Class: SpectrumHash::Splash

Inherits:
Object
  • Object
show all
Defined in:
lib/spectrum_hash/splash.rb

Constant Summary collapse

DEFAULT_SPLASH_API_URI = 
'http://splash.fiehnlab.ucdavis.edu/splash/it'
DEFAULT_SPECTRUM_TYPE = 
:ms
SPECTRUM_TYPES = 
{ms: 1, nmr: 2, uv_vis: 3, ir: 4, raman: 5}.freeze
RETRIES = 
3
RETRY_WAIT = 
0.1

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(spectrum, options = {}) ⇒ Splash

Returns a new instance of Splash.



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# File 'lib/spectrum_hash/splash.rb', line 15

def initialize(spectrum, options={})
  # options can be version or uri to use a different end point
  @spectrum      = spectrum
  @spectrum_type = options[:spectrum_type] || DEFAULT_SPECTRUM_TYPE
  @api_uri       = options[:uri]           || DEFAULT_SPLASH_API_URI

  # Load the splash if given
  @splash = options[:splash]

  fetch! if @splash.nil?
end

Instance Attribute Details

#api_uri ⇒ Object (readonly)

Returns the value of attribute api_uri.



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# File 'lib/spectrum_hash/splash.rb', line 8

def api_uri
  @api_uri
end

#response ⇒ Object (readonly)

Returns the value of attribute response.



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# File 'lib/spectrum_hash/splash.rb', line 8

def response
  @response
end

#spectrum ⇒ Object (readonly)

Returns the value of attribute spectrum.



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# File 'lib/spectrum_hash/splash.rb', line 8

def spectrum
  @spectrum
end

#spectrum_type ⇒ Object (readonly)

Returns the value of attribute spectrum_type.



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# File 'lib/spectrum_hash/splash.rb', line 8

def spectrum_type
  @spectrum_type
end

#splash ⇒ Object (readonly)

Returns the value of attribute splash.



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# File 'lib/spectrum_hash/splash.rb', line 8

def splash
  @splash
end

Instance Method Details

#distance_to(other) ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 82

def distance_to(other)
  sum = 0
  other_histo = other.histogram_list
  histogram_list.each.with_index(0) do |my_value,i|
    sum += ( my_value - other_histo[i] ).abs
  end
  sum
end

#fetch! ⇒ Object

TODO handle retries



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# File 'lib/spectrum_hash/splash.rb', line 31

def fetch!
  return @splash unless @splash.nil?
  @response = fetch_splash
  @splash = @response.body
end

#hash_block ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 70

def hash_block
  split_splash[3]
end

#histogram_block ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 66

def histogram_block
  split_splash[2]
end

#histogram_list ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 74

def histogram_list
  @histogram_list ||= histogram_block.chars.map{|v| v.to_i }
end

#payload ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 43

def payload
  {
    ions: peak_list,
    type: spectrum_type.to_s.upcase
  }
end

#peak_list ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 37

def peak_list
  @peak_list ||= spectrum.map do |peak|
    {mass: peak.first, intensity: peak.last}
  end
end

#split_splash ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 50

def split_splash
  @split_splash ||= splash.split(/-/)
end

#to_s ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 78

def to_s
  splash
end

#top_ten_block ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 62

def top_ten_block
  split_splash[1]
end

#version ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 54

def version
  "1"
end

#version_block ⇒ Object 



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# File 'lib/spectrum_hash/splash.rb', line 58

def version_block
  split_splash[0]
end