cDeNovoGraph.h

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#ifndef _CDENOVOGRAPH_H
#define _CDENOVOGRAPH_H
 
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
 
#include "core/cParameters.h"
#include "core/cDeNovoGraphNode.h"
#include "core/cPeakListSeries.h"
#include "core/cBricksDatabase.h"
#include "core/cTheoreticalSpectrumList.h"
#include "parallel/cGraphReaderThread.h"
 
class cMainThread;
 
 
using namespace std;
 
 
const long long unsigned maximumcandidates = 1000000000;
 
 
bool compareNodes(cDeNovoGraphNode& node1, cDeNovoGraphNode& node2);
 
 
class cDeNovoGraph {
 
    cParameters* parameters;
    vector<cDeNovoGraphNode> graph;
    cPeaksList sortedpeaklist;
    cBricksDatabase bricksdatabasewithcombinations;
    int lastsystemnode;
    cMainThread* os;
    int startnode;
 
    cGraphReaderThread* graphreaderthread;
 
    bool findPath(int sourcenodeid, int edgeid, int targetnodeid, string& composition, string brickspath, int maximumbricksincombination, vector<nodeEdge>& path, bool& terminatecomputation);
 
    // create vectors of edges from temporary unordered_sets
    void createVectorsOfEdges();
 
    // check whether a path leads to the precursor
    bool finishInPrecursor(int currentnode, double cummass);
 
 
public:
 
    cDeNovoGraph();
 
 
    void initialize(cMainThread& os, cParameters& parameters);
 
 
    int createGraph(bool& terminatecomputation);
 
 
    int removeEdgesFormingPathsNotFinishingInPrecursor(bool& terminatecomputation);
 
 
    int removeEdgesFormingPathsNotStartingFromFirstNode(bool& terminatecomputation);
 
 
    int connectEdgesFormingPathsNotFinishingInPrecursor(bool& terminatecomputation);
 
 
    int connectEdgesFormingPathsNotStartingFromFirstNode(bool& terminatecomputation);
 
 
    int removePathsWhichCanBeSubstitutedByLongerPath(bool& terminatecomputation);
 
 
    void startGraphReader(cCandidateSet& candidates, long long unsigned& count, int scanmode, bool& terminatecomputation);
 
 
    int getNumberOfEdges();
 
 
    void printPaths(cMainThread* os, cDeNovoGraphNode& node, vector<string>& path, vector<string>& composition);
 
 
    string printGraph();
 
 
    cDeNovoGraphNode& operator[](int position);
 
 
    void sortEdgesByPPMError();
 
    
    void sortEdgesByTargetNodeIntensity();
 
    
    cBricksDatabase* getBrickDatabaseWithCombinations();
 
};
 
 
#endif