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#
# = bio/appl/phylip/distance_matrix.rb - phylip distance matrix parser
#
# Copyright:: Copyright (C) 2006
# GOTO Naohisa <ng@bioruby.org>
#
# License:: The Ruby License
#
# $Id: distance_matrix.rb,v 1.3 2007/04/05 23:35:40 trevor Exp $
#
# = About Bio::Phylip::DistanceMatrix
#
# Please refer document of Bio::Phylip::DistanceMatrix class.
#
require 'matrix'
module Bio
module Phylip
# This is a parser class for phylip distance matrix data
# created by dnadist, protdist, or restdist commands.
#
class DistanceMatrix
# creates a new distance matrix object
def initialize(str)
data = str.strip.split(/(?:\r\n|\r|\n)/)
@otus = data.shift.to_s.strip.to_i
prev = nil
data.collect! do |x|
if /\A +/ =~ x and prev then
prev.concat x.strip.split(/\s+/)
nil
else
prev = x.strip.split(/\s+/)
prev
end
end
data.compact!
if data.size != @otus then
raise "inconsistent data (OTUs=#{@otus} but #{data.size} rows)"
end
@otu_names = data.collect { |x| x.shift }
mat = data.collect do |x|
if x.size != @otus then
raise "inconsistent data (OTUs=#{@otus} but #{x.size} columns)"
end
x.collect { |y| y.to_f }
end
@matrix = Matrix.rows(mat, false)
@original_matrix = Matrix.rows(data, false)
end
# distance matrix (returns Ruby's Matrix object)
attr_reader :matrix
# matrix contains values as original strings.
# Use it when you doubt precision of floating-point numbers.
attr_reader :original_matrix
# number of OTUs
attr_reader :otus
# names of OTUs
attr_reader :otu_names
# Generates a new phylip distance matrix formatted text as a string.
def self.generate(matrix, otu_names = nil, options = {})
if matrix.row_size != matrix.column_size then
raise "must be a square matrix"
end
otus = matrix.row_size
names = (0...otus).collect do |i|
name = ((otu_names and otu_names[i]) or "OTU#{i.to_s}")
name
end
data = (0...otus).collect do |i|
x = (0...otus).collect { |j| sprintf("%9.6f", matrix[i, j]) }
x.unshift(sprintf("%-10s", names[i])[0, 10])
str = x[0, 7].join(' ') + "\n"
7.step(otus + 1, 7) do |k|
str << ' ' + x[k, 7].join(' ') + "\n"
end
str
end
sprintf("%5d\n", otus) + data.join('')
end
end #class DistanceMatrix
end #module Phylip
end #module Bio
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