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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: Marc Sturm, Clemens Groepl, Steffen Sass $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_FeatureLinkerBase FeatureLinkerBase
@brief Base class for different FeatureLinker tools.
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPFeatureLinkerBase :
public TOPPBase
{
public:
TOPPFeatureLinkerBase(String name, String description) :
TOPPBase(name, description)
{
}
protected:
void registerOptionsAndFlags_() // only for "unlabeled" algorithms!
{
registerInputFileList_("in", "<files>", StringList(), "input files separated by blanks", true);
setValidFormats_("in", StringList::create("featureXML,consensusXML"));
registerOutputFile_("out", "<file>", "", "Output file", true);
setValidFormats_("out", StringList::create("consensusXML"));
addEmptyLine_();
registerFlag_("keep_subelements", "For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.");
}
ExitCodes common_main_(FeatureGroupingAlgorithm * algorithm,
bool labeled = false)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
StringList ins;
if (labeled) ins << getStringOption_("in");
else ins = getStringList_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// check for valid input
//-------------------------------------------------------------
// check if all input files have the correct type
FileTypes::Type file_type = FileHandler::getType(ins[0]);
for (Size i = 0; i < ins.size(); ++i)
{
if (FileHandler::getType(ins[i]) != file_type)
{
writeLog_("Error: All input files must be of the same type!");
return ILLEGAL_PARAMETERS;
}
}
//-------------------------------------------------------------
// set up algorithm
//-------------------------------------------------------------
Param algorithm_param = getParam_().copy("algorithm:", true);
writeDebug_("Used algorithm parameters", algorithm_param, 3);
algorithm->setParameters(algorithm_param);
//-------------------------------------------------------------
// perform grouping
//-------------------------------------------------------------
// load input
ConsensusMap out_map;
if (file_type == FileTypes::FEATUREXML)
{
vector<FeatureMap<> > maps(ins.size());
FeatureXMLFile f;
for (Size i = 0; i < ins.size(); ++i)
{
f.load(ins[i], maps[i]);
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = maps[i].size();
out_map.getFileDescriptions()[i].unique_id = maps[i].getUniqueId();
// to save memory, remove convex hulls and subordinates:
for (FeatureMap<>::Iterator it = maps[i].begin(); it != maps[i].end();
++it)
{
it->getSubordinates().clear();
it->getConvexHulls().clear();
}
}
// exception for "labeled" algorithms: copy file descriptions
if (labeled)
{
out_map.getFileDescriptions()[1] = out_map.getFileDescriptions()[0];
out_map.getFileDescriptions()[0].label = "light";
out_map.getFileDescriptions()[1].label = "heavy";
}
out_map.updateRanges();
// group
algorithm->group(maps, out_map);
}
else
{
vector<ConsensusMap> maps(ins.size());
ConsensusXMLFile f;
for (Size i = 0; i < ins.size(); ++i)
{
f.load(ins[i], maps[i]);
}
// group
algorithm->group(maps, out_map);
// set file descriptions:
bool keep_subelements = getFlag_("keep_subelements");
if (!keep_subelements)
{
for (Size i = 0; i < ins.size(); ++i)
{
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = maps[i].size();
out_map.getFileDescriptions()[i].unique_id = maps[i].getUniqueId();
}
}
else
{
// components of the output map are not the input maps themselves, but
// the components of the input maps:
algorithm->transferSubelements(maps, out_map);
}
}
// assign unique ids
out_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// annotate output with data processing info
addDataProcessing_(out_map, getProcessingInfo_(DataProcessing::FEATURE_GROUPING));
// write output
ConsensusXMLFile().store(out, out_map);
// some statistics
map<Size, UInt> num_consfeat_of_size;
for (ConsensusMap::const_iterator cmit = out_map.begin(); cmit != out_map.end(); ++cmit)
{
++num_consfeat_of_size[cmit->size()];
}
LOG_INFO << "Number of consensus features:" << endl;
for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin(); i != num_consfeat_of_size.rend(); ++i)
{
LOG_INFO << " of size " << setw(2) << i->first << ": " << setw(6) << i->second << endl;
}
LOG_INFO << " total: " << setw(6) << out_map.size() << endl;
return EXECUTION_OK;
}
};
/// @endcond
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