Class: SequenceServer::BLAST::HSP

Inherits:
Struct
  • Object
show all
Defined in:
lib/sequenceserver/blast/hsp.rb,
lib/sequenceserver/blast/hsp.rb

Overview

Structure to hold generic HSP data for each hit.

HSP class is not used directly. Relevant HSP stats and formatting the alignment changes with BLAST algorithm. We subclass HSP for each BLAST algorithm.

Direct Known Subclasses

BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX

Defined Under Namespace

Classes: BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX

Instance Attribute Summary collapse

Instance Attribute Details

#bit_scoreObject

Returns the value of attribute bit_score

Returns:

  • (Object)

    the current value of bit_score



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def bit_score
  @bit_score
end

#evalueObject

Returns the value of attribute evalue

Returns:

  • (Object)

    the current value of evalue



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def evalue
  @evalue
end

#gapsObject

Returns the value of attribute gaps

Returns:

  • (Object)

    the current value of gaps



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def gaps
  @gaps
end

#hitObject

Returns the value of attribute hit

Returns:

  • (Object)

    the current value of hit



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def hit
  @hit
end

#identityObject

Returns the value of attribute identity

Returns:

  • (Object)

    the current value of identity



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def identity
  @identity
end

#lengthObject

Returns the value of attribute length

Returns:

  • (Object)

    the current value of length



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def length
  @length
end

#midlineObject

Returns the value of attribute midline

Returns:

  • (Object)

    the current value of midline



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def midline
  @midline
end

#numberObject

Returns the value of attribute number

Returns:

  • (Object)

    the current value of number



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def number
  @number
end

#positivesObject

Returns the value of attribute positives

Returns:

  • (Object)

    the current value of positives



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def positives
  @positives
end

#qendObject

Returns the value of attribute qend

Returns:

  • (Object)

    the current value of qend



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def qend
  @qend
end

#qframeObject

Returns the value of attribute qframe

Returns:

  • (Object)

    the current value of qframe



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def qframe
  @qframe
end

#qseqObject

Returns the value of attribute qseq

Returns:

  • (Object)

    the current value of qseq



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def qseq
  @qseq
end

#qstartObject

Returns the value of attribute qstart

Returns:

  • (Object)

    the current value of qstart



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def qstart
  @qstart
end

#scoreObject

Returns the value of attribute score

Returns:

  • (Object)

    the current value of score



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def score
  @score
end

#sendObject

Returns the value of attribute send

Returns:

  • (Object)

    the current value of send



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def send
  @send
end

#sframeObject

Returns the value of attribute sframe

Returns:

  • (Object)

    the current value of sframe



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def sframe
  @sframe
end

#sseqObject

Returns the value of attribute sseq

Returns:

  • (Object)

    the current value of sseq



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def sseq
  @sseq
end

#sstartObject

Returns the value of attribute sstart

Returns:

  • (Object)

    the current value of sstart



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# File 'lib/sequenceserver/blast/hsp.rb', line 9

def sstart
  @sstart
end