[IC:SymbolHash{ :MzXml::Scan#parse_peakso:$YARD::CodeObjects::MethodObject:@signature"{def parse_peaks
      @mz = []
      @mzi = []
      return if @e[:peaksCount] == 0
      if (!@isMzData) then 
        pkelm = @e.at('peaks')
        sym = Rampy::BYTEORDER[pkelm[:byteOrder]]
        sym.upcase! if (pkelm[:precision].to_i > 32)
        data = Base64.decode64(pkelm.inner_text())
        if (pkelm[:compressionType] == 'zlib')
          data = Zlib::Inflate.inflate(data)
        end
        tmp = data.unpack("#{sym}")
        tmp.each_index do |idx|
          if (idx % 2 == 0 ) then 
            @mz.push(tmp[idx])
          else
            @mzi.push(tmp[idx])
          end
        end
      else
        # first, get mz array data
        tmp = scan.search('mzArrayBinary/data')
        sym = Rampy::BYTEORDER[tmp.attr('endian')]
        sym.upcase! if (tmp.attr('precision').to_i > 32)
        @mz = Base64.decode64(tmp.text()).unpack(sym)
        #now for the intensity array
        tmp = scan.search('intenArrayBinary/data')
        sym = Rampy::BYTEORDER[tmp.attr('endian')]
        sym.upcase! if (tmp.attr('precision').to_i > 32)
        @mzi = Base64.decode64(tmp.text()).unpack(sym)
      end
      return 1
    end:@parameters[ :
@lineiB:@files[["lib/mzml.rbiB:@scope:instance:@source"÷def parse_peaks
  @mz = []
  @mzi = []
  return if @e[:peaksCount] == 0
  if (!@isMzData) then 
    pkelm = @e.at('peaks')
    sym = Rampy::BYTEORDER[pkelm[:byteOrder]]
    sym.upcase! if (pkelm[:precision].to_i > 32)
    data = Base64.decode64(pkelm.inner_text())
    if (pkelm[:compressionType] == 'zlib')
      data = Zlib::Inflate.inflate(data)
    end
    tmp = data.unpack("#{sym}")
    tmp.each_index do |idx|
      if (idx % 2 == 0 ) then 
        @mz.push(tmp[idx])
      else
        @mzi.push(tmp[idx])
      end
    end
  else
    # first, get mz array data
    tmp = scan.search('mzArrayBinary/data')
    sym = Rampy::BYTEORDER[tmp.attr('endian')]
    sym.upcase! if (tmp.attr('precision').to_i > 32)
    @mz = Base64.decode64(tmp.text()).unpack(sym)
    #now for the intensity array
    tmp = scan.search('intenArrayBinary/data')
    sym = Rampy::BYTEORDER[tmp.attr('endian')]
    sym.upcase! if (tmp.attr('precision').to_i > 32)
    @mzi = Base64.decode64(tmp.text()).unpack(sym)
  end
  return 1
end:
@name:parse_peaks:@namespaceo:#YARD::CodeObjects::ClassObject:@class_mixinsIC:&YARD::CodeObjects::CodeObjectList[ :@owner@:@superclasso:YARD::CodeObjects::Proxy;:Object:	@obj0;o:$YARD::CodeObjects::ModuleObject;IC;[ ;@;[[@i1;:
MzXml:@childrenIC;[	o:&YARD::CodeObjects::ConstantObject;"@BYTEORDER = {"little" =>"e*", "network"=>"g*", "big"=>"g*"};
i2:@value"4{"little" =>"e*", "network"=>"g*", "big"=>"g*"};[[@i2;"@BYTEORDER = {"little" =>"e*", "network"=>"g*", "big"=>"g*"};:BYTEORDER;@:@docstringIC:YARD::Docstring" :@tag_factoryo:YARD::Tags::Library:@factoryo:YARD::Tags::DefaultFactory :@object@:	@all" :@line_range0:
@tags[ :@ref_tags[ ;)[ :@current_file_has_commentsFo;;"3def parse(xml)
    Hpricot.xml(xml).root
  end;	[["xml0;
i3;[[@i3;;;"/def parse(xml)
  Hpricot.xml(xml).root
end;:
parse;@; IC;!" ;"o;#;$@;&@#;'" ;(0;)[ ;*[ :@visibility:public;)[ ;+F:@explicitT@o;;IC;[ ;@1;o;;;;0;@;[[@i;:MzFile;IC;[o;;"Zdef initialize (mzXmlFile )
      @file = File.open(mzXmlFile, "r")
      @file.readline
      if (@file.readline =~  /mzData/) then
        @isMzData = true
      else 
        @isMzData = false
      end
      @offset = parse_index_offset
      @index = parse_index
      @header = parse_header
      @basepeak = nil
      @file.pos = 0
    end;	[["mzXmlFile0;
i};[[@i};;;"&def initialize (mzXmlFile )
  @file = File.open(mzXmlFile, "r")
  @file.readline
  if (@file.readline =~  /mzData/) then
    @isMzData = true
  else 
    @isMzData = false
  end
  @offset = parse_index_offset
  @index = parse_index
  @header = parse_header
  @basepeak = nil
  @file.pos = 0
end;:initialize;@1; IC;!" ;"o;#;$@;&@7;'" ;(0;)[o:YARD::Tags::Tag
:@types["MzFile;0:
@text"a new instance of +MzFile+;&@7:@tag_name"return;*[ ;-;.;)[ ;+F;/To;;"def isMzData;	[ ;[[@iŒ;;;"!def isMzData
  @isMzData
end;:isMzData;@1; IC;!"UBoolean determining whether the opened file is an mzData file, rather than mzXML;"o;#;$@;&@J;'["UBoolean determining whether the opened file is an mzData file, rather than mzXML;(o:
Range:
begini‹:	exclF:endi‹;)[ ;*[ ;-;.;)[ ;+To;;"def index;	[ ;[[@i;;;"def index
  @index
end;:
index;@1; IC;!"…The scan index read (or computed) from the mzXML/mzData file. A Hash of {scanNum => file_position}
-- 
should work on both file types;"o;#;$@;&@X;'["gThe scan index read (or computed) from the mzXML/mzData file. A Hash of {scanNum => file_position}"-- "#should work on both file types;(o;7;8i;9F;:i;)[ ;*[ ;-;.;)[ ;+To;;"def header;	[ ;[[@i’;;;"def header
  @header
end;:header;@1; IC;!"kThe mzXML/mzData header annotations (should have some useful information in it ;-) ) as REXML::Element;"o;#;$@;&@h;'["kThe mzXML/mzData header annotations (should have some useful information in it ;-) ) as REXML::Element;(o;7;8i‘;9F;:i‘;)[ ;*[ ;-;.;)[ ;+To;;"Tdef basePeak 
      return @basepeak if @basepeak
      parse_base_peak
    end;	[ ;
i=;[[@i”[@i=;;;"Hdef basePeak 
  return @basepeak if @basepeak
  parse_base_peak
end;:basePeak;@1; IC;!"sThe base peak chromatograph (*WARNING* Calculated the first time it is accessed, which may take a bit of time);"o;#;$@;&@v;'["sThe base peak chromatograph (*WARNING* Calculated the first time it is accessed, which may take a bit of time);(0;)[ ;*[ ;-:protected;)[ ;+T;/To;;"]def parse_index_offset
      return -1 if @isMzData
      r = %r{\<indexOffset\>(\d+)\<\/indexOffset\>}
      seekoffset = -120
      while true 
        self.seek(seekoffset, IO::SEEK_END)
        if (r.match(self.read)) then 
          return  $1.to_i
        end
        seekoffset -= 10
        return -1 if seekoffset <= -1000
      end
    end;	[ ;
i˜;[[@i˜;;;"-def parse_index_offset
  return -1 if @isMzData
  r = %r{\<indexOffset\>(\d+)\<\/indexOffset\>}
  seekoffset = -120
  while true 
    self.seek(seekoffset, IO::SEEK_END)
    if (r.match(self.read)) then 
      return  $1.to_i
    end
    seekoffset -= 10
    return -1 if seekoffset <= -1000
  end
end;:parse_index_offset;@1; IC;!",Parses the indexOffset from mzXML files;"o;#;$@;&@;'["-Parses the indexOffset from mzXML files ;(o;7;8i—;9F;:i—;)[ ;*[ ;-:private;)[ ;+T;/To;;"def parse_index
      if (@offset < 0) then 
        return compute_index
      end
      r= %r{\<offset\s+id=\"(\d+)\"\>(\d+)\<\/offset\>}
      @file.pos = @offset
      index = {}
      while (!@file.eof?) 
        next unless (r.match(@file.readline))
        index[$1.to_i] = $2.to_i
      end
      ## now check the index, otherwise recompute it!!!
      # beginning
      return compute_index if index.empty?
      r =/\<scan|\<spectrum\sid/
      tmpkeys = index.keys.sort
      @file.pos = index[tmpkeys.first]
      if (!(@file.readline =~ r ))
        index = compute_index
      else
        #middle 
        @file.pos = index[tmpkeys[tmpkeys.length/2]]
        if (!(@file.readline =~ r))
          index = compute_index
        else
          #end
          @file.pos = index[tmpkeys.last]
          if (!(@file.readline =~ r))
            index = compute_index
          end
        end
      end
      #reset the file to the first scan position
      @file.pos = index[tmpkeys.first]
      #return the index
      index
    end;	[ ;
i§;[[@i§;;;"ƒdef parse_index
  if (@offset < 0) then 
    return compute_index
  end
  r= %r{\<offset\s+id=\"(\d+)\"\>(\d+)\<\/offset\>}
  @file.pos = @offset
  index = {}
  while (!@file.eof?) 
    next unless (r.match(@file.readline))
    index[$1.to_i] = $2.to_i
  end
  ## now check the index, otherwise recompute it!!!
  # beginning
  return compute_index if index.empty?
  r =/\<scan|\<spectrum\sid/
  tmpkeys = index.keys.sort
  @file.pos = index[tmpkeys.first]
  if (!(@file.readline =~ r ))
    index = compute_index
  else
    #middle 
    @file.pos = index[tmpkeys[tmpkeys.length/2]]
    if (!(@file.readline =~ r))
      index = compute_index
    else
      #end
      @file.pos = index[tmpkeys.last]
      if (!(@file.readline =~ r))
        index = compute_index
      end
    end
  end
  #reset the file to the first scan position
  @file.pos = index[tmpkeys.first]
  #return the index
  index
end;:parse_index;@1; IC;!">Return a hash of scans, where {scan number} = file offset;"o;#;$@;&@;'[">Return a hash of scans, where {scan number} = file offset;(o;7;8i¦;9F;:i¦;)[ ;*[ ;-;@;)[ ;+T;/To;;"adef parse_header
      @file.pos = 0
      r = %r{\<scan\s|\<spectrum\s}
      xml = "" 
      while true
        l = @file.readline
        break if l =~ r
        xml << l 
      end
      if (@isMzData) then 
        xml << "</spectrumList></mzData>"
      else 
        xml << "</msRun></mzXML>"
      end
      xml.empty? ? nil : parse(xml)
    end;	[ ;
iÎ;[[@iÎ;;;"%def parse_header
  @file.pos = 0
  r = %r{\<scan\s|\<spectrum\s}
  xml = "" 
  while true
    l = @file.readline
    break if l =~ r
    xml << l 
  end
  if (@isMzData) then 
    xml << "</spectrumList></mzData>"
  else 
    xml << "</msRun></mzXML>"
  end
  xml.empty? ? nil : parse(xml)
end;:parse_header;@1; IC;!"'Parses the file header information;"o;#;$@;&@›;'["'Parses the file header information;(o;7;8iÍ;9F;:iÍ;)[ ;*[ ;-;@;)[ ;+T;/To;;"2def compute_index 
      @file.rewind
      r = %r{\<scan\snum\=\"(\d+)\"|\<spectrum\sid\=\"(\d+)\"}
      index  = {}
      while (!@file.eof) 
        p = @file.pos
        if (r.match(@file.readline)) then 
          m = $1 ? $1 : $2
          index[m.to_i] = p
        end
      end
      index
    end;	[ ;
ià;[[@ià;;;"def compute_index 
  @file.rewind
  r = %r{\<scan\snum\=\"(\d+)\"|\<spectrum\sid\=\"(\d+)\"}
  index  = {}
  while (!@file.eof) 
    p = @file.pos
    if (r.match(@file.readline)) then 
      m = $1 ? $1 : $2
      index[m.to_i] = p
    end
  end
  index
end;:compute_index;@1; IC;!"3Computes the index by scanning the entire file;"o;#;$@;&@©;'["3Computes the index by scanning the entire file;(o;7;8iß;9F;:iß;)[ ;*[ ;-;@;)[ ;+T;/To;;"¦def parse_base_peak 
      @file.pos = 0
      @basepeak = [[],[]]
      if (@isMzData) 
        # MUCH more expensive to compute
        while (s = next_scan)
          p = get_peaks(s)
          max_int = -1.0
          bp_idx = 0
          p[1].each_index do |i|
            bp_idx = i if p[1][i] > max_int
          end
          @basepeak[0].push(p[0][bp_idx]) 
          @basepeak[0].push(p[1][bp_idx]) 
        end
      else
        numr= %r{\<scan num\=[\"|\'](\d+)[\"|\']}
        bpr= %r{basePeak(\w+)\=[\"|\'](\S+)[\"|\']}
        num = 0
        while(!@file.eof?)
          l = @file.readline
          if (m = numr.match(l))
            num = m[1].to_i
            next
          end
          if (m = bpr.match(l))
            if m[1] == "Mz"
              @basepeak[0].push(num) 
            else
              @basepeak[1].push(m[2].to_f)  
            end
          end
        end
      end
      @basepeak
    end;	[ ;
ið;[[@ið;;;"def parse_base_peak 
  @file.pos = 0
  @basepeak = [[],[]]
  if (@isMzData) 
    # MUCH more expensive to compute
    while (s = next_scan)
      p = get_peaks(s)
      max_int = -1.0
      bp_idx = 0
      p[1].each_index do |i|
        bp_idx = i if p[1][i] > max_int
      end
      @basepeak[0].push(p[0][bp_idx]) 
      @basepeak[0].push(p[1][bp_idx]) 
    end
  else
    numr= %r{\<scan num\=[\"|\'](\d+)[\"|\']}
    bpr= %r{basePeak(\w+)\=[\"|\'](\S+)[\"|\']}
    num = 0
    while(!@file.eof?)
      l = @file.readline
      if (m = numr.match(l))
        num = m[1].to_i
        next
      end
      if (m = bpr.match(l))
        if m[1] == "Mz"
          @basepeak[0].push(num) 
        else
          @basepeak[1].push(m[2].to_f)  
        end
      end
    end
  end
  @basepeak
end;:parse_base_peak;@1; IC;!" ;"o;#;$@;&@·;'" ;(0;)[ ;*[ ;-;>;)[ ;+F;/To;;"4def get_scan_from_curr_pos 
      return nil if (@file.eof)
      xml = ""
      while (!@file.eof )
        l = @file.readline
        if (l =~ /\<\/scan\>|\<\/spectrum\>/) then
          xml.concat(l)
          break 
        end
        xml.concat(l)
      end
      xml.empty? ? nil :  parse(xml)
    end;	[ ;
i;[[@i;;;"def get_scan_from_curr_pos 
  return nil if (@file.eof)
  xml = ""
  while (!@file.eof )
    l = @file.readline
    if (l =~ /\<\/scan\>|\<\/spectrum\>/) then
      xml.concat(l)
      break 
    end
    xml.concat(l)
  end
  xml.empty? ? nil :  parse(xml)
end;:get_scan_from_curr_pos;@1; IC;!" ;"o;#;$@;&@Ã;'" ;(0;)[ ;*[ ;-;>;)[ ;+F;/To;;"fdef scan scanNum
      @file.pos = @index[scanNum]
      Scan.new(get_scan_from_curr_pos)
    end;	[["scanNum0;
i';[[@i';;;"Zdef scan scanNum
  @file.pos = @index[scanNum]
  Scan.new(get_scan_from_curr_pos)
end;:	scan;@1; IC;!"*Return a Scan for a given scan number;"o;#;$@;&@Ï;'["*Return a Scan for a given scan number" ",@param [Fixnum] the scan number to grab;(o;7;8i$;9F;:i&;)[o;2
;3["Fixnum;"the;4"scan number to grab;&@Ï;5"
param;*[ ;-;>;)[ ;+T;/To;;"÷def next_scan
      lastPos = @file.pos
      while (!@file.eof )
        l = @file.readline
        break if l =~ /\<scan|\<spectrum\s/
        lastPos = @file.pos
      end
      @file.pos = lastPos
      Scan.new(get_scan_from_curr_pos)
    end;	[ ;
i2;[[@i2;;;"Ódef next_scan
  lastPos = @file.pos
  while (!@file.eof )
    l = @file.readline
    break if l =~ /\<scan|\<spectrum\s/
    lastPos = @file.pos
  end
  @file.pos = lastPos
  Scan.new(get_scan_from_curr_pos)
end;:next_scan;@1; IC;!"¹Return a Scan node for the next scan sequentially encountered with respect to the file. 
This may not correspond to any notion of scan ordering by ms_level, retention time, etc., it is 
simply related to file read position. 

This method pays no attention to the last scan called in your routines. If you made any other API 
calls that change the file read position (most methods do), the result will be unexpected. Use at your own risk  :-P;"o;#;$@;&@ç;'["]Return a Scan node for the next scan sequentially encountered with respect to the file. "eThis may not correspond to any notion of scan ordering by ms_level, retention time, etc., it is "+simply related to file read position. " "gThis method pays no attention to the last scan called in your routines. If you made any other API "ycalls that change the file read position (most methods do), the result will be unexpected. Use at your own risk  :-P;(o;7;8i+;9F;:i0;)[ ;*[ ;-;>;)[ ;+T;/T;@1;@; IC;!" ;"o;#;$@;&@1;'" ;(0;)[ ;*[ :@aliases{ :@attributesIC; {:
classIC; { :@symbolize_valueT;IC; {	;<IC; {:
write0:	read@h;KT;=IC; {;L0;M@v;KT;;IC; {;L0;M@X;KT;6IC; {;L0;M@J;KT;KT;KT;)[ ;+F:@instance_mixinsIC;[o;;;;@;o:"YARD::CodeObjects::RootObject;IC;[ ;@
;[ ;:	root;IC;[@;@
;0; IC;!" 
;"o;#;$@;&@
;'" ;)[ ;*[ ;H{ ;IIC; {;JIC; { ;KT;IC; { ;KT;KT;)[ ;+F;NIC;[ ;@
;@1;@;@
; IC;!"{== MzXML
ds: Angel Pizarro

A pure-Ruby implementation of the excellent C RAMP mzXML/mzData parsing library from 
the Trans Proteomic Pipeline project. 
See the {Seattle Proteome Center}[http://tools.proteomecenter.org/software.php] 
Web site for more information

Currently the library is pretty stripped down and only handles mzXML 2.X and 3.0 files.
The methods are greatly reduced to what I thought made sense from a usage perspective. 
Specifically, the InstrumentStruct and RunHeaderStruct are not yet parsed, and the ScanHeaderStruct
is actually just a XML node. 
===USAGE:

    require 'mzxml'
    mzxml =  MzXml::MzFile.new("test.mzXML")
    index = mzxml.index # Returns a hash of scan numbers and the file byte position
    # get the first scan number
    firstScanNumber = index.keys.sort.first
    # could also just ask for next_scan like "mzxml.next_scan"
    # now got get it!
    scan = mzxml.scan(firstScanNumber)

    # "scan" is now MzXml::Scan object with mz, intensity arrays retrieved lazily from either Scan#mz and Scan#i
    # get the whole mz array
    mz = scan.mz
    # get just the 23rd mz value
    mz_23 = scan.mz(23);"o;#;$@;&@;'[!"== MzXML"ds: Angel Pizarro" "ZA pure-Ruby implementation of the excellent C RAMP mzXML/mzData parsing library from "+the Trans Proteomic Pipeline project. "USee the {Seattle Proteome Center}[http://tools.proteomecenter.org/software.php] ""Web site for more information" "\Currently the library is pretty stripped down and only handles mzXML 2.X and 3.0 files."\The methods are greatly reduced to what I thought made sense from a usage perspective. "hSpecifically, the InstrumentStruct and RunHeaderStruct are not yet parsed, and the ScanHeaderStruct""is actually just a XML node. "===USAGE:" "    require 'mzxml'"1    mzxml =  MzXml::MzFile.new("test.mzXML")"X    index = mzxml.index # Returns a hash of scan numbers and the file byte position"$    # get the first scan number"0    firstScanNumber = index.keys.sort.first"C    # could also just ask for next_scan like "mzxml.next_scan""    # now got get it!"+    scan = mzxml.scan(firstScanNumber)" "u    # "scan" is now MzXml::Scan object with mz, intensity arrays retrieved lazily from either Scan#mz and Scan#i"!    # get the whole mz array"    mz = scan.mz"%    # get just the 23rd mz value"    mz_23 = scan.mz(23);(o;7;8i;9F;:i/;)[ ;*[ ;H{ ;IIC; {;JIC; { ;KT;IC; { ;KT;KT;)[ ;+T;NIC;[ ;@;[[@i6;:	Scan;IC;[o;;"fdef initialize(elem)
      @e = elem
      @mz = nil
      @mzi = nil
      parse_peaks()
    end;	[["	elem0;
i9;[[@i9;;;"Rdef initialize(elem)
  @e = elem
  @mz = nil
  @mzi = nil
  parse_peaks()
end;;1;@; IC;!" ;"o;#;$@;&@D;'" ;(0;)[o;2
;3["	Scan;0;4"a new instance of +Scan+;&@D;5"return;*[ ;-;.;)[ ;+F;/To;;"
def e;	[ ;[[@i?;;;"def e
  @e
end;:e;@; IC;!"'Returns the value of attribute +e+;"o;#;$@;&@W;'"'Returns the value of attribute +e+;(0;)[ ;*[ ;-;.;)[ ;+F@o;;"4def method_missing m
      @e[m.to_sym]
    end;	[["m0;
ie;[[@ie;;;",def method_missing m
  @e[m.to_sym]
end;:method_missing;@; IC;!" ;"o;#;$@;&@c;'" ;(0;)[ ;*[ ;-;>;)[ ;+F;/To;;"_def retention_time_sec
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    end;	[ ;
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    end;	[ ;
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