Class: Cytogenetics::Chromosome

Inherits:
Object
  • Object
show all
Includes:
BandReader
Defined in:
lib/cytogenetics/chromosome.rb

Class Attribute Summary collapse

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from BandReader

#bands, #read_file

Constructor Details

#initialize(*args) ⇒ Chromosome

Returns a new instance of Chromosome.

Raises:

  • (ArgumentError) 


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# File 'lib/cytogenetics/chromosome.rb', line 17

def initialize(*args)
  config_logging()
  chr = args[0]
  chr = chr.to_s  if chr.is_a?Fixnum

  raise ArgumentError, "#{chr} is not a valid chromosome identifier." unless (chr.is_a? String and chr.match(/^\d+|X|Y$/))
  @name = chr
  @aberrations = []
  #@normal_bands = bands(@name, File.open("HsBands.txt", 'r')) if (args.length > 1 and args[1].eql? true) ## TODO quit hardcoding
end

Class Attribute Details

.normal_bands ⇒ Object

Returns the value of attribute normal_bands.



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# File 'lib/cytogenetics/chromosome.rb', line 12

def normal_bands
  @normal_bands
end

Instance Attribute Details

#aberrations ⇒ Object (readonly)

Returns the value of attribute aberrations.



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# File 'lib/cytogenetics/chromosome.rb', line 15

def aberrations
  @aberrations
end

#name ⇒ Object (readonly)

Returns the value of attribute name.



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# File 'lib/cytogenetics/chromosome.rb', line 15

def name
  @name
end

Instance Method Details

#aberration(obj) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/cytogenetics/chromosome.rb', line 32

def aberration(obj)
  raise ArgumentError, "Not an Aberration object" unless obj.is_a? Aberration

  #obj.breakpoints.each do |bp|
  #  log.warn("Band #{bp.to_s} doesn't exist. Removing.") if @normal_bands.index(bp.to_s).nil?
  #end

  ## TODO Deal with bands, HOWEVER because the chromosome has aberration objects breakpoints can include
  ## bands for which no chromosome object is created

  #obj.breakpoints.reject {|bp|
  #  @normal_bands.index(bp.to_s).nil?
  #}

  @aberrations << obj
end

#breakpoints ⇒ Object 



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# File 'lib/cytogenetics/chromosome.rb', line 49

def breakpoints
  bps = []
  @aberrations.each { |a| bps << a.breakpoints }
  return bps
end

#config_logging ⇒ Object 



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# File 'lib/cytogenetics/chromosome.rb', line 64

def config_logging
  @log = Cytogenetics.logger
  #@log.progname = self.class.name
end

#fragments ⇒ Object 



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# File 'lib/cytogenetics/chromosome.rb', line 55

def fragments
  frags = []
  @aberrations.each do |a|
    frags << a.fragments
  end
  frags
end

#to_s ⇒ Object 



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# File 'lib/cytogenetics/chromosome.rb', line 28

def to_s
  "#{@name}"
end