X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fdisembl%2Fbiopython-1.50%2FBio%2FStdHandler.py;fp=binaries%2Fsrc%2Fdisembl%2Fbiopython-1.50%2FBio%2FStdHandler.py;h=58070215bb7c3d03a796a67c959872c14017384c;hb=f47da0247a9f9a8ac55571234064a0d3ded06b6c;hp=0000000000000000000000000000000000000000;hpb=6ff5fdd71d597d015fdc1df7eb0a352f8086eaa9;p=jabaws.git
diff --git a/binaries/src/disembl/biopython-1.50/Bio/StdHandler.py b/binaries/src/disembl/biopython-1.50/Bio/StdHandler.py
new file mode 100644
index 0000000..5807021
--- /dev/null
+++ b/binaries/src/disembl/biopython-1.50/Bio/StdHandler.py
@@ -0,0 +1,770 @@
+# Standard Content and Dispatch handlers for the Bioformat IO system
+# This is a Python module.
+"""This module is DEPRECATED.
+
+Andrew Dalke is no longer maintaining Martel or Bio.Mindy, and these modules
+and associate ones like Bio.StdHandler are now deprecated. They are no longer
+used in any of the current Biopython parsers, and are likely to be removed
+in a future release.
+"""
+
+import warnings
+warnings.warn("Martel and those parts of Biopython depending on it" \
+ +" directly (such as Bio.Mindy and Bio.StdHandler) are now" \
+ +" deprecated, and will be removed in a future release of"\
+ +" Biopython. If you want to continue to use this code,"\
+ +" please get in contact with the Biopython developers via"\
+ +" the mailing lists to avoid its permanent removal from"\
+ +" Biopython.", \
+ DeprecationWarning)
+
+from xml.sax import handler
+from Martel import Parser, Dispatch
+from Bio import Std, Decode
+
+###################################
+
+# Helper functions to make functions
+
+def add_int_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self.%s = int(self.get_characters())
+""" % attrname
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self.%s = self.get_characters()
+""" % attrname
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_dict_handler(klass, tag, attrname, key):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self.%s["%s"] = self.get_characters()
+""" % (attrname, key)
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_decode_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self.save_characters()
+ self._decode_%s = attrs.get("bioformat:decode", None)
+ def end(self, tag):
+ if self._decode_%s is not None:
+ s = Decode.make_decoder(self._decode_%s)(s)
+ self.%s = self.get_characters()
+""" % (tag, tag, tag, attrname)
+ d = {"Decode": Decode}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_first_text_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ if self.%s is None:
+ self.save_characters()
+ def end(self, tag):
+ if self.%s is None:
+ self.%s = self.get_characters()
+""" % (attrname, attrname, attrname)
+ d = {}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+def add_text_block_handler(klass, tag, joinattr, defaultjoin, attrname):
+ assert not hasattr(klass, "start_" + tag), "existing method exists"
+ assert not hasattr(klass, "end_" + tag), "existing method exists"
+ assert not hasattr(klass, "start_"+tag+"_block"), "existing method exists"
+ assert not hasattr(klass, "end_" +tag+"_block"), "existing method exists"
+ s = """if 1:
+ def start_block(self, tag, attrs):
+ self._%(tag)s_join_func = Decode.make_decoder(attrs.get(%(joinattr)r, %(defaultjoin)r))
+ self._%(tag)s_lines = []
+ def end_block(self, tag):
+ self.%(attrname)s = self._%(tag)s_join_func(self._%(tag)s_lines)
+ def start(self, tag, attrs):
+ self.save_characters()
+ def end(self, tag):
+ self._%(tag)s_lines.append(self.get_characters())
+""" % locals()
+ d = {"Decode": Decode}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+ setattr(klass, "start_" + tag + "_block", d["start_block"])
+ setattr(klass, "end_" + tag + "_block", d["end_block"])
+
+def add_value_handler(klass, tag, attrname):
+ assert not hasattr(klass, "start_" +tag), "existing method exists"
+ assert not hasattr(klass, "end_" +tag), "existing method exists"
+ s = """if 1:
+ def start(self, tag, attrs):
+ self._%(tag)s_name = attrs["name"]
+ self._%(tag)s_decode = attrs.get("bioformat:decode", None)
+ self.save_characters()
+ def end(self, tag):
+ s = self.get_characters()
+ if self._%(tag)s_decode is not None:
+ s = Decode.make_decoder(self._%(tag)s_decode)(s)
+ self.%(attrname)s[self._%(tag)s_name] = s
+""" % locals()
+ d = {"Decode": Decode}
+ exec s in d
+ setattr(klass, "start_" + tag, d["start"])
+ setattr(klass, "end_" + tag, d["end"])
+
+
+#################################
+
+class ConvertHandler(handler.ContentHandler):
+ """Used to read records and produce output"""
+ def __init__(self, record_builder, writer, record_tag = "record"):
+ handler.ContentHandler.__init__(self)
+ self.record_builder = record_builder
+ self.writer = writer
+ self.record_tag = record_tag
+
+ def startDocument(self):
+ self.inside_record = 0
+ self.characters = self.ignore_characters
+
+ def startElement(self, tag, attrs):
+ if self.inside_record:
+ self.record_builder.startElement(tag, attrs)
+ elif tag == self.record_tag:
+ self.record_builder.startDocument()
+ self.inside_record = 1
+ self.characters = self.record_builder.characters
+ self.record_builder.startElement(tag, attrs)
+
+ def endElement(self, tag):
+ if self.inside_record:
+ self.record_builder.endElement(tag)
+ if tag == self.record_tag:
+ self.record_builder.endDocument()
+ self.writer.write(self.record_builder.document)
+ self.inside_record = 0
+ self.characters = self.ignore_characters
+
+ def ignore_characters(self, s):
+ pass
+
+class ConvertDispatchHandler(Dispatch.Dispatcher):
+ """Used to read records and produce output through a Dispatcher"""
+ def __init__(self, record_builder, writer, record_tag = "record"):
+ setattr(self, "end_" + record_tag, self.write_record)
+ Dispatch.Dispatcher.__init__(self,
+ remap = {record_tag: "bioformat:"}
+ )
+ self.acquire(record_builder)
+ self.record_builder = record_builder
+ self.writer = writer
+ self.record_tag = record_tag
+ def write_record(self, tag):
+ self.writer.write(self.record_builder.document)
+
+
+
+class RecognizeHandler(handler.ContentHandler, handler.ErrorHandler):
+ def __init__(self):
+ self.recognized = 1
+ self.exc = None
+
+ def fatalError(self, exc):
+ if isinstance(exc, Parser.ParserIncompleteException):
+ pass
+ else:
+ self.recognized = 0
+ self.exc = exc
+ raise exc
+
+ error = fatalError
+
+ def endElement(self, tag):
+ if tag == "record":
+ raise Parser.ParserException("we finished a record!")
+
+
+
+class Handle_dbid(Dispatch.Callback):
+ def start_dbid(self, tag, attrs):
+ self.attrs = attrs
+ self.save_characters()
+
+ def end_dbid(self, tag):
+ text = self.get_characters()
+ self.callback(text, self.attrs)
+
+
+class Handle_description(Dispatch.Callback):
+ def start_description_block(self, tag, attrs):
+ j = attrs.get("join", None)
+ if j is None:
+ self.join_fctn = Decode.join_fixspaces
+ else:
+ self.join_fctn = Decode.make_typechecked_decoder(j, list, str)
+ self.descriptions = []
+ def start_description(self, tag, attrs):
+ self.save_characters()
+ def end_description(self, tag):
+ x = self.get_characters()
+ self.descriptions.append(x)
+ def end_description_block(self, tag):
+ self.callback(self.join_fctn(self.descriptions))
+
+#### There can be multiple dbxref_dbids in a dbxref
+# DR EMBL; X64411; CAA45756.1; -.
+# <..dbname style="swiss">EMBL
+# X64411
+# CAA45756.1
+#
+###
+# DR P35156, YPUI_BACSU, F;
+# P35156
+# YPUI_BACSU
+#
+#
+
+def _fixup_sp_pattern(exp):
+ import re
+ import Martel
+ exp = Martel.select_names(exp, (Std.dbxref_dbname.tag,Std.dbxref_dbid.tag))
+
+ e = exp._find_groups(Std.dbxref_dbname.tag)
+ assert len(e) == 1
+ e = e[0]
+ e.name = "dbname"
+ dbstyle = e.attrs["style"]
+ e.attrs = {}
+ e = exp._find_groups(Std.dbxref_dbid.tag)
+ assert len(e) == 2
+ e[0].name = "primary_dbid"
+ primary_type = e[0].attrs["type"]
+ e[0].attrs = {}
+ e[1].name = "secondary_dbid"
+ secondary_type = e[1].attrs["type"]
+ e[1].attrs = {}
+ pattern = str(exp) + "$"
+ pat = re.compile(pattern)
+ return pat, dbstyle, primary_type, secondary_type
+
+# Turns out these 'fast' versions speed up the dbxref code by about
+# a factor of 2.
+
+# DR PIR; S08427; S08427.
+_fast_dbxref_sp_general_data = None
+def _fast_dbxref_sp_general(s):
+ global _fast_dbxref_sp_general_data
+ if _fast_dbxref_sp_general_data is None:
+ from Bio.expressions.swissprot import sprot38
+ _fast_dbxref_sp_general_data = _fixup_sp_pattern(
+ sprot38.real_DR_general)
+
+ pat, dbstyle, primary_type, secondary_type = _fast_dbxref_sp_general_data
+
+ m = pat.match(s)
+ assert m is not None, "Ill-formated sp-general dxbref: %r" % s
+ return (
+ (dbstyle, m.group("dbname"), primary_type,
+ m.group("primary_dbid"), 0),
+ (dbstyle, m.group("dbname"), secondary_type,
+ m.group("secondary_dbid"), 0)
+ )
+
+# DR PFAM; PF01018; GTP1_OBG; 1.
+# DR PROSITE; PS00905; GTP1_OBG; 1.
+
+_fast_dbxref_sp_prosite_data = None
+def _fast_dbxref_sp_prosite(s):
+ global _fast_dbxref_sp_prosite_data
+
+ if _fast_dbxref_sp_prosite_data is None:
+ from Bio.expressions.swissprot import sprot38
+ _fast_dbxref_sp_prosite_data = _fixup_sp_pattern(
+ sprot38.real_DR_prosite)
+
+ pat, dbstyle, primary_type, secondary_type = _fast_dbxref_sp_prosite_data
+ m = pat.match(s)
+ assert m is not None, "Ill-formated sp-prosite dxbref: %r" % s
+ return (
+ (dbstyle, m.group("dbname"), primary_type,
+ m.group("primary_dbid"), 0),
+ (dbstyle, m.group("dbname"), secondary_type,
+ m.group("secondary_dbid"), 0)
+ )
+
+
+# DR EMBL; M36407; AAA33110.1; -.
+_fast_dbxref_sp_embl_data = None
+def _fast_dbxref_sp_embl(s):
+ global _fast_dbxref_sp_embl_data
+
+ if _fast_dbxref_sp_embl_data is None:
+ from Bio.expressions.swissprot import sprot38
+ _fast_dbxref_sp_embl_data = _fixup_sp_pattern(
+ sprot38.real_DR_embl)
+
+ pat, dbstyle, primary_type, secondary_type = _fast_dbxref_sp_embl_data
+ m = pat.match(s)
+ assert m is not None, "Ill-formated sp-embl dxbref: %r" % s
+ return (
+ (dbstyle, m.group("dbname"), primary_type,
+ m.group("primary_dbid"), 0),
+ (dbstyle, m.group("dbname"), secondary_type,
+ m.group("secondary_dbid"), 0)
+ )
+
+_fast_dbxref_parser_table = {
+ "sp-general": _fast_dbxref_sp_general,
+ "sp-prosite": _fast_dbxref_sp_prosite,
+ "sp-embl": _fast_dbxref_sp_embl,
+}
+
+class Handle_dbxref(Dispatch.Callback):
+ def __init__(self, callback):
+ Dispatch.Callback.__init__(self, callback)
+ self.supported_features.append("fast-sp-dbxref")
+ self.slow_callback = self.callback
+ def start_dbxref(self, tag, attrs):
+ self.negate = 0
+ self.dbname = None
+ self.dbids = []
+ self.info = []
+
+ def start_dbxref_dbname(self, tag, attrs):
+ assert self.dbname is None, "cannot set the dbname twice"
+ self.dbname_style = attrs.get("style", "unknown")
+ self.save_characters()
+ def end_dbxref_dbname(self, tag):
+ self.dbname = self.get_characters()
+
+ def start_dbxref_dbid(self, tag, attrs):
+ d = attrs.get("dbname", None)
+ if d is None:
+ assert self.dbname is not None, "must set the dbname"
+ self.info.append( (self.dbname_style, self.dbname,
+ attrs.get("type", "primary")) )
+ else:
+ self.info.append( ("bioformat", d,
+ attrs.get("type", "primary")) )
+ self.save_characters()
+
+ def end_dbxref_dbid(self, tag):
+ self.dbids.append( self.get_characters())
+
+ def start_dbxref_negate(self, tag, attrs):
+ self.negate = 1
+
+ def end_dbxref(self, tag):
+ cb = self.slow_callback
+ if cb is None:
+ return
+ negate = self.negate
+ for ( (dbname_style, dbname, idtype), dbid) in zip(self.info,
+ self.dbids):
+ self.slow_callback(dbname_style, dbname, idtype, dbid, negate)
+
+ def start_fast_dbxref(self, tag, attrs):
+ style = attrs["style"]
+ self._fast_parser = _fast_dbxref_parser_table[style]
+ self.save_characters()
+ self.slow_callback = None
+ def end_fast_dbxref(self, tag):
+ for info in self._fast_parser(self.get_characters()):
+ self.callback(*info)
+ self.slow_callback = self.callback
+
+##################
+class Handle_sequence(Dispatch.Callback):
+ global_alphabet = None
+ def start_(self, tag, attrs):
+ self.global_alphabet = None
+
+ def start_sequence_block(self, tag, attrs):
+ self.local_alphabet = attrs.get("alphabet", None)
+ self.gapchar = attrs.get("gapchar", None)
+ self.stopchar = attrs.get("stopchar", None)
+ j = attrs.get("join", None)
+ if j is not None:
+ self.join_func = Decode.make_typechecked_decoder(j, list, str)
+ else:
+ self.join_func = None
+ self.sequences = []
+
+ def end_sequence_block(self, tag):
+ f = self.join_func
+ if f is not None:
+ seq = self.f(self.sequences)
+ else:
+ seq = "".join(self.sequences).replace(" ", "")
+ alphabet = self.local_alphabet or self.global_alphabet or "unknown"
+ self.callback( (alphabet, seq, self.gapchar, self.stopchar) )
+
+ def start_alphabet(self, tag, attrs):
+ self.global_alphabet = attrs["alphabet"]
+
+ def start_sequence(self, tag, attrs):
+ self.save_characters()
+ def end_sequence(self, tag):
+ self.sequences.append(self.get_characters())
+
+class Feature:
+ def __init__(self, name, description, location, qualifiers):
+ self.name = name
+ self.description = description
+ self.location = location
+ self.qualifiers = qualifiers
+ def __str__(self):
+ return "Feature %r %r %s num_qualifiers = %d" % \
+ (self.name, self.description, self.location,
+ len(self.qualifiers))
+
+
+class Handle_feature_location(Dispatch.Callback):
+ def __init__(self, callback, settings = {}):
+ Dispatch.Callback.__init__(self, callback)
+ self.settings = settings
+
+ def start_feature(self, tag, attrs):
+ self.location_style = attrs.get("location-style",
+ self.settings["location-style"])
+ j = attrs.get("join-feature", None)
+ if j is None:
+ self.text_join_func = "".join
+ else:
+ self.text_join_func = Decode.make_typechecked_decoder(j, list, str)
+
+ self.location_start = None
+ self.location_end = None
+ self.text_lines = []
+
+ def end_feature(self, tag):
+ if self.location_start or self.location_end:
+ if self.text_lines:
+ raise TypeError("Cannot have both location text and start/end")
+ self.callback(self.location_style,
+ (self.location_start, self.location_end))
+ else:
+ self.callback(self.location_style,
+ (self.text_join_func(self.text_lines), None))
+
+ def start_feature_location(self, tag, attrs):
+ self.save_characters()
+ def end_feature_location(self, tag):
+ self.text_lines.append(self.get_characters())
+
+add_text_handler(Handle_feature_location, "feature_location_start",
+ "location_start")
+add_text_handler(Handle_feature_location, "feature_location_end",
+ "location_end")
+
+##################################
+
+class Handle_feature_qualifier(Dispatch.Callback):
+ def __init__(self, callback, settings):
+ self.settings = settings
+ Dispatch.Callback.__init__(self, callback)
+
+ def start_feature_qualifier(self, tag, attrs):
+ self.name = None
+ self.description = []
+ qj = attrs.get("join-qualifier", None)
+ if qj is None:
+ self.join = self.settings["qualifier_join_func"]
+ else:
+ self.join = Decode.make_typechecked_decoder(qj, list, str)
+
+ def end_feature_qualifier(self, tag):
+ self.callback(self.name, self.join(self.description))
+
+ def start_feature_qualifier_description(self, tag, attrs):
+ self.save_characters()
+ def end_feature_qualifier_description(self, tag):
+ self.description.append(self.get_characters())
+
+add_text_handler(Handle_feature_qualifier, "feature_qualifier_name", "name")
+
+####################
+
+class Handle_features(Dispatch.Callback):
+ def __init__(self, callback):
+ Dispatch.Callback.__init__(self, callback)
+ self.settings = {}
+
+ self.acquire(Handle_feature_location(self.add_location, self.settings))
+
+ self.acquire(Handle_feature_qualifier(self.add_feature_qualifier,
+ self.settings))
+
+ def start_feature_block(self, tag, attrs):
+ jf = attrs.get("join-description", None)
+ if jf is None:
+ self.join_feature_description = Decode.join_fixspaces
+ else:
+ self.join_feature_description = Decode.make_typechecked_decoder(
+ jf, list, str)
+
+ self.settings["location-style"] = attrs.get("location-style", None)
+
+ jq = attrs.get("join-qualifier", None)
+ if jq is None:
+ self.settings["qualifier_join_func"] = Decode.join_fixspaces
+ else:
+ self.settings["qualifier_join_func"] = \
+ Decode.make_typechecked_decoder(jq, list, str)
+ self.features = []
+
+ def end_feature_block(self, tag):
+ self.callback(self.features)
+ self.features = None
+
+ def start_feature(self, tag, attrs):
+ self.name = None
+ self.description = []
+ self.location = None
+ self.qualifiers = []
+
+ def start_feature_description(self, tag, attrs):
+ self.save_characters()
+ def end_feature_description(self, tag):
+ self.description.append(self.get_characters())
+
+ def end_feature(self, tag):
+ self.features.append(Feature(
+ self.name,
+ self.join_feature_description(self.description),
+ self.location,
+ self.qualifiers))
+
+ def add_feature_qualifier(self, name, description):
+ self.qualifiers.append((name, description))
+
+ def add_location(self, style, location_info):
+ self.location = (style, location_info)
+
+add_text_handler(Handle_features, "feature_name", "name")
+
+
+############## Search handlers
+
+class Handle_hsp_seqalign(Dispatch.Callback):
+ def start_hsp(self, tag, attrs):
+ self.query_name = None # "Query"
+ self.subject_name = None # "Sbjct"
+
+ self.query_seq = "" # the actual text of the sequence
+ self.homology_seq = ""
+ self.subject_seq = ""
+
+ self.query_start_loc = None
+ self.query_end_loc = None
+
+ self.subject_start_loc = None
+ self.subject_end_loc = None
+
+ def end_hsp(self, tag):
+ self.callback(self)
+
+ def start_hsp_seqalign(self, tag, attrs):
+ self.sub_leader = None
+
+ def start_hsp_seqalign_query_seq(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_query_seq(self, tag):
+ s = self.get_characters()
+ self.query_seq += s
+ self.sub_query_seq_len = len(s)
+
+ def start_hsp_seqalign_homology_seq(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_homology_seq(self, tag):
+ query_leader = self.leader_size
+ query_seq_len = self.sub_query_seq_len
+ line = self.get_characters()
+ s = line[query_leader:query_leader+query_seq_len]
+ assert len(s) == query_seq_len, (len(s), query_seq_len, line)
+ self.homology_seq += s
+
+ def start_hsp_seqalign_subject_seq(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_subject_seq(self, tag):
+ self.subject_seq += self.get_characters()
+
+ def start_hsp_seqalign_query_leader(self, tag, attrs):
+ self.save_characters()
+ def end_hsp_seqalign_query_leader(self, tag):
+ self.leader_size = len(self.get_characters())
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_query_name",
+ "query_name")
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_subject_name",
+ "subject_name")
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_query_start",
+ "query_start_loc")
+add_text_handler(Handle_hsp_seqalign, "hsp_seqalign_query_end",
+ "query_end_loc")
+
+add_first_text_handler(Handle_hsp_seqalign, "hsp_seqalign_subject_start",
+ "subject_start_loc")
+add_text_handler(Handle_hsp_seqalign, "hsp_seqalign_subject_end",
+ "subject_end_loc")
+
+
+
+
+#############################
+
+class Handle_hsp(Dispatch.Callback):
+ def __init__(self, callback):
+ Dispatch.Callback.__init__(self, callback)
+ self.acquire(Handle_hsp_seqalign(self.add_hsp_seqs))
+
+ def start_hsp(self, tag, attrs):
+ self.hsp_values = {} # expect, p, identities, ...
+ self.strands = {}
+ self.frames = {}
+
+ def end_hsp(self, tag):
+ self.callback(self.hsp_values,
+ self.hsp_info,
+ self.strands, self.frames,
+ )
+
+ def start_hsp_strand(self, tag, attrs):
+ self.strands[attrs["which"]] = attrs["strand"]
+
+ def start_hsp_frame(self, tag, attrs):
+ self.getting_frame = attrs["which"]
+ self.save_characters()
+
+ def end_hsp_frame(self, tag):
+ self.frames[self.getting_frame] = self.get_characters()
+ self.getting_frame = None
+
+ def add_hsp_seqs(self, hsp_info):
+ self.hsp_info = hsp_info
+
+ def start_hsp_value(self, tag, attrs):
+ self.value_convert = attrs.get("bioformat:decode", None)
+ self.value_name = attrs["name"]
+ self.save_characters()
+
+ def end_hsp_value(self, tag):
+ s = self.get_characters()
+ if self.value_name is not None:
+ if self.value_name == "float":
+ s = float(s)
+ else:
+ s = Decode.make_decoder(self.value_convert)(s)
+ self.hsp_values[self.value_name] = s
+
+#############################
+
+
+class Handle_search_table(Dispatch.Callback):
+ def start_search_table_value(self, tag, attrs):
+ self.value_name = attrs["name"]
+ self.value_decode = attrs.get("bioformat:decode", None)
+ self.save_characters()
+ def end_search_table_value(self, tag):
+ s = self.get_characters()
+ if self.value_decode is not None:
+ x = self.value_decode
+ if x == "int":
+ s = int(s)
+ elif x == "float":
+ s = float(s)
+ else:
+ s = Decode.make_decoder(x)(s)
+ self.values[self.value_name] = s
+
+ def start_search_table(self, tag, attrs):
+ self.data = []
+ def end_search_table(self, tag):
+ self.callback(self.data)
+ self.data = None
+
+ def start_search_table_entry(self, tag, attrs):
+ self.description = None
+ self.values = {}
+
+ def end_search_table_entry(self, tag):
+ self.data.append( (self.description, self.values) )
+ self.description = self.values = None
+
+add_text_handler(Handle_search_table, "search_table_description",
+ "description")
+
+#############################
+
+class Handle_search_header(Dispatch.Callback):
+ def start_(self, tag, attrs):
+ self.dict = {}
+ self.query_description = None
+
+ def end_search_header(self, tag):
+ d = self.dict
+ d["query_description"] = self.query_description
+ self.callback(d)
+
+add_text_block_handler(Handle_search_header, "query_description",
+ "join-query", "join|fixspaces", "query_description")
+
+add_text_dict_handler(Handle_search_header, "application_name",
+ "dict", "appname")
+add_text_dict_handler(Handle_search_header, "application_version",
+ "dict", "appversion")
+add_text_dict_handler(Handle_search_header, "database_name",
+ "dict", "dbname")
+add_text_dict_handler(Handle_search_header, "database_num_sequences",
+ "dict", "db_num_sequences")
+add_text_dict_handler(Handle_search_header, "database_num_letters",
+ "dict", "db_num_letters")
+add_text_dict_handler(Handle_search_header, "query_size",
+ "dict", "query_size")
+
+
+#############################
+
+class Handle_search_info(Dispatch.Callback):
+ def start_(self, tag, attrs):
+ self.parameters = {}
+ self.statistics = {}
+
+ def end_(self, tag):
+ self.callback(self.parameters, self.statistics)
+
+add_value_handler(Handle_search_info, "search_parameter", "parameters")
+add_value_handler(Handle_search_info, "search_statistic", "statistics")