OpenMS: LibSVMEncoder.h Source File

Go to the documentation of this file.
00001 // --------------------------------------------------------------------------
00002 //                   OpenMS -- Open-Source Mass Spectrometry
00003 // --------------------------------------------------------------------------
00004 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
00005 // ETH Zurich, and Freie Universitaet Berlin 2002-2012.
00006 //
00007 // This software is released under a three-clause BSD license:
00008 //  * Redistributions of source code must retain the above copyright
00009 //    notice, this list of conditions and the following disclaimer.
00010 //  * Redistributions in binary form must reproduce the above copyright
00011 //    notice, this list of conditions and the following disclaimer in the
00012 //    documentation and/or other materials provided with the distribution.
00013 //  * Neither the name of any author or any participating institution
00014 //    may be used to endorse or promote products derived from this software
00015 //    without specific prior written permission.
00016 // For a full list of authors, refer to the file AUTHORS.
00017 // --------------------------------------------------------------------------
00018 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
00019 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
00020 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
00021 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
00022 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
00023 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
00024 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
00025 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
00026 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
00027 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
00028 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
00029 //
00030 // --------------------------------------------------------------------------
00031 // $Maintainer: Sandro Andreotti $
00032 // $Authors: Nico Pfeifer $
00033 // --------------------------------------------------------------------------
00034 
00035 #ifndef OPENMS_FORMAT_LIBSVMENCODER_H
00036 #define OPENMS_FORMAT_LIBSVMENCODER_H
00037 
00038 #include <OpenMS/DATASTRUCTURES/String.h>
00039 #include <OpenMS/CHEMISTRY/AASequence.h>
00040 #include <svm.h>
00041 
00042 #include <vector>
00043 #include <utility>
00044 
00045 namespace OpenMS
00046 {
00055   class OPENMS_DLLAPI LibSVMEncoder
00056   {
00057 public:
00059     LibSVMEncoder();
00061     ~LibSVMEncoder();
00062 
00072     void encodeCompositionVector(const String & sequence, std::vector<std::pair<Int, DoubleReal> > & encoded_vector, const String & allowed_characters = "ACDEFGHIKLMNPQRSTVWY");
00073 
00083     void encodeCompositionVectors(const std::vector<String> & sequences, const String & allowed_characters, std::vector<std::vector<std::pair<Int, DoubleReal> > > & composition_vectors);
00085     svm_node * encodeLibSVMVector(const std::vector<std::pair<Int, DoubleReal> > & feature_vector);
00086 
00088     void encodeLibSVMVectors(const std::vector<std::vector<std::pair<Int, DoubleReal> > > & feature_vectors, std::vector<svm_node *> & libsvm_vectors);
00089 
00091     svm_problem * encodeLibSVMProblem(const std::vector<svm_node *> & vectors,
00092                                       std::vector<DoubleReal> & labels);
00093 
00095     svm_problem * encodeLibSVMProblemWithCompositionVectors(const std::vector<String> & sequences,
00096                                                             std::vector<DoubleReal> & labels,
00097                                                             const String & allowed_characters);
00098 
00100     svm_problem * encodeLibSVMProblemWithCompositionAndLengthVectors(const std::vector<String> & sequences,
00101                                                                      std::vector<DoubleReal> & labels,
00102                                                                      const String & allowed_characters,
00103                                                                      UInt                maximum_sequence_length);
00104 
00106     svm_problem * encodeLibSVMProblemWithCompositionLengthAndWeightVectors(const std::vector<String> & sequences,
00107                                                                            std::vector<DoubleReal> & labels,
00108                                                                            const String & allowed_characters);
00109 
00111     bool storeLibSVMProblem(const String & filename, const svm_problem * problem) const;
00112 
00114     svm_problem * loadLibSVMProblem(const String & filename);
00115 
00117     void encodeOligoBorders(String                                                                                       sequence,
00118                             UInt                                                                             k_mer_length,
00119                             const String & allowed_characters,
00120                             UInt                                        border_length,
00121                             std::vector<std::pair<Int, DoubleReal> > & libsvm_vector,
00122                             bool                                                                                             strict = false,
00123                             bool                                                                                             unpaired = false,
00124                             bool                                                                                             length_encoding = false);
00125 
00127     svm_problem * encodeLibSVMProblemWithOligoBorderVectors(const std::vector<String> & sequences,
00128                                                             std::vector<DoubleReal> & labels,
00129                                                             UInt                           k_mer_length,
00130                                                             const String & allowed_characters,
00131                                                             UInt                           border_length,
00132                                                             bool                                                   strict = false,
00133                                                             bool                                                   unpaired = false,
00134                                                             bool                                                   length_encoding = false);
00135 
00137     void encodeProblemWithOligoBorderVectors(const std::vector<AASequence> & sequences,
00138                                              UInt                                                       k_mer_length,
00139                                              const String & allowed_characters,
00140                                              UInt                                                       border_length,
00141                                              std::vector<std::vector<std::pair<Int, DoubleReal> > > & vectors);
00142 
00149     void libSVMVectorToString(svm_node * vector, String & output);
00150 
00157     void libSVMVectorsToString(svm_problem * vector, String & output);
00158 
00165     void encodeOligo(const AASequence & sequence,
00166                      UInt k_mer_length,
00167                      const String & allowed_characters,
00168                      std::vector<std::pair<Int, DoubleReal> > & values,
00169                      bool is_right_border = false);
00170 
00176     static void destroyProblem(svm_problem * problem);
00177 
00178 private:
00180     static bool cmpOligos_(std::pair<Int, DoubleReal> a,
00181                            std::pair<Int, DoubleReal> b);
00182 
00183   };
00184 
00185 } // namespace OpenMS
00186 
00187 #endif // OPENMS_FORMAT_LIBSVMENCODER_H