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 960

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

Instance Attribute Details

#align_lenObject (readonly)

aligned length


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

def align_len
  @align_len
end

#bit_scoreObject (readonly)

bit score


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

def bit_score
  @bit_score
end

#evalueObject (readonly)

e-value


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

def evalue
  @evalue
end

#gapsObject (readonly)

Gaps (number of gaps)


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

def gaps
  @gaps
end

#hit_frameObject (readonly)

frame of the hit


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

def hit_frame
  @hit_frame
end

#hit_fromObject (readonly)

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


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# File 'lib/bio/appl/blast/format0.rb', line 1218

def hit_from
  @hit_from
end

#hit_strandObject (readonly)

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


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# File 'lib/bio/appl/blast/format0.rb', line 1110

def hit_strand
  @hit_strand
end

#hit_toObject (readonly)

end position of the hit (including its position)


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# File 'lib/bio/appl/blast/format0.rb', line 1222

def hit_to
  @hit_to
end

#hseqObject (readonly)

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


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# File 'lib/bio/appl/blast/format0.rb', line 1202

def hseq
  @hseq
end

#identityObject (readonly)

Identity (number of identical nucleotides or amino acids)


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

def identity
  @identity
end

#midlineObject (readonly)

middle line of the alignment of the hsp


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

def midline
  @midline
end

#percent_gapsObject (readonly)

percent of gaps


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

def percent_gaps
  @percent_gaps
end

#percent_identityObject (readonly)

percent of identical nucleotides or amino acids


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

def percent_identity
  @percent_identity
end

#percent_positiveObject (readonly)

percent of positive hit amino acids or nucleotides


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

def percent_positive
  @percent_positive
end

#positiveObject (readonly)

Positives (number of positive hit amino acids or nucleotides)


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

def positive
  @positive
end

#qseqObject (readonly)

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


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

def qseq
  @qseq
end

#query_frameObject (readonly)

frame of the query


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# File 'lib/bio/appl/blast/format0.rb', line 1074

def query_frame
  @query_frame
end

#query_fromObject (readonly)

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


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# File 'lib/bio/appl/blast/format0.rb', line 1210

def query_from
  @query_from
end

#query_strandObject (readonly)

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


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

def query_strand
  @query_strand
end

#query_toObject (readonly)

end position of the query (including its position)


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# File 'lib/bio/appl/blast/format0.rb', line 1214

def query_to
  @query_to
end

#scoreObject (readonly)

score


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

def score
  @score
end

#stat_methodObject (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 1117

def stat_method
  @stat_method
end