Class: Bio::LazyBlast::Report

Inherits:
Object
  • Object
show all
Includes:
Enumerable
Defined in:
lib/bio/appl/blast/lazyblastxml.rb

Defined Under Namespace

Classes: Iteration

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename) ⇒ Report

Returns a new instance of Report.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 9

def initialize(filename)
  @filename = filename
  @reader = LibXML::XML::Reader.file(@filename)
  @nodes = Enumerator.new do |yielder|
    while @reader.read 
      yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT
    end
  end
  setup_report_values
end

Instance Attribute Details

#db ⇒ Object (readonly)

Returns the value of attribute db.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def db
  @db
end

#program ⇒ Object (readonly)

Returns the value of attribute program.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def program
  @program
end

#query_def ⇒ Object (readonly)

Returns the value of attribute query_def.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def query_def
  @query_def
end

#query_id ⇒ Object (readonly)

Returns the value of attribute query_id.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def query_id
  @query_id
end

#query_len ⇒ Object (readonly)

Returns the value of attribute query_len.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def query_len
  @query_len
end

#statistics ⇒ Object (readonly)

Returns the value of attribute statistics.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def statistics
  @statistics
end

#version ⇒ Object (readonly)

Returns the value of attribute version.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 7

def version
  @version
end

Instance Method Details

#each ⇒ Object Also known as: each_iteration 



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 51

def each
  @nodes.each{|node| yield Iteration.new(node) if node.name == "Iteration"}
end

#rewind ⇒ Object 



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 56

def rewind
  @reader.close
  @reader = LibXML::XML::Reader.file(@filename)
  @nodes = Enumerator.new do |yielder|
    while @reader.read 
      yielder << @reader if @reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT
    end
  end
end

#setup_report_values ⇒ Object 



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 20

def setup_report_values
  @statistics = Hash.new
  @nodes.each do |node|
    return if node.name == "BlastOutput_iterations"
    case node.name
    when 'BlastOutput_program'
      @program = node.read_inner_xml
    when 'BlastOutput_version'
      @version = node.read_inner_xml
    when 'BlastOutput_db'
      @db = node.read_inner_xml
    when 'BlastOutput_query-ID'
      @query_id = node.read_inner_xml
    when 'BlastOutput_query-def'
      @query_def = node.read_inner_xml
    when 'BlastOutput_query-len'
      @query_len = node.read_inner_xml.to_i
    when 'Parameters_matrix'
      @statistics['matrix'] = node.read_inner_xml
    when 'Parameters_expect'
      @statistics['expect'] = node.read_inner_xml.to_i
    when 'Parameters_gap-open'
      @statistics['gap-open'] = node.read_inner_xml.to_i
    when 'Parameters_gap-extend'
      @statistics['gap-extend'] = node.read_inner_xml.to_i
    when 'Parameters_filter'
      @statistics['filter'] = node.read_inner_xml
    end
  end
end