bool CPeptideDatabase::readPepList(char* fn){
FILE* f=fopen(fn,"rt");
char pep[64];
float rt1,rt2;
int charge;
double mass;
char basePep[64];
char name[32];
int i,j;
bool bFound;
while(!feof(f)){
fscanf(f,"%s\t%f\t%f\t%d\t%lf\n",pep,&rt1,&rt2,&charge,&mass);
//match base peptide to database;
strcpy(basePep,"");
for(i=0;i<strlen(pep);i++){
if(isalpha(pep[i])) strncat(basePep,&pep[i],1);
}
//iterate through all proteins for match
bFound=false;
for(i=0;i<vDB.size();i++){
if(strstr(&vDB[i].strSeq[0],basePep)!=NULL){
bFound=true;
strncpy(name,&vDB[i].strName[0],31);
name[31]='\0';
addPeptide(pep,name,rt1,rt2,charge,mass);
}
}
if(!bFound) cout << basePep << " not found." << endl;
}
fclose(f);
return true;
}
ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
int groupId)
: name_(name), q_(0.0), qemp_(0.0), pep_(0.0), p_(0.0), score_(0.0),
isDecoy_(isDecoy), groupId_(groupId), specCountsUnique_(0u), specCountsAll_(0u) {
if (!peptide.name.empty()) addPeptide(peptide);
}