Class: Bio::Blast::Report::Hit

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

Overview

Bio::Blast::Report::Hit

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initializeHit

Returns a new instance of Hit


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# File 'lib/bio/appl/blast/report.rb', line 255

def initialize
  @hsps = []
end

Instance Attribute Details

#accessionObject Also known as: target_id

Accession


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# File 'lib/bio/appl/blast/report.rb', line 271

def accession
  @accession
end

#definitionObject Also known as: target_def

Definition line of subject


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# File 'lib/bio/appl/blast/report.rb', line 269

def definition
  @definition
end

#hit_idObject

SeqId of subject


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# File 'lib/bio/appl/blast/report.rb', line 265

def hit_id
  @hit_id
end

#hspsObject (readonly)

Returns an Array of Bio::Blast::Report::Hsp objects.


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# File 'lib/bio/appl/blast/report.rb', line 260

def hsps
  @hsps
end

#lenObject Also known as: target_len

Length of subject


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# File 'lib/bio/appl/blast/report.rb', line 267

def len
  @len
end

#numObject

Hit number


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# File 'lib/bio/appl/blast/report.rb', line 263

def num
  @num
end

#query_defObject

Compatible method with Bio::Fasta::Report::Hit class.


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

def query_def
  @query_def
end

#query_idObject

Compatible method with Bio::Fasta::Report::Hit class.


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

def query_id
  @query_id
end

#query_lenObject

Compatible method with Bio::Fasta::Report::Hit class.


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

def query_len
  @query_len
end

Instance Method Details

#bit_scoreObject


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

def bit_score;        @hsps.first.bit_score;        end

#eachObject

Iterates on each Hsp object.


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# File 'lib/bio/appl/blast/report.rb', line 274

def each
  @hsps.each do |x|
    yield x
  end
end

#evalueObject

Shortcut methods for the best Hsp, some are also compatible with Bio::Fasta::Report::Hit class.


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# File 'lib/bio/appl/blast/report.rb', line 296

def evalue;           @hsps.first.evalue;           end

#identityObject


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# File 'lib/bio/appl/blast/report.rb', line 298

def identity;         @hsps.first.identity;         end

#lap_atObject


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# File 'lib/bio/appl/blast/report.rb', line 310

def lap_at
  [ query_start, query_end, target_start, target_end ]
end

#midlineObject


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# File 'lib/bio/appl/blast/report.rb', line 304

def midline;          @hsps.first.midline;          end

#overlapObject


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# File 'lib/bio/appl/blast/report.rb', line 300

def overlap;          @hsps.first.align_len;        end

#percent_identityObject


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

def percent_identity; @hsps.first.percent_identity; end

#query_endObject


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

def query_end;        @hsps.first.query_to;         end

#query_seqObject


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# File 'lib/bio/appl/blast/report.rb', line 302

def query_seq;        @hsps.first.qseq;             end

#query_startObject


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# File 'lib/bio/appl/blast/report.rb', line 306

def query_start;      @hsps.first.query_from;       end

#target_endObject


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

def target_end;       @hsps.first.hit_to;           end

#target_seqObject


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

def target_seq;       @hsps.first.hseq;             end

#target_startObject


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# File 'lib/bio/appl/blast/report.rb', line 308

def target_start;     @hsps.first.hit_from;         end