Class: Bio::LazyBlast::Report::Iteration::Hit::Hsp

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(reader) ⇒ Hsp

Returns a new instance of Hsp.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 141

def initialize(reader)
  @nodes = Enumerator.new do |yielder|
    until (reader.name == "Hsp" and reader.node_type == LibXML::XML::Reader::TYPE_END_ELEMENT) or !reader.read
      yielder << reader if reader.node_type == LibXML::XML::Reader::TYPE_ELEMENT
    end
  end
  setup_hsp_values
end

Instance Attribute Details

#align_len ⇒ Object (readonly)

Returns the value of attribute align_len.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def align_len
  @align_len
end

#bit_score ⇒ Object (readonly)

Returns the value of attribute bit_score.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def bit_score
  @bit_score
end

#density ⇒ Object (readonly)

Returns the value of attribute density.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def density
  @density
end

#evalue ⇒ Object (readonly)

Returns the value of attribute evalue.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def evalue
  @evalue
end

#gaps ⇒ Object (readonly)

Returns the value of attribute gaps.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def gaps
  @gaps
end

#hit_frame ⇒ Object (readonly)

Returns the value of attribute hit_frame.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def hit_frame
  @hit_frame
end

#hit_from ⇒ Object (readonly)

Returns the value of attribute hit_from.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def hit_from
  @hit_from
end

#hit_to ⇒ Object (readonly)

Returns the value of attribute hit_to.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def hit_to
  @hit_to
end

#hseq ⇒ Object (readonly)

Returns the value of attribute hseq.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def hseq
  @hseq
end

#identity ⇒ Object (readonly)

Returns the value of attribute identity.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def identity
  @identity
end

#midline ⇒ Object (readonly)

Returns the value of attribute midline.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def midline
  @midline
end

#mismatch_count ⇒ Object (readonly)

Returns the value of attribute mismatch_count.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def mismatch_count
  @mismatch_count
end

#num ⇒ Object (readonly)

Returns the value of attribute num.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def num
  @num
end

#percent_identity ⇒ Object (readonly)

Returns the value of attribute percent_identity.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def percent_identity
  @percent_identity
end

#positive ⇒ Object (readonly)

Returns the value of attribute positive.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def positive
  @positive
end

#qseq ⇒ Object (readonly)

Returns the value of attribute qseq.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def qseq
  @qseq
end

#query_frame ⇒ Object (readonly)

Returns the value of attribute query_frame.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def query_frame
  @query_frame
end

#query_from ⇒ Object (readonly)

Returns the value of attribute query_from.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def query_from
  @query_from
end

#query_to ⇒ Object (readonly)

Returns the value of attribute query_to.



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 139

def query_to
  @query_to
end

Instance Method Details

#setup_hsp_values ⇒ Object 



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# File 'lib/bio/appl/blast/lazyblastxml.rb', line 150

def setup_hsp_values
  @nodes.each do |node|
    case node.name
    when 'Hsp_num'
      @num = node.read_inner_xml.to_i
    when 'Hsp_bit-score'
      @bit_score = node.read_inner_xml.to_f
    when 'Hsp_evalue'
      @evalue = node.read_inner_xml.to_f
    when 'Hsp_query-from'
      @query_from = node.read_inner_xml.to_i
    when 'Hsp_query-to'
      @query_to = node.read_inner_xml.to_i
    when 'Hsp_query-frame'
      @query_frame = node.read_inner_xml.to_i
    when 'Hsp_hit-frame'
      @hit_frame = node.read_inner_xml.to_i
    when 'Hsp_identity'
      @identity = node.read_inner_xml.to_i
    when 'Hsp_positive'
      @positive = node.read_inner_xml.to_i
    when 'Hsp_align-len'
      @align_len = node.read_inner_xml.to_i
    when 'Hsp_qseq'
      @qseq = node.read_inner_xml
    when 'Hsp_hseq'
      @hseq = node.read_inner_xml
    when 'Hsp_midline'
      @midline = node.read_inner_xml
    end
  end
end