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Cleanup print_outputs() #15

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Cleanup print_outputs() #15

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a464db5
Removed unreachable part of the code
nielsdg Nov 13, 2016
08dd85e
Refactor unnecessarily large if-else
nielsdg Nov 13, 2016
63528c7
Fix wrong condition in print_outputs
nielsdg Nov 13, 2016
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137 changes: 32 additions & 105 deletions hmm_lib.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1136,127 +1136,54 @@ void print_outputs(int codon_start, int start_t, int end_t, int frame, char* out
int* insert, int* c_delete, int insert_id, int delete_id, int format, char* temp_str_ptr, unsigned int multiple) {

int i;
char tab[] = "\t";

if (codon_start != 1 && codon_start != -1)
return;



if (codon_start == 1) {

//sprintf(temp_str_ptr, "%d\t%d\t+\t%d\t%lf\t", start_t, end_t, frame, final_score);
if (codon_start == 1)
sprintf(temp_str_ptr, "%d\t%d\t+\t%d\t", start_t, end_t, frame);
strcat(output_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "I:");
strcat(output_buffer, temp_str_ptr);

else
sprintf(temp_str_ptr, "%d\t%d\t-\t%d\t", start_t, end_t, frame);

for (i=0; i<insert_id; i++) {
sprintf(temp_str_ptr, "%d,", insert[i]);
strcat(output_buffer, temp_str_ptr);
}
strcat(output_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "I:");
strcat(output_buffer, temp_str_ptr);

sprintf(temp_str_ptr, "\tD:");
for (i = 0; i < insert_id; i++) {
sprintf(temp_str_ptr, "%d,", insert[i]);
strcat(output_buffer, temp_str_ptr);
}

for (i=0; i<delete_id; i++) {
sprintf(temp_str_ptr, "%d,", c_delete[i]);
strcat(output_buffer, temp_str_ptr);
}
sprintf(temp_str_ptr, "\tD:");
strcat(output_buffer, temp_str_ptr);

sprintf(temp_str_ptr, "\n");
for (i = 0; i < delete_id; i++) {
sprintf(temp_str_ptr, "%d,", c_delete[i]);
strcat(output_buffer, temp_str_ptr);
}

sprintf(temp_str_ptr, "%s_%d_%d_+\n", sequence_head_short, start_t, end_t);

if(multiple) strcat(aa_buffer, tab);

strcat(aa_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "\n");
strcat(output_buffer, temp_str_ptr);

if (codon_start == 1)
sprintf(temp_str_ptr, "%s_%d_%d_+\n", sequence_head_short, start_t, end_t);
strcat(dna_buffer, temp_str_ptr);

get_protein(dna,protein,1);
sprintf(temp_str_ptr, "%s\n", protein);
strcat(aa_buffer, temp_str_ptr);
if (format == 0) {
sprintf(temp_str_ptr, "%s\n", dna);
} else if (format == 1) {
sprintf(temp_str_ptr, "%s\n", dna_f);
}
strcat(dna_buffer, temp_str_ptr);

} else if (codon_start == -1) {
//sprintf(temp_str_ptr, "%d\t%d\t-\t%d\t%lf\t", start_t, end_t, frame, final_score);
sprintf(temp_str_ptr, "%d\t%d\t-\t%d\t", start_t, end_t, frame);
strcat(output_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "I:");
strcat(output_buffer, temp_str_ptr);

for (i = 0; i < insert_id; i++) {
sprintf(temp_str_ptr, "%d,", insert[i]);
strcat(output_buffer, temp_str_ptr);
}

sprintf(temp_str_ptr, "\tD:");
strcat(output_buffer, temp_str_ptr);

for (i=0; i<delete_id; i++) {
sprintf(temp_str_ptr, "%d,", c_delete[i]);
strcat(output_buffer, temp_str_ptr);
}

sprintf(temp_str_ptr, "\n");
strcat(output_buffer, temp_str_ptr);

else
sprintf(temp_str_ptr, "%s_%d_%d_-\n", sequence_head_short, start_t, end_t);

if(multiple) strcat(aa_buffer, tab);
strcat(aa_buffer, temp_str_ptr);
if(multiple) strcat(aa_buffer, "\t");

strcat(aa_buffer, temp_str_ptr);

sprintf(temp_str_ptr, "%s_%d_%d_+\n", sequence_head_short, start_t, end_t);
strcat(dna_buffer, temp_str_ptr);

get_protein(dna,protein,1);
sprintf(temp_str_ptr, "%s\n", protein);
strcat(aa_buffer, temp_str_ptr);
if (format == 0) {
sprintf(temp_str_ptr, "%s\n", dna);
} else if (format == 1) {
sprintf(temp_str_ptr, "%s\n", dna_f);
}
strcat(dna_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "%s_%d_%d_+\n", sequence_head_short, start_t, end_t);
strcat(dna_buffer, temp_str_ptr);

} else if (codon_start == -1) {
get_protein(dna,protein,1);
sprintf(temp_str_ptr, "%s\n", protein);
strcat(aa_buffer, temp_str_ptr);
if (format == 0)
sprintf(temp_str_ptr, "%s\n", dna);
else if (format == 1)
sprintf(temp_str_ptr, "%s\n", dna_f);

//sprintf(temp_str_ptr, "%d\t%d\t-\t%d\t%lf\t", start_t, end_t, frame, final_score);
sprintf(temp_str_ptr, "%d\t%d\t-\t%d\t", start_t, end_t, frame);
strcat(output_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "I:");
strcat(output_buffer, temp_str_ptr);

for (i = 0; i < insert_id; i++) {
sprintf(temp_str_ptr, "%d,", insert[i]);
strcat(output_buffer, temp_str_ptr);
}

sprintf(temp_str_ptr, "\tD:");
strcat(aa_buffer, temp_str_ptr);
sprintf(temp_str_ptr, "%s_%d_%d_-\n", sequence_head_short, start_t, end_t);
strcat(dna_buffer, temp_str_ptr);

get_protein(dna,protein,-1);
get_rc_dna(dna, dna1);
get_rc_dna_indel(dna_f, dna_f1);
sprintf(temp_str_ptr, "%s\n", protein);
if(multiple) strcat(aa_buffer, tab);
strcat(aa_buffer, temp_str_ptr);

if (format == 0) {
sprintf(temp_str_ptr, "%s\n", dna1);
} else if (format == 1) {
sprintf(temp_str_ptr, "%s\n", dna_f1);
}
strcat(dna_buffer, temp_str_ptr);
}
strcat(dna_buffer, temp_str_ptr);
}