def get_features_for_seqid(self, seqid):
rval = gtlib.gt_feature_index_get_features_for_seqid(self.fi,
seqid)
if rval:
a = Array(rval, True)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
else:
return None
def create_from_ptr(cls, node_ptr, newref=False):
if node_ptr == 0 or node_ptr == None:
gterror("GenomeNode pointer cannot be NULL (was: " + str(node_ptr) + ")")
n = cls()
if newref:
n.own = True
n.gn = gtlib.gt_genome_node_ref(node_ptr)
else:
n.own = False
n.gn = node_ptr
n._as_parameter_ = n.gn
return n
def create_from_ptr(cls, node_ptr, newref=False):
if node_ptr == 0 or node_ptr == None:
gterror("GenomeNode pointer cannot be NULL (was: "+ str(node_ptr) +
")")
n = cls()
if newref:
n.own = True
n.gn = gtlib.gt_genome_node_ref(node_ptr)
else:
n.own = False
n.gn = node_ptr
n._as_parameter_ = n.gn
return n
def get_features_for_range(self, start, end, seqid):
from ctypes import byref
a = Array.create()
err = Error()
rng = Range(start, end)
rval = gtlib.gt_feature_index_get_features_for_range(self.fi, a,
seqid, byref(rng), err)
if rval != 0:
gterror(err)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
def get_features_for_seqid(self, seqid):
err = Error()
result = []
rval = gtlib.gt_feature_index_get_features_for_seqid(
self.fi, seqid.encode('UTF-8'), err)
if rval:
a = Array(rval, True)
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
else:
gterror(err)
return result
def get_features_for_seqid(self, seqid):
err = Error()
result = []
rval = gtlib.gt_feature_index_get_features_for_seqid(self.fi,
seqid, err._as_parameter_)
if rval:
a = Array(rval, True)
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result
else:
gterror(err)
return result
def get_features_for_range(self, start, end, seqid):
from ctypes import byref
a = Array.create()
err = Error()
rng = Range(start, end)
rval = gtlib.gt_feature_index_get_features_for_range(
self.fi, a, seqid, byref(rng), err)
if rval != 0:
gterror(err)
result = []
for i in range(a.size()):
fptr = gtlib.gt_genome_node_ref(a.get(i))
result.append(FeatureNode.create_from_ptr(fptr))
return result