Class: Bio::Blast::Report::Hsp

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

Overview

Bio::Blast::Report::Hsp

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Hsp

Returns a new instance of Hsp.



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# File 'lib/bio/appl/blast/report.rb', line 275

def initialize
  @hsp = {}
end

Instance Attribute Details

#align_len ⇒ Object

Length of the alignment used



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# File 'lib/bio/appl/blast/report.rb', line 311

def align_len
  @align_len
end

#bit_score ⇒ Object

Score (in bits) of HSP



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# File 'lib/bio/appl/blast/report.rb', line 283

def bit_score
  @bit_score
end

#density ⇒ Object

Score density



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# File 'lib/bio/appl/blast/report.rb', line 313

def density
  @density
end

#evalue ⇒ Object

E-value of HSP



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# File 'lib/bio/appl/blast/report.rb', line 287

def evalue
  @evalue
end

#gaps ⇒ Object

Number of gaps in HSP



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# File 'lib/bio/appl/blast/report.rb', line 309

def gaps
  @gaps
end

#hit_frame ⇒ Object

Translation frame of subject



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# File 'lib/bio/appl/blast/report.rb', line 303

def hit_frame
  @hit_frame
end

#hit_from ⇒ Object

Start of HSP in subject



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# File 'lib/bio/appl/blast/report.rb', line 293

def hit_from
  @hit_from
end

#hit_to ⇒ Object

End of HSP



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# File 'lib/bio/appl/blast/report.rb', line 295

def hit_to
  @hit_to
end

#hseq ⇒ Object

Alignment string for subject (with gaps)



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# File 'lib/bio/appl/blast/report.rb', line 317

def hseq
  @hseq
end

#hsp ⇒ Object (readonly)

Returns the value of attribute hsp.



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# File 'lib/bio/appl/blast/report.rb', line 278

def hsp
  @hsp
end

#identity ⇒ Object

Number of identities in HSP



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# File 'lib/bio/appl/blast/report.rb', line 305

def identity
  @identity
end

#midline ⇒ Object

Formating middle line



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# File 'lib/bio/appl/blast/report.rb', line 319

def midline
  @midline
end

#mismatch_count ⇒ Object

Available only for ‘-m 8’ format outputs.



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# File 'lib/bio/appl/blast/report.rb', line 323

def mismatch_count
  @mismatch_count
end

#num ⇒ Object

HSP number



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# File 'lib/bio/appl/blast/report.rb', line 281

def num
  @num
end

#pattern_from ⇒ Object

Start of PHI-BLAST pattern



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# File 'lib/bio/appl/blast/report.rb', line 297

def pattern_from
  @pattern_from
end

#pattern_to ⇒ Object

End of PHI-BLAST pattern



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# File 'lib/bio/appl/blast/report.rb', line 299

def pattern_to
  @pattern_to
end

#percent_identity ⇒ Object

Available only for ‘-m 8’ format outputs.



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# File 'lib/bio/appl/blast/report.rb', line 321

def percent_identity
  @percent_identity
end

#positive ⇒ Object

Number of positives in HSP



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# File 'lib/bio/appl/blast/report.rb', line 307

def positive
  @positive
end

#qseq ⇒ Object

Alignment string for the query (with gaps)



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# File 'lib/bio/appl/blast/report.rb', line 315

def qseq
  @qseq
end

#query_frame ⇒ Object

Translation frame of query



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# File 'lib/bio/appl/blast/report.rb', line 301

def query_frame
  @query_frame
end

#query_from ⇒ Object

Start of HSP in query



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# File 'lib/bio/appl/blast/report.rb', line 289

def query_from
  @query_from
end

#query_to ⇒ Object

End of HSP



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# File 'lib/bio/appl/blast/report.rb', line 291

def query_to
  @query_to
end

#score ⇒ Object

Sscore of HSP



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# File 'lib/bio/appl/blast/report.rb', line 285

def score
  @score
end