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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Immanuel Luhn$
// $Authors: Immanuel Luhn$
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/ANALYSIS/ID/IDRipper.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <QDir>
using std::vector;
using std::pair;
using std::map;
using namespace OpenMS;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page TOPP_IDRipper IDRipper
@brief IDRipper splits the protein/peptide identification of an idXML file into several idXML files according their annotated file origin.
<center>
<table>
<tr>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> potential predecessor tools </td>
<td VALIGN="middle" ROWSPAN=3> \f$ \longrightarrow \f$ IDRipper\f$ \longrightarrow \f$</td>
<td ALIGN = "center" BGCOLOR="#EBEBEB"> potential successor tools </td>
</tr>
<tr>
<td VALIGN="middle" ALIGN ="center" ROWSPAN=1> @ref TOPP_IDFilter</td>
<td VALIGN="middle" ALIGN ="center" ROWSPAN=1> @ref TOPP_IDMapper</td>
</tr>
</table>
</center>
<B>Example</B>
<p>Assuming each peptide identification in a given idXML-file is annotated with its file origin (e.g. IDRipper_test.idXML) :</p>
@p <tt><userParam type="string" name="file_origin" value="IDMerger1_test.idXML"/></tt> or <br />
@p <tt><userParam type="string" name="file_origin" value="IDMerger2_test.idXML"/></tt>
<p>Obviously the file contains protein/peptide identifications of IDMerger1_test.idXML and IDMerger2_test.idXML.</p>
<p>Calling IDRipper with an input file (here: @p -in IDRipper_test.idXML) and an output directory (via @p out or @p out_path) will
result in two idXML-files stored in the specified directory and named according their file origin.</p>
<p>In theory, merging files with @p IDMerger and rip the resulting file with @p IDSplitter will result in the original input files.
<B>NOTE: The meta value file origin is removed by the <tt>IDSplitter</tt>!!</B>
<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_IDRipper.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_IDRipper.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPIDRipper :
public TOPPBase
{
public:
TOPPIDRipper() :
TOPPBase("IDRipper", "Split protein/peptide identification file into several files according annotated file origin.")
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<file>", "", "idXML-file, whereas the protein/peptide identifications must be tagged with file_origin");
setValidFormats_("in", StringList::create("idXML"));
registerOutputFile_("out", "<file>", "", "The path to the file is used as the output directory.", false, false);
setValidFormats_("out", StringList::create("idXML"));
registerStringOption_("out_path", "<file>", "", "Directory for the idXML-files after ripping according file_origin tag. If out_path is set, out is ignored.", false, false);
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String file_name = getStringOption_("in");
String out_dir = getStringOption_("out");
String out_dir_ = getStringOption_("out_path");
String output_directory;
//if neither 'out' nor 'out_dir' is set throw an exception
if (out_dir.empty() && out_dir_.empty())
{
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Please specify an output directory! There are two options to do so. Use 'out' to specify the directory and basename of the resulting files, or use 'out_path' to specify a path");
}
QString dir = (!out_dir.empty()) ?
QFileInfo(out_dir.toQString()).absolutePath()
: QFileInfo(out_dir_.toQString()).absolutePath();
if (!QDir(dir).exists())
throw Exception::InvalidParameter(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Specified path does not exist");
output_directory = dir.toStdString();
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
IdXMLFile().load(file_name, proteins, peptides);
//ensure protein and peptide identifications are presented, otherwise we don't have to rip anything anyhow
if (proteins.empty() || peptides.empty())
{
throw Exception::Precondition(__FILE__, __LINE__, __PRETTY_FUNCTION__, "idXML file has to store protein and peptide identifications!");
}
map<String, pair<vector<ProteinIdentification>, vector<PeptideIdentification> > > ripped;
// rip the idXML-file into several idXML according to the annotated file origin
IDRipper ripper;
ripper.rip(ripped, proteins, peptides);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
map<String, pair<vector<ProteinIdentification>, vector<PeptideIdentification> > >::iterator it;
for (it = ripped.begin(); it != ripped.end(); ++it)
{
QString output = output_directory.toQString();
// create full absolute path with filename
String out = QDir::toNativeSeparators(output.append(QString("/")).append(it->first.toQString())).toStdString();
IdXMLFile().store(out, it->second.first, it->second.second);
}
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPIDRipper tool;
return tool.main(argc, argv);
}
/// @endcond
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