/usr/include/OpenMS/COMPARISON/CLUSTERING/SILACClustering.h is in libopenms-dev 1.11.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | // --------------------------------------------------------------------------
// 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: Lars Nilse $
// $Authors: Bastian Blank $
// --------------------------------------------------------------------------
#include <OpenMS/COMPARISON/CLUSTERING/HierarchicalClustering.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SILACPattern.h>
#ifndef OPENMS_COMPARISON_CLUSTERING_SILACCLUSTERING_H
#define OPENMS_COMPARISON_CLUSTERING_SILACCLUSTERING_H
namespace OpenMS
{
/**
* @brief Clustering implementation for SILAC stuff.
*
* It cleans up the results of the hierarchical clustering for the search of
* labeled and unlabeled peptide data. It removes too small clusters and joins
* clusters with small gaps that the clustering split on purpose.
*
* @warning The cleanups will not work on random data
*/
class OPENMS_DLLAPI SILACClustering :
public HierarchicalClustering<SILACPattern *>
{
public:
const DoubleReal rt_min;
const DoubleReal rt_max_spacing;
SILACClustering(const PointCoordinate & cluster_dimension, DoubleReal rt_min, DoubleReal rt_max_spacing) :
HierarchicalClustering<SILACPattern *>(cluster_dimension), rt_min(rt_min), rt_max_spacing(rt_max_spacing)
{}
/**
*/
void cluster();
protected:
/**
* @brief Remove clusters smaller then rt_min
*/
void removeSmall_();
/**
* @brief Join clusters with holes less then rt_max_spacing
*/
void joinLarge_();
};
}
#endif /* OPENMS_COMPARISON_CLUSTERING_HIERARCHICALCLUSTERING_H */
|