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

Instance Method Summary collapse

Constructor Details

#initialize(data) ⇒ HSP

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 949

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

Instance Attribute Details

#align_len ⇒ Object (readonly)

aligned length



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

def align_len
  @align_len
end

#bit_score ⇒ Object (readonly)

bit score



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# File 'lib/bio/appl/blast/format0.rb', line 1052

def bit_score
  @bit_score
end

#evalue ⇒ Object (readonly)

e-value



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# File 'lib/bio/appl/blast/format0.rb', line 1059

def evalue
  @evalue
end

#gaps ⇒ Object (readonly)

Gaps (number of gaps)



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

def gaps
  @gaps
end

#hit_frame ⇒ Object (readonly)

frame of the hit



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# File 'lib/bio/appl/blast/format0.rb', line 1066

def hit_frame
  @hit_frame
end

#hit_from ⇒ Object (readonly)

start position of the hit (the first position is 1)



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# File 'lib/bio/appl/blast/format0.rb', line 1207

def hit_from
  @hit_from
end

#hit_strand ⇒ Object (readonly)

strand of the hit (“Plus” or “Minus” or nil)



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# File 'lib/bio/appl/blast/format0.rb', line 1099

def hit_strand
  @hit_strand
end

#hit_to ⇒ Object (readonly)

end position of the hit (including its position)



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# File 'lib/bio/appl/blast/format0.rb', line 1211

def hit_to
  @hit_to
end

#hseq ⇒ Object (readonly)

hit sequence (with gaps) of the alignment of the hsp



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# File 'lib/bio/appl/blast/format0.rb', line 1191

def hseq
  @hseq
end

#identity ⇒ Object (readonly)

Identity (number of identical nucleotides or amino acids)



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

def identity
  @identity
end

#midline ⇒ Object (readonly)

middle line of the alignment of the hsp



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# File 'lib/bio/appl/blast/format0.rb', line 1195

def midline
  @midline
end

#percent_gaps ⇒ Object (readonly)

percent of gaps



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# File 'lib/bio/appl/blast/format0.rb', line 1087

def percent_gaps
  @percent_gaps
end

#percent_identity ⇒ Object (readonly)

percent of identical nucleotides or amino acids



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

def percent_identity
  @percent_identity
end

#percent_positive ⇒ Object (readonly)

percent of positive hit amino acids or nucleotides



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# File 'lib/bio/appl/blast/format0.rb', line 1080

def percent_positive
  @percent_positive
end

#positive ⇒ Object (readonly)

Positives (number of positive hit amino acids or nucleotides)



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

def positive
  @positive
end

#qseq ⇒ Object (readonly)

query sequence (with gaps) of the alignment of the hsp



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# File 'lib/bio/appl/blast/format0.rb', line 1188

def qseq
  @qseq
end

#query_frame ⇒ Object (readonly)

frame of the query



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# File 'lib/bio/appl/blast/format0.rb', line 1063

def query_frame
  @query_frame
end

#query_from ⇒ Object (readonly)

start position of the query (the first position is 1)



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# File 'lib/bio/appl/blast/format0.rb', line 1199

def query_from
  @query_from
end

#query_strand ⇒ Object (readonly)

strand of the query (“Plus” or “Minus” or nil)



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

def query_strand
  @query_strand
end

#query_to ⇒ Object (readonly)

end position of the query (including its position)



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# File 'lib/bio/appl/blast/format0.rb', line 1203

def query_to
  @query_to
end

#score ⇒ Object (readonly)

score



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# File 'lib/bio/appl/blast/format0.rb', line 1055

def score
  @score
end

#stat_method ⇒ Object (readonly)

statistical method for calculating evalue and/or score (nil or a string) (note that composition-based statistics for blastp or tblastn were enabled by default after NCBI BLAST 2.2.17)



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# File 'lib/bio/appl/blast/format0.rb', line 1106

def stat_method
  @stat_method
end