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LibSVMEncoder.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/String.h>
38 #include <OpenMS/CHEMISTRY/AASequence.h>
39 #include <OpenMS/ANALYSIS/SVM/SVMWrapper.h>
40 #include <svm.h>
41
42 #include <vector>
43 #include <utility>
44
45 namespace OpenMS
46 {
55 class OPENMS_DLLAPI LibSVMEncoder
56 {
57 public:
59 LibSVMEncoder();
61 ~LibSVMEncoder();
62
72 void encodeCompositionVector(const String & sequence, std::vector<std::pair<Int, double> > & encoded_vector, const String & allowed_characters = "ACDEFGHIKLMNPQRSTVWY");
73
83 void encodeCompositionVectors(const std::vector<String> & sequences, const String & allowed_characters, std::vector<std::vector<std::pair<Int, double> > > & composition_vectors);
85 svm_node * encodeLibSVMVector(const std::vector<std::pair<Int, double> > & feature_vector);
86
88 void encodeLibSVMVectors(const std::vector<std::vector<std::pair<Int, double> > > & feature_vectors, std::vector<svm_node *> & libsvm_vectors);
89
91 svm_problem * encodeLibSVMProblem(const std::vector<svm_node *> & vectors,
92 std::vector<double> & labels);
93
95 svm_problem * encodeLibSVMProblemWithCompositionVectors(const std::vector<String> & sequences,
96 std::vector<double> & labels,
97 const String & allowed_characters);
98
104 svm_problem * encodeLibSVMProblemWithCompositionAndLengthVectors(const std::vector<String> & sequences,
105 std::vector<double> & labels,
106 const String & allowed_characters,
107 UInt maximum_sequence_length);
108
114 svm_problem * encodeLibSVMProblemWithCompositionLengthAndWeightVectors(const std::vector<String> & sequences,
115 std::vector<double> & labels,
116 const String & allowed_characters);
117
119 bool storeLibSVMProblem(const String & filename, const svm_problem * problem) const;
120
122 svm_problem * loadLibSVMProblem(const String & filename);
123
125 void encodeOligoBorders(String sequence,
126 UInt k_mer_length,
127 const String & allowed_characters,
128 UInt border_length,
129 std::vector<std::pair<Int, double> > & libsvm_vector,
130 bool strict = false,
131 bool unpaired = false,
132 bool length_encoding = false);
133
135 svm_problem * encodeLibSVMProblemWithOligoBorderVectors(const std::vector<String> & sequences,
136 std::vector<double> & labels,
137 UInt k_mer_length,
138 const String & allowed_characters,
139 UInt border_length,
140 bool strict = false,
141 bool unpaired = false,
142 bool length_encoding = false);
143
145 void encodeProblemWithOligoBorderVectors(const std::vector<AASequence> & sequences,
146 UInt k_mer_length,
147 const String & allowed_characters,
148 UInt border_length,
149 std::vector<std::vector<std::pair<Int, double> > > & vectors);
150
157 void libSVMVectorToString(svm_node * vector, String & output);
158
165 void libSVMVectorsToString(svm_problem * vector, String & output);
166
173 void encodeOligo(const AASequence & sequence,
174 UInt k_mer_length,
175 const String & allowed_characters,
176 std::vector<std::pair<Int, double> > & values,
177 bool is_right_border = false);
178
184 static void destroyProblem(svm_problem * problem);
185
186 static std::vector<double> predictPeptideRT(const std::vector<String> & sequences,
187 SVMWrapper& svm,
188 const String & allowed_characters = "ACDEFGHIKLMNPQRSTVWY",
189 UInt maximum_sequence_length = 50)
190 {
191 std::vector<double> predicted_retention_times;
192
193 LibSVMEncoder encoder;
194 std::vector<double> temp_rts;
195 temp_rts.resize(sequences.size(), 0);
196 svm_problem * prediction_data =
197 encoder.encodeLibSVMProblemWithCompositionAndLengthVectors(sequences,
198 temp_rts,
199 allowed_characters,
200 maximum_sequence_length);
201 svm.predict(prediction_data, predicted_retention_times);
202 LibSVMEncoder::destroyProblem(prediction_data);
203 return predicted_retention_times;
204 }
205
206 private:
208 static bool cmpOligos_(std::pair<Int, double> a,
209 std::pair<Int, double> b);
210
211 };
212
213 } // namespace OpenMS
214
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::LibSVMEncoder::encodeLibSVMProblemWithCompositionAndLengthVectors
svm_problem * encodeLibSVMProblemWithCompositionAndLengthVectors(const std::vector< String > &sequences, std::vector< double > &labels, const String &allowed_characters, UInt maximum_sequence_length)
creates composition vectors with additional length information for &#39;sequences&#39; and stores them in Lib...
AASequence.h
OpenMS::LibSVMEncoder::destroyProblem
static void destroyProblem(svm_problem *problem)
frees all the memory of the svm_problem instance
OpenMS::LibSVMEncoder::predictPeptideRT
static std::vector< double > predictPeptideRT(const std::vector< String > &sequences, SVMWrapper &svm, const String &allowed_characters="ACDEFGHIKLMNPQRSTVWY", UInt maximum_sequence_length=50)
Definition: LibSVMEncoder.h:186
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::SVMWrapper
Serves as a wrapper for the libsvm.
Definition: SVMWrapper.h:79
String.h
SVMWrapper.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::LibSVMEncoder
Serves for encoding sequences into feature vectors.
Definition: LibSVMEncoder.h:55
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::SVMWrapper::predict
void predict(struct svm_problem *problem, std::vector< double > &predicted_labels)
predicts the labels using the trained model