# File lib/bio/appl/genscan/report.rb
 66 def initialize(report)
 67   @predictions = []
 68   @genscan_version = nil
 69   @date_run   = nil
 70   @time       = nil
 71   @query_name = nil
 72   @length     = nil
 73   @gccontent  = nil
 74   @isochore   = nil
 75   @matrix     = nil
 76 
 77   report.each_line("\n") do |line|
 78     case line
 79     when /^GENSCAN/
 80       parse_headline(line)
 81     when /^Sequence/
 82       parse_sequence(line)
 83     when /^Parameter/
 84       parse_parameter(line)
 85     when /^Predicted genes/
 86       break
 87     end
 88   end
 89 
 90   # rests
 91   i = report.index(/^Predicted gene/)
 92   j = report.index(/^Predicted peptide sequence/)
 93 
 94   # genes/exons
 95   genes_region = report[i...j]
 96   genes_region.each_line("\n") do |line|
 97     if /Init|Intr|Term|PlyA|Prom|Sngl/ =~ line
 98       gn, en = line.strip.split(" +")[0].split(/\./).map {|ii| ii.to_i }
 99       add_exon(gn, en, line)
100     end
101   end
102 
103   # sequences (peptide|CDS)
104   sequence_region = report[j...report.size]
105   sequence_region.gsub!(/^Predicted .+?:/, '')
106   sequence_region.gsub!(/^\s*$/, '')
107   sequence_region.split(Bio::FastaFormat::RS).each do |ff|
108     add_seq(Bio::FastaFormat.new(ff))
109   end
110 end