text: /*
   Copyright (C) 2003 Ronald C Beavis, all rights reserved
   X! tandem 
   This software is a component of the X! proteomics software
   development project
  
  Use of this software governed by the Artistic license, as reproduced here:
  
  The Artistic License for all X! software, binaries and documentation
  
  Preamble
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  Package may be copied, such that the Copyright Holder maintains some 
  semblance of artistic control over the development of the package, 
  while giving the users of the package the right to use and distribute 
  the Package in a more-or-less customary fashion, plus the right to 
  make reasonable modifications. 
  
  Definitions
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  	Holder, and derivatives of that collection of files created through 
  	textual modification. 
  
  "Standard Version" refers to such a Package if it has not been modified, 
  	or has been modified in accordance with the wishes of the Copyright 
  	Holder as specified below. 
  
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  	for the package. 
  
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  "Reasonable copying fee" is whatever you can justify on the basis of 
  	media cost, duplication charges, time of people involved, and so on. 
  	(You will not be required to justify it to the Copyright Holder, but 
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  d.	make other distribution arrangements with the Copyright Holder. 
  
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  However, you may distribute this Package in aggregate with other 
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  output from the programs of this Package do not automatically fall 
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  fall under the restrictions of Paragraphs 3 and 4, provided that you 
  do not represent such an executable image as a Standard Version of 
  this Package. 
  
  7. C subroutines (or comparably compiled subroutines in other languages) 
  supplied by you and linked into this Package in order to emulate 
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  The End 
  */
  
  #ifndef XMLTAXONOMY_H
  #define XMLTAXONOMY_H
  
  // File version: 2003-07-01
  
  /*
   * the XmlTaxonomy object is used to create a list of sequnece list files, based on
   * an XML file that can be used to create lists of sequence list files to be
   * modelled. The format for this file is as follows:
  
  <?xml version="1.0"?>
  <bioml label="x! taxon-to-file matching list">
  	<taxon label="nr other mammals">
  		<file format="peptide" URL="c:/x-bang/fasta/nr-Other-Mammalia.fasta" />
  	</taxon>
  	<taxon label="nr yeast">
  		<file format="peptide" URL="c:/x-bang/fasta/nr-Saccharomyces-cerevisiae.fasta" />
  	</taxon>
  	<taxon label="ensembl Homo sapiens">
  		<file format="peptide" URL="c:/x-bang/fasta/Homo_sapiens.pep.known.fasta" />
  		<file format="peptide" URL="c:/x-bang/fasta/Homo_sapiens.pep.novel.fasta" />
  		<!-- "peptide" entries correspond to protein sequence files in either FASTA or PRO formats -->
  		<file format="saps" URL="c:/x-bang/fasta/Homo_sapiens.pep.known.xml" />
  		<!-- "saps" entries correspond to known single amino acid polymorphisms, in BIOML format 
  				NOTE: these entries only apply to X! Tandem or P3 implimentations	-->
  		<file format="spectrum" URL="c:/x-bang/fasta/Homo_sapiens.pep.known.hlf" />
  		<file format="spectrum" URL="c:/x-bang/fasta/Homo_sapiens.pep.novel.hlf" />
  		<!-- "spectrum" entries correspond to annotated spectrum libraries in either XML or HLF formats -->
  	</taxon>
  </bioml>
  
   * A list of file nodes, containing the path to a sequence list file, is associated with
   * a "taxon" label by being contained within the taxon object tags. The XmlTaxonomy object
   * checks for the availability of these files and stores the paths for later use.
   */
  
  class XmlTaxonomy
  {
  public:
  	XmlTaxonomy(void);
  	virtual ~XmlTaxonomy(void);
  
  	vector<string> m_vstrPaths; // the path names associated with a taxon
  	string m_strTaxonPath; // the path to the taxonomy file
  	string m_strTaxon; // the name of the desired taxon
  	enum tax_type	{
  		SEQUENCE = 1,
  		SPECTRUM = 2
  	} TAX_TYPE;
  	bool load(const string &_p,const string &_t,const string &_y);
  };
  #endif
  