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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: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/APPLICATIONS/TOPPBase.h>
using namespace OpenMS;
using namespace std;
//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------
/**
@page UTILS_DeMeanderize DeMeanderize
@brief Repairs MALDI experiments which were spotted line by line.
<B>The command line parameters of this tool are:</B>
@verbinclude UTILS_DeMeanderize.cli
<B>INI file documentation of this tool:</B>
@htmlinclude UTILS_DeMeanderize.html
*/
// We do not want this class to show up in the docu:
/// @cond TOPPCLASSES
class TOPPDeMeanderize :
public TOPPBase
{
public:
TOPPDeMeanderize() :
TOPPBase("DeMeanderize", "Orders the spectra of MALDI spotting plates correctly.", false)
{
}
protected:
void registerOptionsAndFlags_()
{
registerInputFile_("in", "<mzML-file>", "", "Input experiment file, containing the wrongly sorted spectra.");
setValidFormats_("in", StringList::create("mzML"));
registerOutputFile_("out", "<mzML-file>", "", "Output experiment file with correctly sorted spectra.");
setValidFormats_("out", StringList::create("mzML"));
registerIntOption_("num_spots_per_row", "<integer>", 48, "Number of spots in one column, until next row is spotted.", false);
setMinInt_("num_spots_per_row", 1);
registerDoubleOption_("RT_distance", "<integer>", 1.0, "RT distance between two spots which is used to calculated pseudo RT.", false, true);
setMinFloat_("RT_distance", 0.0);
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in(getStringOption_("in"));
String out(getStringOption_("out"));
Size num_spots_per_row(getIntOption_("num_spots_per_row"));
DoubleReal RT_distance(getDoubleOption_("RT_distance"));
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
PeakMap exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
ProgressLogger pl;
pl.setLogType(log_type_);
pl.startProgress(0, exp.size(), "Assigning pseudo RTs.");
Size num_ms1(0), num_ms1_base(0), row_counter(0);
bool row_to_reverse(false);
DoubleReal actual_RT(0);
for (Size i = 0; i != exp.size(); ++i)
{
pl.setProgress(i);
if (row_to_reverse)
{
actual_RT = (DoubleReal)(num_ms1_base + (num_spots_per_row - row_counter)) * RT_distance;
writeDebug_("RT=" + String(actual_RT) + " (modified, row_counter=" + String(row_counter) + ")", 1);
}
else
{
actual_RT = (DoubleReal)num_ms1 * RT_distance;
writeDebug_("RT=" + String(actual_RT), 1);
}
exp[i].setRT(actual_RT);
if (exp[i].getMSLevel() == 1)
{
if (++row_counter >= num_spots_per_row)
{
row_counter = 0;
if (row_to_reverse)
{
row_to_reverse = false;
}
else
{
row_to_reverse = true;
}
}
++num_ms1;
if (!row_to_reverse)
{
num_ms1_base = num_ms1;
}
}
}
pl.endProgress();
// sort the spectra according to their new RT
exp.sortSpectra();
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
f.store(out, exp);
return EXECUTION_OK;
}
};
int main(int argc, const char ** argv)
{
TOPPDeMeanderize tool;
return tool.main(argc, argv);
}
/// @endcond
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