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Viewing changes to source/FORMAT/MzQuantMLFile.C

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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source/FORMAT/MzQuantMLFile.C
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Mathias Walzer $
 
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// $Authors: Mathias Walzer $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/FORMAT/MzQuantMLFile.h>
 
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#include <OpenMS/FORMAT/CVMappingFile.h>
 
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#include <OpenMS/FORMAT/VALIDATORS/XMLValidator.h>
 
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#include <OpenMS/FORMAT/HANDLERS/MzQuantMLHandler.h>
 
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#include <OpenMS/SYSTEM/File.h>
 
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//~ #include <OpenMS/FORMAT/VALIDATORS/MzQuantMLValidator.h>
 
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namespace OpenMS
 
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{
 
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        MzQuantMLFile::MzQuantMLFile()
 
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                : XMLFile("/SCHEMAS/mzQuantML0.1.7.xsd","0.1.7")
 
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        {
 
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        }
 
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        MzQuantMLFile::~MzQuantMLFile()
 
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        {
 
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        }
 
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        void MzQuantMLFile::load(const String& filename, ConsensusMap& cm)
 
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        {
 
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                Internal::MzQuantMLHandler handler(cm, filename, schema_version_, *this);
 
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                parse_(filename, &handler);
 
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        }
 
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        void MzQuantMLFile::store(const String& filename, const ConsensusMap& cm) const
 
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        {
 
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                Internal::MzQuantMLHandler handler(cm, filename, schema_version_, *this);
 
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                save_(filename, &handler);
 
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        }
 
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        //~ TODO
 
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        //~ bool MzQuantMLFile::isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings)
 
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        //~ {
 
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                //~ //load mapping
 
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                //~ CVMappings mapping;
 
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                //~ CVMappingFile().load(File::find("/MAPPING/mzQuantML-mapping.xml"),mapping);
 
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                //~ //load cvs
 
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                //~ ControlledVocabulary cv;
 
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                //~ cv.loadFromOBO("MS",File::find("/CV/psi-ms.obo"));
 
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                //~ cv.loadFromOBO("PATO",File::find("/CV/quality.obo"));
 
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                //~ cv.loadFromOBO("UO",File::find("/CV/unit.obo"));
 
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                //~ cv.loadFromOBO("BTO",File::find("/CV/brenda.obo"));
 
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                //~ cv.loadFromOBO("GO",File::find("/CV/goslim_goa.obo"));
 
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                //~ //validate
 
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                //~ Internal::MzQuantMLValidator v(mapping, cv);
 
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                //~ bool result = v.validate(filename, errors, warnings);
 
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                //~ return result;
 
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        //~ }
 
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}// namespace OpenMS
 
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