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// =============================================================== //
// //
// File : ali_sequence.cxx //
// Purpose : //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include "ali_sequence.hxx"
// ---------------------
// ALI_SEQUENCE
int ALI_SEQUENCE::check()
{
unsigned char *seq_buf;
unsigned long i;
seq_buf = seq;
for (i = 0; i < seq_len; i++, seq_buf++)
if (*seq_buf > 6)
ali_fatal_error("STOP");
return 1;
}
char *ALI_SEQUENCE::string()
{
char *str, *str_buf;
unsigned char *seq_buf;
unsigned long i;
str = (char *) CALLOC((unsigned int) seq_len + 1, sizeof(char));
str_buf = str;
seq_buf = seq;
for (i = 0; i < seq_len; i++) {
*(str_buf++) = *(seq_buf++);
}
*str_buf = '\0';
ali_sequence_to_string((unsigned char*) str, seq_len);
return str;
}
// --------------------------
// ALI_NORM_SEQUENCE
ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(char *Name, char *String)
{
unsigned long counter;
unsigned char *s;
int dot_flag;
char *str;
// Count only _BASES_
for (counter = 0, str = String; *str != '\0'; str++)
if (ali_is_base(*str))
counter++;
seq_len = counter;
seq = (unsigned char*) CALLOC((unsigned int) seq_len, sizeof(unsigned char));
dots = (unsigned char **) CALLOC((unsigned int) (seq_len/8)+1, sizeof(unsigned char));
seq_name = strdup(Name);
if (seq == 0 || dots == 0 || seq_name == 0) {
ali_fatal_error("Out of memory");
}
dot_flag = 0;
(*dots)[0] |= (unsigned char) (1<<7);
for (counter = 0, str = String, s = seq; *str != '\0'; str++) {
if (ali_is_base(*str)) {
*s++ = ali_base_to_number(*str);
dot_flag = 0;
counter++;
}
else {
if (dot_flag == 0 && ali_is_dot(*str)) {
(*dots)[(counter/8)] |= (unsigned char) (1<<(7-(counter%8)));
dot_flag = 1;
}
}
}
}
ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(ALI_SEQUENCE *SEQ)
{
unsigned long counter, pos;
unsigned char *s;
int dot_flag;
unsigned char *str;
for (counter = pos = 0, str = SEQ->sequence();
pos < SEQ->length(); pos++, str++)
if (ali_is_base(*str))
counter++;
seq_len = counter;
seq = (unsigned char*) CALLOC((unsigned int) seq_len, sizeof(unsigned char));
dots = (unsigned char **) CALLOC((unsigned int) (seq_len/8)+1, sizeof(unsigned char));
seq_name = strdup(SEQ->name());
if (seq == 0 || dots == 0 || seq_name == 0) {
ali_fatal_error("Out of memory");
}
dot_flag = 0;
(*dots)[0] |= (unsigned char) (1<<7);
for (counter = pos = 0, str = SEQ->sequence(), s = seq;
pos < SEQ->length(); str++, pos++) {
if (ali_is_base(*str)) {
*s++ = *str;
dot_flag = 0;
counter++;
}
else {
if (dot_flag == 0 && ali_is_dot(*str)) {
(*dots)[(counter/8)] |= (unsigned char) (1<<(7-(counter%8)));
dot_flag = 1;
}
}
}
}
char *ALI_NORM_SEQUENCE::string()
{
char *str, *str_buf;
unsigned char *seq_buf;
unsigned long i;
str = (char *) CALLOC((unsigned int) seq_len + 1, sizeof(char));
if (str == 0)
ali_fatal_error("Out of memory");
for (i = seq_len, str_buf = str, seq_buf = seq; i-- > 0;)
*str_buf++ = *seq_buf++;
*str_buf = '\0';
ali_sequence_to_string((unsigned char*) str, seq_len);
return str;
}
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