ref.h

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//file: ref.h
#ifndef REF_H
#define REF_H
#include <iostream>
#include <string>
#include <vector>
#include "gberr.h"

#ifndef LINE
#define LINE 83
#endif

enum refType {normal, thesis, unpub, submit, inpres, patent, abnormal};

class jinfo
{
 public:
        jinfo();
        /* load info from Journal Line.  Return 1 for missing vol and page
         * return 0 if normal */
        int load(const string &jl) throw(gberr); 
        void getYear(const string &jj); //if no year info year will be nothing

        /* what type of journal is, abnormal? */
        refType type;

        string key() const; //make a unique key for paper
        void clear();

        friend class ref;

 private:
        string jo;  // name of the journal, such as Science, Nature, etc.
        string vol;
        string iss;
        string pgb;
        string pge;
        string yr;
        string affil; //affiliation, deparments, universities etc.
};

class ref
{
 public:
        ref() : auth(), titl(), jnl(), med(), pubmed() { }

        /* simply read in from ins and ln without formating and processing
         * return 0 if normal; otherwise, error numbers 
         * 1 for missing vol and/or page */
        int read(istream &ins, string &ln);
        /* return 1 or higher if some error. return 0 if correct */
        int dump(ostream &seq, ostream &pap, ostream &aut);
        int writeProtein(ostream &seq, ostream &pap, ostream &aut);
        string key() const;  // make a key for paper
        string title() const { return titl; }
        
 private:
        void clear(); // needs to clear fields between succesive reads
        /*convert author string to vector<string> authorList */
        void au2list(); 
        string fullName(); //returns the full name of an author from JOURNAL if exist
        //at the same time remove the author from the JOURNAL record
        void rmSubmit();

        /* helper function only used inside this class */
        friend void rmAuthorPunc(string &s); //removes punctuations from author
        friend void rmJournalDot(string &s); //remove dots in journal names

   string auth; // AUTHOR required
        string titl; // TITLE
        string jnl;  // JOURNAL field
        string med;     // Medline key  Optional
        string pubmed;  // PUBMED key   Optional
        string rmk;  // REMARK Optional field in a reference
        jinfo parsedJ;  // parsed journal line: jnl
        vector<string> authorList;  // list of author names
};

#endif