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// --------------------------------------------------------------------------
// 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: Clemens Groepl $
// $Authors: $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/TransformationXMLFile.h>
#include <OpenMS/SYSTEM/File.h>
#include <iostream>
#include <fstream>
using namespace std;
namespace OpenMS
{
TransformationXMLFile::TransformationXMLFile() :
XMLHandler("", "1.0"),
XMLFile("/SCHEMAS/TrafoXML_1_0.xsd", "1.0"),
params_(), data_(), model_type_()
{
}
void TransformationXMLFile::load(const String & filename, TransformationDescription & transformation)
{
//Filename for error messages in XMLHandler
file_ = filename;
params_.clear();
data_.clear();
model_type_.clear();
parse_(filename, this);
transformation.setDataPoints(data_);
transformation.fitModel(model_type_, params_);
}
void TransformationXMLFile::store(String filename, const TransformationDescription & transformation)
{
if (transformation.getModelType() == "")
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__, "will not write a transformation with empty name");
}
//open stream
std::ofstream os(filename.c_str());
if (!os)
{
throw Exception::UnableToCreateFile(__FILE__, __LINE__, __PRETTY_FUNCTION__, filename);
}
os.precision(writtenDigits<DoubleReal>());
//write header
os << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" << "\n";
//add XSLT file if it can be found
os << "<TrafoXML version=\"" << getVersion() << "\" xsi:noNamespaceSchemaLocation=\"http://open-ms.sourceforge.net/schemas/TrafoXML_1_0.xsd\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">" << "\n";
// open tag
os << "\t<Transformation name=\"" << transformation.getModelType()
<< "\">\n";
// write parameters
Param params;
transformation.getModelParameters(params);
for (Param::ParamIterator it = params.begin(); it != params.end(); ++it)
{
if (it->value.valueType() != DataValue::EMPTY_VALUE)
{
switch (it->value.valueType())
{
case DataValue::INT_VALUE:
os << "\t\t<Param type=\"int\" name=\"" << it->name << "\" value=\"" << it->value.toString() << "\"/>\n";
break;
case DataValue::DOUBLE_VALUE:
os << "\t\t<Param type=\"float\" name=\"" << it->name << "\" value=\"" << it->value.toString() << "\"/>\n";
break;
case DataValue::STRING_VALUE:
case DataValue::STRING_LIST:
case DataValue::INT_LIST:
case DataValue::DOUBLE_LIST:
os << "\t\t<Param type=\"string\" name=\"" << it->name << "\" value=\"" << it->value.toString() << "\"/>\n";
break;
default: // no other value types are supported!
fatalError(STORE, String("Unsupported parameter type of parameter '") + it->name + "' with value '" + it->value.toString() + "'");
break;
}
}
}
//write pairs
Size pairs_size = transformation.getDataPoints().size();
if (pairs_size != 0)
{
os << "\t\t<Pairs count=\"" << pairs_size << "\">\n";
for (Size i = 0; i < pairs_size; ++i)
{
os << "\t\t\t<Pair from=\"" << transformation.getDataPoints()[i].first << "\" to=\"" << transformation.getDataPoints()[i].second << "\"/>\n";
}
os << "\t\t</Pairs>\n";
}
// close tag
os << "\t</Transformation>\n";
//write footer
os << "</TrafoXML>" << "\n";
//close stream
os.close();
}
void TransformationXMLFile::startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes)
{
String element = sm_.convert(qname);
if (element == "TrafoXML")
{
//check file version against schema version
DoubleReal file_version = attributeAsDouble_(attributes, "version");
if (file_version > version_.toDouble())
{
warning(LOAD, String("The XML file (") + file_version + ") is newer than the parser (" + version_ + "). This might lead to undefined program behavior.");
}
}
else if (element == "Transformation")
{
model_type_ = attributeAsString_(attributes, "name");
}
else if (element == "Param")
{
String type = attributeAsString_(attributes, "type");
if (type == "int")
{
params_.setValue(attributeAsString_(attributes, "name"), attributeAsInt_(attributes, "value"));
}
else if (type == "float")
{
params_.setValue(attributeAsString_(attributes, "name"), attributeAsDouble_(attributes, "value"));
}
else if (type == "string")
{
params_.setValue(attributeAsString_(attributes, "name"), String(attributeAsString_(attributes, "value")));
}
else
{
error(LOAD, String("Unsupported parameter type: '") + type + "'");
}
}
else if (element == "Pairs")
{
data_.reserve(attributeAsInt_(attributes, "count"));
}
else if (element == "Pair")
{
data_.push_back(make_pair(attributeAsDouble_(attributes, "from"), attributeAsDouble_(attributes, "to")));
}
else
{
warning(LOAD, String("Unknown element: '") + element + "'");
}
}
} // namespace OpenMS
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