lib/bio/appl/blast/xmlparser.rb in bio-1.2.1 vs lib/bio/appl/blast/xmlparser.rb in bio-1.3.0

@@ -5,11 +5,11 @@
 #              Mitsuteru C. Nakao <[e-mail]>
 # Copyright::  Copyright (C) 2003 
 #              Toshiaki Katayama <[e-mail]>
 # License::    The Ruby License
 #
-# $Id: xmlparser.rb,v 1.17 2007/04/05 23:35:39 trevor Exp $
+# $Id:$
 #
 # == Description
 # 
 # A parser for blast XML report (format 7) based on the XMLParser.
 # This file is automatically loaded by bio/appl/blast/report.rb if
@@ -113,38 +113,55 @@
       when 'BlastOutput_query-len'
         @query_len = hash[tag].to_i
       end
     end
 
-    def xmlparser_parse_parameters(hash)
-      labels = { 
-        'matrix'       => 'Parameters_matrix',
-        'expect'       => 'Parameters_expect',
-        'include'      => 'Parameters_include',
-        'sc-match'     => 'Parameters_sc-match',
-        'sc-mismatch'  => 'Parameters_sc-mismatch',
-        'gap-open'     => 'Parameters_gap-open',
-        'gap-extend'   => 'Parameters_gap-extend',
-        'filter'       => 'Parameters_filter',
-        'pattern'      => 'Parameters_pattern',
-        'entrez-query' => 'Parameters_entrez-query',
-      }
-      labels.each do |k,v|
+    # set parameter of the key as val
+    def xml_set_parameter(key, val)
+      #labels = { 
+      #  'matrix'       => 'Parameters_matrix',
+      #  'expect'       => 'Parameters_expect',
+      #  'include'      => 'Parameters_include',
+      #  'sc-match'     => 'Parameters_sc-match',
+      #  'sc-mismatch'  => 'Parameters_sc-mismatch',
+      #  'gap-open'     => 'Parameters_gap-open',
+      #  'gap-extend'   => 'Parameters_gap-extend',
+      #  'filter'       => 'Parameters_filter',
+      #  'pattern'      => 'Parameters_pattern',
+      #  'entrez-query' => 'Parameters_entrez-query',
+      #}
+      k = key.sub(/\AParameters\_/, '')
+      @parameters[k] =
         case k
-        when 'filter', 'matrix'
-          @parameters[k] = hash[v].to_s
+        when 'expect', 'include'
+          val.to_f
+        when /\Agap\-/, /\Asc\-/
+          val.to_i
         else
-          @parameters[k] = hash[v].to_i
+          val
         end
+    end
+
+    def xmlparser_parse_parameters(hash)
+      hash.each do |k, v|
+        xml_set_parameter(k, v)
       end
     end
 
     def xmlparser_parse_iteration(tag, hash)
       case tag
       when 'Iteration_iter-num'
         @iterations.last.num = hash[tag].to_i
       when 'Iteration_message'
         @iterations.last.message = hash[tag].to_s
+
+        # for new BLAST XML format
+      when 'Iteration_query-ID'
+        @iterations.last.query_id = hash[tag].to_s
+      when 'Iteration_query-def'
+        @iterations.last.query_def = hash[tag].to_s
+      when 'Iteration_query-len'
+        @iterations.last.query_len = hash[tag].to_i
       end
     end
 
     def xmlparser_parse_hit(tag, hash)
       hit = @iterations.last.hits.last