public SalzbergWordStringKernel(int size, PluginEstimate pie) : this(modshogunPINVOKE.new_SalzbergWordStringKernel__SWIG_2(size, PluginEstimate.getCPtr(pie)), true)
{
if (modshogunPINVOKE.SWIGPendingException.Pending)
{
throw modshogunPINVOKE.SWIGPendingException.Retrieve();
}
}
public SalzbergWordStringKernel(StringWordFeatures l, StringWordFeatures r, PluginEstimate pie) : this(modshogunPINVOKE.new_SalzbergWordStringKernel__SWIG_4(StringWordFeatures.getCPtr(l), StringWordFeatures.getCPtr(r), PluginEstimate.getCPtr(pie)), true)
{
if (modshogunPINVOKE.SWIGPendingException.Pending)
{
throw modshogunPINVOKE.SWIGPendingException.Retrieve();
}
}
public static void Main()
{
modshogun.init_shogun_with_defaults();
bool reverse = false;
int order = 3;
int gap = 0;
String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, EAlphabet.DNA);
StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order-1, order, gap, false);
charfeat = new StringCharFeatures(fm_test_dna, EAlphabet.DNA);
StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat, order-1, order, gap, false);
BinaryLabels labels = new BinaryLabels(Load.load_labels("../data/label_train_dna.dat"));
PluginEstimate pie = new PluginEstimate();
pie.set_labels(labels);
pie.set_features(feats_train);
pie.train();
SalzbergWordStringKernel kernel = new SalzbergWordStringKernel(feats_train, feats_train, pie, labels);
double[,] km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
pie.set_features(feats_test);
BinaryLabels.obtain_from_generic(pie.apply()).get_labels();
double[,] km_test=kernel.get_kernel_matrix();
modshogun.exit_shogun();
}
internal static ArrayList run(IList para)
{
bool reverse = false;
modshogun.init_shogun_with_defaults();
int order = (int)((int?)para[0]);
int gap = (int)((int?)para[1]);
string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, DNA);
StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order-1, order, gap, false);
charfeat = new StringCharFeatures(fm_test_dna, DNA);
StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat, order-1, order, gap, false);
Labels labels = new Labels(Load.load_labels("../data/label_train_dna.dat"));
PluginEstimate pie = new PluginEstimate();
pie.set_labels(labels);
pie.set_features(feats_train);
pie.train();
SalzbergWordStringKernel kernel = new SalzbergWordStringKernel(feats_train, feats_train, pie, labels);
DoubleMatrix km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
pie.set_features(feats_test);
pie.apply().get_labels();
DoubleMatrix km_test =kernel.get_kernel_matrix();
ArrayList result = new ArrayList();
result.Add(km_train);
result.Add(km_test);
result.Add(kernel);
modshogun.exit_shogun();
return result;
}
public static void Main()
{
modshogun.init_shogun_with_defaults();
bool reverse = false;
int order = 3;
int gap = 0;
String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
StringCharFeatures charfeat = new StringCharFeatures(fm_train_dna, EAlphabet.DNA);
StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order - 1, order, gap, false);
charfeat = new StringCharFeatures(fm_test_dna, EAlphabet.DNA);
StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat, order - 1, order, gap, false);
BinaryLabels labels = new BinaryLabels(Load.load_labels("../data/label_train_dna.dat"));
PluginEstimate pie = new PluginEstimate();
pie.set_labels(labels);
pie.set_features(feats_train);
pie.train();
SalzbergWordStringKernel kernel = new SalzbergWordStringKernel(feats_train, feats_train, pie, labels);
double[,] km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
pie.set_features(feats_test);
BinaryLabels.obtain_from_generic(pie.apply()).get_labels();
double[,] km_test = kernel.get_kernel_matrix();
modshogun.exit_shogun();
}
public HistogramWordStringKernel(StringWordFeatures l, StringWordFeatures r, PluginEstimate pie) : this(modshogunPINVOKE.new_HistogramWordStringKernel__SWIG_2(StringWordFeatures.getCPtr(l), StringWordFeatures.getCPtr(r), PluginEstimate.getCPtr(pie)), true) {
if (modshogunPINVOKE.SWIGPendingException.Pending) throw modshogunPINVOKE.SWIGPendingException.Retrieve();
}
public HistogramWordStringKernel(int size, PluginEstimate pie) : this(modshogunPINVOKE.new_HistogramWordStringKernel__SWIG_1(size, PluginEstimate.getCPtr(pie)), true) {
if (modshogunPINVOKE.SWIGPendingException.Pending) throw modshogunPINVOKE.SWIGPendingException.Retrieve();
}
internal static HandleRef getCPtr(PluginEstimate obj) {
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public SalzbergWordStringKernel(StringWordFeatures l, StringWordFeatures r, PluginEstimate pie, Labels labels) : this(modshogunPINVOKE.new_SalzbergWordStringKernel__SWIG_3(StringWordFeatures.getCPtr(l), StringWordFeatures.getCPtr(r), PluginEstimate.getCPtr(pie), Labels.getCPtr(labels)), true) {
if (modshogunPINVOKE.SWIGPendingException.Pending) throw modshogunPINVOKE.SWIGPendingException.Retrieve();
}
public SalzbergWordStringKernel(int size, PluginEstimate pie, Labels labels) : this(modshogunPINVOKE.new_SalzbergWordStringKernel__SWIG_1(size, PluginEstimate.getCPtr(pie), Labels.getCPtr(labels)), true) {
if (modshogunPINVOKE.SWIGPendingException.Pending) throw modshogunPINVOKE.SWIGPendingException.Retrieve();
}
internal static HandleRef getCPtr(PluginEstimate obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
