Class Bio::PAML::Codeml::ReportSingle
In: lib/bio/appl/paml/codeml/report.rb
Parent: Bio::PAML::Common::Report

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)

  >> 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);"

Methods

new  

Attributes

alpha  [R] 
tree  [R] 
tree_length  [R] 
tree_log_likelihood  [R] 

Public Class methods

Do not use

[Source]

     # File lib/bio/appl/paml/codeml/report.rb, line 367
367:       def initialize(codeml_report)
368:         @tree_log_likelihood = pull_tree_log_likelihood(codeml_report)
369:         @tree_length = pull_tree_length(codeml_report)
370:         @alpha = pull_alpha(codeml_report)
371:         @tree = pull_tree(codeml_report)
372:       end

[Validate]