Class: Bio::Blast::Default::Report

Inherits:

Object

• Object
• Bio::Blast::Default::Report

show all

Defined in:

lib/bio/appl/blast/format0.rb

Overview

Defined Under Namespace

Classes: AlwaysNil, F0dbstat, HSP, Hit, Iteration

Constant Summary

DELIMITER =

< DB

RS = "\nBLAST"

DELIMITER_OVERRUN =

(Integer) excess read size included in DELIMITER.

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Instance Attribute Summary (collapse)

• - (Object) db_len readonly

  Returns the value of attribute db_len.

• - (Object) db_num readonly

  Returns the value of attribute db_num.

• - (Object) eff_space readonly

  Returns the value of attribute eff_space.

• - (Object) entry_overrun readonly

  piece of next entry.

• - (Object) expect readonly

  Returns the value of attribute expect.

• - (Object) gap_extend readonly

  Returns the value of attribute gap_extend.

• - (Object) gap_open readonly

  Returns the value of attribute gap_open.

• - (Object) iterations readonly

  (PSI-BLAST) Returns iterations.

• - (Object) matrix readonly

  Returns the value of attribute matrix.

• - (Object) num_hits readonly

  Returns the value of attribute num_hits.

• - (Object) posted_date readonly

  Returns the value of attribute posted_date.

• - (Object) sc_match readonly

  Returns the value of attribute sc_match.

• - (Object) sc_mismatch readonly

  Returns the value of attribute sc_mismatch.

Class Method Summary (collapse)

• + (Object) delegate_to_f0dbstat(*names)

  Defines attributes which delegate to @f0dbstat objects.

• + (Object) open(filename, *mode)

  Opens file by using Bio::FlatFile.open.

Instance Method Summary (collapse)

• - (Boolean) converged?

  (PSI-BLAST) Same as iterations.last.converged?.

• - (Object) db

  Returns the name (filename or title) of the database.

• - (Object) each_hit (also: #each)

  Iterates over each hit of the last iteration.

• - (Object) each_iteration

  (PSI-BLAST) Iterates over each iteration.

• - (Object) entropy

  Same as iterations.last.entropy.

• - (Object) gapped_entropy

  Same as iterations.last.gapped_entropy.

• - (Object) gapped_kappa

  Same as iterations.last.gapped_kappa.

• - (Object) gapped_lambda

  Same as iterations.last.gapped_lambda.

• - (Object) hits

  Same as iterations.last.hits.

• - (Report) initialize(*arg) constructor

  def.

• - (Object) kappa

  Same as iterations.last.kappa.

• - (Object) lambda

  Same as iterations.last.lambda.

• - (Object) message

  (PSI-BLAST) Same as iterations.last.message.

• - (Object) pattern

  (PHI-BLAST) Same as iterations.first.pattern.

• - (Object) pattern_positions

  (PHI-BLAST) Same as iterations.first.pattern_positions.

• - (Object) program

  Returns program name.

• - (Object) query_def

  Returns definition of the query.

• - (Object) query_len

  Returns length of the query.

• - (Object) reference

  Returns the bibliography reference of the BLAST software.

• - (Object) references

  Returns the bibliography references of the BLAST software.

• - (Object) to_s

  Returns whole entry as a string.

• - (Object) version

  Returns version of the program.

• - (Object) version_date

  Returns released date of the program.

• - (Object) version_number

  Returns version number string of the program.

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# File 'lib/bio/appl/blast/format0.rb', line 53

def initialize(*arg)
  raise 'cannot use StringScanner_R'
end

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# File 'lib/bio/appl/blast/format0.rb', line 102

def db_len
  @db_len
end

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# File 'lib/bio/appl/blast/format0.rb', line 98

def db_num
  @db_num
end

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# File 'lib/bio/appl/blast/format0.rb', line 110

def eff_space
  @eff_space
end

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# File 'lib/bio/appl/blast/format0.rb', line 65

def entry_overrun
  @entry_overrun
end

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# File 'lib/bio/appl/blast/format0.rb', line 134

def expect
  @expect
end

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# File 'lib/bio/appl/blast/format0.rb', line 130

def gap_extend
  @gap_extend
end

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# File 'lib/bio/appl/blast/format0.rb', line 126

def gap_open
  @gap_open
end

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# File 'lib/bio/appl/blast/format0.rb', line 71

def iterations
  @iterations
end

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# File 'lib/bio/appl/blast/format0.rb', line 114

def matrix
  @matrix
end

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# File 'lib/bio/appl/blast/format0.rb', line 138

def num_hits
  @num_hits
end

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# File 'lib/bio/appl/blast/format0.rb', line 106

def posted_date
  @posted_date
end

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# File 'lib/bio/appl/blast/format0.rb', line 118

def sc_match
  @sc_match
end

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# File 'lib/bio/appl/blast/format0.rb', line 122

def sc_mismatch
  @sc_mismatch
end

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# File 'lib/bio/appl/blast/format0.rb', line 90

def self.delegate_to_f0dbstat(*names)
  names.each do |x|
    module_eval("def #{x}; @f0dbstat.#{x}; end")
  end
end

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# File 'lib/bio/appl/blast/format0.rb', line 48

def self.open(filename, *mode)
  Bio::FlatFile.open(self, filename, *mode)
end

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# File 'lib/bio/appl/blast/format0.rb', line 221

def converged?
  @iterations.last.converged?
end

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# File 'lib/bio/appl/blast/format0.rb', line 245

def db
  unless defined?(@db)
    if /Database *\: *(.*)/m =~ @f0database then
      a = $1.split(/^/)
      a.pop if a.size > 1
      @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
    end
  end #unless
  @db
end

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# File 'lib/bio/appl/blast/format0.rb', line 196

def each_hit
  @iterations.last.each do |x|
    yield x
  end
end

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# File 'lib/bio/appl/blast/format0.rb', line 186

def each_iteration
  @iterations.each do |x|
    yield x
  end
end

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# File 'lib/bio/appl/blast/format0.rb', line 146

def entropy;        @iterations.last.entropy;        end

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# File 'lib/bio/appl/blast/format0.rb', line 153

def gapped_entropy; @iterations.last.gapped_entropy; end

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# File 'lib/bio/appl/blast/format0.rb', line 149

def gapped_kappa;   @iterations.last.gapped_kappa;   end

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# File 'lib/bio/appl/blast/format0.rb', line 151

def gapped_lambda;  @iterations.last.gapped_lambda;  end

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# File 'lib/bio/appl/blast/format0.rb', line 207

def hits
  @iterations.last.hits
end

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# File 'lib/bio/appl/blast/format0.rb', line 142

def kappa;          @iterations.last.kappa;          end

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# File 'lib/bio/appl/blast/format0.rb', line 144

def lambda;         @iterations.last.lambda;         end

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# File 'lib/bio/appl/blast/format0.rb', line 213

def message
  @iterations.last.message
end

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# File 'lib/bio/appl/blast/format0.rb', line 173

def pattern; @iterations.first.pattern; end

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# File 'lib/bio/appl/blast/format0.rb', line 178

def pattern_positions
  @iterations.first.pattern_positions
end

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# File 'lib/bio/appl/blast/format0.rb', line 156

def program;        format0_parse_header; @program;        end

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# File 'lib/bio/appl/blast/format0.rb', line 168

def query_def; format0_parse_query; @query_def; end

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# File 'lib/bio/appl/blast/format0.rb', line 165

def query_len; format0_parse_query; @query_len; end

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# File 'lib/bio/appl/blast/format0.rb', line 229

def reference
  references[0]
end

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# File 'lib/bio/appl/blast/format0.rb', line 235

def references
  unless defined?(@references)
    @references = @f0references.collect do |x|
      x.to_s.gsub(/\s+/, ' ').strip
    end
  end #unless
  @references
end

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# File 'lib/bio/appl/blast/format0.rb', line 74

def to_s; @entry; end

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# File 'lib/bio/appl/blast/format0.rb', line 158

def version;        format0_parse_header; @version;        end

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# File 'lib/bio/appl/blast/format0.rb', line 162

def version_date;   format0_parse_header; @version_date;   end

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# File 'lib/bio/appl/blast/format0.rb', line 160

def version_number; format0_parse_header; @version_number; end