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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html">LibSVMEncoder</a></li> </ul>
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<p>Serves for encoding sequences into feature vectors.
<a href="classOpenMS_1_1LibSVMEncoder.html#details">More...</a></p>
<p><code>#include <<a class="el" href="LibSVMEncoder_8h_source.html">OpenMS/FORMAT/LibSVMEncoder.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a8fd830149e5e33446b65d0f988c49e2f"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a8fd830149e5e33446b65d0f988c49e2f">LibSVMEncoder</a> ()</td></tr>
<tr class="memdesc:a8fd830149e5e33446b65d0f988c49e2f"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a8fd830149e5e33446b65d0f988c49e2f">More...</a><br/></td></tr>
<tr class="separator:a8fd830149e5e33446b65d0f988c49e2f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a316f01d46fc8b58acf85fbe0d92ebeb9"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a316f01d46fc8b58acf85fbe0d92ebeb9">~LibSVMEncoder</a> ()</td></tr>
<tr class="memdesc:a316f01d46fc8b58acf85fbe0d92ebeb9"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a316f01d46fc8b58acf85fbe0d92ebeb9">More...</a><br/></td></tr>
<tr class="separator:a316f01d46fc8b58acf85fbe0d92ebeb9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6a55c55c9a1b6bb89a28ad2d01f6c282"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a6a55c55c9a1b6bb89a28ad2d01f6c282">encodeCompositionVector</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &sequence, std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > &encoded_vector, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters="ACDEFGHIKLMNPQRSTVWY")</td></tr>
<tr class="memdesc:a6a55c55c9a1b6bb89a28ad2d01f6c282"><td class="mdescLeft"> </td><td class="mdescRight">stores a composition vector of 'sequence' in 'encoded_vector' <a href="#a6a55c55c9a1b6bb89a28ad2d01f6c282">More...</a><br/></td></tr>
<tr class="separator:a6a55c55c9a1b6bb89a28ad2d01f6c282"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae7616d10bd510a300474854327595f4b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#ae7616d10bd510a300474854327595f4b">encodeCompositionVectors</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &sequences, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters, std::vector< std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > &composition_vectors)</td></tr>
<tr class="memdesc:ae7616d10bd510a300474854327595f4b"><td class="mdescLeft"> </td><td class="mdescRight">stores composition vectors of the sequences given by 'sequence' in 'composition_vectors' <a href="#ae7616d10bd510a300474854327595f4b">More...</a><br/></td></tr>
<tr class="separator:ae7616d10bd510a300474854327595f4b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adc354fac28608905af89d54965ac9831"><td class="memItemLeft" align="right" valign="top">svm_node * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#adc354fac28608905af89d54965ac9831">encodeLibSVMVector</a> (const std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > &feature_vector)</td></tr>
<tr class="memdesc:adc354fac28608905af89d54965ac9831"><td class="mdescLeft"> </td><td class="mdescRight">encodes the feature vector in LibSVM compliant format <a href="#adc354fac28608905af89d54965ac9831">More...</a><br/></td></tr>
<tr class="separator:adc354fac28608905af89d54965ac9831"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6928bd2e1b05f88227ec2a8ea6dc2d66"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a6928bd2e1b05f88227ec2a8ea6dc2d66">encodeLibSVMVectors</a> (const std::vector< std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > &feature_vectors, std::vector< svm_node * > &libsvm_vectors)</td></tr>
<tr class="memdesc:a6928bd2e1b05f88227ec2a8ea6dc2d66"><td class="mdescLeft"> </td><td class="mdescRight">encodes the feature vectors in LibSVM compliant format <a href="#a6928bd2e1b05f88227ec2a8ea6dc2d66">More...</a><br/></td></tr>
<tr class="separator:a6928bd2e1b05f88227ec2a8ea6dc2d66"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2ea48476fb89be562d3034a405c33995"><td class="memItemLeft" align="right" valign="top">svm_problem * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a2ea48476fb89be562d3034a405c33995">encodeLibSVMProblem</a> (const std::vector< svm_node * > &vectors, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &labels)</td></tr>
<tr class="memdesc:a2ea48476fb89be562d3034a405c33995"><td class="mdescLeft"> </td><td class="mdescRight">encodes the LibSVM compliant vectors into a LibSVM compliant structure <a href="#a2ea48476fb89be562d3034a405c33995">More...</a><br/></td></tr>
<tr class="separator:a2ea48476fb89be562d3034a405c33995"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a06f713b79fd3fc8854aa4d3161379d8f"><td class="memItemLeft" align="right" valign="top">svm_problem * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a06f713b79fd3fc8854aa4d3161379d8f">encodeLibSVMProblemWithCompositionVectors</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &sequences, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &labels, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters)</td></tr>
<tr class="memdesc:a06f713b79fd3fc8854aa4d3161379d8f"><td class="mdescLeft"> </td><td class="mdescRight">creates composition vectors for 'sequences' and stores them in LibSVM compliant format <a href="#a06f713b79fd3fc8854aa4d3161379d8f">More...</a><br/></td></tr>
<tr class="separator:a06f713b79fd3fc8854aa4d3161379d8f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af88c607a510497211033ebe3bc9e3f32"><td class="memItemLeft" align="right" valign="top">svm_problem * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#af88c607a510497211033ebe3bc9e3f32">encodeLibSVMProblemWithCompositionAndLengthVectors</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &sequences, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &labels, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> maximum_sequence_length)</td></tr>
<tr class="memdesc:af88c607a510497211033ebe3bc9e3f32"><td class="mdescLeft"> </td><td class="mdescRight">creates composition vectors with additional length information for 'sequences' and stores them in LibSVM compliant format <a href="#af88c607a510497211033ebe3bc9e3f32">More...</a><br/></td></tr>
<tr class="separator:af88c607a510497211033ebe3bc9e3f32"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a934185e9bc3cf943fd6ca10d84c3a50e"><td class="memItemLeft" align="right" valign="top">svm_problem * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a934185e9bc3cf943fd6ca10d84c3a50e">encodeLibSVMProblemWithCompositionLengthAndWeightVectors</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &sequences, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &labels, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters)</td></tr>
<tr class="memdesc:a934185e9bc3cf943fd6ca10d84c3a50e"><td class="mdescLeft"> </td><td class="mdescRight">creates composition vectors with additional length and average weight information for 'sequences' and stores them in LibSVM compliant format <a href="#a934185e9bc3cf943fd6ca10d84c3a50e">More...</a><br/></td></tr>
<tr class="separator:a934185e9bc3cf943fd6ca10d84c3a50e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab9a514a9fd405b986cd85ef4d3b9ea54"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#ab9a514a9fd405b986cd85ef4d3b9ea54">storeLibSVMProblem</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename, const svm_problem *problem) const </td></tr>
<tr class="memdesc:ab9a514a9fd405b986cd85ef4d3b9ea54"><td class="mdescLeft"> </td><td class="mdescRight">stores the LibSVM-encoded data in a text file that can be used by the LibSVM applications (svm-scale, svm-train,...) <a href="#ab9a514a9fd405b986cd85ef4d3b9ea54">More...</a><br/></td></tr>
<tr class="separator:ab9a514a9fd405b986cd85ef4d3b9ea54"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a022ef62449e1ef4547d07d3f1bdb0596"><td class="memItemLeft" align="right" valign="top">svm_problem * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a022ef62449e1ef4547d07d3f1bdb0596">loadLibSVMProblem</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &filename)</td></tr>
<tr class="memdesc:a022ef62449e1ef4547d07d3f1bdb0596"><td class="mdescLeft"> </td><td class="mdescRight">loads the LibSVM-encoded data stored in 'filename' <a href="#a022ef62449e1ef4547d07d3f1bdb0596">More...</a><br/></td></tr>
<tr class="separator:a022ef62449e1ef4547d07d3f1bdb0596"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a14d0f15718f7ce8574d28b3155b700cf"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a14d0f15718f7ce8574d28b3155b700cf">encodeOligoBorders</a> (<a class="el" href="classOpenMS_1_1String.html">String</a> sequence, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> k_mer_length, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> border_length, std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > &libsvm_vector, bool strict=false, bool unpaired=false, bool length_encoding=false)</td></tr>
<tr class="memdesc:a14d0f15718f7ce8574d28b3155b700cf"><td class="mdescLeft"> </td><td class="mdescRight">encodes the borders of the sequence as k_mer oligos and stores them in 'libsvm_vector' <a href="#a14d0f15718f7ce8574d28b3155b700cf">More...</a><br/></td></tr>
<tr class="separator:a14d0f15718f7ce8574d28b3155b700cf"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af7de985006b4a0673bd1942fd282f3c8"><td class="memItemLeft" align="right" valign="top">svm_problem * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#af7de985006b4a0673bd1942fd282f3c8">encodeLibSVMProblemWithOligoBorderVectors</a> (const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > &sequences, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &labels, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> k_mer_length, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> border_length, bool strict=false, bool unpaired=false, bool length_encoding=false)</td></tr>
<tr class="memdesc:af7de985006b4a0673bd1942fd282f3c8"><td class="mdescLeft"> </td><td class="mdescRight">creates oligo border vectors vectors for 'sequences' and stores them in LibSVM compliant format <a href="#af7de985006b4a0673bd1942fd282f3c8">More...</a><br/></td></tr>
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<tr class="memitem:a3bdbe58670b5a2ba93b3962a5c419623"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a3bdbe58670b5a2ba93b3962a5c419623">encodeProblemWithOligoBorderVectors</a> (const std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > &sequences, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> k_mer_length, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> border_length, std::vector< std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > &vectors)</td></tr>
<tr class="memdesc:a3bdbe58670b5a2ba93b3962a5c419623"><td class="mdescLeft"> </td><td class="mdescRight">creates oligo border vectors vectors for 'sequences' and stores them in 'vectors' <a href="#a3bdbe58670b5a2ba93b3962a5c419623">More...</a><br/></td></tr>
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<tr class="memitem:ae755e074b7667b38b2e173c46d7791c8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#ae755e074b7667b38b2e173c46d7791c8">libSVMVectorToString</a> (svm_node *vector, <a class="el" href="classOpenMS_1_1String.html">String</a> &output)</td></tr>
<tr class="memdesc:ae755e074b7667b38b2e173c46d7791c8"><td class="mdescLeft"> </td><td class="mdescRight">stores a string representation of the encoded sequence 'vector' in 'output' <a href="#ae755e074b7667b38b2e173c46d7791c8">More...</a><br/></td></tr>
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<tr class="memitem:a9c1ad079376ba0f55d414e1c584e4569"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a9c1ad079376ba0f55d414e1c584e4569">libSVMVectorsToString</a> (svm_problem *vector, <a class="el" href="classOpenMS_1_1String.html">String</a> &output)</td></tr>
<tr class="memdesc:a9c1ad079376ba0f55d414e1c584e4569"><td class="mdescLeft"> </td><td class="mdescRight">stores a string representation of the encoded sequences in 'vectors' in 'output' <a href="#a9c1ad079376ba0f55d414e1c584e4569">More...</a><br/></td></tr>
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<tr class="memitem:ad7203656eb6d92da3a2552064ee05831"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#ad7203656eb6d92da3a2552064ee05831">encodeOligo</a> (const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> &sequence, <a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> k_mer_length, const <a class="el" href="classOpenMS_1_1String.html">String</a> &allowed_characters, std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > &values, bool is_right_border=false)</td></tr>
<tr class="memdesc:ad7203656eb6d92da3a2552064ee05831"><td class="mdescLeft"> </td><td class="mdescRight">encodes an <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> instance in oligo encoding <a href="#ad7203656eb6d92da3a2552064ee05831">More...</a><br/></td></tr>
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Static Public Member Functions</h2></td></tr>
<tr class="memitem:a94f559ce6231df530c5f7627415cd0c1"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a94f559ce6231df530c5f7627415cd0c1">destroyProblem</a> (svm_problem *problem)</td></tr>
<tr class="memdesc:a94f559ce6231df530c5f7627415cd0c1"><td class="mdescLeft"> </td><td class="mdescRight">frees all the memory of the svm_problem instance <a href="#a94f559ce6231df530c5f7627415cd0c1">More...</a><br/></td></tr>
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Static Private Member Functions</h2></td></tr>
<tr class="memitem:a070d7b3d971b30a61bcc2cbe5db9c9ed"><td class="memItemLeft" align="right" valign="top">static bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1LibSVMEncoder.html#a070d7b3d971b30a61bcc2cbe5db9c9ed">cmpOligos_</a> (std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > a, std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > b)</td></tr>
<tr class="memdesc:a070d7b3d971b30a61bcc2cbe5db9c9ed"><td class="mdescLeft"> </td><td class="mdescRight">comparator for oligos encoded by encodeOligo <a href="#a070d7b3d971b30a61bcc2cbe5db9c9ed">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Serves for encoding sequences into feature vectors. </p>
<p>The class can be used to construct composition vectors for sequences. Additionally the vectors can be encoded into the libsvm format. </p>
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<p>Constructor. </p>
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<td class="memname">~<a class="el" href="classOpenMS_1_1LibSVMEncoder.html">LibSVMEncoder</a> </td>
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<p>Destructor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">static bool cmpOligos_ </td>
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<td class="paramtype">std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > </td>
<td class="paramname"><em>a</em>, </td>
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<p>comparator for oligos encoded by encodeOligo </p>
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<td class="memname">static void destroyProblem </td>
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<p>frees all the memory of the svm_problem instance </p>
<p>This function is used to free all the memory used by 'problem' </p>
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<td class="memname">void encodeCompositionVector </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<td class="paramtype">std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > & </td>
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<p>stores a composition vector of 'sequence' in 'encoded_vector' </p>
<p>The allowed characters given by 'allowed_characters' are counted in the sequence 'sequence' and the relative frequency of the letters are sored in the composition vector. The first entry of the vector (<UInt, DoubleReal>) corresponds to the first letter of 'allowed_characters' that has a non zero frequency in 'sequence' and its corresponding relative frequency... </p>
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<td class="memname">void encodeCompositionVectors </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td>
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<td class="paramtype">std::vector< std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > & </td>
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<p>stores composition vectors of the sequences given by 'sequence' in 'composition_vectors' </p>
<p>The allowed characters given by 'allowed_characters' are counted in the sequences 'sequences' and the relative frequency of the letters are sored in the composition vectors. The first entry of the first vector (<UInt, DoubleReal>) corresponds to the first letter of 'allowed_characters' that has a non zero frequency in the first 'sequence' and its corresponding relative frequency... </p>
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<td class="paramtype">const std::vector< svm_node * > & </td>
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<p>encodes the LibSVM compliant vectors into a LibSVM compliant structure </p>
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<p>creates composition vectors with additional length information for 'sequences' and stores them in LibSVM compliant format </p>
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<p>creates composition vectors with additional length and average weight information for 'sequences' and stores them in LibSVM compliant format </p>
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<p>creates composition vectors for 'sequences' and stores them in LibSVM compliant format </p>
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<p>creates oligo border vectors vectors for 'sequences' and stores them in LibSVM compliant format </p>
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<td class="memname">svm_node* encodeLibSVMVector </td>
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<td class="paramtype">const std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > & </td>
<td class="paramname"><em>feature_vector</em></td><td>)</td>
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<p>encodes the feature vector in LibSVM compliant format </p>
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<td class="memname">void encodeLibSVMVectors </td>
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<td class="paramtype">const std::vector< std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > & </td>
<td class="paramname"><em>feature_vectors</em>, </td>
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<td class="paramtype">std::vector< svm_node * > & </td>
<td class="paramname"><em>libsvm_vectors</em> </td>
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<p>encodes the feature vectors in LibSVM compliant format </p>
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<td class="memname">void encodeOligo </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> & </td>
<td class="paramname"><em>sequence</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>k_mer_length</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>allowed_characters</em>, </td>
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<td class="paramtype">std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > & </td>
<td class="paramname"><em>values</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>is_right_border</em> = <code>false</code> </td>
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<p>encodes an <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> instance in oligo encoding </p>
<p>This function is used to get the oligo encoding for <a class="el" href="classOpenMS_1_1AASequence.html" title="Representation of a peptide/protein sequence. ">AASequence</a> 'sequence'. If a residue is modified, it gets an extra oligo function. </p>
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<td class="memname">void encodeOligoBorders </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> </td>
<td class="paramname"><em>sequence</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>k_mer_length</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>border_length</em>, </td>
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<td class="paramtype">std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > & </td>
<td class="paramname"><em>libsvm_vector</em>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>strict</em> = <code>false</code>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>unpaired</em> = <code>false</code>, </td>
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<td class="paramtype">bool </td>
<td class="paramname"><em>length_encoding</em> = <code>false</code> </td>
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<p>encodes the borders of the sequence as k_mer oligos and stores them in 'libsvm_vector' </p>
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<td class="memname">void encodeProblemWithOligoBorderVectors </td>
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<td class="paramtype">const std::vector< <a class="el" href="classOpenMS_1_1AASequence.html">AASequence</a> > & </td>
<td class="paramname"><em>sequences</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>k_mer_length</em>, </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>allowed_characters</em>, </td>
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<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>border_length</em>, </td>
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<td class="paramtype">std::vector< std::vector< std::pair< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > > > & </td>
<td class="paramname"><em>vectors</em> </td>
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<p>creates oligo border vectors vectors for 'sequences' and stores them in 'vectors' </p>
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<td class="memname">void libSVMVectorsToString </td>
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<td class="paramtype">svm_problem * </td>
<td class="paramname"><em>vector</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<p>stores a string representation of the encoded sequences in 'vectors' in 'output' </p>
<p>This function can be used if one wants to print the feature vectors that are used in the libsvm. </p>
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<td class="memname">void libSVMVectorToString </td>
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<td class="paramtype">svm_node * </td>
<td class="paramname"><em>vector</em>, </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
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<p>stores a string representation of the encoded sequence 'vector' in 'output' </p>
<p>This function can be used if one wants to print one feature vector that is used in the libsvm. </p>
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<td class="memname">svm_problem* loadLibSVMProblem </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em></td><td>)</td>
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<p>loads the LibSVM-encoded data stored in 'filename' </p>
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<td class="memname">bool storeLibSVMProblem </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>filename</em>, </td>
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<td class="paramtype">const svm_problem * </td>
<td class="paramname"><em>problem</em> </td>
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<p>stores the LibSVM-encoded data in a text file that can be used by the LibSVM applications (svm-scale, svm-train,...) </p>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:30 using doxygen 1.8.5</font></TD>
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