seqinfo.h

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//file:seqinfo.h for use by feature1.h and gbhead.h
#ifndef SEQINFO_H
#define SEQINFO_H
#include <set>
//#include <vector>
#include <string>
#include "strformat.h"

/* should have just one count for all subsequences */
struct seqinfo {
   const char* name() const {return acc;}
   //for GB sequences their key name is represented by acc
   char type[20]; //such as ss-RNA, mRNA, DNA,  etc.  
        bool linear;
   char acc[20];
   char org[60];
   char locus[17];  // is getting longer!
        char seg[12];
   char div[4];
   int len;
        int cdsCount;   // count CDS subsequences
        int sourCount;  // source sequence count
        int mrnaCount;  // count mRNA subsequences
        int rnaCount;
        int rptCount; //repeat_region count
        int tokCount;
        int subcnt;  // count all subsequences, safer and faster; all the
        // other counts can be removed in the future

        seqinfo();
        bool isseg() const {return seg[0] != '\0';}
        void nameseg(char sgn[]) const; //obtain a name for the segseq
        //based on locus name
        //vector<string> sk; //all subkeys for this sequence
        set<string> sk; //all subkeys for this sequence
        //sometimes subkey generated may have the same name
        
        // helper function
        void getcntstr(char cntstr[]) { itoa(subcnt++, cntstr); }

        /* get count as string */
        string getcntstr();
};

#endif