class MzID::PSM
class to represent a single peptide-spectrum match (PSM
)
Public Class Methods
new(h={})
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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
Public Instance Methods
add_pep_ev(pep_ev)
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add the peptide evidence
# 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()
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get ID
# File lib/mzid/psm.rb, line 25 def get_id() @id end
get_mods()
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get modifications
# File lib/mzid/psm.rb, line 37 def get_mods() @mods end
get_pass_threshold()
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get pass threshold flag
# File lib/mzid/psm.rb, line 41 def get_pass_threshold() @pass_thresh end
get_pep()
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get peptide sequence
# File lib/mzid/psm.rb, line 27 def get_pep() @pep end
get_pep_ev()
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get peptide evidence
# File lib/mzid/psm.rb, line 39 def get_pep_ev() @pep_evidence end
get_pep_ref()
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get peptide reference
# File lib/mzid/psm.rb, line 31 def get_pep_ref() @peptide_ref end
get_spec_num()
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get spectrum number
# File lib/mzid/psm.rb, line 35 def get_spec_num() @spec_num end
get_spec_prob()
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get spectral probability
# File lib/mzid/psm.rb, line 29 def get_spec_prob() @spec_prob end
get_spec_ref()
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get spectrum reference
# File lib/mzid/psm.rb, line 33 def get_spec_ref() @spec_ref end
set_pep(pep)
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set the peptide sequence
# File lib/mzid/psm.rb, line 48 def set_pep(pep) @pep = pep end
set_spec_prob(prob)
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set the spectral probability
# File lib/mzid/psm.rb, line 50 def set_spec_prob(prob) @spec_prob = prob end
to_s()
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output PSM
as string
# File lib/mzid/psm.rb, line 58 def to_s() "[#{@spec_num}; Pep: #{@pep}; SpecProb: #{@spec_prob}; Mods #{@mods.to_s}]" end