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

#initializeHsp

Returns a new instance of Hsp


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# File 'lib/bio/appl/blast/report.rb', line 318

def initialize
  @hsp = {}
end

Instance Attribute Details

#align_lenObject

Length of the alignment used


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# File 'lib/bio/appl/blast/report.rb', line 354

def align_len
  @align_len
end

#bit_scoreObject

Score (in bits) of HSP


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# File 'lib/bio/appl/blast/report.rb', line 326

def bit_score
  @bit_score
end

#densityObject

Score density


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# File 'lib/bio/appl/blast/report.rb', line 356

def density
  @density
end

#evalueObject

E-value of HSP


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# File 'lib/bio/appl/blast/report.rb', line 330

def evalue
  @evalue
end

#gapsObject

Number of gaps in HSP


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# File 'lib/bio/appl/blast/report.rb', line 352

def gaps
  @gaps
end

#hit_frameObject

Translation frame of subject


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# File 'lib/bio/appl/blast/report.rb', line 346

def hit_frame
  @hit_frame
end

#hit_fromObject

Start of HSP in subject


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# File 'lib/bio/appl/blast/report.rb', line 336

def hit_from
  @hit_from
end

#hit_toObject

End of HSP


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# File 'lib/bio/appl/blast/report.rb', line 338

def hit_to
  @hit_to
end

#hseqObject

Alignment string for subject (with gaps)


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# File 'lib/bio/appl/blast/report.rb', line 360

def hseq
  @hseq
end

#hspObject (readonly)

Returns the value of attribute hsp


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

def hsp
  @hsp
end

#identityObject

Number of identities in HSP


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# File 'lib/bio/appl/blast/report.rb', line 348

def identity
  @identity
end

#midlineObject

Formating middle line


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# File 'lib/bio/appl/blast/report.rb', line 362

def midline
  @midline
end

#mismatch_countObject

Available only for '-m 8' format outputs.


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# File 'lib/bio/appl/blast/report.rb', line 366

def mismatch_count
  @mismatch_count
end

#numObject

HSP number


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# File 'lib/bio/appl/blast/report.rb', line 324

def num
  @num
end

#pattern_fromObject

Start of PHI-BLAST pattern


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# File 'lib/bio/appl/blast/report.rb', line 340

def pattern_from
  @pattern_from
end

#pattern_toObject

End of PHI-BLAST pattern


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# File 'lib/bio/appl/blast/report.rb', line 342

def pattern_to
  @pattern_to
end

#percent_identityObject

Available only for '-m 8' format outputs.


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# File 'lib/bio/appl/blast/report.rb', line 364

def percent_identity
  @percent_identity
end

#positiveObject

Number of positives in HSP


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# File 'lib/bio/appl/blast/report.rb', line 350

def positive
  @positive
end

#qseqObject

Alignment string for the query (with gaps)


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# File 'lib/bio/appl/blast/report.rb', line 358

def qseq
  @qseq
end

#query_frameObject

Translation frame of query


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# File 'lib/bio/appl/blast/report.rb', line 344

def query_frame
  @query_frame
end

#query_fromObject

Start of HSP in query


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# File 'lib/bio/appl/blast/report.rb', line 332

def query_from
  @query_from
end

#query_toObject

End of HSP


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# File 'lib/bio/appl/blast/report.rb', line 334

def query_to
  @query_to
end

#scoreObject

Sscore of HSP


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# File 'lib/bio/appl/blast/report.rb', line 328

def score
  @score
end