class Bio::PAML::Codeml::ReportSingle

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);"

Attributes

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

Public Class Methods

new(codeml_report) click to toggle source

Do not use

# 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