Class: MzID::PSM

Inherits:
Object
  • Object
show all
Defined in:
lib/mzid/psm.rb

Overview

class to represent a single peptide-spectrum match (PSM)

Instance Method Summary collapse

Constructor Details

#initialize(h = {}) ⇒ PSM

Returns a new instance of PSM.



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# File 'lib/mzid/psm.rb', line 8

def initialize(h={})
  @id = h.has_key?(:id) ? h[:id] : nil
  @pep = h.has_key?(:pep) ? h[:pep] : nil
  @spec_prob = h.has_key?(:spec_prob) ? h[:spec_prob] : nil
  @peptide_ref= h.has_key?(:pep_ref) ? h[:pep_ref] : nil
  @spec_ref = h.has_key?(:spec_ref) ? h[:spec_ref] : nil
  @spec_num = h.has_key?(:spec_num) ? h[:spec_num] : nil
  @mods = h.has_key?(:mods) ? h[:mods] : nil
  @pep_evidence = h.has_key?(:pep_ev) ? h[:pep_ev] : nil
  @pass_thresh = h.has_key?(:pass_threshold) ? h[:pass_threshold] : nil
end

Instance Method Details

#add_pep_ev(pep_ev) ⇒ Object

add the peptide evidence



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# File 'lib/mzid/psm.rb', line 54

def add_pep_ev(pep_ev) @pep_evidence.nil? ? @pep_evidence = [pep_ev] : @pep_evidence.push(pep_ev) end

#get_id ⇒ Object

– get methods ++

get ID



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# File 'lib/mzid/psm.rb', line 25

def get_id() @id end

#get_mods ⇒ Object

get modifications



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# File 'lib/mzid/psm.rb', line 37

def get_mods() @mods end

#get_pass_threshold ⇒ Object

get pass threshold flag



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# File 'lib/mzid/psm.rb', line 41

def get_pass_threshold() @pass_thresh end

#get_pep ⇒ Object

get peptide sequence



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# File 'lib/mzid/psm.rb', line 27

def get_pep() @pep end

#get_pep_ev ⇒ Object

get peptide evidence



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# File 'lib/mzid/psm.rb', line 39

def get_pep_ev() @pep_evidence end

#get_pep_ref ⇒ Object

get peptide reference



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# File 'lib/mzid/psm.rb', line 31

def get_pep_ref() @peptide_ref end

#get_spec_num ⇒ Object

get spectrum number



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# File 'lib/mzid/psm.rb', line 35

def get_spec_num() @spec_num end

#get_spec_prob ⇒ Object

get spectral probability



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# File 'lib/mzid/psm.rb', line 29

def get_spec_prob() @spec_prob end

#get_spec_ref ⇒ Object

get spectrum reference



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# File 'lib/mzid/psm.rb', line 33

def get_spec_ref() @spec_ref end

#set_pep(pep_seq) ⇒ Object

set peptide



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# File 'lib/mzid/psm.rb', line 48

def set_pep(pep) @pep = pep end

#set_spec_prob(prob) ⇒ Object

set the spectral probability



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# File 'lib/mzid/psm.rb', line 50

def set_spec_prob(prob) @spec_prob = prob end

#to_s ⇒ Object

output PSM as string



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# File 'lib/mzid/psm.rb', line 58

def to_s() "[#{@spec_num}; Pep: #{@pep}; SpecProb: #{@spec_prob}; Mods #{@mods.to_s}]" end