source: tags/initial/NALIGNER/ali_sequence.hxx

#ifndef _ALI_SEQUENCE_INC_
#define _ALI_SEQUENCE_INC_

#include <string.h>
#include <malloc.h>

#include "ali_misc.hxx"


class ALI_SEQUENCE {
        unsigned char *seq;
        char *seq_name;
        unsigned long seq_len;
public:
        ALI_SEQUENCE(char *name, char *str) {
                seq = (unsigned char *) str;
                seq_len = strlen(str);
                seq_name = strdup(name);
                ali_string_to_sequence(str);
                if (seq_name == 0) ali_fatal_error("Out of memory");
        }
        ALI_SEQUENCE(char *name, unsigned char *str, unsigned long str_len) {
                seq = str;
                seq_len = str_len;
                seq_name = strdup(name);
        }
        ~ALI_SEQUENCE(void) {
                if (seq)
                        free((char *) seq);
                if (seq_name)
                        free((char *) seq_name);
        }
        unsigned char *sequence(void) {
                return seq;
        }
        unsigned char base(unsigned long position) {
                return seq[position];
        }
        int check(void);
        char *string(void); 
        char *name(void) {
                return seq_name;
        }
        unsigned long length(void) {
                return seq_len;
        }
};


class ALI_NORM_SEQUENCE {
        unsigned char *seq;
        char *seq_name;
        unsigned char **dots;
        unsigned long seq_len;
public:
        ALI_NORM_SEQUENCE(char *name, char *str);
        ALI_NORM_SEQUENCE(ALI_SEQUENCE *sequence);
        ~ALI_NORM_SEQUENCE(void) {
                if (seq)
                        free((char *) seq);
                if (seq_name)
                        free((char *) seq_name);
                if (dots)
                        free((char *) dots);
        }
        unsigned char *sequence(void) {
                return seq;
        }
        unsigned char base(unsigned long position) {
                return seq[position];
        }
        char *string(void);
        char *name(void) {
                return seq_name;
        }
        unsigned long length(void) {
                return seq_len;
        }
        int is_begin(unsigned long pos) {
                if (dots == 0)
                        return 0;
                else {
                   if (pos > seq_len)
                        return 1;
                        else
                      return (((*dots)[pos/8] & (unsigned char) (1<<(7-(pos%8)))) != 0);
                }
        }
};

#endif