head.h

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#ifndef PHEAD_H
#define PHEAD_H
#include <iostream.h>
#include <fstream.h>
#include <string>
#include <list>
#include <map>

#define LINE 83
#define DATAIDX 17    //starting index of data field
        
void getField(ifstream &ins, string &tit, char ll[]);
void getAccField(ifstream &ins, string &ff, char ll[]);
void getf(ifstream &ins, string &s, char l[], int fs);

class accession {  //for accession subfield in ref
        private:
        char acc[15];
        string status;
        string moltype;  //only required field
        string residu;
        string label;
        string crossRef;
        string expSource;
        char genetics[20];
        string note;

        public:
        void read(ifstream &ins, char ln[]);
        void clear();  //change to default empty values of all members
};
        

class ref {  //references one or more
        private:
        char key[20];
        string auth;
        string cit;  //one of journal, book, submission, citation
        string descrip; //for submission type only
        string titl;
        //string crossRef;
        string cont;
        string note;
        string acc;
        char citype[15]; //citation type
        char medid[15];
        list<accession> refacc;

        public:
        void read(ifstream &ins, char ln[]);
        void clear();

};

class genetics {
        private:
        char key[15];
        string gene;
        string gxref;
        string mapos; //map_position
        char genome[70];
        string gorigin;  //no occurance in pir1.dat
        char gcode[30];
        char startCodon[5];
        string intron;
        string otherProduct; //not found in pir1.dat
        string note;
        string mobele;
        
        public:
        genetics();
        void read(ifstream &ins, char ln[]);
        void clear();
};

class func {
        private:
        char key[60];  //this field not being used now
        string descrip;
        string pathway;
        string note;

        public:
        func();
        void read(ifstream &ins, char ln[]);
        void clear();
        void write(ostream &ou) const;
};

class feature {
        private:
        string loc;
        string feat;

        public:
        void read(ifstream &ins, char ln[]);
        void write(ostream &ous) const;
        void clear();
};

class protein {
 private:
   char entry[24];  //this is the key of the protein 
        char type[24];
        string title;
        string altName;  //alternate_name
        string contains;
        string org;
        string date;
        string acc;  //this field not processed now
        list<ref> reflist;
        string comm;
        list<genetics> genlist;
        string cplx;  //complex
        list<func> funclist;
        string superfam;
        string keywd;
        list<feature> felist;
        char *seq;
        int seqlen;
        int seqmaxlen;
        int cksm;  //checksum defined in GCG

        void creatDate(ostream &ous) const;
        void revDate(ostream &ous) const;
        void tcDate(ostream &ous) const;
        bool seqRevised() const {return date.find("#sequence_revision") != string::npos; }
        bool textChanged() const {return date.find("#text_change") != string::npos;}

 public:
        static char rel[12];  //for the release version of pir
        protein();
        ~protein();
        void read(ifstream &ins, char ln[]);  //ln should be first line
        void write(ostream &ous);
        string fname() const; //return the species object name
        string cname() const;
        bool orgNamed() const {return org.find("#formal_name") != string::npos;}
        //got scientific name
        const char *key() const {return entry;}
        void clear();
};

#endif