Class: Bio::PAML::Codeml::ReportSingle

Inherits:
Bio::PAML::Common::Report show all
Defined in:
lib/bio/appl/paml/codeml/report.rb

Overview

ReportSingle is a simpler parser for a codeml report

containing a single run. This is retained for 
backward compatibility mostly.

The results of a single model (old style report parser)

–

>> buf = BioTestFile.read('paml/codeml/output.txt')

++

>> single = Bio::PAML::Codeml::Report.new(buf)

>> single.tree_log_likelihood
=> -1817.465211

>> single.tree_length
=> 0.77902

>> single.alpha
=> 0.58871

>> single.tree
=> "(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);"

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(codeml_report) ⇒ ReportSingle

Do not use



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# File 'lib/bio/appl/paml/codeml/report.rb', line 367

def initialize(codeml_report)
  @tree_log_likelihood = pull_tree_log_likelihood(codeml_report)
  @tree_length = pull_tree_length(codeml_report)
  @alpha = pull_alpha(codeml_report)
  @tree = pull_tree(codeml_report)
end

Instance Attribute Details

#alpha ⇒ Object (readonly)

Returns the value of attribute alpha.



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

def alpha
  @alpha
end

#tree ⇒ Object (readonly)

Returns the value of attribute tree.



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

def tree
  @tree
end

#tree_length ⇒ Object (readonly)

Returns the value of attribute tree_length.



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

def tree_length
  @tree_length
end

#tree_log_likelihood ⇒ Object (readonly)

Returns the value of attribute tree_log_likelihood.



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

def tree_log_likelihood
  @tree_log_likelihood
end