Gmapres.h

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#ifndef GMAPRES_H
#define GMAPRES_H

#include "GenModel.h"
#include <iostream>
#include <fstream>
#include "Range.h"
#include <set>

using namespace std;

//vector<int> getNumbers(const string &str);
//string deleteChr(const string &str, char c);
//int getInt(const string &str);
//getInt and getNumbers moved to strforamt.h

//pair<string,string> breakString(const string &str, const string &sep);
//void trimLeadingSpace(string &str);

class Gmapalnseg {
   public: 
      Gmapalnseg() { }
      Gmapalnseg(const string &ln);
      Gmapalnseg(const Gmapalnseg &ga) : cr(ga.cr), gr(ga.gr), iden(ga.iden) { }
      Gmapalnseg(const vector<int> &row);
      ~Gmapalnseg() { }
      friend ostream& operator<<(ostream &ous, const Gmapalnseg &as);
      const Range& grange() const { return gr; }
      int length() const { return min(cr.length(), gr.length()); }
      int identity() const { return iden; }
      int idenxlen() const { return length() * iden; }
      const Range& cDNARange() const { return cr; }
      const Range& genomicRange() const { return gr; }

   private:
      Range cr, gr;
      int iden;
};

class Gmapath {
   public:
      Gmapath() { }
      Gmapath(const string &pathstr, const string &dircstr, 
            const string &covstr, const string &tcovstr, const string &idenstr);
      ~Gmapath();
      void addAlnSeg(Gmapalnseg *as) { align.push_back(as); }
      void assignAln(vector<Gmapalnseg*> &as);
      friend ostream& operator<<(ostream &ous, const Gmapath &pa);
      Noschain makeNoschain();
      Alnchain makeAlnchain();
      Alnchainid makeAlnchainid(const string &estid);

      Alnchainid* makeAlnchainidPtr(const string &estid);
      int modelDirection() const { return modirect; }
      void setDirection(int d) { modirect=d; }
      char genomicDirection() const { return grange.direction(); }
      string genomicId() const { return gid; }
      double getIdentity() const { return iden; }
      double getCoverage() const { return cov; }
      int numberOfSegments() const { return align.size(); }
      bool emptyAlignment() const { return align.empty(); }
      bool isGood() const;
      int alnLength() const;
      void trimEnds();

      static void setTrimCutoff(float ct) { trimcutoff=ct; }
      static void setMinimumLength(int min) { minLEN=min; }
      static void setMinimumCoverage(float min) { minCOV=min; }
      static void setMinimumIdentity(float min) { minIDEN=min; }
      static void setTrimShortIntronlen(int min) { trimShortIntronlen=min; }


   private:
      // should use the index of the array in holding class
      //int pathid;
      int modirect; // +1 for +, -1 for -, 0 for ?
      string gid;
      double cov, trimcov, iden;
      int match, mismatch, indel, unknown;
      Range crange, grange;
      int estlen;
      vector<Gmapalnseg*> align;

      static float trimcutoff;
      static int alnlenL;
      static int minLEN;
      static float minCOV;
      static float minIDEN;
      static int trimShortIntronlen;
};

class Gmapres {
   public:
      Gmapres() { }
      Gmapres(const string &id, int np) : cid(id), numpath(np), paths() { }
      ~Gmapres();
      void addPath(Gmapath &gp) { paths.push_back(&gp); }
      void addPath(Gmapath *gp) { paths.push_back(gp); }
      void addAlignment(vector<Gmapalnseg*> &aln, int idx);
      friend ostream& operator<<(ostream &ous, const Gmapres &res);
      void storeChain(map<string, set<Noschain> > &chainstore, float idencut);
      void storeChain(map<string, map<Alnchain,int> > &chainstore);
      void storeChain(map<string, set<Alnchainid> > &chainstore);
      void storeChain(map<string, set<Alnchainid*, lessChainPtr> > &chainstore);
      int strandByESTName() const;
      void guessDirection();
      const string& ESTId() const { return cid; }

      /*
      static void setMinimumLength(int lc) { minpathlength=lc; }
      static void setMinimumCoverage(double mc) { mincoverage=mc; }
      static void setMinimumIdentity(double mi) { minidentity=mi; }
      */
      static void setMaximumIntron(int maxil) { maxintron=maxil; }
      static void setMinimumIntron(int minil);
      static void setDangleExon(const pair<int,int> &dang) { dangleinlen=dang.first; danglexlen=dang.second; }


   private:
      int numpath;
      vector<Gmapath*> paths;
      string cid; // cDNA identifer string

      //static int minpathlength;
      //static double mincoverage;
      //static double minidentity;

      static int maxintron;
      static int minintron;
      static int dangleinlen;
      static int danglexlen;
};

#endif