int main(int argc, const char *argv[]) {
simple_loops();
conditionals();
early_exits();
jumps();
switches();
big_switch();
boolean_operators();
boolop_loops();
do_fallthrough();
static_func();
return 0;
}
int jump(vector<int>& nums) {
if(nums.size() <= 1)return 0;
vector<int> jumps(nums.size(),2147483647);
jumps[0] = 0;
int pos=0;
for(int i=0;i<nums.size();i++){
if(i+nums[i] > pos){
if(i+nums[i] >= nums.size()-1)return jumps[i]+1;
for(int j=pos+1;j<=i+nums[i];j++){
jumps[j] = jumps[i]+1;
}
pos = i+nums[i];
}
}
return jumps[nums.size()-1];
}
int main(int argc, char **argv) {
InputParams params; vector<char *> paramStrs; paramStrs.resize(2);
paramStrs[0] = "INPUT_FASTA";
paramStrs[1] = "OUTPUT_FILES_PREFIX";
if(argc==1) params.readParams("tagsearchspecs.params"); else params.readParams(argv[1]);
if(!params.confirmParams(paramStrs)) {
cerr << "ERROR: Parameters file ";
if(argc==1) cerr<<"tagsearchspecs.params"; else cerr<<argv[1];
cerr << " is incomplete. One of the following is missing: INPUT_FASTA, OUTPUT_FILES_PREFIX\n";
return -1;
}
char *dbFN = params.getValue(paramStrs[0]);
char *outputPrefix = params.getValue(paramStrs[1]);
unsigned int tagLen = params.paramPresent("TAG_LEN")?(unsigned int) params.getValueInt("TAG_LEN"):6;
unsigned int maxNumMissedPeaks = params.paramPresent("MAX_MISSED_PEAKS")?(unsigned int) params.getValueInt("MAX_MISSED_PEAKS"):1;
// int numJumps = params.paramPresent("DOUBLE_AA_JUMPS")?(int) params.getValueInt("DOUBLE_AA_JUMPS"):1;
// short minMatchFlanking = params.paramPresent("MATCH_TAG_FLANKING_MASSES")?(short) params.getValueInt("MATCH_TAG_FLANKING_MASSES"):1;
// float minRatio = params.paramPresent("MIN_RATIO")?(float) params.getValueDouble("MIN_RATIO"):0;
float peakTol = params.paramPresent("TOLERANCE_PEAK")?(float) params.getValueDouble("TOLERANCE_PEAK"):0.5;
// float pmTol = params.paramPresent("TOLERANCE_PM")?(float) params.getValueDouble("TOLERANCE_PM"):1;
int specType = params.paramPresent("SPEC_TYPE_MSMS")?((int) params.getValueInt("SPEC_TYPE_MSMS")?1:0):0;
float ionOffset = specType?AAJumps::massHion:0;
bool maxParsimony = (bool)params.paramPresent("MAX_PARSIMONY")?((int) params.getValueInt("MAX_PARSIMONY")?1:0):0;
float maxCharge = params.paramPresent("MAX_PEAK_CHARGE")?(float) params.getValueDouble("MAX_PEAK_CHARGE"):1.0;
float missingPeakPenalty = params.paramPresent("PENALTY_MISSING_PEAK")?(float) params.getValueDouble("PENALTY_MISSING_PEAK"):-1.0;
float noisePeakPenalty = params.paramPresent("PENALTY_NOISE_PEAK")?(float) params.getValueDouble("PENALTY_NOISE_PEAK"):-1.0;
SpecSet specSet; short loadOk=0;
if(params.paramPresent("INPUT_SPECS")) loadOk=specSet.LoadSpecSet_pkl(params.getValue("INPUT_SPECS"));
else if(params.paramPresent("INPUT_SPECS_PKLBIN")) loadOk=specSet.LoadSpecSet_pklbin(params.getValue("INPUT_SPECS_PKLBIN"));
if (loadOk<=0 or specSet.size()==0) { cerr<<"Error loading spectra!\n"; return -1; }
vector<float> specScores(specSet.size());
for(unsigned int specIdx=0; specIdx<specSet.size(); specIdx++) {
specSet[specIdx].addZPMpeaks(peakTol, ionOffset, true);
specScores[specIdx]=0; for(unsigned int peakIdx=0; peakIdx<specSet[specIdx].size();peakIdx++) specScores[specIdx]+=specSet[specIdx][peakIdx][1];
}
DB_fasta db; if(db.Load(dbFN)<=0) return -1;
db.replaceAA('L','I'); db.replaceAA('K','Q');
FILE *pepsFID = (FILE *)fopen("tmp_matches.txt","wb");
fprintf(pepsFID,"SpecIdx\tPeptide\tTag pos\tTag score\tPerc peptide score\tProtIdx\tProtein\n");
vector<Tag> tags; AAJumps jumps(1);
list<pair<int,string> > matches;
vector<list<ProteinMatch> > proteinHits(specSet.size()); ProteinMatch curMatch; string tmpString;
vector<list<unsigned int> > matchedTagsIdx; list<unsigned int>::iterator iterIdx;
vector<list<float> > matchedTagsScores; list<float>::iterator iterScores;
vector<list<unsigned int> > matchedTagsPos; list<unsigned int>::iterator iterPos;
for(unsigned int protIdx=0; protIdx<db.size(); protIdx++) {
cout<<"Processing protein "<<protIdx+1<<" out of "<<db.size()<<"..."; cout.flush();
if(ExtractTags(db[protIdx], tags, tagLen)) {
//cerr<<"Tags: "; for(unsigned int i=0;i<tags.size();i++) cerr<<"("<<i<<","<<tags[i].asString(tmpString)<<")"; cerr<<"\n"; cerr.flush();
MatchTagsToSpectra(specSet,tags,peakTol,maxCharge,missingPeakPenalty,noisePeakPenalty,maxNumMissedPeaks,matchedTagsIdx,matchedTagsScores,matchedTagsPos);
for(unsigned int specIdx=0; specIdx<specSet.size(); specIdx++)
if(matchedTagsIdx[specIdx].size()) {
iterScores = matchedTagsScores[specIdx].begin();
iterPos = matchedTagsPos[specIdx].begin();
for(iterIdx=matchedTagsIdx[specIdx].begin(); iterIdx!=matchedTagsIdx[specIdx].end(); iterIdx++,iterScores++,iterPos++) {
curMatch.set(protIdx,*iterScores,(*iterScores)/specScores[specIdx],tags[*iterIdx].asString(tmpString),specSet[specIdx][*iterPos][0]);
proteinHits[specIdx].push_back(curMatch);
}
}
}
cout<<"done\n"; cout.flush();
}
vector<list<int> > simpleProteinHits(specSet.size());
if(maxParsimony) {
for(unsigned int specIdx=0; specIdx<specSet.size(); specIdx++) { simpleProteinHits[specIdx].clear();
for(list<ProteinMatch>::iterator iter=proteinHits[specIdx].begin(); iter!=proteinHits[specIdx].end(); iter++)
simpleProteinHits[specIdx].push_back(iter->protIdx);
}
MaximumParsimony(simpleProteinHits);
}
for(unsigned int specIdx=0; specIdx<specSet.size(); specIdx++) { if(proteinHits[specIdx].empty()) continue;
for(list<ProteinMatch>::iterator iter=proteinHits[specIdx].begin(); iter!=proteinHits[specIdx].end(); iter++) {
if(maxParsimony and simpleProteinHits[specIdx].front()!=iter->protIdx) continue;
curMatch = *iter;
fprintf(pepsFID,"%d\t%s\t%.1f\t%.1f\t%.1f\t%d",specIdx+1,curMatch.peptide.c_str(),curMatch.tagPos,curMatch.score,curMatch.percScore,curMatch.protIdx);
fprintf(pepsFID,"\t%s %s\n",db.getID(curMatch.protIdx),db.getDesc(curMatch.protIdx));
}
}
fclose(pepsFID);
return 0;
}
