kzseq.h

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#ifndef KZ_SEQ_H
#define KZ_SEQ_H
#include <fstream.h>
#include <sys/types.h>

/* $Id: kzseq.h,v 1.1.1.1 2007-07-13 03:44:06 kzhou Exp $ */

class kzseq {
 private:
        char *seq;        //the sequence data string 
        //stored in UPPER case
        char *header;
        int slen; /* bytes in seq, not including '\0' */
        int maxlen; //maximum allocated space 
        bool rc;  //wheather the seq string is derived from
        //the original sequence by reverse-complement

 public:
        kzseq();
        kzseq(int alloc);  //if alloc = 0, no allocation of 
        //dynamic memory
        ~kzseq();
        bool readSeq(ifstream &infs, char ln[]);  
        //reads in the one sequence at 
        //a time, return true if success 
        //will use old allocated memory
        void fastRead(caddr_t hstart, caddr_t sstart, size_t seqLen);
        const char* seqchar() const {return seq; }
        int seqlen() const { return slen; }
        int headlen() const { return strlen(header); }
        const char* seqhead() const {return header; }
        const char* getHeader() const { return header; }
        void getName(char name[]) const;
        void revcomp(char rc[]) const; //create an reverse complement string
        //the String will be in UPPER case
        kzseq& revcomp(); //reverse complement the sequence only
        //the resulting sequence string will be in UPPER case
        //the original sequence will be changed
        void seq2upper();
        void polyATsize(int &pA, int &pT) const;
        bool isDNA() const;
        kzseq &operator=(const kzseq &ks);
        void copyRevcomp(const kzseq &ks);  //creates a copy and reverse-complement it
};

unsigned long* readIndex(char inf[], int &seqCnt);
#endif