Exemple #1
0
    DBL_MATRIX PeakListCollection::mergeAll(double drt, double dmz, double dz, double dint)
    {
        //preprocessing: delete empty PeakLists from c_
        for(unsigned int i = 0; i < c_.size(); i++){
            if(c_[i].size() == 0){
                c_.erase(c_.begin() + i);
            }
        }

        unsigned int oldSize = c_.size();

        // initialization

        //fill correspondenceMap with rt-values
        correspondenceMap_.clear();
        correspondenceMap_.resize(oldSize);

        for(unsigned int i = 0; i < oldSize; i++){
            correspondenceMap_[i].resize(c_[i].size());
            for(unsigned int j = 0; j < c_[i].size(); j++){
                //create map_item to write to correspondenceMap
                map_item tempItem;
                //origin information contains the PeakList index and rt value
                originInformation o;
                o.rt = c_[i][j].getRt();
                o.mz = c_[i][j].getMz();
                o.intensity = c_[i][j].getAbundance();
                o.originPeakList = i;
                o.originPeak = j;
                tempItem.push_back( o );
                correspondenceMap_[i][j] = tempItem;
            }
        }

        //PeakLists are not merged in the beginning --> fill with 1
        plContent_.clear();
        plContent_.resize(oldSize,1);

        //build distance matrix
        DistanceMatrix D = buildDistanceMatrix_(drt,dmz,dz,dint);

        //merge, until there is only one PeakList left

        while(D.size() > 1){
            //find cheapest assignment
            unsigned int merge_lower = D.getMin_LowerIndex();
            unsigned int merge_upper = D.getMin_HigherIndex();

            //merge peaklists into a new one
            mergePeakLists_(merge_lower, merge_upper, c_, drt, dmz, dz, dint);

            //update distance matrix
            updateDistanceMatrix_(D, merge_lower, merge_upper, drt, dmz, dz, dint);
        }

        return calculateRtCorrespondencesFromCorrespondenceMap_(oldSize);

    }
Exemple #2
0
    DBL_MATRIX PeakListCollection::getAlignment(double drt, double dmz, double dz, double dint, AccelerationFlag flag = NORMAL, int param = 0)
    {

        //Create a copy of c_ to work on
        std::vector<PeakList> pls = c_;

        unsigned int oldSize = pls.size();

        // initialization

        //fill correspondenceMap with rt-values
        correspondenceMap_.clear();
        correspondenceMap_.resize(oldSize);

        for(unsigned int i = 0; i < oldSize; i++){
            correspondenceMap_[i].resize(pls[i].size());
            for(unsigned int j = 0; j < pls[i].size(); j++){
                //create map_item to write to correspondenceMap
                map_item tempItem;
                //origin information contains the PeakList index and rt value
                originInformation o;
                o.rt = c_[i][j].getRt();
                o.mz = c_[i][j].getMz();
                o.intensity = c_[i][j].getAbundance();
                o.originPeakList = i;
                o.originPeak = j;
                tempItem.push_back( o );
                correspondenceMap_[i][j] = tempItem;
            }
        }

        //PeakLists are not merged in the beginning --> fill with 1
        plContent_.clear();
        plContent_.resize(oldSize,1);

        DistanceMatrix D;
        if(flag == NORMAL){
            //build distance matrix
            D = buildDistanceMatrix_(drt,dmz,dz,dint);
        }

        if(flag == REFERENCE){
            //first, merge PeakList n with one other --> last PeakList contains PeakList n
            if(param==0){
                //select first two peaklists
                unsigned int merge_lower = param;
                unsigned int merge_upper = 1;

                //merge peaklists into a new one
                mergePeakLists_(merge_lower, merge_upper, pls, drt, dmz, dz, dint);
            }else{
                //select first and n'th PeakList
                unsigned int merge_lower = 0;
                unsigned int merge_upper = param;

                //merge peaklists into a new one
                mergePeakLists_(merge_lower, merge_upper, pls, drt, dmz, dz, dint);
            }
        }

        //merge, until there is only one PeakList left
        bool exit = false;
        while(!exit){
            //find cheapest assignment
            unsigned int merge_lower = 0;
            unsigned int merge_upper = 1;
            switch(flag){
            case NORMAL:
                merge_lower = D.getMin_LowerIndex();
                merge_upper = D.getMin_HigherIndex();
                break;

            case FAST:
                //select last two PeakList
                merge_lower = pls.size()-2;
                merge_upper = pls.size()-1;
                break;

            case REFERENCE:
                //select last two PeakList
                merge_lower = pls.size()-2;
                merge_upper = pls.size()-1;
                break;
            }

            //merge peaklists into a new one
            mergePeakLists_(merge_lower, merge_upper, pls, drt, dmz, dz, dint);


            switch(flag){
            case NORMAL:
                //update distance matrix
                updateDistanceMatrix_(D, merge_lower, merge_upper, drt, dmz, dz, dint);
                if(D.size()==1){
                    exit = true;
                }
                break;

            case FAST:
                if(pls.size()==1){
                    exit = true;
                }
                break;

            case REFERENCE:
                if(pls.size()==1){
                    exit = true;
                }
                break;
            }
        }

        DBL_MATRIX rtc = calculateRtCorrespondencesFromCorrespondenceMap_(oldSize);

        return rtc;


    }