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


314
315
316
# File 'lib/bio/appl/blast/report.rb', line 314

def initialize
  @hsp = {}
end

Instance Attribute Details

#align_lenObject

Length of the alignment used


350
351
352
# File 'lib/bio/appl/blast/report.rb', line 350

def align_len
  @align_len
end

#bit_scoreObject

Score (in bits) of HSP


322
323
324
# File 'lib/bio/appl/blast/report.rb', line 322

def bit_score
  @bit_score
end

#densityObject

Score density


352
353
354
# File 'lib/bio/appl/blast/report.rb', line 352

def density
  @density
end

#evalueObject

E-value of HSP


326
327
328
# File 'lib/bio/appl/blast/report.rb', line 326

def evalue
  @evalue
end

#gapsObject

Number of gaps in HSP


348
349
350
# File 'lib/bio/appl/blast/report.rb', line 348

def gaps
  @gaps
end

#hit_frameObject

Translation frame of subject


342
343
344
# File 'lib/bio/appl/blast/report.rb', line 342

def hit_frame
  @hit_frame
end

#hit_fromObject

Start of HSP in subject


332
333
334
# File 'lib/bio/appl/blast/report.rb', line 332

def hit_from
  @hit_from
end

#hit_toObject

End of HSP


334
335
336
# File 'lib/bio/appl/blast/report.rb', line 334

def hit_to
  @hit_to
end

#hseqObject

Alignment string for subject (with gaps)


356
357
358
# File 'lib/bio/appl/blast/report.rb', line 356

def hseq
  @hseq
end

#hspObject (readonly)

Returns the value of attribute hsp


317
318
319
# File 'lib/bio/appl/blast/report.rb', line 317

def hsp
  @hsp
end

#identityObject

Number of identities in HSP


344
345
346
# File 'lib/bio/appl/blast/report.rb', line 344

def identity
  @identity
end

#midlineObject

Formating middle line


358
359
360
# File 'lib/bio/appl/blast/report.rb', line 358

def midline
  @midline
end

#mismatch_countObject

Available only for '-m 8' format outputs.


362
363
364
# File 'lib/bio/appl/blast/report.rb', line 362

def mismatch_count
  @mismatch_count
end

#numObject

HSP number


320
321
322
# File 'lib/bio/appl/blast/report.rb', line 320

def num
  @num
end

#pattern_fromObject

Start of PHI-BLAST pattern


336
337
338
# File 'lib/bio/appl/blast/report.rb', line 336

def pattern_from
  @pattern_from
end

#pattern_toObject

End of PHI-BLAST pattern


338
339
340
# File 'lib/bio/appl/blast/report.rb', line 338

def pattern_to
  @pattern_to
end

#percent_identityObject

Available only for '-m 8' format outputs.


360
361
362
# File 'lib/bio/appl/blast/report.rb', line 360

def percent_identity
  @percent_identity
end

#positiveObject

Number of positives in HSP


346
347
348
# File 'lib/bio/appl/blast/report.rb', line 346

def positive
  @positive
end

#qseqObject

Alignment string for the query (with gaps)


354
355
356
# File 'lib/bio/appl/blast/report.rb', line 354

def qseq
  @qseq
end

#query_frameObject

Translation frame of query


340
341
342
# File 'lib/bio/appl/blast/report.rb', line 340

def query_frame
  @query_frame
end

#query_fromObject

Start of HSP in query


328
329
330
# File 'lib/bio/appl/blast/report.rb', line 328

def query_from
  @query_from
end

#query_toObject

End of HSP


330
331
332
# File 'lib/bio/appl/blast/report.rb', line 330

def query_to
  @query_to
end

#scoreObject

Sscore of HSP


324
325
326
# File 'lib/bio/appl/blast/report.rb', line 324

def score
  @score
end