head.h

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#ifndef GBHEAD_H
#define GBHEAD_H
#include <iostream>
#include "seqinfo.h"
#include "date.h"

#ifndef LINE
#define LINE 84
#endif

/*file: head.h
 * model representing header information of each GenBank record
 * The part that is not repeated
 * From LOCUS to REFERENCE */

class head
{
  public:
   head();
   head(const head& hd);
   ~head();

         /* read from LOCUS line to ORGANISM */
   void getHead(istream &ins, char ln[]);

        /* parse the first line of GenBank record into a seqinfo object and 
         * a Date objects */
   void loadSeqInfo(seqinfo &si, Date &gd);
        /* If the header contains the SEGMENT     1 of 2
         * or not 
         * */
   bool isseg() const {return seg[0] != '\0';}
        /* if the first segment
         * */
   bool firstSeg() const;
        /* for output
         */
   void segmentOut(ostream &SOUF, char ss[], const seqinfo &mseq) const;
   //ss is the name for the seqmented sequence
   char *phylogeny() const;

         /* get SOURCE as char pointer */
         inline char* getSource() const { return source; }
         //char *getSource() const;
         inline char* getOrganism() const { return org; }

         /* dump in the ace format; I am discarding SOURCE=human */
   void dump(ostream &SOUF, seqinfo &si) const;
   friend ostream &operator<<(ostream &ous, const head &h);
   //this one is only used for debuging aid
   
  private:
   void outAcc(ostream &so) const;
   char locus[LINE+1];   // the Locus line
   char ver[35]; 
        char seg[12];

   /* source may contain organism or organ or cell type
    * info, not well organiszed; I found this not useful and often
         * redundant with the source feature. I am discarding this field if it
         * is just human. 
    */
         char *source;

   char *def, *acess, *keywd, *org, *phyl;
   //release 115.0 has eliminted the NID line!!!
   //but some recoreds still contains it!!
   //program has to deal with this at this time 2000-05-02
};
#endif