entry_t copy_entry(entry_t other){
entry_t r = NULL;
if(other == NULL){
return NULL;
}
switch(other->type_tag){
case ENTRY_INT:
r = new_entry_int(
other->e.scalar_int,
other->name);
break;
case ENTRY_STR:
r = new_entry_str(
other->e.scalar_str,
other->name);
break;
case ENTRY_MAP:
r = new_entry_map(copy_config(other->e.conf), other->name);
break;
case ENTRY_SEQ:
r = new_entry_seq(copy_sequence(other->e.seq), other->name);
break;
default: //NULL
r = new_entry_null();
}
return r;
}
/* make a copy for editing sequence in sequences array */
int make_copy_for_editor (int seq_id) {
int num_seq;
num_seq = sequences->num_seq;
sequences = realloc_sequences (sequences, num_seq);
sequences->sequence[num_seq] = copy_sequence (sequences->sequence[seq_id]);
extend_unique_name (sequences->sequence[num_seq]);
sequences->num_seq ++;
return num_seq;
}
/****************************************************************************
* Remove from an alignment any sequence whose ID is not in a given list.
*
* N.B. It is NOT an error for the given list to contain sequence IDs that
* are not in the alignment.
****************************************************************************/
ALIGNMENT_T* remove_alignment_seqs
(STRING_LIST_T* seqs_to_keep,
ALIGNMENT_T* alignment)
{
// Extract the names of the sequences in the alignment.
STRING_LIST_T* alignment_species = get_species_names(alignment);
int num_species = get_num_strings(alignment_species);
// Count how many sequences will be in the new alignment.
int i_species;
int num_final = 0;
for (i_species = 0; i_species < num_species; i_species++) {
char* this_species = get_nth_string(i_species, alignment_species);
if (have_string(this_species, seqs_to_keep)) {
num_final++;
} else {
if (verbosity >= NORMAL_VERBOSE) {
fprintf(stderr, "Removing %s from alignment.\n", this_species);
}
}
}
// Allocate space for the new sequences.
SEQ_T** new_sequences = (SEQ_T**)mm_malloc(num_final * sizeof(SEQ_T*));
// Copy the sequences.
int final_index = 0;
num_species = get_num_strings(seqs_to_keep);
for (i_species = 0; i_species < num_species; i_species++) {
char* this_species = get_nth_string(i_species, seqs_to_keep);
// If the requested ID is in the alignment, then copy over the sequence.
if (have_string(this_species, alignment_species)) {
SEQ_T* this_seq
= get_alignment_sequence_by_name(this_species, alignment);
new_sequences[final_index] = copy_sequence(this_seq);
final_index++;
}
}
// Allocate and return the new alignment.
char *consensus = NULL;
copy_string(&consensus, get_consensus_string(alignment));
ALIGNMENT_T* new_alignment
= allocate_alignment(get_alignment_name(alignment),
get_alignment_description(alignment),
num_final,
new_sequences,
consensus);
return(new_alignment);
}
int save_change_to_sequence (int seq_id, SEQUENCE *s) {
int i, num_seq;
num_seq = sequences->num_seq;
for (i = 0; i < num_seq; i++) {
if (seq_id == sequences->sequence[i]->id) {
free_sequence (sequences->sequence[i]);
sequences->sequence[i] = copy_sequence (s);
if (sequences->sequence[i] == NULL) return -1;
}
}
return 0;
}