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#include "base_comp.h"
#include "text_output.h"
#include "edge.h"
#include "dna_utils.h"
#include "seq_results.h"
void sequence_info(char *seq_name,
char *sequence,
int start,
int end,
int seq_structure,
int seq_type)
{
double base_comp[5];
double aa_comp[25];
char aa[] = {"ABCDEFGHIKLMNPQRSTVWYZX*-"};
int i;
double aa_mass[25];
int seq_length;
seq_length = end - start + 1;
vmessage("Sequence %s: %d to %d\n", seq_name, start, end);
if (seq_type == 1) {
if (seq_structure == 0) {
vmessage("linear ");
} else {
vmessage("circular ");
}
vmessage("DNA\n");
set_char_set(DNA);
get_base_comp(&sequence[start-1], seq_length, base_comp);
vmessage("Sequence composition\n");
vmessage("\tA %d (%.2f%%) C %d (%.2f%%) G %d (%.2f%%) T %d (%.2f%%) - %d (%.2f%%)\n",
(int)base_comp[0], base_comp[0]/seq_length*100.0,
(int)base_comp[1], base_comp[1]/seq_length*100.0,
(int)base_comp[2], base_comp[2]/seq_length*100.0,
(int)base_comp[3], base_comp[3]/seq_length*100.0,
(int)base_comp[4], base_comp[4]/seq_length*100.0);
vmessage("Mass %f\n", get_base_comp_mass((int)base_comp[0],
(int)base_comp[1],
(int)base_comp[2],
(int)base_comp[3]));
} else {
vmessage("Protein\n");
set_char_set(PROTEIN);
get_aa_comp(&sequence[start-1], seq_length, aa_comp);
get_aa_comp_mass(aa_comp, aa_mass);
/* amino acid name */
vmessage("AA ");
for (i = 0; i < 13; i++) {
vmessage(" %-5c", aa[i]);
}
vmessage("\n");
/* number of each aa */
vmessage("N ");
for (i = 0; i < 13; i++) {
vmessage("%-6g", aa_comp[i]);
}
vmessage("\n");
/* % of each aa */
vmessage("%% ");
for (i = 0; i < 13; i++) {
vmessage("%-6.1f", aa_comp[i]/seq_length*100.0);
}
vmessage("\n");
/* mass of each aa */
vmessage("M ");
for (i = 0; i < 13; i++) {
vmessage("%-6.0f", aa_mass[i]);
}
vmessage("\n\n");
/* amino acid name */
vmessage("AA ");
for (i = 13; i < 25; i++) {
vmessage(" %-5c", aa[i]);
}
vmessage("\n");
/* number of each aa */
vmessage("N ");
for (i = 13; i < 25; i++) {
vmessage("%-6g", aa_comp[i]);
}
vmessage("\n");
/* % of each aa */
vmessage("%% ");
for (i = 13; i < 25; i++) {
vmessage("%-6.1f", aa_comp[i]/seq_length*100.0);
}
vmessage("\n");
/* mass of each aa */
vmessage("M ");
for (i = 13; i < 25; i++) {
vmessage("%-6.0f", aa_mass[i]);
}
vmessage("\n");
}
}
double get_seq_mass (int seq_num)
{
double mass = 0.0;
if (GetSeqType(seq_num) == 1) {
double base_comp[5];
get_base_comp(GetSeqSequence(seq_num), GetSeqLength(seq_num),
base_comp);
mass = get_base_comp_mass((int)base_comp[0],
(int)base_comp[1],
(int)base_comp[2],
(int)base_comp[3]);
} else {
double aa_mass[25];
double aa_comp[25];
int i;
get_aa_comp(GetSeqSequence(seq_num), GetSeqLength(seq_num), aa_comp);
get_aa_comp_mass(aa_comp, aa_mass);
for (i = 0; i < 25; i++) {
mass += aa_mass[i];
}
}
return mass;
}
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