libopenms-dev 1.11.1-5 / usr / include / OpenMS / FORMAT / MzMLFile.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_MZMLFILE_H
#define OPENMS_FORMAT_MZMLFILE_H

#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/MzMLHandler.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/METADATA/DocumentIdentifier.h>

namespace OpenMS
{
  /**
      @brief File adapter for MzML files

      This implementation does currently not support the whole functionality of MzML.
      Some minor features are still missing:
          - chromatograms

      @todo Implement chromatograms (Andreas)

      @ingroup FileIO
  */
  class OPENMS_DLLAPI MzMLFile :
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    ///Default constructor
    MzMLFile();
    ///Destructor
    ~MzMLFile();

    /// Mutable access to the options for loading/storing
    PeakFileOptions& getOptions();

    /// Non-mutable access to the options for loading/storing
    const PeakFileOptions& getOptions() const;

    /// set options for loading/storing
    void setOptions(const PeakFileOptions &);

    /**
        @brief Loads a map from a MzML file.

        @p map has to be a MSExperiment or have the same interface.

        @exception Exception::FileNotFound is thrown if the file could not be opened
        @exception Exception::ParseError is thrown if an error occurs during parsing
    */
    template <typename MapType>
    void load(const String& filename, MapType& map)
    {
      map.reset();

      //set DocumentIdentifier
      map.setLoadedFileType(filename);
      map.setLoadedFilePath(filename);

      Internal::MzMLHandler<MapType> handler(map, filename, getVersion(), *this);
      handler.setOptions(options_);
      //handler can throw parse error and other errors - catch those here - they are the cause for a parse error - report accordingly
      try
      {
        parse_(filename, &handler);
      }
      catch (Exception::BaseException& e)
      {
        std::string expr;
        expr.append(e.getFile());
        expr.append("@");
        std::stringstream ss;
        ss << e.getLine(); // we need c++11!! maybe in 2012?
        expr.append(ss.str());
        expr.append("-");
        expr.append(e.getFunction());
        std::string mess = "- due to that error of type ";
        mess.append(e.getName());
        throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, expr, mess);
      }

    }

    /**
        @brief Stores a map in a MzML file.

        @p map has to be a MSExperiment or have the same interface.

        @exception Exception::UnableToCreateFile is thrown if the file could not be created
    */
    template <typename MapType>
    void store(const String& filename, const MapType& map) const
    {
      Internal::MzMLHandler<MapType> handler(map, filename, getVersion(), *this);
      handler.setOptions(options_);
      save_(filename, &handler);
    }

    /**
        @brief Checks if a file validates against the XML schema.

    @exception Exception::FileNotFound is thrown if the file cannot be found.
    */
    bool isValid(const String& filename, std::ostream& os = std::cerr);

    /**
        @brief Checks if a file is valid with respect to the mapping file and the controlled vocabulary.

        @param filename File name of the file to be checked.
        @param errors Errors during the validation are returned in this output parameter.
        @param warnings Warnings during the validation are returned in this output parameter.

        @exception Exception::FileNotFound is thrown if the file could not be opened
    */
    bool isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings);

private:

    /// Options for loading / storing
    PeakFileOptions options_;

    /// Location of indexed mzML schema
    String indexed_schema_location_;
  };

} // namespace OpenMS

#endif // OPENMS_FOMAT_MZMLFILE_H