ESTCombined.h

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#ifndef ESTCOMBINED_H
#define ESTCOMBINED_H

#include "GenModel.h"
#include <string>
#include "bioseq.h"

using namespace std;

class ESTCombined {
   public:
      ESTCombined() { }
      ESTCombined(const Noschain &seg, int count, const string &chrom)
         : ex(&seg), gid(chrom), numest(count) { }
      void write(ostream& mod, ostream &exon, ostream &track, char sep='\t') const;

      static int id;  // id counter
      static int exonid; // autocounter, not multithread safe yet
      static const char modelheader[];
      static const char exonheader[];
      static const char trackheader[];

   private:
      const Noschain *ex;
      string gid;
      int numest;
};

class ESTModel : public Noschain {
   public:
      explicit ESTModel(const Noschain &seg, int nume, const string &chrom) 
         : Noschain(seg), numest(nume), gid(chrom) { }
      explicit ESTModel(const Noschain &seg, int nume, const string &chrom, const string &gs, int cngid);
      void setGenomic(const string &gs) { gseq=&gs; }
      void write(ostream& mod, ostream &exon, ostream &track, 
            ostream &ousest, ostream &ouspep, char sep='\t') const;
      const DNA& getseq() const { return estseq; }
      const Protein& getpep() const { return pep; }
      //int genomicIndex(int mrnaidx) const;

      static const char modelheader[];
      static const char exonheader[];
      static const char trackheader[];

   private:
      string gid;
      int congid; // congregate id
      int numest;
      const string *gseq;
      DNA estseq;
      int orfb, orfe; // longest orf range [b,e) C-style index
      Protein pep;

      static int id;
      static int exonid;
      static int shortestorf;
};

#endif