# File lib/bio/io/flatfile/indexer.rb, line 79
79:           def initialize
80:             @namestyle = self.class::NAMESTYLE
81:             @secondary = NameSpaces.new
82:             @errorlog = []
83:           end

     # File lib/bio/io/flatfile/indexer.rb, line 98
 98:           def add_secondary_namespaces(*names)
 99:             DEBUG.print "add_secondary_namespaces: #{names.inspect}\n"
100:             names.each do |x|
101:               unless x.is_a?(NameSpace) then
102:                 y = @namestyle[x]
103:                 raise 'unknown secondary namespace' unless y
104:                 @secondary << y
105:               end
106:             end
107:             true
108:           end

     # File lib/bio/io/flatfile/indexer.rb, line 164
164:           def close_flatfile
165:             DEBUG.print "close flatfile #{@flatfilename.inspect}\n"
166:             @flatfile.close
167:           end

     # File lib/bio/io/flatfile/indexer.rb, line 122
122:           def each
123:             @flatfile.each do |x|
124:               @entry = x
125:               pos = @flatfile.entry_start_pos
126:               len = @flatfile.entry_ended_pos - @flatfile.entry_start_pos
127:               begin
128:                 yield pos, len
129:               rescue RuntimeError, NameError => evar
130:                 DEBUG.print "Caught error: #{evar.inspect}\n"
131:                 DEBUG.print "in #{@flatfilename.inspect} position #{pos}\n"
132:                 DEBUG.print "===begin===\n"
133:                 DEBUG.print @flatfile.entry_raw.to_s.chomp
134:                 DEBUG.print "\n===end===\n"
135:                 @errorlog << [ evar, @flatfilename, pos ]
136:                 if @fatal then
137:                   DEBUG.print "Fatal error occurred, stop creating index...\n"
138:                   raise evar
139:                 else
140:                   DEBUG.print "This entry shall be incorrectly indexed.\n"
141:                 end
142:               end #rescue
143:             end
144:           end

     # File lib/bio/io/flatfile/indexer.rb, line 111
111:           def open_flatfile(fileid, file)
112:             @fileid = fileid
113:             @flatfilename = file
114:             DEBUG.print "fileid=#{fileid} file=#{@flatfilename.inspect}\n"
115:             @flatfile = Bio::FlatFile.open(@dbclass, file, 'rb')
116:             @flatfile.raw = nil
117:             @flatfile.entry_pos_flag = true
118:             @entry = nil
119:           end

     # File lib/bio/io/flatfile/indexer.rb, line 146
146:           def parse_primary
147:             r = self.primary.proc.call(@entry)
148:             unless r.is_a?(String) and r.length > 0
149:               #@fatal = true
150:               raise 'primary id must be a non-void string (skipped this entry)'
151:             end
152:             r
153:           end

     # File lib/bio/io/flatfile/indexer.rb, line 155
155:           def parse_secondary
156:             self.secondary.each do |x|
157:               p = x.proc.call(@entry)
158:               p.each do |y|
159:                 yield x.name, y if y.length > 0
160:               end
161:             end
162:           end

    # File lib/bio/io/flatfile/indexer.rb, line 87
87:           def set_primary_namespace(name)
88:             DEBUG.print "set_primary_namespace: #{name.inspect}\n"
89:             if name.is_a?(NameSpace) then
90:               @primary = name
91:             else
92:               @primary = @namestyle[name] 
93:             end
94:             raise 'unknown primary namespace' unless @primary
95:             @primary
96:           end