddCount = 0;
double maxScore;
int bigCount = 0;
int twoCount = 0;
double bigScore = 0;
double bigMass;
double unknownMass;
for (size_t b = 0; b<spec.size(); b++){
//if(spec[b].getScoreCard(0).simpleScore==0) continue;
maxScore = 0;
unknownMass = 0;
for (int q = 0; q<spec[b]->sizePrecursor(); q++){
if (spec[b]->getTopPeps(q)->singletList.size() == 0) continue;
list<kSingletScoreCard>::iterator it = spec[b]->getTopPeps(q)->singletList.begin();
if (it->simpleScore>spec[b]->getScoreCard(0).simpleScore){
if (it->simpleScore>maxScore) {
maxScore = it->simpleScore;
unknownMass = spec[b]->getPrecursor(q).monoMass - it->mass;
}
}
}
if (maxScore>0) oddCount++;
if (maxScore>3) bigCount++;
if (maxScore>3 && spec[b]->getScoreCard(0).simpleScore>0 && maxScore>spec[b]->getScoreCard(0).simpleScore * 2) twoCount++;
if (maxScore>bigScore) {
bigScore = maxScore;
bigMass = unknownMass;
}
}
cout << " Diagnostics:" << endl;
cout << " Odd counts " << oddCount << " of " << spec.size() << endl;
cout << " Big counts " << bigCount << " of " << oddCount << endl;
cout << " Two fold " << twoCount << " of " << bigCount << endl;
cout << " Biggest Score: " << bigScore << " Mass: " << bigMass << endl;
cout << endl;
}
bool KData::getBoundaries(double mass1, double mass2, vector<int>& index, bool* buffer){
int sz=(int)massList.size();
if(mass1>massList[sz-1].mass) return false;
int lower=0;
int mid=sz/2;
int upper=sz;
int i;
int low;
int high;
vector<int> v;
//binary search to closest mass
while(massList[mid].mass!=mass1){
if(lower>=upper) break;
if(mass1<massList[mid].mass){
upper=mid-1;
mid=(lower+upper)/2;
} else {
lower=mid+1;
mid=(lower+upper)/2;
}
if(mid==sz) {
mid--;
break;
}
}
//Adjust if needed
if(massList[mid].mass<mass1) mid++;
if(mid>0 && massList[mid-1].mass>mass1) mid--;
if(massList[mid].mass>mass2) return false;
if(mid==sz) return false;
low=mid;
//binary search to next mass
lower=0;
mid=sz/2;
upper=sz;
while(massList[mid].mass!=mass2){
if(lower>=upper) break;
if(mass2<massList[mid].mass){
upper=mid-1;
mid=(lower+upper)/2;
} else {
lower=mid+1;
mid=(lower+upper)/2;
}
if(mid==sz) {
mid--;
break;
}
}
//Adjust if needed
if(massList[mid].mass>mass2) mid--;
if(mid<sz-1 && massList[mid+1].mass<mass2) mid++;
if(mid<0) return false;
high=mid;
sz=(int)spec.size();
memset(buffer,false,sz);
for (i = low; i <= high; i++) buffer[massList[i].index]=true;
index.clear();
for (i = 0; i < sz; i++) {
if(buffer[i]) index.push_back(i);
}
return true;
/* old method
for(i=low;i<=high;i++) v.push_back(massList[i].index);
//Sort indexes and copy to final array, removing duplicates.
//This may be a potentially slow step and should be profiled
qsort(&v[0],v.size(),sizeof(int),compareInt);
index.clear();
index.push_back(v[0]);
mid=(int)v.size();
for(i=1;i<mid;i++){
if(v[i]!=v[i-1]) index.push_back(v[i]);
}
return true;
*/
}
//Get the list of spectrum array indexes to search based on desired mass
bool KData::getBoundaries2(double mass, double prec, vector<int>& index, bool* buffer){
int sz=(int)massList.size();
int lower=0;
int mid=sz/2;
int upper=sz;
int i;
vector<int> v;
double minMass = mass - (mass/1000000*prec);
double maxMass = mass + (mass/1000000*prec);
//binary search to closest mass
while(massList[mid].mass<minMass || massList[mid].mass>maxMass){
if(lower>=upper) break;
if(mass<massList[mid].mass){
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(massList[mid].mass<minMass || massList[mid].mass>maxMass) return false;
v.push_back(massList[mid].index);
//check left
i=mid;
while(i>0){
i--;
if(massList[i].mass<minMass) break;
v.push_back(massList[i].index);
}
//check right
i=mid;
while(i<(sz-1)){
i++;
if(massList[i].mass>maxMass) break;
v.push_back(massList[i].index);
}
sz = (int)spec.size();
memset(buffer, false, sz);
for (i = 0; i < (int)v.size(); i++) buffer[v[i]] = true;
index.clear();
for (i = 0; i < sz; i++) {
if (buffer[i]) index.push_back(i);
}
return true;
//Sort indexes and copy to final array, removing duplicates.
//This may be a potentially slow step and should be profiled
qsort(&v[0],v.size(),sizeof(int),compareInt);
index.clear();
index.push_back(v[0]);
mid=(int)v.size();
for(i=1;i<mid;i++){
if(v[i]!=v[i-1]) index.push_back(v[i]);
}
return true;
}
int KData::getCounterMotif(int motifIndex, int counterIndex){
if (motifIndex>=motifCount) return -1;
return motifs[motifIndex].counterMotif[counterIndex];
}
kLinker& KData::getLink(int i){
return link[i];
}
double KData::getMaxMass(){
if(massList.size()==0) return 0;
else return massList[massList.size()-1].mass;
}
double KData::getMinMass(){
if(massList.size()==0) return 0;
else return massList[0].mass;
}
int KData::getMotifCount(){
return motifCount;
}
int KData::getXLIndex(int motifIndex, int xlIndex){
if (motifIndex >= motifCount) return -1;
return motifs[motifIndex].xlIndex[xlIndex];
}
void KData::initHardklor(){
hs2.noBase = true;
hs4.noBase = true;
CHardklorVariant hv;
hv.addAtom(107, 2);
hv.addEnrich(107, 2, params->enrichment);
hs2.variant->push_back(hv);
hv.clear();
hv.addAtom(107, 4);
hv.addEnrich(107, 2, params->enrichment);
hs4.variant->push_back(hv);
hv.clear();
hs.winSize = hs2.winSize = hs4.winSize = 10;
hs.peptide = hs2.peptide = hs4.peptide = 4;
hs.sn = hs2.sn = hs4.sn = 0;
hs.depth = hs2.depth = hs4.depth = 3;
hs.minCharge = hs2.minCharge = hs4.minCharge = 2;
hs.maxCharge = hs2.maxCharge = hs4.maxCharge = 8;
hs.algorithm = Version2;
if (params->instrument == 1) hs.msType = hs2.msType = hs4.msType = FTICR;
else hs.msType = hs2.msType = hs4.msType = OrbiTrap;
hs.res400 = hs2.res400 = hs4.res400 = params->ms1Resolution;
hs.corr = 0.875;
hs2.corr = hs4.corr = 0.85;
hs.centroid = hs2.centroid = hs4.centroid = true;
strcpy(hs.inFile, "PLTmp.ms1");
strcpy(hs2.inFile, "PLTmp.ms1");
strcpy(hs4.inFile, "PLTmp.ms1");
hs.fileFormat = hs2.fileFormat = hs4.fileFormat = ms1;
CHardklorVariant hkv;
vector<CHardklorVariant> pepVariants;
pepVariants.clear();
pepVariants.push_back(hkv);
averagine = new CAveragine*[params->threads]();
mercury = new CMercury8*[params->threads]();
h = new CHardklor2*[params->threads]();
hO = new CHardklor*[params->threads]();
mutexHardklor = new Mutex[params->threads]();
bHardklor = new bool[params->threads]();
for (int a = 0; a<params->threads; a++){
averagine[a] = new CAveragine(NULL, NULL);
mercury[a] = new CMercury8(NULL);
if (a == 0) models = new CModelLibrary(averagine[a], mercury[a]);
h[a] = new CHardklor2(averagine[a], mercury[a], models);
h[a]->Echo(false);
h[a]->SetResultsToMemory(true);
hO[a] = new CHardklor(averagine[a], mercury[a]);
hO[a]->Echo(false);
hO[a]->SetResultsToMemory(true);
Threading::CreateMutex(&mutexHardklor[a]);
bHardklor[a] = false;
}
models->eraseLibrary();
models->buildLibrary(2, 8, pepVariants);
}
CnpxModificationInfo KData::makeModificationInfo(vector<kPepMod>& mods, string peptide, bool n15, bool nTerm, bool cTerm){
CnpxModificationInfo mi;
for (size_t i = 0; i<mods.size(); i++){
if (mods[i].pos == -1) mi.mod_nterm_mass = mods[i].mass;
else if (mods[i].pos == -2) mi.mod_cterm_mass = mods[i].mass;
else {
CnpxModAminoAcidMass maam;
maam.position=(int)mods[i].pos + 1;
maam.mass=mods[i].mass + aa.getAAMass(peptide[mods[i].pos], n15);
maam.variable=mods[i].mass;
mi.mod_aminoacid_mass.push_back(maam);
}
}
if (nTerm && aa.getFixedModMass('$') != 0)mi.mod_nterm_mass += aa.getFixedModMass('$');
if (cTerm && aa.getFixedModMass('%') != 0)mi.mod_cterm_mass += aa.getFixedModMass('%');
mi.mod_nterm_mass += aa.getFixedModMass('n');
mi.mod_cterm_mass += aa.getFixedModMass('c');
if (mi.mod_nterm_mass != 0) mi.mod_nterm_mass += 1.00782503;
if (mi.mod_cterm_mass != 0) mi.mod_cterm_mass += 17.00273963;
for (size_t i = 0; i<peptide.size(); i++){
if (aa.getFixedModMass(peptide[i])>0) {
CnpxModAminoAcidMass maam;
maam.position=(int)i + 1;
maam.mass=aa.getAAMass(peptide[i], n15);
maam.staticMass=aa.getFixedModMass(peptide[i]);
mi.mod_aminoacid_mass.push_back(maam);
}
}
return mi;