def __init__(self, filename, sepn=None, use_sa=1, print_flag=0):
self.thisown = 0
if sepn == None:
sepn = []
# Need to change directory because the C code works only on UNIX
old_workdir = os.getcwd()
new_workdir, new_filename = os.path.split(filename)
if len(new_workdir):
os.chdir(new_workdir)
self.this = FS.new_Index(new_filename, sepn, use_sa, print_flag)
# Return to old working directory
if len(new_workdir):
os.chdir(old_workdir)
self.thisown = 1
self.__dict__.update(FS.Index_get_data(self))
def kNN_srch(self, qseq, M, kNN, stype=FS_BINS, ptype=SARRAY, qdef=""):
hits_dict = FS.Index_kNN_srch(self, qseq, M, kNN, stype, ptype, qdef)
return HitList(hits_dict)
def rng_srch(self, qseq, M, rng, stype=FS_BINS, ptype=SARRAY, qdef=""):
hits_dict = FS.Index_rng_srch(self, qseq, M, rng, M.conv_type, stype,
ptype, qdef)
return HitList(hits_dict)
def get_unique_bin_size(self, bin):
return FS.Index_get_unique_bin_size(self, bin)
def print_stats(self, options=3):
return FS.Index_print_stats(self, options)
def print_bin(self, bin, options=1):
return FS.Index_print_bin(self, bin, options)
def seq2bin(self, seq):
return FS.Index_seq2bin(self, seq)
def __str__(self):
return FS.Index___str__(self)
def save(self, filename):
return FS.Index_save(self, filename)
def __del__(self):
if self.thisown:
FS.delete_Index(self)
def _get_ix_data(I):
return FS.Index_get_data(I)
def _get_db(I):
return db(FS.Index_s_db_get(I), new=False, own=False)
def threaded_search(self, srch_args):
results = FS.Index_threaded_search(self, srch_args)
return [HitList(r) for r in results]