Class: Bio::Blast::Default::Report::HSP

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/blast/format0.rb

Overview

Bio::Blast::Default::Report::HSP holds information about the hsp (high-scoring segment pair).

Direct Known Subclasses

Bl2seq::Report::HSP, WU::Report::HSP

Instance Attribute Summary (collapse)

Class Method Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (HSP) initialize(data)

Creates new HSP object. It is designed to be called only internally from the Bio::Blast::Default::Report::Hit class. Users should not call the method directly.



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# File 'lib/bio/appl/blast/format0.rb', line 967

def initialize(data)
  @f0score = data.shift
  @f0alignment = []
  while r = data[0] and /^(Query|Sbjct)\:/ =~ r
    @f0alignment << data.shift
  end
end

Instance Attribute Details

- (Object) align_len (readonly)

Returns the value of attribute align_len



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# File 'lib/bio/appl/blast/format0.rb', line 1109

def align_len
  @align_len
end

- (Object) bit_score (readonly)

Returns the value of attribute bit_score



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# File 'lib/bio/appl/blast/format0.rb', line 1070

def bit_score
  @bit_score
end

- (Object) evalue (readonly)

Returns the value of attribute evalue



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# File 'lib/bio/appl/blast/format0.rb', line 1077

def evalue
  @evalue
end

- (Object) gaps (readonly)

Returns the value of attribute gaps



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# File 'lib/bio/appl/blast/format0.rb', line 1102

def gaps
  @gaps
end

- (Object) hit_frame (readonly)

Returns the value of attribute hit_frame



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# File 'lib/bio/appl/blast/format0.rb', line 1084

def hit_frame
  @hit_frame
end

- (Object) hit_from (readonly)

Returns the value of attribute hit_from



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# File 'lib/bio/appl/blast/format0.rb', line 1225

def hit_from
  @hit_from
end

- (Object) hit_strand (readonly)

Returns the value of attribute hit_strand



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# File 'lib/bio/appl/blast/format0.rb', line 1117

def hit_strand
  @hit_strand
end

- (Object) hit_to (readonly)

Returns the value of attribute hit_to



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# File 'lib/bio/appl/blast/format0.rb', line 1229

def hit_to
  @hit_to
end

- (Object) hseq (readonly)

Returns the value of attribute hseq



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# File 'lib/bio/appl/blast/format0.rb', line 1209

def hseq
  @hseq
end

- (Object) identity (readonly)

Returns the value of attribute identity



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# File 'lib/bio/appl/blast/format0.rb', line 1088

def identity
  @identity
end

- (Object) midline (readonly)

Returns the value of attribute midline



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# File 'lib/bio/appl/blast/format0.rb', line 1213

def midline
  @midline
end

- (Object) percent_gaps (readonly)

Returns the value of attribute percent_gaps



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# File 'lib/bio/appl/blast/format0.rb', line 1105

def percent_gaps
  @percent_gaps
end

- (Object) percent_identity (readonly)

Returns the value of attribute percent_identity



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# File 'lib/bio/appl/blast/format0.rb', line 1091

def percent_identity
  @percent_identity
end

- (Object) percent_positive (readonly)

Returns the value of attribute percent_positive



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# File 'lib/bio/appl/blast/format0.rb', line 1098

def percent_positive
  @percent_positive
end

- (Object) positive (readonly)

Returns the value of attribute positive



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# File 'lib/bio/appl/blast/format0.rb', line 1095

def positive
  @positive
end

- (Object) qseq (readonly)

Returns the value of attribute qseq



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# File 'lib/bio/appl/blast/format0.rb', line 1206

def qseq
  @qseq
end

- (Object) query_frame (readonly)

Returns the value of attribute query_frame



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# File 'lib/bio/appl/blast/format0.rb', line 1081

def query_frame
  @query_frame
end

- (Object) query_from (readonly)

Returns the value of attribute query_from



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# File 'lib/bio/appl/blast/format0.rb', line 1217

def query_from
  @query_from
end

- (Object) query_strand (readonly)

Returns the value of attribute query_strand



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# File 'lib/bio/appl/blast/format0.rb', line 1113

def query_strand
  @query_strand
end

- (Object) query_to (readonly)

Returns the value of attribute query_to



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# File 'lib/bio/appl/blast/format0.rb', line 1221

def query_to
  @query_to
end

- (Object) score (readonly)

Returns the value of attribute score



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# File 'lib/bio/appl/blast/format0.rb', line 1073

def score
  @score
end

- (Object) stat_method (readonly)

Returns the value of attribute stat_method



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# File 'lib/bio/appl/blast/format0.rb', line 1124

def stat_method
  @stat_method
end

Class Method Details

+ (Object) method_after_parse_alignment(*names)

Defines attributes which call parse_alignment before accessing.



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# File 'lib/bio/appl/blast/format0.rb', line 1198

def self.method_after_parse_alignment(*names)
  names.each do |x|
    module_eval("def #{x}; parse_alignment; @#{x}; end")
  end
end

+ (Object) method_after_parse_score(*names)

Defines attributes which call parse_score before accessing.



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# File 'lib/bio/appl/blast/format0.rb', line 1062

def self.method_after_parse_score(*names)
  names.each do |x|
    module_eval("def #{x}; parse_score; @#{x}; end")
  end
end