1 from Martel import Dispatch
2 from Bio import Search, StdHandler
3
17
18 - def start_(self, name, attrs):
26
27 - def end_(self, name):
37
42
47
48 - def add_hsp(self, hsp_values, hsp_handler, strands, frames):
49 self.hsps.append(Search.HSP(hsp_handler.query_seq,
50 hsp_handler.homology_seq,
51 hsp_handler.subject_seq,
52
53
54 (hsp_handler.query_start_loc,
55 hsp_handler.query_end_loc),
56 (hsp_handler.subject_start_loc,
57 hsp_handler.subject_end_loc),
58
59 hsp_handler.query_name,
60 hsp_handler.subject_name,
61
62 self.algorithm,
63
64 hsp_values))
65
68
70 self.algorithm = Search.Algorithm(info["appname"],
71 info["appversion"])
72 self.database = Search.Database(info["dbname"],
73 info["db_num_letters"],
74 info["db_num_sequences"])
75 self.query = Search.Query("XXX spam", "XXX eggs",
76 info["query_description"],
77 info["query_size"])
78
82
83 StdHandler.add_text_block_handler(BuildSearch, "hit_description",
84 "join-description", "join|fixspaces",
85 "hit_description")
86
87 StdHandler.add_int_handler(BuildSearch, "hit_length", "hit_length")
88
89 make_builder = BuildSearch
90