Class: MS::Parser::MzXML::Regexp

Inherits:
Object
  • Object
show all
Includes:
MS::Parser::MzXML
Defined in:
lib/ms/parser/mzxml/regexp.rb

Defined Under Namespace

Classes: MsRun

Constant Summary collapse

@@first_scan_regexp = 
/<scan /o
@@scan_re =

def msrun(file, opts={}) end

/<scan.*?num="(\d+)"(.*?)<\/scan>/mo

Constants included from MS::Parser::MzXML

Base_dir_for_parsers

Constants included from XMLStyleParser

XMLStyleParser::File_required, XMLStyleParser::Parser_precedence

Constants included from MS::Parser

MS::Parser::Mzdata_regexp, MS::Parser::Mzxml_regexp

Instance Attribute Summary

Attributes included from XMLStyleParser

#method

Attributes included from MS::Parser

#version

Class Method Summary collapse

Instance Method Summary collapse

Methods included from MS::Parser::MzXML

#_el, #basic_info, fix_bad_scan_tags, fix_bad_scan_tags_from_io, has_bad_scan_tag?, has_bad_scan_tag_from_io?, has_bad_scan_tag_from_string?, new, #precursor_mz_and_inten_by_scan, #precursor_mz_by_scan_for_path, #precursor_mz_by_scan_num, #scans_by_num, #start_and_end_mz

Methods included from XMLStyleParser

available_xml_parsers, choose_parser, require_parse_files, require_parsers

Methods included from MS::Parser

filetype_and_version, new

Constructor Details

#initialize(method = :msrun, version = '1.0') ⇒ Regexp

Returns a new instance of Regexp.



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# File 'lib/ms/parser/mzxml/regexp.rb', line 9

def initialize(method=:msrun, version='1.0')
  @method = method
  @version = version
end

Class Method Details

.by_scan_num(file, regex) ⇒ Object

(array will likely start at 1!)



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# File 'lib/ms/parser/mzxml/regexp.rb', line 36

def self.by_scan_num(file, regex)
  arr = []
  File.open(file) do |fh|
    string = fh.read 
    matches = string.scan(@@scan_re)
    matches.each do |matched|
      if inner_match = regex.match(matched[1])
        index = matched[0].to_i
        arr[index] = yield(inner_match)
      end
    end
  end
  arr
end

.precursor_mz_and_intensity_by_scan(file) ⇒ Object 



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# File 'lib/ms/parser/mzxml/regexp.rb', line 30

def self.precursor_mz_and_intensity_by_scan(file)
  prec_re = /msLevel="2".*?<precursorMz precursorIntensity="([\d\.]+)".*?>([\d\.]+)<\/precursorMz>/mo
  self.by_scan_num(file, prec_re) {|match_obj| match_obj.captures.reverse}
end

.precursor_mz_by_scan(file) ⇒ Object

Returns array where array = precursorMz Parent scans armme not arrayed Values are strings. Array index likely starts at 1! @TODO: replace the use of a yield block



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# File 'lib/ms/parser/mzxml/regexp.rb', line 55

def self.precursor_mz_by_scan(file)
  prec_re = /msLevel="2".*?<precursorMz.*?>([\d\.]+)<\/precursorMz>/mo
  self.by_scan_num(file, prec_re) {|match_obj| match_obj.captures[0]}
end

Instance Method Details

#msrun(file) ⇒ Object

returns a MS::MsRun Object



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# File 'lib/ms/parser/mzxml/regexp.rb', line 19

def msrun(file)
  fh = File.open(file) 
  get_header(fh)

  fh.close
end

#parse(file) ⇒ Object 



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# File 'lib/ms/parser/mzxml/regexp.rb', line 14

def parse(file)
  send(@method, file) 
end