コード例 #1
0
 def index(self, persist=True):
     """(re)builds the interval tree index into the interval list you
     have stored.
     
     .. note: interval tree performance will not be obtained unless 
     the user *explicitly* calls this method.  This is typically 
     called after a set of intervals has been added.
     
     :param persist: permanently store the index on disk
     :type persist: bool
     """
     refcountdict = None
     tbl = self.hdf_group._f_getChild(INTERVAL_TABLE)
     tree_group = self.hdf_group._f_getChild(INTERVAL_INDEX_GROUP)
     for rname, idx in self.indexes.iteritems():
         # see if index needs to be generated
         if (idx.tree is None) or idx.dirty:
             # count number of items for each reference
             if refcountdict is None:
                 refcountdict = self._get_ref_count_dict()
             # iterate and insert all intervals
             tree = IntervalTree(refcountdict[rname])            
             cur_id = 1
             for row in tbl.where('ref == rname'):
                 start = row[START_COL_NAME]
                 end = row[END_COL_NAME]
                 tree.insert(cur_id, start, end, row.nrow)
                 cur_id += 1
             # update index
             idx.tree = tree
             idx.dirty = False
         # save for future use
         if persist:
             tree.tohdf(tree_group, rname)
コード例 #2
0
 def _init_index(self):
     if not INTERVAL_INDEX_GROUP in self.hdf_group:
         h5file = self._get_hdf_file()
         h5file.createGroup(self.hdf_group, INTERVAL_INDEX_GROUP)
     parentgroup = self.hdf_group._f_getChild(INTERVAL_INDEX_GROUP)
     self.indexes = {}
     for rname in self.get_rnames():
         idx = self._Index()
         # load index if it exists
         if rname in parentgroup:
             tree = IntervalTree.fromhdf(parentgroup._f_getChild(rname))
             idx.tree = tree
         self.indexes[rname] = idx