gfeature.h

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#ifndef GFEATURE_H
#define GFEATURE_H

#include "Range.h"
#include "validqualifier.h"
#include <vector>
//#include <set>
#include <map>

using namespace std;

class InvalidQualifier : public exception {
   public:
      InvalidQualifier(const string &msg) {
         errmsg=msg;
      }
      const char* what() const throw() { return errmsg.c_str(); }
      ~InvalidQualifier() throw() { }

   private:
      string errmsg;
};

class Gfeature {
   public:
      Gfeature() : type(), qual(0), exons(), has_start(true), has_end(true) { }
      Gfeature(vector<string> &loc, const string &ftype, map<string,string> *qls) throw (InvalidQualifier);
      ~Gfeature() { delete qual; }
      void writeGBTab() const;
      const string& getQualifier(const string &key) const;
      const string& getType() const { return type; }
      const string& featureType() const { return type; }
      //virtual void addCoding(vector<Gfeature*> &m, 
      //      vector<Gfeature*> &c) { }
      void writeGBTab(ostream &ous) const;

   protected:
      map<string,string> *qual; 
      string type;
      vector<Range> exons;
      bool has_start;
      bool has_end;

      static bool validq(const string &ql) { 
         return vq->valid(ql); }

   private:
      ostream& writeGBLocation(ostream &ous) const;

      static ValidQualifier* vq;
};

class Genefeature : public Gfeature {
   public:
      Genefeature() : Gfeature(), mRNA(), CDS() { }
      Genefeature(vector<string> &loc, const string &ftype, 
            map<string,string> *qls) throw (InvalidQualifier)  
         : Gfeature(loc,ftype,qls), mRNA(), CDS() {}
      void addCoding(vector<Gfeature*> &m, 
            vector<Gfeature*> &c) {
         mRNA=m; CDS=c; }
      const string& proteinid() const { return CDS[0]->getQualifier("protein_id"); }
      const string& product() const {
         return CDS[0]->getQualifier("product"); }
      bool deflineBetter(const string &oldef) const;
      ostream& writeGBTable(ostream &ous) const;
      int numberOfCoding() const { return CDS.size(); }

   private:
      vector<Gfeature*> mRNA;
      vector<Gfeature*> CDS;
};

#endif