std::vector<std::string> IndexedFastaReader::Names(void) const
{
REQUIRE_FAIDX_LOADED;
std::vector<std::string> names;
names.reserve(NumSequences());
for (size_t i = 0; i < NumSequences(); ++i)
names.push_back(faidx_iseq(handle_, i));
return names;
}
std::string IndexedFastaReader::Name(const size_t idx) const
{
REQUIRE_FAIDX_LOADED;
if (idx >= NumSequences())
throw std::runtime_error("FASTA index out of range");
return std::string(faidx_iseq(handle_, idx));
}
/*
* set the "active" sequence in a given direction
*/
int
Set_Active_Seq(int seq_num,
int direction)
{
/* nip */
if (direction == -1)
active_seq = seq_num;
if (direction == HORIZONTAL) {
horizontal = seq_num;
} else if (direction == VERTICAL) {
vertical = seq_num;
} else {
return -1;
}
/*
* HACK to deal with h and v set to be the same value, default to the
* latest change and set the other to be -1
*/
/* if (horizontal == vertical) {
if (direction == HORIZONTAL){
vertical = -1;
} else if (direction == VERTICAL) {
horizontal = -1;
}
}*/
/*yy:Set horizontal sequence as active sequence in sequence array
*/
if (horizontal == vertical){
if (direction == HORIZONTAL) {
vertical = -1;
}else if (direction == VERTICAL) {
if( NumSequences() > 1 ){
horizontal = 0;
}else if (NumSequences()==1) {
vertical = -1;
horizontal = 0;
}
}
}
return 0;
}
/* check if adding same sequence name, if are, remove previous seq */
void RemoveDuplicateSeq(Tcl_Interp *interp,
char *name)
{
int n_seqs;
int i;
/*
* need to check if entry_name already exists in the database. If it does
* then must delete current sequence (and all its results) and add the
* new entry_name
*/
n_seqs = NumSequences();
for (i = 0; i < n_seqs; i++) {
if (strcmp(name, GetSeqName(i)) == 0) {
verror(ERR_WARN, "RemoveDuplicateSeq",
"%s already exists in. Removing previous sequence and adding new sequence\n", name);
DeleteSequence(interp, i--);
n_seqs--;
}
}
}
