//------------------------------------------------------------
static void
writeLCF(BookCaseDB& db, info_lib *mmdb,
const char *bcname,
hashTable<CC_String,BTCollectable> &hd)
{
DBTable *out = db.DB::table(DATABASE_STDIO,
LOCATOR_CODE, BT_NUM_LOCATOR_FIELDS,
DB::CREATE);
hashTableIterator<CC_String,BTCollectable> loc_it( hd );
while ( ++loc_it ) {
CC_String *locator_str = ( CC_String *)loc_it.key();
const char *locator = (const char *)*locator_str;
BTCollectable *loc_val = ( BTCollectable *)loc_it.value();
const char *opaque, *nodeloc;
char* reflabel;
nodeloc = opaque = (const char *)loc_val->get_value();
reflabel = strchr(opaque, '\t');
*reflabel++ = 0;
const char *nodeOID = to_oid(mmdb, bcname, nodeloc);
#ifdef FISH_DEBUG
DBUG_PRINT("LCF", ("LCF entry: L:%s->O:%s\n",
locator, nodeOID));
#endif
out->insert(STRING_CODE, locator,
OID_CODE, nodeOID,
STRING_CODE, reflabel,
NULL);
}
delete out;
}
void CFeatTrim::x_TrimLocation(const TSeqPos from, const TSeqPos to,
const bool set_partial,
CRef<CSeq_loc>& loc)
{
if (loc.IsNull()) {
return;
}
bool partial_start = false;
bool partial_stop = false;
const auto strand = loc->GetStrand();
for(CSeq_loc_CI loc_it(*loc); loc_it; ++loc_it) {
const auto& current_range = loc_it.GetRange();
const auto current_from = current_range.GetFrom();
const auto current_to = current_range.GetTo();
CRef<CSeq_id> current_seqid = Ref(new CSeq_id());
current_seqid->Assign(loc_it.GetSeq_id());
// May be able to do this more succinctly and efficiently using CSeq_loc::Intersect
if ((current_to < from) ||
(current_from > to)) {
CRef<CSeq_loc> trim(new CSeq_loc(*current_seqid,
current_from,
current_to,
strand));
loc = loc->Subtract(*trim, 0, NULL, NULL);
if (current_to < from) {
partial_start = true;
}
if (current_from > to) {
partial_stop = true;
}
continue;
}
if (current_from < from) {
CRef<CSeq_loc> trim(new CSeq_loc(*current_seqid,
current_from,
from-1,
strand));
loc = loc->Subtract(*trim, 0, NULL, NULL);
partial_start = true;
}
if (current_to > to) {
CRef<CSeq_loc> trim(new CSeq_loc(*current_seqid,
to+1,
current_to,
strand));
loc = loc->Subtract(*trim, 0, NULL, NULL);
partial_stop = true;
}
}
if (loc->IsNull() || !set_partial) {
return;
}
if (strand == eNa_strand_minus) {
swap(partial_start, partial_stop);
}
if (partial_start) {
loc->SetPartialStart(true, eExtreme_Biological);
}
if (partial_stop) {
loc->SetPartialStop(true, eExtreme_Biological);
}
}
