SGInterface.cpp

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#include <shogun/ui/GUICommands.h>
#include <shogun/ui/SGInterface.h>
#include <shogun/ui/SyntaxHighLight.h>

#include <shogun/lib/config.h>
#include <shogun/lib/memory.h>
#include <shogun/lib/ShogunException.h>
#include <shogun/mathematics/Math.h>
#include <shogun/lib/Hash.h>
#include <shogun/lib/Set.h>
#include <shogun/lib/Signal.h>

#include <shogun/classifier/svm/SVM.h>
#include <shogun/classifier/svm/pr_loqo.h>
#include <shogun/machine/LinearMachine.h>
#include <shogun/classifier/mkl/MKL.h>
#include <shogun/kernel/WeightedDegreePositionStringKernel.h>
#include <shogun/kernel/WeightedDegreeStringKernel.h>
#include <shogun/kernel/CommWordStringKernel.h>
#include <shogun/kernel/WeightedCommWordStringKernel.h>
#include <shogun/kernel/LinearKernel.h>
#include <shogun/kernel/CombinedKernel.h>
#include <shogun/kernel/CustomKernel.h>
#include <shogun/kernel/SalzbergWordStringKernel.h>
#include <shogun/kernel/WaveletKernel.h>
#include <shogun/features/SimpleFeatures.h>
#include <shogun/features/PolyFeatures.h>
#include <shogun/preprocessor/SortWordString.h>

#include <shogun/structure/Plif.h>
#include <shogun/structure/PlifArray.h>
#include <shogun/structure/PlifBase.h>
#include <shogun/structure/DynProg.h>
#include <shogun/structure/IntronList.h>
#include <shogun/structure/SegmentLoss.h>

#include <ctype.h>

using namespace shogun;

CSGInterface* interface=NULL;
CSyntaxHighLight hilight;

#if defined(HAVE_CMDLINE)
#define USAGE(method) "", ""
#define USAGE_I(method, in) "", " " in ""
#define USAGE_O(method, out) "" out " = ", ""
#define USAGE_IO(method, in, out) "" out " = ", " " in ""
#define USAGE_COMMA " "
#define USAGE_STR ""
#elif defined(HAVE_R)
#define USAGE(method) "sg('", "')"
#define USAGE_I(method, in) "sg('", "', " in ")"
#define USAGE_O(method, out) "[" out "] <- sg('", "')"
#define USAGE_IO(method, in, out) "[" out "] <- sg('", "', " in ")"
#define USAGE_COMMA ", "
#define USAGE_STR "'"
#else
#define USAGE(method) "sg('", "')"
#define USAGE_I(method, in) "sg('", "', " in ")"
#define USAGE_O(method, out) "[" out "]=sg('", "')"
#define USAGE_IO(method, in, out) "[" out "]=sg('", "', " in ")"
#define USAGE_COMMA ", "
#define USAGE_STR "'"
#endif

CSGInterfaceMethod sg_methods[]=
{
    { "Features", NULL, NULL, NULL },
    {
        N_PR_LOQO,
        (&CSGInterface::cmd_pr_loqo),
        USAGE_IO(N_PR_LOQO,
            "'Var1', Var1, 'Var2', Var2", "results")
    },
    {
        N_LOAD_FEATURES,
        (&CSGInterface::cmd_load_features),
        USAGE_I(N_LOAD_FEATURES,
            "filename" USAGE_COMMA "feature_class" USAGE_COMMA "type" USAGE_COMMA "target[" USAGE_COMMA "size[" USAGE_COMMA "comp_features]]")
    },
    {
        N_SAVE_FEATURES,
        (&CSGInterface::cmd_save_features),
        USAGE_I(N_SAVE_FEATURES, "filename" USAGE_COMMA "type" USAGE_COMMA "target")
    },
    {
        N_CLEAN_FEATURES,
        (&CSGInterface::cmd_clean_features),
        USAGE_I(N_CLEAN_FEATURES, USAGE_STR "TRAIN|TEST" USAGE_STR )
    },
    {
        N_GET_FEATURES,
        (&CSGInterface::cmd_get_features),
        USAGE_IO(N_GET_FEATURES, USAGE_STR "TRAIN|TEST" USAGE_STR, "features")
    },
    {
        N_ADD_FEATURES,
        (&CSGInterface::cmd_add_features),
        USAGE_I(N_ADD_FEATURES,
            USAGE_STR "TRAIN|TEST" USAGE_STR USAGE_COMMA "features[" USAGE_COMMA "DNABINFILE|<ALPHABET>]")
    },
    {
        N_ADD_MULTIPLE_FEATURES,
        (&CSGInterface::cmd_add_multiple_features),
        USAGE_I(N_ADD_MULTIPLE_FEATURES,
            USAGE_STR "TRAIN|TEST" USAGE_STR USAGE_COMMA "repetitions" USAGE_COMMA "features[" USAGE_COMMA "DNABINFILE|<ALPHABET>]")
    },
    {
        N_ADD_DOTFEATURES,
        (&CSGInterface::cmd_add_dotfeatures),
        USAGE_I(N_ADD_DOTFEATURES,
            USAGE_STR "TRAIN|TEST" USAGE_STR USAGE_COMMA "features[" USAGE_COMMA "DNABINFILE|<ALPHABET>]")
    },
    {
        N_SET_FEATURES,
        (&CSGInterface::cmd_set_features),
        USAGE_I(N_SET_FEATURES,
            USAGE_STR "TRAIN|TEST" USAGE_STR
            USAGE_COMMA "features["
            USAGE_COMMA "DNABINFILE|<ALPHABET>]["
            USAGE_COMMA "[from_position_list|slide_window]"
            USAGE_COMMA "window size"
            USAGE_COMMA "[position_list|shift]"
            USAGE_COMMA "skip")
    },
    {
        N_SET_REF_FEAT,
        (&CSGInterface::cmd_set_reference_features),
        USAGE_I(N_SET_REF_FEAT, USAGE_STR "TRAIN|TEST" USAGE_STR)
    },
    {
        N_DEL_LAST_FEATURES,
        (&CSGInterface::cmd_del_last_features),
        USAGE_I(N_DEL_LAST_FEATURES, USAGE_STR "TRAIN|TEST" USAGE_STR )
    },
    {
        N_CONVERT,
        (&CSGInterface::cmd_convert),
        USAGE_I(N_CONVERT, USAGE_STR "TRAIN|TEST" USAGE_STR 
                USAGE_COMMA "from_class"
                USAGE_COMMA "from_type"
                USAGE_COMMA "to_class"
                USAGE_COMMA "to_type["
                USAGE_COMMA "order"
                USAGE_COMMA "start"
                USAGE_COMMA "gap"
                USAGE_COMMA "reversed]")
    },
    {
        N_RESHAPE,
        (&CSGInterface::cmd_reshape),
        USAGE_I(N_RESHAPE, USAGE_STR "TRAIN|TEST"
                USAGE_COMMA "num_feat"
                USAGE_COMMA "num_vec")
    },
    {
        N_LOAD_LABELS,
        (&CSGInterface::cmd_load_labels),
        USAGE_I(N_LOAD_LABELS, "filename"
                USAGE_COMMA USAGE_STR "TRAIN|TARGET" USAGE_STR)
    },
    {
        N_SET_LABELS,
        (&CSGInterface::cmd_set_labels),
        USAGE_I(N_SET_LABELS, USAGE_STR "TRAIN|TEST" USAGE_STR
                USAGE_COMMA "labels")
    },
    {
        N_GET_LABELS,
        (&CSGInterface::cmd_get_labels),
        USAGE_IO(N_GET_LABELS, USAGE_STR "TRAIN|TEST" USAGE_STR, "labels")
    },


    { "Kernel", NULL, NULL },
    {
        N_SET_KERNEL_NORMALIZATION,
        (&CSGInterface::cmd_set_kernel_normalization),
        USAGE_I(N_SET_KERNEL_NORMALIZATION, "IDENTITY|AVGDIAG|SQRTDIAG|FIRSTELEMENT|VARIANCE|ZEROMEANCENTER"
                USAGE_COMMA "size[" USAGE_COMMA "kernel-specific parameters]")
    },
    {
        N_SET_KERNEL,
        (&CSGInterface::cmd_set_kernel),
        USAGE_I(N_SET_KERNEL, "type" USAGE_COMMA "size[" USAGE_COMMA "kernel-specific parameters]")
    },
    {
        N_ADD_KERNEL,
        (&CSGInterface::cmd_add_kernel),
        USAGE_I(N_ADD_KERNEL, "weight" USAGE_COMMA "kernel-specific parameters")
    },
    {
        N_DEL_LAST_KERNEL,
        (&CSGInterface::cmd_del_last_kernel),
        USAGE(N_DEL_LAST_KERNEL)
    },
    {
        N_INIT_KERNEL,
        (&CSGInterface::cmd_init_kernel),
        USAGE_I(N_INIT_KERNEL, USAGE_STR "TRAIN|TEST" USAGE_STR)
    },
    {
        N_CLEAN_KERNEL,
        (&CSGInterface::cmd_clean_kernel),
        USAGE(N_CLEAN_KERNEL)
    },
    {
        N_SAVE_KERNEL,
        (&CSGInterface::cmd_save_kernel),
        USAGE_I(N_SAVE_KERNEL, "filename" USAGE_COMMA USAGE_STR "TRAIN|TEST" USAGE_STR)
    },
    {
        N_GET_KERNEL_MATRIX,
        (&CSGInterface::cmd_get_kernel_matrix),
        USAGE_IO(N_GET_KERNEL_MATRIX, "[" USAGE_STR "TRAIN|TEST" USAGE_STR, "K]")
    },
    {
        N_SET_WD_POS_WEIGHTS,
        (&CSGInterface::cmd_set_WD_position_weights),
        USAGE_I(N_SET_WD_POS_WEIGHTS, "W[" USAGE_COMMA USAGE_STR "TRAIN|TEST" USAGE_STR "]")
    },
    {
        N_GET_SUBKERNEL_WEIGHTS,
        (&CSGInterface::cmd_get_subkernel_weights),
        USAGE_O(N_GET_SUBKERNEL_WEIGHTS, "W")
    },
    {
        N_SET_SUBKERNEL_WEIGHTS,
        (&CSGInterface::cmd_set_subkernel_weights),
        USAGE_I(N_SET_SUBKERNEL_WEIGHTS, "W")
    },
    {
        N_SET_SUBKERNEL_WEIGHTS_COMBINED,
        (&CSGInterface::cmd_set_subkernel_weights_combined),
        USAGE_I(N_SET_SUBKERNEL_WEIGHTS_COMBINED, "W" USAGE_COMMA "idx")
    },
    {
        N_GET_DOTFEATURE_WEIGHTS_COMBINED,
        (&CSGInterface::cmd_get_dotfeature_weights_combined),
        USAGE_IO(N_GET_DOTFEATURE_WEIGHTS_COMBINED,  USAGE_STR "TRAIN|TEST" USAGE_STR, "W")
    },
    {
        N_SET_DOTFEATURE_WEIGHTS_COMBINED,
        (&CSGInterface::cmd_set_dotfeature_weights_combined),
        USAGE_I(N_SET_DOTFEATURE_WEIGHTS_COMBINED, "W" USAGE_COMMA "idx")
    },
    {
        N_SET_LAST_SUBKERNEL_WEIGHTS,
        (&CSGInterface::cmd_set_last_subkernel_weights),
        USAGE_I(N_SET_LAST_SUBKERNEL_WEIGHTS, "W")
    },
    {
        N_GET_WD_POS_WEIGHTS,
        (&CSGInterface::cmd_get_WD_position_weights),
        USAGE_O(N_GET_WD_POS_WEIGHTS, "W")
    },
    {
        N_GET_LAST_SUBKERNEL_WEIGHTS,
        (&CSGInterface::cmd_get_last_subkernel_weights),
        USAGE_O(N_GET_LAST_SUBKERNEL_WEIGHTS, "W")
    },
    {
        N_COMPUTE_BY_SUBKERNELS,
        (&CSGInterface::cmd_compute_by_subkernels),
        USAGE_O(N_COMPUTE_BY_SUBKERNELS, "W")
    },
    {
        N_INIT_KERNEL_OPTIMIZATION,
        (&CSGInterface::cmd_init_kernel_optimization),
        USAGE(N_INIT_KERNEL_OPTIMIZATION)
    },
    {
        N_GET_KERNEL_OPTIMIZATION,
        (&CSGInterface::cmd_get_kernel_optimization),
        USAGE_O(N_GET_KERNEL_OPTIMIZATION, "W")
    },
    {
        N_DELETE_KERNEL_OPTIMIZATION,
        (&CSGInterface::cmd_delete_kernel_optimization),
        USAGE(N_DELETE_KERNEL_OPTIMIZATION)
    },
    {
        N_USE_DIAGONAL_SPEEDUP,
        (&CSGInterface::cmd_use_diagonal_speedup),
        USAGE_I(N_USE_DIAGONAL_SPEEDUP, USAGE_STR "0|1" USAGE_STR)
    },
    {
        N_SET_KERNEL_OPTIMIZATION_TYPE,
        (&CSGInterface::cmd_set_kernel_optimization_type),
        USAGE_I(N_SET_KERNEL_OPTIMIZATION_TYPE, USAGE_STR "FASTBUTMEMHUNGRY|SLOWBUTMEMEFFICIENT" USAGE_STR)
    },
    {
        N_SET_SOLVER,
        (&CSGInterface::cmd_set_solver),
        USAGE_I(N_SET_SOLVER, USAGE_STR "AUTO|CPLEX|GLPK|INTERNAL" USAGE_STR)
    },
    {
        N_SET_CONSTRAINT_GENERATOR,
        (&CSGInterface::cmd_set_constraint_generator),
        USAGE_I(N_SET_CONSTRAINT_GENERATOR, USAGE_STR "LIBSVM_ONECLASS|LIBSVM_MULTICLASS|LIBSVM"
                "|SVMLIGHT|LIGHT|SVMLIGHT_ONECLASS|GPBTSVM|MPDSVM|GNPPSVM|GMNPSVM"
                USAGE_STR)
    },
    {
        N_SET_PRIOR_PROBS,
        (&CSGInterface::cmd_set_prior_probs),
        USAGE_I(N_SET_PRIOR_PROBS, USAGE_STR "pos probs, neg_probs" USAGE_STR)
    },
    {
        N_SET_PRIOR_PROBS_FROM_LABELS,
        (&CSGInterface::cmd_set_prior_probs_from_labels),
        USAGE_I(N_SET_PRIOR_PROBS_FROM_LABELS, USAGE_STR "labels" USAGE_STR)
    },
#ifdef USE_SVMLIGHT
    {
        N_RESIZE_KERNEL_CACHE,
        (&CSGInterface::cmd_resize_kernel_cache),
        USAGE_I(N_RESIZE_KERNEL_CACHE, "size")
    },
#endif //USE_SVMLIGHT


    { "Distance", NULL, NULL },
    {
        N_SET_DISTANCE,
        (&CSGInterface::cmd_set_distance),
        USAGE_I(N_SET_DISTANCE, "type" USAGE_COMMA "data type[" USAGE_COMMA "distance-specific parameters]")
    },
    {
        N_INIT_DISTANCE,
        (&CSGInterface::cmd_init_distance),
        USAGE_I(N_INIT_DISTANCE, USAGE_STR "TRAIN|TEST" USAGE_STR)
    },
    {
        N_GET_DISTANCE_MATRIX,
        (&CSGInterface::cmd_get_distance_matrix),
        USAGE_O(N_GET_DISTANCE_MATRIX, "D")
    },


    { "Classifier", NULL, NULL },
    {
        N_CLASSIFY,
        (&CSGInterface::cmd_classify),
        USAGE_O(N_CLASSIFY, "result")
    },
    {
        N_SVM_CLASSIFY,
        (&CSGInterface::cmd_classify),
        USAGE_O(N_SVM_CLASSIFY, "result")
    },
    {
        N_CLASSIFY_EXAMPLE,
        (&CSGInterface::cmd_classify_example),
        USAGE_IO(N_CLASSIFY_EXAMPLE, "feature_vector_index", "result")
    },
    {
        N_SVM_CLASSIFY_EXAMPLE,
        (&CSGInterface::cmd_classify_example),
        USAGE_IO(N_SVM_CLASSIFY_EXAMPLE, "feature_vector_index", "result")
    },
    {
        N_GET_CLASSIFIER,
        (&CSGInterface::cmd_get_classifier),
        USAGE_IO(N_GET_CLASSIFIER, "[index in case of MultiClassSVM]", "bias" USAGE_COMMA "weights")
    },
    {
        N_GET_CLUSTERING,
        (&CSGInterface::cmd_get_classifier),
        USAGE_O(N_GET_CLUSTERING, "radi" USAGE_COMMA "centers|merge_distances" USAGE_COMMA "pairs")
    },
    {
        N_NEW_SVM,
        (&CSGInterface::cmd_new_classifier),
        USAGE_I(N_NEW_SVM, USAGE_STR "LIBSVM_ONECLASS|LIBSVM_MULTICLASS|LIBSVM"
                "|SVMLIGHT|LIGHT|LIGHT_ONECLASS|SVMLIN|GPBTSVM|MPDSVM|GNPPSVM|GMNPSVM"
                "|SUBGRADIENTSVM|WDSVMOCAS|SVMOCAS|SVMSGD|SVMBMRM|SVMPERF"
                "|KERNELPERCEPTRON|PERCEPTRON|LIBLINEAR_LR|LIBLINEAR_L2|LDA"
                "|LPM|LPBOOST|SUBGRADIENTLPM|KNN" USAGE_STR)
    },
    {
        N_NEW_CLASSIFIER,
        (&CSGInterface::cmd_new_classifier),
        USAGE_I(N_NEW_CLASSIFIER, USAGE_STR "LIBSVM_ONECLASS|LIBSVM_MULTICLASS"
                "|LIBSVM|SVMLIGHT|LIGHT|LIGHT_ONECLASS|SVMLIN|GPBTSVM|MPDSVM|GNPPSVM|GMNPSVM"
                "|SUBGRADIENTSVM|WDSVMOCAS|SVMOCAS|SVMSGD|SVMBMRM|SVMPERF"
                "|KERNELPERCEPTRON|PERCEPTRON|LIBLINEAR_LR|LIBLINEAR_L2|LDA"
                "|LPM|LPBOOST|SUBGRADIENTLPM|KNN" USAGE_STR)
    },
    {
        N_NEW_REGRESSION,
        (&CSGInterface::cmd_new_classifier),
        USAGE_I(N_NEW_REGRESSION, USAGE_STR "SVRLIGHT|LIBSVR|KRR" USAGE_STR)
    },
    {
        N_NEW_CLUSTERING,
        (&CSGInterface::cmd_new_classifier),
        USAGE_I(N_NEW_CLUSTERING, USAGE_STR "KMEANS|HIERARCHICAL" USAGE_STR)
    },
    {
        N_LOAD_CLASSIFIER,
        (&CSGInterface::cmd_load_classifier),
        USAGE_O(N_LOAD_CLASSIFIER, "filename" USAGE_COMMA "type")
    },
    {
        N_SAVE_CLASSIFIER,
        (&CSGInterface::cmd_save_classifier),
        USAGE_I(N_SAVE_CLASSIFIER, "filename")
    },
    {
        N_GET_NUM_SVMS,
        (&CSGInterface::cmd_get_num_svms),
        USAGE_O(N_GET_NUM_SVMS, "number of SVMs in MultiClassSVM")
    },
    {
        N_GET_SVM,
        (&CSGInterface::cmd_get_svm),
        USAGE_IO(N_GET_SVM, "[index in case of MultiClassSVM]", "bias" USAGE_COMMA "alphas")
    },
    {
        N_SET_SVM,
        (&CSGInterface::cmd_set_svm),
        USAGE_I(N_SET_SVM, "bias" USAGE_COMMA "alphas")
    },
    {
        N_SET_LINEAR_CLASSIFIER,
        (&CSGInterface::cmd_set_linear_classifier),
        USAGE_I(N_SET_LINEAR_CLASSIFIER, "bias" USAGE_COMMA "w")
    },
    {
        N_GET_SVM_OBJECTIVE,
        (&CSGInterface::cmd_get_svm_objective),
        USAGE_O(N_GET_SVM_OBJECTIVE, "objective")
    },
    {
        N_COMPUTE_SVM_PRIMAL_OBJECTIVE,
        (&CSGInterface::cmd_compute_svm_primal_objective),
        USAGE_O(N_COMPUTE_SVM_PRIMAL_OBJECTIVE, "objective")
    },
    {
        N_COMPUTE_SVM_DUAL_OBJECTIVE,
        (&CSGInterface::cmd_compute_svm_dual_objective),
        USAGE_O(N_COMPUTE_SVM_DUAL_OBJECTIVE, "objective")
    },
    {
        N_COMPUTE_MKL_PRIMAL_OBJECTIVE,
        (&CSGInterface::cmd_compute_svm_primal_objective),
        USAGE_O(N_COMPUTE_MKL_PRIMAL_OBJECTIVE, "objective")
    },
    {
        N_COMPUTE_MKL_DUAL_OBJECTIVE,
        (&CSGInterface::cmd_compute_mkl_dual_objective),
        USAGE_O(N_COMPUTE_MKL_DUAL_OBJECTIVE, "objective")
    },
    {
        N_COMPUTE_RELATIVE_MKL_DUALITY_GAP,
        (&CSGInterface::cmd_compute_relative_mkl_duality_gap),
        USAGE_O(N_COMPUTE_RELATIVE_MKL_DUALITY_GAP, "gap")
    },
    {
        N_COMPUTE_ABSOLUTE_MKL_DUALITY_GAP,
        (&CSGInterface::cmd_compute_absolute_mkl_duality_gap),
        USAGE_O(N_COMPUTE_ABSOLUTE_MKL_DUALITY_GAP, "gap")
    },
    {
        N_DO_AUC_MAXIMIZATION,
        (&CSGInterface::cmd_do_auc_maximization),
        USAGE_I(N_DO_AUC_MAXIMIZATION, USAGE_STR "auc" USAGE_STR)
    },
    {
        N_SET_PERCEPTRON_PARAMETERS,
        (&CSGInterface::cmd_set_perceptron_parameters),
        USAGE_I(N_SET_PERCEPTRON_PARAMETERS, "learnrate" USAGE_COMMA "maxiter")
    },
    {
        N_TRAIN_CLASSIFIER,
        (&CSGInterface::cmd_train_classifier),
        USAGE_I(N_TRAIN_CLASSIFIER, "[classifier-specific parameters]")
    },
    {
        N_TRAIN_REGRESSION,
        (&CSGInterface::cmd_train_classifier),
        USAGE(N_TRAIN_REGRESSION)
    },
    {
        N_TRAIN_CLUSTERING,
        (&CSGInterface::cmd_train_classifier),
        USAGE(N_TRAIN_CLUSTERING)
    },
    {
        N_SVM_TRAIN,
        (&CSGInterface::cmd_train_classifier),
        USAGE_I(N_SVM_TRAIN, "[classifier-specific parameters]")
    },
    {
        N_SVMQPSIZE,
        (&CSGInterface::cmd_set_svm_qpsize),
        USAGE_I(N_SVMQPSIZE, "size")
    },
    {
        N_SVMMAXQPSIZE,
        (&CSGInterface::cmd_set_svm_max_qpsize),
        USAGE_I(N_SVMMAXQPSIZE, "size")
    },
    {
        N_SVMBUFSIZE,
        (&CSGInterface::cmd_set_svm_bufsize),
        USAGE_I(N_SVMBUFSIZE, "size")
    },
    {
        N_C,
        (&CSGInterface::cmd_set_svm_C),
        USAGE_I(N_C, "C1[" USAGE_COMMA "C2]")
    },
    {
        N_SVM_EPSILON,
        (&CSGInterface::cmd_set_svm_epsilon),
        USAGE_I(N_SVM_EPSILON, "epsilon")
    },
    {
        N_SVR_TUBE_EPSILON,
        (&CSGInterface::cmd_set_svr_tube_epsilon),
        USAGE_I(N_SVR_TUBE_EPSILON, "tube_epsilon")
    },
    {
        N_SVM_NU,
        (&CSGInterface::cmd_set_svm_nu),
        USAGE_I(N_SVM_NU, "nu")
    },
    {
        N_MKL_PARAMETERS,
        (&CSGInterface::cmd_set_svm_mkl_parameters),
        USAGE_I(N_MKL_PARAMETERS, "weight_epsilon" USAGE_COMMA "C_MKL [" USAGE_COMMA "mkl_norm ]")
    },
    {
      N_ENT_LAMBDA,
      (&CSGInterface::cmd_set_elasticnet_lambda),
      USAGE_I(N_ENT_LAMBDA, "ent_lambda")
    },
    {
      N_MKL_BLOCK_NORM,
      (&CSGInterface::cmd_set_mkl_block_norm),
      USAGE_I(N_MKL_BLOCK_NORM, "mkl_block_norm")
    },
    {
        N_SVM_MAX_TRAIN_TIME,
        (&CSGInterface::cmd_set_max_train_time),
        USAGE_I(N_SVM_MAX_TRAIN_TIME, "max_train_time")
    },
    {
        N_USE_SHRINKING,
        (&CSGInterface::cmd_set_svm_shrinking_enabled),
        USAGE_I(N_USE_SHRINKING, "enable_shrinking")
    },
    {
        N_USE_BATCH_COMPUTATION,
        (&CSGInterface::cmd_set_svm_batch_computation_enabled),
        USAGE_I(N_USE_BATCH_COMPUTATION, "enable_batch_computation")
    },
    {
        N_USE_LINADD,
        (&CSGInterface::cmd_set_svm_linadd_enabled),
        USAGE_I(N_USE_LINADD, "enable_linadd")
    },
    {
        N_SVM_USE_BIAS,
        (&CSGInterface::cmd_set_svm_bias_enabled),
        USAGE_I(N_SVM_USE_BIAS, "enable_bias")
    },
    {
        N_MKL_USE_INTERLEAVED_OPTIMIZATION,
        (&CSGInterface::cmd_set_mkl_interleaved_enabled),
        USAGE_I(N_MKL_USE_INTERLEAVED_OPTIMIZATION, "enable_interleaved_optimization")
    },
    {
        N_KRR_TAU,
        (&CSGInterface::cmd_set_krr_tau),
        USAGE_I(N_KRR_TAU, "tau")
    },


    { "Preprocessors", NULL, NULL },
    {
        N_ADD_PREPROC,
        (&CSGInterface::cmd_add_preproc),
        USAGE_I(N_ADD_PREPROC, "preproc[, preproc-specific parameters]")
    },
    {
        N_DEL_PREPROC,
        (&CSGInterface::cmd_del_preproc),
        USAGE(N_DEL_PREPROC)
    },
    {
        N_ATTACH_PREPROC,
        (&CSGInterface::cmd_attach_preproc),
        USAGE_I(N_ATTACH_PREPROC, USAGE_STR "TRAIN|TEST" USAGE_STR USAGE_COMMA "force")
    },
    {
        N_CLEAN_PREPROC,
        (&CSGInterface::cmd_clean_preproc),
        USAGE(N_CLEAN_PREPROC)
    },


    { "HMM", NULL, NULL },
    {
        N_NEW_HMM,
        (&CSGInterface::cmd_new_hmm),
        USAGE_I(N_NEW_HMM, "N" USAGE_COMMA "M")
    },
    {
        N_LOAD_HMM,
        (&CSGInterface::cmd_load_hmm),
        USAGE_I(N_LOAD_HMM, "filename")
    },
    {
        N_SAVE_HMM,
        (&CSGInterface::cmd_save_hmm),
        USAGE_I(N_SAVE_HMM, "filename[" USAGE_COMMA "save_binary]")
    },
    {
        N_GET_HMM,
        (&CSGInterface::cmd_get_hmm),
        USAGE_O(N_GET_HMM, "p" USAGE_COMMA "q" USAGE_COMMA "a" USAGE_COMMA "b")
    },
    {
        N_APPEND_HMM,
        (&CSGInterface::cmd_append_hmm),
        USAGE_I(N_APPEND_HMM, "p" USAGE_COMMA "q" USAGE_COMMA "a" USAGE_COMMA "b")
    },
    {
        N_APPEND_MODEL,
        (&CSGInterface::cmd_append_model),
        USAGE_I(N_APPEND_MODEL, USAGE_STR "filename" USAGE_STR "[" USAGE_COMMA "base1" USAGE_COMMA "base2]")
    },
    {
        N_SET_HMM,
        (&CSGInterface::cmd_set_hmm),
        USAGE_I(N_SET_HMM, "p" USAGE_COMMA "q" USAGE_COMMA "a" USAGE_COMMA "b")
    },
    {
        N_SET_HMM_AS,
        (&CSGInterface::cmd_set_hmm_as),
        USAGE_I(N_SET_HMM_AS, "POS|NEG|TEST")
    },
    {
        N_CHOP,
        (&CSGInterface::cmd_set_chop),
        USAGE_I(N_CHOP, "chop")
    },
    {
        N_PSEUDO,
        (&CSGInterface::cmd_set_pseudo),
        USAGE_I(N_PSEUDO, "pseudo")
    },
    {
        N_LOAD_DEFINITIONS,
        (&CSGInterface::cmd_load_definitions),
        USAGE_I(N_LOAD_DEFINITIONS, "filename" USAGE_COMMA "init")
    },
    {
        N_HMM_CLASSIFY,
        (&CSGInterface::cmd_hmm_classify),
        USAGE_O(N_HMM_CLASSIFY, "result")
    },
    {
        N_ONE_CLASS_LINEAR_HMM_CLASSIFY,
        (&CSGInterface::cmd_one_class_linear_hmm_classify),
        USAGE_O(N_ONE_CLASS_LINEAR_HMM_CLASSIFY, "result")
    },
    {
        N_ONE_CLASS_HMM_CLASSIFY,
        (&CSGInterface::cmd_one_class_hmm_classify),
        USAGE_O(N_ONE_CLASS_HMM_CLASSIFY, "result")
    },
    {
        N_ONE_CLASS_HMM_CLASSIFY_EXAMPLE,
        (&CSGInterface::cmd_one_class_hmm_classify_example),
        USAGE_IO(N_ONE_CLASS_HMM_CLASSIFY_EXAMPLE, "feature_vector_index", "result")
    },
    {
        N_HMM_CLASSIFY_EXAMPLE,
        (&CSGInterface::cmd_hmm_classify_example),
        USAGE_IO(N_HMM_CLASSIFY_EXAMPLE, "feature_vector_index", "result")
    },
    {
        N_OUTPUT_HMM,
        (&CSGInterface::cmd_output_hmm),
        USAGE(N_OUTPUT_HMM)
    },
    {
        N_OUTPUT_HMM_DEFINED,
        (&CSGInterface::cmd_output_hmm_defined),
        USAGE(N_OUTPUT_HMM_DEFINED)
    },
    {
        N_HMM_LIKELIHOOD,
        (&CSGInterface::cmd_hmm_likelihood),
        USAGE_O(N_HMM_LIKELIHOOD, "likelihood")
    },
    {
        N_LIKELIHOOD,
        (&CSGInterface::cmd_likelihood),
        USAGE(N_LIKELIHOOD)
    },
    {
        N_SAVE_LIKELIHOOD,
        (&CSGInterface::cmd_save_likelihood),
        USAGE_I(N_SAVE_LIKELIHOOD, "filename[" USAGE_COMMA "save_binary]")
    },
    {
        N_GET_VITERBI_PATH,
        (&CSGInterface::cmd_get_viterbi_path),
        USAGE_IO(N_GET_VITERBI_PATH, "dim", "path" USAGE_COMMA "likelihood")
    },
    {
        N_VITERBI_TRAIN_DEFINED,
        (&CSGInterface::cmd_viterbi_train_defined),
        USAGE(N_VITERBI_TRAIN_DEFINED)
    },
    {
        N_VITERBI_TRAIN,
        (&CSGInterface::cmd_viterbi_train),
        USAGE(N_VITERBI_TRAIN)
    },
    {
        N_BAUM_WELCH_TRAIN,
        (&CSGInterface::cmd_baum_welch_train),
        USAGE(N_BAUM_WELCH_TRAIN)
    },
    {
        N_BAUM_WELCH_TRAIN_DEFINED,
        (&CSGInterface::cmd_baum_welch_train_defined),
        USAGE(N_BAUM_WELCH_TRAIN_DEFINED)
    },
    {
        N_BAUM_WELCH_TRANS_TRAIN,
        (&CSGInterface::cmd_baum_welch_trans_train),
        USAGE(N_BAUM_WELCH_TRANS_TRAIN)
    },
    {
        N_LINEAR_TRAIN,
        (&CSGInterface::cmd_linear_train),
        USAGE(N_LINEAR_TRAIN)
    },
    {
        N_SAVE_PATH,
        (&CSGInterface::cmd_save_path),
        USAGE_I(N_SAVE_PATH, "filename[" USAGE_COMMA "save_binary]")
    },
    {
        N_CONVERGENCE_CRITERIA,
        (&CSGInterface::cmd_convergence_criteria),
        USAGE_I(N_CONVERGENCE_CRITERIA, "num_iterations" USAGE_COMMA "epsilon")
    },
    {
        N_NORMALIZE,
        (&CSGInterface::cmd_normalize),
        USAGE_I(N_NORMALIZE, "[keep_dead_states]")
    },
    {
        N_ADD_STATES,
        (&CSGInterface::cmd_add_states),
        USAGE_I(N_ADD_STATES, "states" USAGE_COMMA "value")
    },
    {
        N_PERMUTATION_ENTROPY,
        (&CSGInterface::cmd_permutation_entropy),
        USAGE_I(N_PERMUTATION_ENTROPY, "width" USAGE_COMMA "seqnum")
    },
    {
        N_RELATIVE_ENTROPY,
        (&CSGInterface::cmd_relative_entropy),
        USAGE_O(N_RELATIVE_ENTROPY, "result")
    },
    {
        N_ENTROPY,
        (&CSGInterface::cmd_entropy),
        USAGE_O(N_ENTROPY, "result")
    },
    {
        (char*) N_SET_FEATURE_MATRIX,
        (&CSGInterface::cmd_set_feature_matrix),
        (char*) USAGE_I(N_SET_FEATURE_MATRIX, "features")
    },
    {
        (char*) N_SET_FEATURE_MATRIX_SPARSE,
        (&CSGInterface::cmd_set_feature_matrix_sparse),
        (char*) USAGE_I(N_SET_FEATURE_MATRIX_SPARSE, "sp1" USAGE_COMMA "sp2" )
    },
    {
        N_NEW_PLUGIN_ESTIMATOR,
        (&CSGInterface::cmd_new_plugin_estimator),
        USAGE_I(N_NEW_PLUGIN_ESTIMATOR, "pos_pseudo" USAGE_COMMA "neg_pseudo")
    },
    {
        N_TRAIN_ESTIMATOR,
        (&CSGInterface::cmd_train_estimator),
        USAGE(N_TRAIN_ESTIMATOR)
    },
    {
        N_PLUGIN_ESTIMATE_CLASSIFY_EXAMPLE,
        (&CSGInterface::cmd_plugin_estimate_classify_example),
        USAGE_IO(N_PLUGIN_ESTIMATE_CLASSIFY_EXAMPLE, "feature_vector_index", "result")
    },
    {
        N_PLUGIN_ESTIMATE_CLASSIFY,
        (&CSGInterface::cmd_plugin_estimate_classify),
        USAGE_O(N_PLUGIN_ESTIMATE_CLASSIFY, "result")
    },
    {
        N_SET_PLUGIN_ESTIMATE,
        (&CSGInterface::cmd_set_plugin_estimate),
        USAGE_I(N_SET_PLUGIN_ESTIMATE, "emission_probs" USAGE_COMMA "model_sizes")
    },
    {
        N_GET_PLUGIN_ESTIMATE,
        (&CSGInterface::cmd_get_plugin_estimate),
        USAGE_O(N_GET_PLUGIN_ESTIMATE, "emission_probs" USAGE_COMMA "model_sizes")
    },
    { "Signals", NULL, NULL },
    {
        N_SIGNALS_SET_MODEL,
        (&CSGInterface::cmd_signals_set_model),
        USAGE_I(N_SIGNALS_SET_MODEL, "arg1")
    },
    {
        N_SIGNALS_SET_POSITIONS,
        (&CSGInterface::cmd_signals_set_positions),
        USAGE_I(N_SIGNALS_SET_POSITIONS, "positions")
    },
    {
        N_SIGNALS_SET_LABELS,
        (&CSGInterface::cmd_signals_set_labels),
        USAGE_I(N_SIGNALS_SET_LABELS, "labels")
    },
    {
        N_SIGNALS_SET_SPLIT,
        (&CSGInterface::cmd_signals_set_split),
        USAGE_I(N_SIGNALS_SET_SPLIT, "split")
    },
    {
        N_SIGNALS_SET_TRAIN_MASK,
        (&CSGInterface::cmd_signals_set_train_mask),
        USAGE_I(N_SIGNALS_SET_TRAIN_MASK, "")
    },
    {
        N_SIGNALS_ADD_FEATURE,
        (&CSGInterface::cmd_signals_add_feature),
        USAGE_I(N_SIGNALS_ADD_FEATURE, "feature")
    },
    {
        N_SIGNALS_ADD_KERNEL,
        (&CSGInterface::cmd_signals_add_kernel),
        USAGE_I(N_SIGNALS_ADD_KERNEL, "kernelparam")
    },
    {
        N_SIGNALS_RUN,
        (&CSGInterface::cmd_signals_run),
        USAGE_I(N_SIGNALS_RUN, "arg1")
    },
    { "Structure", NULL, NULL },
    {
        N_BEST_PATH,
        (&CSGInterface::cmd_best_path),
        USAGE_I(N_BEST_PATH, "from" USAGE_COMMA "to")
    },
    {
        N_BEST_PATH_2STRUCT,
        (&CSGInterface::cmd_best_path_2struct),
        USAGE_IO(N_BEST_PATH_2STRUCT, "p"
                USAGE_COMMA "q" 
                USAGE_COMMA "cmd_trans"
                USAGE_COMMA "seq"
                USAGE_COMMA "pos"
                USAGE_COMMA "genestr"
                USAGE_COMMA "penalties"
                USAGE_COMMA "penalty_info"
                USAGE_COMMA "nbest"
                USAGE_COMMA "content_weights"
                USAGE_COMMA "segment_sum_weights",
            "prob" USAGE_COMMA "path" USAGE_COMMA "pos")
    },
    {
        (char*) N_SET_PLIF_STRUCT,
        (&CSGInterface::cmd_set_plif_struct),
        (char*) USAGE_I(N_SET_PLIF_STRUCT, "id"
                USAGE_COMMA "name"
                USAGE_COMMA "limits"
                USAGE_COMMA "penalties"
                USAGE_COMMA "transform"
                USAGE_COMMA "min_value"
                USAGE_COMMA "max_value"
                USAGE_COMMA "use_cache"
                USAGE_COMMA "use_svm")
    },
    {
        (char*) N_GET_PLIF_STRUCT,
        (&CSGInterface::cmd_get_plif_struct),
        (char*) USAGE_O(N_GET_PLIF_STRUCT, "id"
                USAGE_COMMA "name"
                USAGE_COMMA "limits"
                USAGE_COMMA "penalties"
                USAGE_COMMA "transform"
                USAGE_COMMA "min_value"
                USAGE_COMMA "max_value"
                USAGE_COMMA "use_cache"
                USAGE_COMMA "use_svm")
    },
    {
        (char*) N_PRECOMPUTE_SUBKERNELS,
        (&CSGInterface::cmd_precompute_subkernels),
        (char*) USAGE(N_PRECOMPUTE_SUBKERNELS)
    },
    {
        (char*) N_PRECOMPUTE_CONTENT_SVMS,
        (&CSGInterface::cmd_precompute_content_svms),
        (char*) USAGE_I(N_PRECOMPUTE_CONTENT_SVMS, "sequence"
                USAGE_COMMA "position_list"
                USAGE_COMMA "weights")
    },
    {
        (char*) N_GET_LIN_FEAT,
        (&CSGInterface::cmd_get_lin_feat),
        (char*) USAGE_O(N_GET_LIN_FEAT, "lin_feat")
    },
    {
        (char*) N_SET_LIN_FEAT,
        (&CSGInterface::cmd_set_lin_feat),
        (char*) USAGE_I(N_SET_LIN_FEAT, "lin_feat")
    },
    {
        (char*) N_INIT_DYN_PROG,
        (&CSGInterface::cmd_init_dyn_prog),
        (char*) USAGE_I(N_INIT_DYN_PROG, "num_svms")
    },
    {
        (char*) N_CLEAN_UP_DYN_PROG,
        (&CSGInterface::cmd_clean_up_dyn_prog),
        (char*) USAGE(N_CLEAN_UP_DYN_PROG)
    },
    {
        (char*) N_INIT_INTRON_LIST,
        (&CSGInterface::cmd_init_intron_list),
        (char*) USAGE_I(N_INIT_INTRON_LIST, "start_positions"
                USAGE_COMMA "end_positions"
                USAGE_COMMA "quality")
    },
    {
        (char*) N_PRECOMPUTE_TILING_FEATURES,
        (&CSGInterface::cmd_precompute_tiling_features),
        (char*) USAGE_I(N_PRECOMPUTE_TILING_FEATURES, "intensities"
                USAGE_COMMA "probe_pos"
                USAGE_COMMA "tiling_plif_ids")
    },
    {
        (char*) N_LONG_TRANSITION_SETTINGS,
        (&CSGInterface::cmd_long_transition_settings),
        (char*) USAGE_I(N_LONG_TRANSITION_SETTINGS, "use_long_transitions"
                USAGE_COMMA "threshold"
                USAGE_COMMA "max_len")
    },

    {
        (char*) N_SET_MODEL,
        (&CSGInterface::cmd_set_model),
        (char*) USAGE_I(N_SET_MODEL, "content_weights"
                USAGE_COMMA "transition_pointers"
                USAGE_COMMA "use_orf"
                USAGE_COMMA "mod_words")
    },

    {
        (char*) N_BEST_PATH_TRANS,
        (&CSGInterface::cmd_best_path_trans),
        USAGE_IO(N_BEST_PATH_TRANS, "p"
                USAGE_COMMA "q"
                USAGE_COMMA "nbest"
                USAGE_COMMA "seq_path"
                USAGE_COMMA "a_trans"
                USAGE_COMMA "segment_loss",
            "prob" USAGE_COMMA "path" USAGE_COMMA "pos")
    },
    {
        N_BEST_PATH_TRANS_DERIV,
        (&CSGInterface::cmd_best_path_trans_deriv),
        USAGE_IO(N_BEST_PATH_TRANS_DERIV,
            USAGE_COMMA "my_path"
            USAGE_COMMA "my_pos"
            USAGE_COMMA "p"
            USAGE_COMMA "q"
            USAGE_COMMA "cmd_trans"
            USAGE_COMMA "seq"
            USAGE_COMMA "pos"
            USAGE_COMMA "genestr"
            USAGE_COMMA "penalties"
            USAGE_COMMA "state_signals"
            USAGE_COMMA "penalty_info"
            USAGE_COMMA "dict_weights"
            USAGE_COMMA "mod_words ["
            USAGE_COMMA "segment_loss"
            USAGE_COMMA "segmend_ids_mask]", "p_deriv"
            USAGE_COMMA "q_deriv"
            USAGE_COMMA "cmd_deriv"
            USAGE_COMMA "penalties_deriv"
            USAGE_COMMA "my_scores"
            USAGE_COMMA "my_loss")
    },

    { "POIM", NULL, NULL },
    {
        N_COMPUTE_POIM_WD,
        (&CSGInterface::cmd_compute_POIM_WD),
        USAGE_IO(N_COMPUTE_POIM_WD, "max_order" USAGE_COMMA "distribution", "W")
    },
    {
        N_GET_SPEC_CONSENSUS,
        (&CSGInterface::cmd_get_SPEC_consensus),
        USAGE_O(N_GET_SPEC_CONSENSUS, "W")
    },
    {
        N_GET_SPEC_SCORING,
        (&CSGInterface::cmd_get_SPEC_scoring),
        USAGE_IO(N_GET_SPEC_SCORING, "max_order", "W")
    },
    {
        N_GET_WD_CONSENSUS,
        (&CSGInterface::cmd_get_WD_consensus),
        USAGE_O(N_GET_WD_CONSENSUS, "W")
    },
    {
        N_GET_WD_SCORING,
        (&CSGInterface::cmd_get_WD_scoring),
        USAGE_IO(N_GET_WD_SCORING, "max_order", "W")
    },


    { "Utility", NULL, NULL },
    {
        N_CRC,
        (&CSGInterface::cmd_crc),
        USAGE_IO(N_CRC, "string", "crc32")
    },
    {
        N_SYSTEM,
        (&CSGInterface::cmd_system),
        USAGE_I(N_SYSTEM, "system_command")
    },
    {
        N_EXIT,
        (&CSGInterface::cmd_exit),
        USAGE(N_EXIT)
    },
    {
        N_QUIT,
        (&CSGInterface::cmd_exit),
        USAGE(N_QUIT)
    },
    {
        N_EXEC,
        (&CSGInterface::cmd_exec),
        USAGE_I(N_EXEC, "filename")
    },
    {
        N_SET_OUTPUT,
        (&CSGInterface::cmd_set_output),
        USAGE_I(N_SET_OUTPUT, USAGE_STR "STDERR|STDOUT|filename" USAGE_STR)
    },
    {
        N_SET_THRESHOLD,
        (&CSGInterface::cmd_set_threshold),
        USAGE_I(N_SET_THRESHOLD, "threshold")
    },
    {
        N_INIT_RANDOM,
        (&CSGInterface::cmd_init_random),
        USAGE_I(N_INIT_RANDOM, "value_to_initialize_RNG_with")
    },
    {
        N_THREADS,
        (&CSGInterface::cmd_set_num_threads),
        USAGE_I(N_THREADS, "num_threads")
    },
    {
        N_TRANSLATE_STRING,
        (&CSGInterface::cmd_translate_string),
        USAGE_IO(N_TRANSLATE_STRING,
            "string, order, start", "translation")
    },
    {
        N_CLEAR,
        (&CSGInterface::cmd_clear),
        USAGE(N_CLEAR)
    },
    {
        N_TIC,
        (&CSGInterface::cmd_tic),
        USAGE(N_TIC)
    },
    {
        N_TOC,
        (&CSGInterface::cmd_toc),
        USAGE(N_TOC)
    },
    {
        N_PRINT,
        (&CSGInterface::cmd_print),
        USAGE_I(N_PRINT, "msg")
    },
    {
        N_ECHO,
        (&CSGInterface::cmd_echo),
        USAGE_I(N_ECHO, "level")
    },
    {
        N_LOGLEVEL,
        (&CSGInterface::cmd_loglevel),
        USAGE_I(N_LOGLEVEL, USAGE_STR "ALL|DEBUG|INFO|NOTICE|WARN|ERROR|CRITICAL|ALERT|EMERGENCY" USAGE_STR)
    },
    {
        N_SYNTAX_HIGHLIGHT,
        (&CSGInterface::cmd_syntax_highlight),
        USAGE_I(N_SYNTAX_HIGHLIGHT, USAGE_STR "ON|OFF" USAGE_STR)
    },
    {
        N_PROGRESS,
        (&CSGInterface::cmd_progress),
        USAGE_I(N_PROGRESS, USAGE_STR "ON|OFF" USAGE_STR)
    },
    {
        N_GET_VERSION,
        (&CSGInterface::cmd_get_version),
        USAGE_O(N_GET_VERSION, "version")
    },
    {
        N_HELP,
        (&CSGInterface::cmd_help),
        USAGE(N_HELP)
    },
    {
        N_WHOS,
        (&CSGInterface::cmd_whos),
        USAGE(N_WHOS)
    },
    {
        N_SEND_COMMAND,
        (&CSGInterface::cmd_send_command),
        NULL
    },
    {
        N_RUN_PYTHON,
        (&CSGInterface::cmd_run_python),
        USAGE_IO(N_RUN_PYTHON,
            "'Var1', Var1, 'Var2', Var2,..., python_function", "results")
    },
    {
        N_RUN_OCTAVE,
        (&CSGInterface::cmd_run_octave),
        USAGE_IO(N_RUN_OCTAVE,
            "'Var1', Var1, 'Var2', Var2,..., octave_function", "results")
    },
    {
        N_RUN_R,
        (&CSGInterface::cmd_run_r),
        USAGE_IO(N_RUN_R,
            "'Var1', Var1, 'Var2', Var2,..., r_function", "results")
    },
    {NULL, NULL, NULL}        /* Sentinel */
};


CSGInterface::CSGInterface(bool print_copyright)
: CSGObject(),
    ui_classifier(new CGUIClassifier(this)),
    ui_distance(new CGUIDistance(this)),
    ui_features(new CGUIFeatures(this)),
    ui_hmm(new CGUIHMM(this)),
    ui_kernel(new CGUIKernel(this)),
    ui_labels(new CGUILabels(this)),
    ui_math(new CGUIMath(this)),
    ui_pluginestimate(new CGUIPluginEstimate(this)),
    ui_preproc(new CGUIPreprocessor(this)),
    ui_time(new CGUITime(this)),
  ui_structure(new CGUIStructure(this))/*,
/   ui_signals(new CGUISignals(this))*/
{
    if (print_copyright)
    {
        version->print_version();
        SG_PRINT("( seeding random number generator with %u (seed size %d))\n",
                CMath::get_seed(), RNG_SEED_SIZE);
#ifdef USE_LOGCACHE
        SG_PRINT( "initializing log-table (size=%i*%i*%i=%2.1fMB) ... ) ",
                CMath::get_log_range(),CMath::get_log_accuracy(),sizeof(float64_t),
                CMath::get_log_range()*CMath::get_log_accuracy()*sizeof(float64_t)/(1024.0*1024.0));
#else
        SG_PRINT("determined range for x in log(1+exp(-x)) is:%d )\n", CMath::get_log_range());
#endif 
    }

    reset();
}

CSGInterface::~CSGInterface()
{
    delete ui_classifier;
    delete ui_hmm;
    delete ui_pluginestimate;
    delete ui_kernel;
    delete ui_preproc;
    delete ui_features;
    delete ui_labels;
    delete ui_math;
    delete ui_structure;
    //delete ui_signals; 
    delete ui_time;
    delete ui_distance;

    if (file_out)
        fclose(file_out);
}

void CSGInterface::reset()
{
    m_lhs_counter=0;
    m_rhs_counter=0;
    m_nlhs=0;
    m_nrhs=0;
    m_legacy_strptr=NULL;
    file_out=NULL;
    echo=true;
}

void CSGInterface::translate_arg(CSGInterface* source, CSGInterface* target)
{
    switch (source->get_argument_type())
    {
        case SCALAR_INT:
            target->set_int(source->get_int());
            break;
        case SCALAR_REAL:
            target->set_real(source->get_real());
            break;
        case SCALAR_BOOL:
            target->set_bool(source->get_bool());
            break;
        case VECTOR_BOOL:
            {
                bool* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_BYTE:
            {
                uint8_t* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_CHAR:
            {
                char* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_INT:
            {
                int32_t* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_REAL:
            {
                float64_t* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_SHORTREAL:
            {
                float32_t* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_SHORT:
            {
                int16_t* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }
        case VECTOR_WORD:
            {
                uint16_t* v=NULL;
                int32_t len=0;
                source->get_vector(v, len);
                target->set_vector(v, len);
                SG_FREE(v);
                break;
            }

        case STRING_BYTE:
            {
                int32_t num_str=0;
                int32_t max_str_len=0;
                SGString<uint8_t>* strs=NULL;
                source->get_string_list(strs, num_str, max_str_len);
                target->set_string_list(strs, num_str);
                SG_FREE(strs);
                break;
            }
        case STRING_CHAR:
            {
                int32_t num_str=0;
                int32_t max_str_len=0;
                SGString<char>* strs;
                source->get_string_list(strs, num_str,max_str_len);
                target->set_string_list(strs, num_str);
                SG_FREE(strs);
                break;
            }
        case STRING_INT:
            {
                int32_t num_str=0;
                int32_t max_str_len=0;
                SGString<int32_t>* strs;
                source->get_string_list(strs, num_str,max_str_len);
                target->set_string_list(strs, num_str);
                SG_FREE(strs);
                break;
            }
        case STRING_SHORT:
            {
                int32_t num_str=0;
                int32_t max_str_len=0;
                SGString<int16_t>* strs=NULL;
                source->get_string_list(strs, num_str, max_str_len);
                target->set_string_list(strs, num_str);
                SG_FREE(strs);
                break;
            }
        case STRING_WORD:
            {
                int32_t num_str=0;
                int32_t max_str_len=0;
                SGString<uint16_t>* strs=NULL;
                source->get_string_list(strs, num_str, max_str_len);
                target->set_string_list(strs, num_str);
                SG_FREE(strs);
                break;
            }
        case DENSE_INT:
            {
                int32_t num_feat=0;
                int32_t num_vec=0;
                int32_t* fmatrix=NULL;
                source->get_matrix(fmatrix, num_feat, num_vec);
                target->set_matrix(fmatrix, num_feat, num_vec);
                SG_FREE(fmatrix);
                break;
            }
        case DENSE_REAL:
            {
                int32_t num_feat=0;
                int32_t num_vec=0;
                float64_t* fmatrix=NULL;
                source->get_matrix(fmatrix, num_feat, num_vec);
                target->set_matrix(fmatrix, num_feat, num_vec);
                SG_FREE(fmatrix);
                break;
            }
        case DENSE_SHORT:
            {
                int32_t num_feat=0;
                int32_t num_vec=0;
                int16_t* fmatrix=NULL;
                source->get_matrix(fmatrix, num_feat, num_vec);
                target->set_matrix(fmatrix, num_feat, num_vec);
                SG_FREE(fmatrix);
                break;
            }
        case DENSE_SHORTREAL:
            {
                int32_t num_feat=0;
                int32_t num_vec=0;
                float32_t* fmatrix=NULL;
                source->get_matrix(fmatrix, num_feat, num_vec);
                target->set_matrix(fmatrix, num_feat, num_vec);
                SG_FREE(fmatrix);
                break;
            }
        case DENSE_WORD:
            {
                int32_t num_feat=0;
                int32_t num_vec=0;
                uint16_t* fmatrix=NULL;
                source->get_matrix(fmatrix, num_feat, num_vec);
                target->set_matrix(fmatrix, num_feat, num_vec);
                SG_FREE(fmatrix);
                break;
            }
            /*
        case NDARRAY_BYTE:
            {
                uint8_t* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }
        case NDARRAY_CHAR:
            {
                char* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }
        case NDARRAY_INT:
            {
                int32_t* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }
        case NDARRAY_REAL:
            {
                float64_t* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }
        case NDARRAY_SHORTREAL:
            {
                float32_t* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }
        case NDARRAY_SHORT:
            {
                int16_t* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }
        case NDARRAY_WORD:
            {
                uint16_t* a=NULL;
                int32_t* dims=NULL;
                int32_t num_dims=0;
                source->get_ndarray(a, dims, num_dims);
                target->set_ndarray(a, dims, num_dims);
                SG_FREE(a);
                SG_FREE(dims);
                break;
            }*/
        case SPARSE_REAL:
            {
                int32_t num_feat=0;
                int32_t num_vec=0;
                SGSparseVector<float64_t>* fmatrix=NULL;
                source->get_sparse_matrix(fmatrix, num_feat, num_vec);
                int64_t nnz=0;
                for (int32_t i=0; i<num_vec; i++)
                    nnz+=fmatrix[i].num_feat_entries;
                target->set_sparse_matrix(fmatrix, num_feat, num_vec, nnz);
                SG_FREE(fmatrix);
                break;
            }

        default:
            SG_ERROR("unknown return type");
            break;
    }
}

// commands

/* Features */

bool CSGInterface::cmd_load_features()
{
    if (m_nrhs<8 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);
    char* fclass=get_str_from_str_or_direct(len);
    char* type=get_str_from_str_or_direct(len);
    char* target=get_str_from_str_or_direct(len);
    int32_t size=get_int_from_int_or_str();
    int32_t comp_features=get_int_from_int_or_str();

    bool success=ui_features->load(
        filename, fclass, type, target, size, comp_features);

    SG_FREE(filename);
    SG_FREE(fclass);
    SG_FREE(type);
    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_save_features()
{
    if (m_nrhs<5 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);
    char* type=get_str_from_str_or_direct(len);
    char* target=get_str_from_str_or_direct(len);

    bool success=ui_features->save(filename, type, target);

    SG_FREE(filename);
    SG_FREE(type);
    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_clean_features()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);

    bool success=ui_features->clean(target);

    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_get_features()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t tlen=0;
    char* target=get_string(tlen);
    CFeatures* feat=NULL;

    if (strmatch(target, "TRAIN"))
        feat=ui_features->get_train_features();
    else if (strmatch(target, "TEST"))
        feat=ui_features->get_test_features();
    else
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }
    SG_FREE(target);

    ASSERT(feat);

    switch (feat->get_feature_class())
    {
        case C_SIMPLE:
        {
            int32_t num_feat=0;
            int32_t num_vec=0;

            switch (feat->get_feature_type())
            {
                case F_BYTE:
                {
                    uint8_t* fmatrix=((CSimpleFeatures<uint8_t> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                case F_CHAR:
                {
                    char* fmatrix=((CSimpleFeatures<char> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                case F_DREAL:
                {
                    float64_t* fmatrix=((CSimpleFeatures<float64_t> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                case F_INT:
                {
                    int32_t* fmatrix=((CSimpleFeatures<int32_t> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                case F_SHORT:
                {
                    int16_t* fmatrix=((CSimpleFeatures<int16_t> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                case F_SHORTREAL:
                {
                    float32_t* fmatrix=((CSimpleFeatures<float32_t> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                case F_WORD:
                {
                    uint16_t* fmatrix=((CSimpleFeatures<uint16_t> *) feat)->get_feature_matrix(num_feat, num_vec);
                    set_matrix(fmatrix, num_feat, num_vec);
                    break;
                }

                default:
                    SG_NOTIMPLEMENTED;
            }
            break;
        }

        case C_SPARSE:
        {
            switch (feat->get_feature_type())
            {
                case F_DREAL:
                {
                    int64_t nnz=((CSparseFeatures<float64_t>*) feat)->
                        get_num_nonzero_entries();
                    int32_t num_feat=0;
                    int32_t num_vec=0;
                    SGSparseVector<float64_t>* fmatrix=((CSparseFeatures<float64_t>*) feat)->get_sparse_feature_matrix(num_feat, num_vec);
                    SG_INFO("sparse matrix has %d feats, %d vecs and %d nnz elemements\n", num_feat, num_vec, nnz);

                    set_sparse_matrix(fmatrix, num_feat, num_vec, nnz);
                    break;
                }

                default:
                    SG_NOTIMPLEMENTED;
            }
            break;
        }

        case C_STRING:
        {
            int32_t num_str=0;
            int32_t max_str_len=0;
            switch (feat->get_feature_type())
            {
                case F_BYTE:
                {
                    SGString<uint8_t>* fmatrix=((CStringFeatures<uint8_t>*) feat)->get_features(num_str, max_str_len);
                    set_string_list(fmatrix, num_str);
                    break;
                }

                case F_CHAR:
                {
                    SGString<char>* fmatrix=((CStringFeatures<char>*) feat)->get_features(num_str, max_str_len);
                    set_string_list(fmatrix, num_str);
                    break;
                }

                case F_WORD:
                {
                    SGString<uint16_t>* fmatrix=((CStringFeatures<uint16_t>*) feat)->get_features(num_str, max_str_len);
                    set_string_list(fmatrix, num_str);
                    break;
                }

                default:
                    SG_NOTIMPLEMENTED;
            }
            break;
        }

        case C_WD:
        case C_WEIGHTEDSPEC:
        case C_SPEC:
        case C_COMBINED_DOT:
        case C_POLY:
        {

            SGMatrix<float64_t> fmatrix = ((CDotFeatures*) feat)->get_computed_dot_feature_matrix();
            set_matrix(fmatrix.matrix, fmatrix.num_cols, fmatrix.num_rows);
            fmatrix.free_matrix();
            break;
        }

        default:
            SG_NOTIMPLEMENTED;
    }

    return true;
}

bool CSGInterface::cmd_add_features()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    return do_set_features(true, false);
}

bool CSGInterface::cmd_add_multiple_features()
{
    if ((m_nrhs!=4 && m_nrhs<5) || !create_return_values(0))
        return false;

    int32_t repetitions=get_int();

    ASSERT(repetitions>=1);

    return do_set_features(true, false, repetitions);
}

bool CSGInterface::cmd_add_dotfeatures()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    return do_set_features(true, true);
}

bool CSGInterface::cmd_set_features()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    return do_set_features(false, false);
}

bool CSGInterface::do_set_features(bool add, bool check_dot, int32_t repetitions)
{
    int32_t tlen=0;
    char* target=get_string(tlen);
    if (!strmatch(target, "TRAIN") && !strmatch(target, "TEST"))
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }

    CFeatures* feat=NULL;
    int32_t num_feat=0;
    int32_t num_vec=0;

    switch (get_argument_type())
    {
        case SPARSE_REAL:
        {
            SGSparseVector<float64_t>* fmatrix=NULL;
            get_sparse_matrix(fmatrix, num_feat, num_vec);

            feat=new CSparseFeatures<float64_t>();
            ((CSparseFeatures<float64_t>*) feat)->
                set_sparse_feature_matrix(SGSparseMatrix<float64_t>(fmatrix, num_feat, num_vec));
            break;
        }

        case DENSE_REAL:
        {
            float64_t* fmatrix=NULL;
            get_matrix(fmatrix, num_feat, num_vec);

            feat=new CSimpleFeatures<float64_t>(0);
            ((CSimpleFeatures<float64_t>*) feat)->
                set_feature_matrix(fmatrix, num_feat, num_vec);

            if (m_nrhs==6)
                feat = create_custom_real_features((CSimpleFeatures<float64_t>*) feat);
            
            break;
        }

        case DENSE_INT:
        {
            int32_t* fmatrix=NULL;
            get_matrix(fmatrix, num_feat, num_vec);

            feat=new CSimpleFeatures<int32_t>(0);
            ((CSimpleFeatures<int32_t>*) feat)->
                set_feature_matrix(fmatrix, num_feat, num_vec);
            break;
        }

        case DENSE_SHORT:
        {
            int16_t* fmatrix=NULL;
            get_matrix(fmatrix, num_feat, num_vec);

            feat=new CSimpleFeatures<int16_t>(0);
            ((CSimpleFeatures<int16_t>*) feat)->
                set_feature_matrix(fmatrix, num_feat, num_vec);
            break;
        }

        case DENSE_WORD:
        {
            uint16_t* fmatrix=NULL;
            get_matrix(fmatrix, num_feat, num_vec);

            feat=new CSimpleFeatures<uint16_t>(0);
            ((CSimpleFeatures<uint16_t>*) feat)->
                set_feature_matrix(fmatrix, num_feat, num_vec);
            break;
        }

        case DENSE_SHORTREAL:
        {
            float32_t* fmatrix=NULL;
            get_matrix(fmatrix, num_feat, num_vec);

            feat=new CSimpleFeatures<float32_t>(0);
            ((CSimpleFeatures<float32_t>*) feat)->
                set_feature_matrix(fmatrix, num_feat, num_vec);
            break;
        }

        case STRING_CHAR:
        {
            if (m_nrhs<4)
                SG_ERROR("Please specify alphabet!\n");

            int32_t num_str=0;
            int32_t max_str_len=0;
            SGString<char>* fmatrix=NULL;
            get_string_list(fmatrix, num_str, max_str_len);

            int32_t alphabet_len=0;
            char* alphabet_str=get_string(alphabet_len);
            ASSERT(alphabet_str);

            if (strmatch(alphabet_str, "DNABINFILE"))
            {
                SG_FREE(alphabet_str);

                ASSERT(fmatrix[0].string);
                feat=new CStringFeatures<uint8_t>(DNA);

                try
                {
                    ((CStringFeatures<uint8_t>*) feat)->load_ascii_file(fmatrix[0].string);
                }
                catch (...)
                {
                    SG_UNREF(feat);
                    SG_ERROR("Couldn't load DNA features from file.\n");
                }
                feat=create_custom_string_features((CStringFeatures<uint8_t>*) feat);
                break;
            }
            else
            {
                bool convert_to_word=false;
                bool convert_to_ulong=false;
                CAlphabet* alphabet=NULL;
                if (strmatch(alphabet_str, "DNAWORD"))
                {
                    alphabet=new CAlphabet(DNA);
                    convert_to_word=true;
                }
                else if (strmatch(alphabet_str, "DNAULONG"))
                {
                    alphabet=new CAlphabet(DNA);
                    convert_to_ulong=true;
                }
                else
                    alphabet=new CAlphabet(alphabet_str, alphabet_len);

                SG_REF(alphabet);
                SG_FREE(alphabet_str);

                feat=new CStringFeatures<char>(alphabet);

                if (!((CStringFeatures<char>*) feat)->set_features(fmatrix, num_str, max_str_len))
                {
                    SG_UNREF(alphabet);
                    SG_UNREF(feat);
                    SG_ERROR("Couldnt set byte string features.\n");
                }

                SG_UNREF(alphabet);

                if (convert_to_word || convert_to_ulong)
                    convert_to_bitembedding(feat, convert_to_word, convert_to_ulong);
            }

            obtain_from_single_string(feat);
            break;
        }

        case STRING_BYTE:
        {
            if (m_nrhs<4)
                SG_ERROR("Please specify alphabet!\n");

            int32_t num_str=0;
            int32_t max_str_len=0;
            SGString<uint8_t>* fmatrix=NULL;
            get_string_list(fmatrix, num_str, max_str_len);

            int32_t alphabet_len=0;
            char* alphabet_str=get_string(alphabet_len);
            ASSERT(alphabet_str);
            CAlphabet* alphabet=NULL;
            alphabet=new CAlphabet(alphabet_str, alphabet_len);
            SG_FREE(alphabet_str);

            feat=new CStringFeatures<uint8_t>(alphabet);
            if (!((CStringFeatures<uint8_t>*) feat)->set_features(fmatrix, num_str, max_str_len))
            {
                SG_UNREF(alphabet);
                SG_UNREF(feat);
                SG_ERROR("Couldnt set byte string features.\n");
            }
            feat=create_custom_string_features((CStringFeatures<uint8_t>*) feat);
            break;
        }

        default:
            SG_ERROR("Wrong argument type %d.\n", get_argument_type());
    }

    if (check_dot && !feat->has_property(FP_DOT))
    {
        SG_UNREF(feat);
        SG_ERROR("Feature type not supported by DOT Features\n");
    }

    if (strmatch(target, "TRAIN"))
    {
        if (!add)
            ui_features->set_train_features(feat);
        else if (check_dot)
        {
            for (int32_t i=0; i<repetitions; i++)
            ui_features->add_train_dotfeatures((CDotFeatures*) feat);
        }
        else
        {
            for (int32_t i=0; i<repetitions; i++)
            ui_features->add_train_features(feat);
        }
    }
    else
    {
        if (!add)
            ui_features->set_test_features(feat);
        else if (check_dot)
        {
            for (int32_t i=0; i<repetitions; i++)
                ui_features->add_test_dotfeatures((CDotFeatures*) feat);
        }
        else
        {
            for (int32_t i=0; i<repetitions; i++)
                ui_features->add_test_features(feat);
        }
    }

    SG_FREE(target);

    return true;
}

bool CSGInterface::cmd_set_reference_features()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);

    bool success=ui_features->set_reference_features(target);

    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_del_last_features()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);
    bool success=ui_features->del_last_feature_obj(target);

    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_convert()
{
    if (m_nrhs<5 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);
    CFeatures* features=ui_features->get_convert_features(target);
    if (!features)
    {
        SG_FREE(target);
        SG_ERROR("No \"%s\" features available.\n", target);
    }

    char* from_class=get_str_from_str_or_direct(len);
    char* from_type=get_str_from_str_or_direct(len);
    char* to_class=get_str_from_str_or_direct(len);
    char* to_type=get_str_from_str_or_direct(len);

    CFeatures* result=NULL;
    if (strmatch(from_class, "SIMPLE"))
    {
        if (strmatch(from_type, "REAL"))
        {
            if (strmatch(to_class, "SPARSE") &&
                strmatch(to_type, "REAL"))
            {
                result=ui_features->convert_simple_real_to_sparse_real(
                    ((CSimpleFeatures<float64_t>*) features));
            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type REAL

        else if (strmatch(from_type, "CHAR"))
        {
            if (strmatch(to_class, "STRING") &&
                strmatch(to_type, "CHAR"))
            {
                result=ui_features->convert_simple_char_to_string_char(
                    ((CSimpleFeatures<char>*) features));
            }
            else if (strmatch(to_class, "SIMPLE"))
            {
                if (strmatch(to_type, "ALIGN") && m_nrhs==8)
                {
                    float64_t gap_cost=get_real_from_real_or_str();
                    result=ui_features->convert_simple_char_to_simple_align(
                        (CSimpleFeatures<char>*) features, gap_cost);
                }
                else
                    SG_NOTIMPLEMENTED;
            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type CHAR

        else if (strmatch(from_type, "WORD"))
        {
            if (strmatch(to_class, "SIMPLE") &&
                strmatch(to_type, "SALZBERG"))
            {
                result=ui_features->convert_simple_word_to_simple_salzberg(
                    (CSimpleFeatures<uint16_t>*) features);
            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type WORD

        else
            SG_NOTIMPLEMENTED;
    } // from_class SIMPLE

    else if (strmatch(from_class, "SPARSE"))
    {
        if (strmatch(from_type, "REAL"))
        {
            if (strmatch(to_class, "SIMPLE") &&
                strmatch(to_type, "REAL"))
            {
                result=ui_features->convert_sparse_real_to_simple_real(
                    (CSparseFeatures<float64_t>*) features);
            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type REAL
        else
            SG_NOTIMPLEMENTED;
    } // from_class SPARSE

    else if (strmatch(from_class, "STRING"))
    {
        if (strmatch(from_type, "CHAR"))
        {
            if (strmatch(to_class, "STRING"))
            {
                int32_t order=1;
                int32_t start=0;
                int32_t gap=0;
                char rev='f';

                if (m_nrhs>6)
                {
                    order=get_int_from_int_or_str();

                    if (m_nrhs>7)
                    {
                        start=get_int_from_int_or_str();

                        if (m_nrhs>8)
                        {
                            gap=get_int_from_int_or_str();

                            if (m_nrhs>9)
                            {
                                char* rev_str=get_str_from_str_or_direct(len);
                                if (rev_str)
                                    rev=rev_str[0];

                                SG_FREE(rev_str);
                            }
                        }
                    }
                }

                if (strmatch(to_type, "BYTE"))
                {
                        result=ui_features->convert_string_char_to_string_generic<char,uint8_t>(
                        (CStringFeatures<char>*) features, order, start,
                        gap, rev);
                }
                else if (strmatch(to_type, "WORD"))
                {
                        result=ui_features->convert_string_char_to_string_generic<char,uint16_t>(
                        (CStringFeatures<char>*) features, order, start,
                        gap, rev);
                }
                else if (strmatch(to_type, "ULONG"))
                {
                    result=ui_features->convert_string_char_to_string_generic<char,uint64_t>(
                    (CStringFeatures<char>*) features, order, start,
                        gap, rev);
                }
                else
                    SG_NOTIMPLEMENTED;
            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type CHAR

        else if (strmatch(from_type, "BYTE"))
        {
            if (strmatch(to_class, "STRING"))
            {
                int32_t order=1;
                int32_t start=0;
                int32_t gap=0;
                char rev='f';

                if (m_nrhs>6)
                {
                    order=get_int_from_int_or_str();

                    if (m_nrhs>7)
                    {
                        start=get_int_from_int_or_str();

                        if (m_nrhs>8)
                        {
                            gap=get_int_from_int_or_str();

                            if (m_nrhs>9)
                            {
                                char* rev_str=get_str_from_str_or_direct(len);
                                if (rev_str)
                                    rev=rev_str[0];

                                SG_FREE(rev_str);
                            }
                        }
                    }
                }

                if (strmatch(to_type, "WORD"))
                {
                    result=ui_features->convert_string_char_to_string_generic<uint8_t,uint16_t>(
                        (CStringFeatures<uint8_t>*) features, order, start,
                        gap, rev);
                }
                else if (strmatch(to_type, "ULONG"))
                {
                    result=ui_features->convert_string_char_to_string_generic<uint8_t,uint64_t>(
                        (CStringFeatures<uint8_t>*) features, order, start,
                        gap, rev);
                }
                else
                    SG_NOTIMPLEMENTED;
            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type uint8_t

        else if (strmatch(from_type, "WORD"))
        {
            if (strmatch(to_class, "SIMPLE") && strmatch(to_type, "TOP"))
            {
                result=ui_features->convert_string_word_to_simple_top(
                    (CStringFeatures<uint16_t>*) features);
            }
            else if (strmatch(to_class, "SPEC") && strmatch(to_type, "WORD") && m_nrhs==7)
            {
                bool use_norm=get_bool();
                result=ui_features->convert_string_byte_to_spec_word((CStringFeatures<uint16_t>*) features, use_norm);

            }
            else
                SG_NOTIMPLEMENTED;
        } // from_type WORD

        else if (strmatch(to_class, "SIMPLE") && strmatch(to_type, "FK"))
        {
            result=ui_features->convert_string_word_to_simple_fk(
                (CStringFeatures<uint16_t>*) features);
        } // to_type FK

        else
            SG_NOTIMPLEMENTED;

    } // from_class STRING

    if (result && ui_features->set_convert_features(result, target))
        SG_INFO("Conversion was successful.\n");
    else
        SG_ERROR("Conversion failed.\n");

    SG_FREE(target);
    SG_FREE(from_class);
    SG_FREE(from_type);
    SG_FREE(to_class);
    SG_FREE(to_type);
    return (result!=NULL);
}

void CSGInterface::convert_to_bitembedding(CFeatures* &features, bool convert_to_word, bool convert_to_ulong)
{
    int32_t order=1;
    int32_t start=0;
    int32_t gap=0;
    char rev='f';

    if (m_nrhs<5)
        return;

    order=get_int();
    // remove arg, for parameters to come
    m_nrhs--;

    if (convert_to_word)
    {
        SG_INFO("Converting into word-bitembedding\n");
        features=ui_features->convert_string_char_to_string_generic<char,uint16_t>(
                (CStringFeatures<char>*) features, order, start, gap, rev);
    }

    if (convert_to_ulong)
    {
        SG_INFO("Converting into ulong-bitembedding\n");
        features=ui_features->convert_string_char_to_string_generic<char,uint64_t>(
                (CStringFeatures<char>*) features, order, start, gap, rev);
    }
}

void CSGInterface::obtain_from_single_string(CFeatures* features)
{
    if (m_nrhs<5)
        return;

    int32_t len=0;
    char* str=get_string(len);
    ASSERT(str);

    if (strmatch(str, "from_position_list"))
    {
        obtain_from_position_list(features);
    }
    else if (strmatch(str, "slide_window"))
    {
        obtain_by_sliding_window(features);
    }
    else
        SG_SERROR("Unknown conversion\n");
}

bool CSGInterface::obtain_from_position_list(CFeatures* features)
{
    int32_t winsize=get_int();

    int32_t* shifts=NULL;
    int32_t num_shift=0;
    get_vector(shifts, num_shift);

    int32_t skip=0;
    if (m_nrhs==8)
        skip=get_int();

    SG_DEBUG("winsize: %d num_shifts: %d skip: %d\n", winsize, num_shift, skip);

    CDynamicArray<int32_t> positions(num_shift+1);

    for (int32_t i=0; i<num_shift; i++)
        positions.set_element(shifts[i], i);

    if (features->get_feature_class()!=C_STRING)
        SG_ERROR("No string features.\n");

    bool success=false;
    switch (features->get_feature_type())
    {
        case F_CHAR:
        {
            success=(((CStringFeatures<char>*) features)->
                obtain_by_position_list(winsize, &positions, skip)>0);
            break;
        }
        case F_BYTE:
        {
            success=(((CStringFeatures<uint8_t>*) features)->
                obtain_by_position_list(winsize, &positions, skip)>0);
            break;
        }
        case F_WORD:
        {
            success=(((CStringFeatures<uint16_t>*) features)->
                obtain_by_position_list(winsize, &positions, skip)>0);
            break;
        }
        case F_ULONG:
        {
            success=(((CStringFeatures<uint64_t>*) features)->
                obtain_by_position_list(winsize, &positions, skip)>0);
            break;
        }
        default:
            SG_ERROR("Unsupported string features type.\n");
    }

    return success;
}

bool CSGInterface::obtain_by_sliding_window(CFeatures* features)
{
    int32_t winsize=get_int();
    int32_t shift=get_int();
    int32_t skip=0;

    if (m_nrhs==8)
        skip=get_int();

    bool success=false;

    ASSERT(features);
    ASSERT(((CFeatures*) features)->get_feature_class()==C_STRING);

    switch (features->get_feature_type())
    {
        case F_CHAR:
            return ( ((CStringFeatures<char>*) features)->obtain_by_sliding_window(winsize, shift, skip)>0);
        case F_BYTE:
            return ( ((CStringFeatures<uint8_t>*) features)->obtain_by_sliding_window(winsize, shift, skip)>0);
        case F_WORD:
            return ( ((CStringFeatures<uint16_t>*) features)->obtain_by_sliding_window(winsize, shift, skip)>0);
        case F_ULONG:
            return ( ((CStringFeatures<uint64_t>*) features)->obtain_by_sliding_window(winsize, shift, skip)>0);
        default:
            SG_SERROR("Unsupported string features type.\n");
            return false;
    }

    return success;
}

bool CSGInterface::cmd_reshape()
{
    if (m_nrhs<4 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);
    int32_t num_feat=get_int_from_int_or_str();
    int32_t num_vec=get_int_from_int_or_str();

    bool success=ui_features->reshape(target, num_feat, num_vec);

    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_load_labels()
{
    if (m_nrhs<4 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);
    char* target=get_str_from_str_or_direct(len);

    bool success=ui_labels->load(filename, target);

    SG_FREE(filename);
    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_set_labels()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    int32_t tlen=0;
    char* target=get_string(tlen);
    if (!strmatch(target, "TRAIN") && !strmatch(target, "TEST"))
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }

    float64_t* lab=NULL;
    int32_t len=0;
    get_vector(lab, len);

    CLabels* labels=new CLabels(len);
    SG_INFO("num labels: %d\n", labels->get_num_labels());

    for (int32_t i=0; i<len; i++)
    {
        if (!labels->set_label(i, lab[i]))
            SG_ERROR("Couldn't set label %d (of %d): %f.\n", i, len, lab[i]);
    }
    SG_FREE(lab);

    if (strmatch(target, "TRAIN"))
        ui_labels->set_train_labels(labels);
    else if (strmatch(target, "TEST"))
        ui_labels->set_test_labels(labels);
    else
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }
    SG_FREE(target);

    return true;
}

bool CSGInterface::cmd_get_labels()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t tlen=0;
    char* target=get_string(tlen);
    CLabels* labels=NULL;

    if (strmatch(target, "TRAIN"))
        labels=ui_labels->get_train_labels();
    else if (strmatch(target, "TEST"))
        labels=ui_labels->get_test_labels();
    else
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }
    SG_FREE(target);

    if (!labels)
        SG_ERROR("No labels.\n");

    int32_t num_labels=labels->get_num_labels();
    float64_t* lab=SG_MALLOC(float64_t, num_labels);

    for (int32_t i=0; i<num_labels ; i++)
        lab[i]=labels->get_label(i);

    set_vector(lab, num_labels);
    SG_FREE(lab);

    return true;
}


bool CSGInterface::cmd_set_kernel_normalization()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* normalization=get_string(len);

    float64_t c=0;
    float64_t r=0;

    if (m_nrhs>=3)
        c=get_real();
    if (m_nrhs>=4)
        r=get_real();

    bool success=ui_kernel->set_normalization(normalization, c, r);

    SG_FREE(normalization);
    return success;
}

bool CSGInterface::cmd_set_kernel()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    SG_DEBUG("SGInterface: set_kernel\n");
    CKernel* kernel=create_kernel();
    return ui_kernel->set_kernel(kernel);
}

bool CSGInterface::cmd_add_kernel()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    float64_t weight=get_real_from_real_or_str();
    // adjust m_nrhs to play well with checks in create_kernel
    m_nrhs--;
    CKernel* kernel=create_kernel();

    SG_DEBUG("SGInterface: add_kernel\n");
    return ui_kernel->add_kernel(kernel, weight);
}

bool CSGInterface::cmd_del_last_kernel()
{
    if (m_nrhs<1 || !create_return_values(0))
        return false;

    return ui_kernel->del_last_kernel();
}

CKernel* CSGInterface::create_kernel()
{
    CKernel* kernel=NULL;
    int32_t len=0;
    char* type=get_str_from_str_or_direct(len);

    SG_DEBUG("set_kernel with type: %s\n", type);

    if (strmatch(type, "COMBINED"))
    {
        if (m_nrhs<3)
            return NULL;

        int32_t size=get_int_from_int_or_str();
        bool append_subkernel_weights=false;
        if (m_nrhs>3)
            append_subkernel_weights=get_bool_from_bool_or_str();

        kernel=ui_kernel->create_combined(size, append_subkernel_weights);
    }
    else if (strmatch(type, "DISTANCE"))
    {
        if (m_nrhs<3)
            return NULL;

        int32_t size=get_int_from_int_or_str();
        float64_t width=1;
        if (m_nrhs>3)
            width=get_real_from_real_or_str();

        kernel=ui_kernel->create_distance(size, width);
    }
    else if (strmatch(type, "WAVELET"))
    {
         
                if (m_nrhs<4)
                        return NULL;

                char* dtype=get_str_from_str_or_direct(len);
                if (strmatch(dtype, "REAL"))
                {
                        int32_t size=get_int_from_int_or_str();
                        float64_t Wdilation=5.0;
                        float64_t Wtranslation=2.0;

                        if (m_nrhs>4)
                        {
                                Wdilation=get_real_from_real_or_str();

                                if (m_nrhs>5)
                                        Wtranslation=get_real_from_real_or_str();
                        }

                        kernel=ui_kernel->create_sigmoid(size, Wdilation, Wtranslation);
                }

                SG_FREE(dtype);
        }
    else if (strmatch(type, "LINEAR"))
    {
        if (m_nrhs<4)
            return NULL;
        if (m_nrhs>5)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        int32_t size=get_int_from_int_or_str();
        float64_t scale=-1;
        if (m_nrhs==5)
            scale=get_real_from_real_or_str();

        if (strmatch(dtype, "BYTE"))
            kernel=ui_kernel->create_linearbyte(size, scale);
        else if (strmatch(dtype, "WORD"))
            kernel=ui_kernel->create_linearword(size, scale);
        else if (strmatch(dtype, "CHAR"))
            kernel=ui_kernel->create_linearstring(size, scale);
        else if (strmatch(dtype, "REAL"))
            kernel=ui_kernel->create_linear(size, scale);
        else if (strmatch(dtype, "SPARSEREAL"))
            kernel=ui_kernel->create_sparselinear(size, scale);

        SG_FREE(dtype);
    }
    else if (strmatch(type, "HISTOGRAM"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "WORD"))
        {
            int32_t size=get_int_from_int_or_str();
            kernel=ui_kernel->create_histogramword(size);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "SALZBERG"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "WORD"))
        {
            int32_t size=get_int_from_int_or_str();
            kernel=ui_kernel->create_salzbergword(size);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "POLYMATCH"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        int32_t size=get_int_from_int_or_str();
        int32_t degree=3;
        bool inhomogene=false;
        bool normalize=true;

        if (m_nrhs>4)
        {
            degree=get_int_from_int_or_str();
            if (m_nrhs>5)
            {
                inhomogene=get_bool_from_bool_or_str();
                if (m_nrhs>6)
                    normalize=get_bool_from_bool_or_str();
            }
        }

        if (strmatch(dtype, "CHAR"))
        {
            kernel=ui_kernel->create_polymatchstring(
                size, degree, inhomogene, normalize);
        }
        else if (strmatch(dtype, "WORD"))
        {
            kernel=ui_kernel->create_polymatchwordstring(
                size, degree, inhomogene, normalize);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "MATCH"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "WORD"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t d=3;
            bool normalize=true;

            if (m_nrhs>4)
                d=get_int_from_int_or_str();
            if (m_nrhs>5)
                normalize=get_bool_from_bool_or_str();

            kernel=ui_kernel->create_matchwordstring(size, d, normalize);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "WEIGHTEDCOMMSTRING") || strmatch(type, "COMMSTRING"))
    {
        char* dtype=get_str_from_str_or_direct(len);
        int32_t size=get_int_from_int_or_str();
        bool use_sign=false;
        char* norm_str=NULL;

        if (m_nrhs>4)
        {
             use_sign=get_bool_from_bool_or_str();

             if (m_nrhs>5)
                norm_str=get_str_from_str_or_direct(len);
        }

        if (strmatch(dtype, "WORD"))
        {
            if (strmatch(type, "WEIGHTEDCOMMSTRING"))
            {
                kernel=ui_kernel->create_commstring(
                    size, use_sign, norm_str, K_WEIGHTEDCOMMWORDSTRING);
            }
            else if (strmatch(type, "COMMSTRING"))
            {
                kernel=ui_kernel->create_commstring(
                    size, use_sign, norm_str, K_COMMWORDSTRING);
            }
        }
        else if (strmatch(dtype, "ULONG"))
        {
            kernel=ui_kernel->create_commstring(
                size, use_sign, norm_str, K_COMMULONGSTRING);
        }

        SG_FREE(dtype);
        SG_FREE(norm_str);
    }
    else if (strmatch(type, "CHI2"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "REAL"))
        {
            int32_t size=get_int_from_int_or_str();
            float64_t width=1;

            if (m_nrhs>4)
                width=get_real_from_real_or_str();

            kernel=ui_kernel->create_chi2(size, width);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "FIXEDDEGREE"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t d=3;
            if (m_nrhs>4)
                d=get_int_from_int_or_str();

            kernel=ui_kernel->create_fixeddegreestring(size, d);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "LOCALALIGNMENT"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR"))
        {
            int32_t size=get_int_from_int_or_str();

            kernel=ui_kernel->create_localalignmentstring(size);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "OLIGO"))
    {
        if (m_nrhs<6)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t k=get_int_from_int_or_str();
            float64_t w=get_real_from_real_or_str();

            kernel=ui_kernel->create_oligo(size, k, w);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "WEIGHTEDDEGREEPOS2") ||
        strmatch(type, "WEIGHTEDDEGREEPOS2_NONORM"))
    {
        if (m_nrhs<7)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR") || strmatch(dtype, "STRING"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t order=get_int_from_int_or_str();
            int32_t max_mismatch=get_int_from_int_or_str();
            int32_t length=get_int_from_int_or_str();
            int32_t* shifts=NULL;
            int32_t l=0;
            get_vector_from_int_vector_or_str(shifts, l);

            ASSERT(l==length);

            bool use_normalization=true;
            if (strmatch(type, "WEIGHTEDDEGREEPOS2_NONORM"))
                use_normalization=false;

            kernel=ui_kernel->create_weighteddegreepositionstring2(
                size, order, max_mismatch, shifts, length,
                use_normalization);

            SG_FREE(shifts);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "WEIGHTEDDEGREEPOS3"))
    {
        if (m_nrhs<7)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR") || strmatch(dtype, "STRING"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t order=get_int_from_int_or_str();
            int32_t max_mismatch=get_int_from_int_or_str();
            int32_t length=get_int_from_int_or_str();
            int32_t mkl_stepsize=get_int_from_int_or_str();
            int32_t* shifts=NULL;
            int32_t l=0;
            get_vector_from_int_vector_or_str(shifts, l);
            ASSERT(l==length);

            float64_t* position_weights=NULL;
            if (m_nrhs>9+length)
            {
                get_vector_from_real_vector_or_str(
                    position_weights, length);
            }

            kernel=ui_kernel->create_weighteddegreepositionstring3(
                size, order, max_mismatch, shifts, length,
                mkl_stepsize, position_weights);

            SG_FREE(position_weights);
            SG_FREE(shifts);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "WEIGHTEDDEGREEPOS"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR") || strmatch(dtype, "STRING"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t order=3;
            int32_t max_mismatch=0;
            int32_t length=0;
            int32_t center=0;
            float64_t step=1;

            if (m_nrhs>4)
            {
                order=get_int_from_int_or_str();

                if (m_nrhs>5)
                {
                    max_mismatch=get_int_from_int_or_str();

                    if (m_nrhs>6)
                    {
                        length=get_int_from_int_or_str();

                        if (m_nrhs>7)
                        {
                            center=get_int_from_int_or_str();

                            if (m_nrhs>8)
                                step=get_real_from_real_or_str();
                        }
                    }
                }
            }

            kernel=ui_kernel->create_weighteddegreepositionstring(
                size, order, max_mismatch, length, center, step);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "WEIGHTEDDEGREE"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR") || strmatch(dtype, "STRING"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t order=3;
            int32_t max_mismatch=0;
            bool use_normalization=true;
            int32_t mkl_stepsize=1;
            bool block_computation=true;
            int32_t single_degree=-1;

            if (m_nrhs>4)
            {
                order=get_int_from_int_or_str();

                if (m_nrhs>5)
                {
                    max_mismatch=get_int_from_int_or_str();

                    if (m_nrhs>6)
                    {
                        use_normalization=get_bool_from_bool_or_str();

                        if (m_nrhs>7)
                        {
                            mkl_stepsize=get_int_from_int_or_str();

                            if (m_nrhs>8)
                            {
                                block_computation=get_int_from_int_or_str();

                                if (m_nrhs>9)
                                    single_degree=get_int_from_int_or_str();
                            }
                        }
                    }
                }
            }

            kernel=ui_kernel->create_weighteddegreestring(
                size, order, max_mismatch, use_normalization,
                mkl_stepsize, block_computation, single_degree);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "WEIGHTEDDEGREERBF"))
    {
        if (m_nrhs<5)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        int32_t size=get_int_from_int_or_str();
        int32_t nof_properties=get_int_from_int_or_str();
        int32_t degree=1;
        float64_t width=1;
        if (m_nrhs>5)
        {
            degree=get_int_from_int_or_str();
            if (m_nrhs>6)
            {
                width=get_real_from_real_or_str();
            }

        }
        //if (strmatch(dtype, "REAL"))
        
        kernel=ui_kernel->create_weighteddegreerbf(size, degree, nof_properties, width);

        SG_FREE(dtype);

    }
    else if (strmatch(type, "SPECTRUMMISMATCHRBF"))
    {
        if (m_nrhs<7)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR") || strmatch(dtype, "STRING"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t degree=get_int_from_int_or_str();
            int32_t max_mismatch=get_int_from_int_or_str();
            float64_t width=get_real_from_real_or_str();
            float64_t* AA_matrix = NULL;

            //int32_t length=128*128;
            //get_vector_from_real_vector_or_str(AA_matrix, length);
            float64_t* helper_matrix=NULL;
            int32_t N=0;
            int32_t M=0;
            get_matrix(helper_matrix, N, M);

            if (N == 128 && M == 128)
            {
                AA_matrix=SG_MALLOC(float64_t, N*M);
                memcpy(AA_matrix, helper_matrix, N*M*sizeof(float64_t)) ;
                kernel=ui_kernel->create_spectrummismatchrbf(size, AA_matrix, max_mismatch, degree, width);
            }
            else
            {
                SG_ERROR("Matrix size %d %d\n", N, M);
            }
        }
        SG_FREE(dtype);

    }

    else if (strmatch(type, "SLIK") || strmatch(type, "LIK"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "CHAR"))
        {
            int32_t size=get_int_from_int_or_str();
            int32_t length=3;
            int32_t inner_degree=3;
            int32_t outer_degree=1;

            if (m_nrhs>4)
            {
                length=get_int_from_int_or_str();

                if (m_nrhs>5)
                {
                    inner_degree=get_int_from_int_or_str();

                    if (m_nrhs>6)
                        outer_degree=get_int_from_int_or_str();
                }
            }

            if (strmatch(type, "SLIK"))
            {
                kernel=ui_kernel->create_localityimprovedstring(
                    size, length, inner_degree, outer_degree,
                    K_SIMPLELOCALITYIMPROVED);
            }
            else
            {
                kernel=ui_kernel->create_localityimprovedstring(
                    size, length, inner_degree, outer_degree,
                    K_LOCALITYIMPROVED);
            }
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "POLY"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        int32_t size=get_int_from_int_or_str();
        int32_t degree=2;
        bool inhomogene=false;
        bool normalize=true;

        if (m_nrhs>4)
        {
            degree=get_int_from_int_or_str();

            if (m_nrhs>5)
            {
                inhomogene=get_bool_from_bool_or_str();

                if (m_nrhs>6)
                    normalize=get_bool_from_bool_or_str();
            }
        }

        if (strmatch(dtype, "REAL"))
        {
            kernel=ui_kernel->create_poly(
                size, degree, inhomogene, normalize);
        }
        else if (strmatch(dtype, "SPARSEREAL"))
        {
            kernel=ui_kernel->create_sparsepoly(
                size, degree, inhomogene, normalize);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "SIGMOID"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "REAL"))
        {
            int32_t size=get_int_from_int_or_str();
            float64_t gamma=0.01;
            float64_t coef0=0;

            if (m_nrhs>4)
            {
                gamma=get_real_from_real_or_str();

                if (m_nrhs>5)
                    coef0=get_real_from_real_or_str();
            }

            kernel=ui_kernel->create_sigmoid(size, gamma, coef0);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "GAUSSIAN")) // RBF
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        int32_t size=get_int_from_int_or_str();
        float64_t width=1;
        if (m_nrhs>4)
            width=get_real_from_real_or_str();

        if (strmatch(dtype, "REAL"))
            kernel=ui_kernel->create_gaussian(size, width);
        else if (strmatch(dtype, "SPARSEREAL"))
            kernel=ui_kernel->create_sparsegaussian(size, width);

        SG_FREE(dtype);
    }
    else if (strmatch(type, "GAUSSIANSHIFT")) // RBF
    {
        if (m_nrhs<7)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "REAL"))
        {
            int32_t size=get_int_from_int_or_str();
            float64_t width=get_real_from_real_or_str();
            int32_t max_shift=get_int_from_int_or_str();
            int32_t shift_step=get_int_from_int_or_str();

            kernel=ui_kernel->create_gaussianshift(
                size, width, max_shift, shift_step);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "CUSTOM"))
    {
        if (m_nrhs!=4 || !create_return_values(0))
            return false;

        float64_t* kmatrix=NULL;
        int32_t num_feat=0;
        int32_t num_vec=0;
        get_matrix(kmatrix, num_feat, num_vec);

        int32_t tlen=0;
        char* ktype=get_string(tlen);

        if (!strmatch(ktype, "DIAG") &&
                !strmatch(ktype, "FULL") &&
                !strmatch(ktype, "FULL2DIAG"))
        {
            SG_FREE(ktype);
            SG_ERROR("Undefined type, not DIAG, FULL or FULL2DIAG.\n");
        }

        bool source_is_diag=false;
        bool dest_is_diag=false;

        if (strmatch(ktype, "FULL2DIAG"))
            dest_is_diag=true;
        else if (strmatch(ktype, "DIAG"))
        {
            source_is_diag=true;
            dest_is_diag=true;
        }

        kernel=ui_kernel->create_custom(kmatrix, num_feat, num_vec,
                source_is_diag, dest_is_diag);
    }
    else if (strmatch(type, "CONST"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "REAL"))
        {
            int32_t size=get_int_from_int_or_str();
            float64_t c=1;
            if (m_nrhs>4)
                c=get_real_from_real_or_str();

            kernel=ui_kernel->create_const(size, c);
        }

        SG_FREE(dtype);
    }
    else if (strmatch(type, "DIAG"))
    {
        if (m_nrhs<4)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "REAL"))
        {
            int32_t size=get_int_from_int_or_str();
            float64_t diag=1;
            if (m_nrhs>4)
                diag=get_real_from_real_or_str();

            kernel=ui_kernel->create_diag(size, diag);
        }

        SG_FREE(dtype);
    }

    else if (strmatch(type, "TPPK"))
    {
        if (m_nrhs!=5)
            return NULL;

        char* dtype=get_str_from_str_or_direct(len);
        if (strmatch(dtype, "INT"))
        {
            int32_t size=get_int_from_int_or_str();
            float64_t* km=NULL;
            int32_t rows=0;
            int32_t cols=0;
            get_matrix(km, rows, cols);
            kernel=ui_kernel->create_tppk(size, km, rows, cols);
        }

        SG_FREE(dtype);
    }
    else
        SG_NOTIMPLEMENTED;

    SG_FREE(type);
    SG_DEBUG("created kernel: %p\n", kernel);
    return kernel;
}


CFeatures* CSGInterface::create_custom_string_features(CStringFeatures<uint8_t>* orig_feat)
{
    CFeatures* feat=orig_feat;

    if (m_nrhs>4)
    {
        int32_t start=-1;
        int32_t order=0;
        int32_t from_order=0;
        bool normalize=true;

        int32_t feature_class_len=0;
        char* feature_class_str=get_string(feature_class_len);
        ASSERT(feature_class_str);
        CAlphabet* alphabet=NULL;
        if (strmatch(feature_class_str, "WD"))
        {
            if (m_nrhs!=7)
                SG_ERROR("Please specify alphabet, WD, order, from_order\n");

            alphabet=new CAlphabet(RAWDNA);
            order=get_int();
            from_order=get_int();
            feat = new CWDFeatures((CStringFeatures<uint8_t>*) feat, order, from_order);
        }
        else if (strmatch(feature_class_str, "WSPEC"))
        {
            if (m_nrhs!=8)
                SG_ERROR("Please specify alphabet, order, WSPEC, start, normalize\n");

            alphabet=new CAlphabet(RAWDNA);
            order=get_int();
            start=get_int();
            normalize=get_bool();
            CStringFeatures<uint16_t>* sf=new CStringFeatures<uint16_t>(RAWDNA);
            sf->obtain_from_char_features((CStringFeatures<uint8_t>*) feat, start, order, 0, normalize);
            sf->add_preprocessor(new CSortWordString());
            sf->apply_preprocessor();
            SG_UNREF(feat);
            feat = new CImplicitWeightedSpecFeatures(sf, normalize);
        }
        SG_FREE(feature_class_str);

        SG_UNREF(alphabet);
    }

    return feat;
}

CFeatures* CSGInterface::create_custom_real_features(CSimpleFeatures<float64_t>* orig_feat)
{
    CFeatures* feat=orig_feat;

    if (m_nrhs==6)
    {
        int32_t degree=0;
        int32_t feature_class_len=0;
        bool normalize;
        char* feature_class_str=get_string(feature_class_len);
        ASSERT(feature_class_str);
        if (strmatch(feature_class_str, "POLY"))
        {
            //if (m_nrhs!=7)
            //  SG_ERROR("Please specify POLY, degree\n");

            degree=get_int();
            normalize = get_bool();
            feat = new CPolyFeatures((CSimpleFeatures<float64_t>*) feat, degree, normalize);

        }
        else    
            SG_ERROR("Unknown feature class: %s\n", feature_class_str);

        SG_FREE(feature_class_str);
    }

    return feat;
}

bool CSGInterface::cmd_init_kernel()
{
    SG_DEPRECATED;
    return true;
}

bool CSGInterface::cmd_clean_kernel()
{
    if (m_nrhs<1 || !create_return_values(0))
        return false;

    return ui_kernel->clean_kernel();
}

bool CSGInterface::cmd_save_kernel()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool success=ui_kernel->save_kernel(filename);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_get_kernel_matrix()
{
    if (m_nrhs>2 || !create_return_values(1))
        return false;

    int32_t len=0;
    char* target=NULL;
    
    if (m_nrhs==2)
        target=get_string(len);
    bool success=ui_kernel->init_kernel(target);

    if (success)
    {
        CKernel* kernel=ui_kernel->get_kernel();
        if (!kernel || !kernel->has_features())
            SG_ERROR("No kernel defined or not initialized.\n");

        SGMatrix<float64_t> km=kernel->get_kernel_matrix<float64_t>();
        set_matrix(km.matrix, km.num_rows, km.num_cols);
    }

    SG_FREE(target);

    return success;
}

bool CSGInterface::cmd_set_WD_position_weights()
{
    if (m_nrhs<2 || m_nrhs>3 || !create_return_values(0))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");

    if (kernel->get_kernel_type()==K_COMBINED)
    {
        kernel=((CCombinedKernel*) kernel)->get_last_kernel();
        if (!kernel)
            SG_ERROR("No last kernel.\n");

        EKernelType ktype=kernel->get_kernel_type();
        if (ktype!=K_WEIGHTEDDEGREE && ktype!=K_WEIGHTEDDEGREEPOS)
            SG_ERROR("Unsupported kernel.\n");
    }

    bool success=false;
    float64_t* weights=NULL;
    int32_t dim=0;
    int32_t len=0;
    get_matrix(weights, dim, len);

    if (kernel->get_kernel_type()==K_WEIGHTEDDEGREE)
    {
        CWeightedDegreeStringKernel* k=
            (CWeightedDegreeStringKernel*) kernel;

        if (dim!=1 && len>0)
            SG_ERROR("Dimension mismatch (should be 1 x seq_length or 0x0\n");

        ui_kernel->init_kernel("TRAIN");
        success=k->set_position_weights(weights, len);
    }
    else
    {
        CWeightedDegreePositionStringKernel* k=
            (CWeightedDegreePositionStringKernel*) kernel;
        char* target=NULL;
        bool is_train=true;

        if (m_nrhs==3)
        {
            int32_t tlen=0;
            target=get_string(tlen);
            if (!target)
            {
                SG_FREE(weights);
                SG_ERROR("Couldn't find second argument to method.\n");
            }

            if (!strmatch(target, "TRAIN") && !strmatch(target, "TEST"))
            {
                SG_FREE(target);
                SG_ERROR("Second argument none of TRAIN or TEST.\n");
            }

            if (strmatch(target, "TEST"))
                is_train=false;
        }
        
        if (dim!=1 && len>0)
        {
            SG_FREE(target);
            SG_ERROR("Dimension mismatch (should be 1 x seq_length or 0x0\n");
            }

        if (dim==0 && len==0)
        {
            if (create_return_values(3))
            {
                if (is_train)
                    success=k->delete_position_weights_lhs();
                else
                    success=k->delete_position_weights_rhs();
            }
            else
                success=k->delete_position_weights();
        }
        else
        {
            if (create_return_values(3))
            {
                if (is_train)
                    success=k->set_position_weights_lhs(weights, dim, len);
                else
                    success=k->set_position_weights_rhs(weights, dim, len);
            }
            else
            {
                ui_kernel->init_kernel("TRAIN");
                k->set_position_weights(SGVector<float64_t>(weights, len));
                success=true;
            }
        }

        SG_FREE(target);
    }

    return success;
}

bool CSGInterface::cmd_get_subkernel_weights()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CKernel *kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("Invalid kernel.\n");

    EKernelType ktype=kernel->get_kernel_type();
    const float64_t* weights=NULL;

    if (ktype==K_COMBINED)
    {
        int32_t num_weights=-1;
        weights=((CCombinedKernel *) kernel)->get_subkernel_weights(num_weights);

        // matrices of shape 1 x num_weight are returned
        set_matrix(weights, 1, num_weights);
        return true;
    }

    int32_t degree=-1;
    int32_t length=-1;

    if (ktype==K_WEIGHTEDDEGREE)
    {
        weights=((CWeightedDegreeStringKernel *) kernel)->
            get_degree_weights(degree, length);
    }
    else if (ktype==K_WEIGHTEDDEGREEPOS)
    {
        weights=((CWeightedDegreePositionStringKernel *) kernel)->
            get_degree_weights(degree, length);
    }
    else
        SG_ERROR("Setting subkernel weights not supported on this kernel.\n");

    if (length==0)
        length=1;

    set_matrix(weights, degree, length);
    return true;
}

bool CSGInterface::cmd_set_subkernel_weights()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");

    bool success=false;
    float64_t* weights=NULL;
    int32_t dim=0;
    int32_t len=0;
    get_matrix(weights, dim, len);

    EKernelType ktype=kernel->get_kernel_type();
    if (ktype==K_WEIGHTEDDEGREE)
    {
        CWeightedDegreeStringKernel* k=
            (CWeightedDegreeStringKernel*) kernel;
        int32_t degree=k->get_degree();
        if (dim!=degree || len<1)
            SG_ERROR("WD: Dimension mismatch (should be (seq_length | 1) x degree) got (%d x %d)\n", len, degree);

        if (len==1)
            len=0;

        success=k->set_weights(SGMatrix<float64_t>(weights, dim, len));
    }
    else if (ktype==K_WEIGHTEDDEGREEPOS)
    {
        CWeightedDegreePositionStringKernel* k=
            (CWeightedDegreePositionStringKernel*) kernel;
        int32_t degree=k->get_degree();
        if (dim!=degree || len<1)
            SG_ERROR("WDPos: Dimension mismatch (should be (seq_length | 1) x degree) got (%d x %d)\n", len, degree);

        if (len==1)
            len=0;

        success=k->set_weights(SGMatrix<float64_t>(weights, dim, len));
    }
    else // all other kernels
    {
        int32_t num_subkernels=kernel->get_num_subkernels();
        if (dim!=1 || len!=num_subkernels)
            SG_ERROR("All: Dimension mismatch (should be 1 x num_subkernels)\n");

        kernel->set_subkernel_weights(SGVector<float64_t>(weights, len));
        success=true;
    }

    return success;
}

bool CSGInterface::cmd_set_subkernel_weights_combined()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");
    if (kernel->get_kernel_type()!=K_COMBINED)
        SG_ERROR("Only works for combined kernels.\n");

    bool success=false;
    float64_t* weights=NULL;
    int32_t dim=0;
    int32_t len=0;
    get_matrix(weights, dim, len);

    int32_t idx=get_int();
    SG_DEBUG("using kernel_idx=%i\n", idx);

    kernel=((CCombinedKernel*) kernel)->get_kernel(idx);
    if (!kernel)
        SG_ERROR("No subkernel at idx %d.\n", idx);

    EKernelType ktype=kernel->get_kernel_type();
    if (ktype==K_WEIGHTEDDEGREE)
    {
        CWeightedDegreeStringKernel* k=
            (CWeightedDegreeStringKernel*) kernel;
        int32_t degree=k->get_degree();
        if (dim!=degree || len<1)
            SG_ERROR("Dimension mismatch (should be de(seq_length | 1) x degree)\n");

        if (len==1)
            len=0;

        success=k->set_weights(SGMatrix<float64_t>(weights, dim, len));
    }
    else if (ktype==K_WEIGHTEDDEGREEPOS)
    {
        CWeightedDegreePositionStringKernel* k=
            (CWeightedDegreePositionStringKernel*) kernel;
        int32_t degree=k->get_degree();
        if (dim!=degree || len<1)
            SG_ERROR("Dimension mismatch (should be de(seq_length | 1) x degree)\n");

        if (len==1)
            len=0;

        success=k->set_weights(SGMatrix<float64_t>(weights, dim, len));
    }
    else // all other kernels
    {
        int32_t num_subkernels=kernel->get_num_subkernels();
        if (dim!=1 || len!=num_subkernels)
            SG_ERROR("Dimension mismatch (should be 1 x num_subkernels)\n");

        kernel->set_subkernel_weights(SGVector<float64_t>(weights, len));
        success=true;
    }

    return success;
}

bool CSGInterface::cmd_get_dotfeature_weights_combined()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t tlen=0;
    char* target=get_string(tlen);
    CFeatures* features=NULL;

    if (strmatch(target, "TRAIN"))
        features=ui_features->get_train_features();
    else if (strmatch(target, "TEST"))
        features=ui_features->get_test_features();
    else
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }
    SG_FREE(target);

    if (!features)
        SG_ERROR("No features.\n");
    if (features->get_feature_class()!=C_COMBINED_DOT)
        SG_ERROR("Only works for combined dot features.\n");

    float64_t* weights=NULL;
    int32_t len=0;
    ((CCombinedDotFeatures*) features)->get_subfeature_weights(&weights, &len);
    set_vector(weights, len);
    SG_FREE(weights);

    return true;
}

bool CSGInterface::cmd_set_dotfeature_weights_combined()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    int32_t tlen=0;
    char* target=get_string(tlen);
    CFeatures* features=NULL;

    if (strmatch(target, "TRAIN"))
        features=ui_features->get_train_features();
    else if (strmatch(target, "TEST"))
        features=ui_features->get_test_features();
    else
    {
        SG_FREE(target);
        SG_ERROR("Unknown target, neither TRAIN nor TEST.\n");
    }
    SG_FREE(target);

    if (!features)
        SG_ERROR("No features.\n");
    if (features->get_feature_class()!=C_COMBINED_DOT)
        SG_ERROR("Only works for combined dot features.\n");

    float64_t* weights=NULL;
    int32_t dim=0;
    int32_t len=0;
    get_matrix(weights, dim, len);

    ((CCombinedDotFeatures*) features)->set_subfeature_weights(weights, len);

    return true;
}

bool CSGInterface::cmd_set_last_subkernel_weights()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");
    if (kernel->get_kernel_type()!=K_COMBINED)
        SG_ERROR("Only works for Combined kernels.\n");

    kernel=((CCombinedKernel*) kernel)->get_last_kernel();
    if (!kernel)
        SG_ERROR("No last kernel.\n");

    bool success=false;
    float64_t* weights=NULL;
    int32_t dim=0;
    int32_t len=0;
    get_matrix(weights, dim, len);

    EKernelType ktype=kernel->get_kernel_type();
    if (ktype==K_WEIGHTEDDEGREE)
    {
        CWeightedDegreeStringKernel* k=(CWeightedDegreeStringKernel*) kernel;
        if (dim!=k->get_degree() || len<1)
            SG_ERROR("Dimension mismatch (should be de(seq_length | 1) x degree)\n");

        if (len==1)
            len=0;

        success=k->set_weights(SGMatrix<float64_t>(weights, dim, len));
    }
    else if (ktype==K_WEIGHTEDDEGREEPOS)
    {
        CWeightedDegreePositionStringKernel* k=
            (CWeightedDegreePositionStringKernel*) kernel;
        if (dim!=k->get_degree() || len<1)
            SG_ERROR("Dimension mismatch (should be de(seq_length | 1) x degree)\n");

        if (len==1)
            len=0;

        success=k->set_weights(SGMatrix<float64_t>(weights, dim, len));
    }
    else // all other kernels
    {
        int32_t num_subkernels=kernel->get_num_subkernels();
        if (dim!=1 || len!=num_subkernels)
            SG_ERROR("Dimension mismatch (should be 1 x num_subkernels)\n");

        kernel->set_subkernel_weights(SGVector<float64_t>(weights, len));
        success=true;
    }

    return success;
}

bool CSGInterface::cmd_get_WD_position_weights()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");

    if (kernel->get_kernel_type()==K_COMBINED)
    {
        kernel=((CCombinedKernel*) kernel)->get_last_kernel();
        if (!kernel)
            SG_ERROR("Couldn't find last kernel.\n");

        EKernelType ktype=kernel->get_kernel_type();
        if (ktype!=K_WEIGHTEDDEGREE && ktype!=K_WEIGHTEDDEGREEPOS)
            SG_ERROR("Wrong subkernel type.\n");
    }

    int32_t len=0;
    const float64_t* position_weights;

    if (kernel->get_kernel_type()==K_WEIGHTEDDEGREE)
        position_weights=((CWeightedDegreeStringKernel*) kernel)->get_position_weights(len);
    else
        position_weights=((CWeightedDegreePositionStringKernel*) kernel)->get_position_weights(len);

    if (position_weights==NULL)
        set_vector(position_weights, 0);
    else
        set_vector(position_weights, len);

    return true;
}

bool CSGInterface::cmd_get_last_subkernel_weights()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    EKernelType ktype=kernel->get_kernel_type();
    if (!kernel)
        SG_ERROR("No kernel.\n");
    if (ktype!=K_COMBINED)
        SG_ERROR("Only works for Combined kernels.\n");

    kernel=((CCombinedKernel*) kernel)->get_last_kernel();
    if (!kernel)
        SG_ERROR("Couldn't find last kernel.\n");

    int32_t degree=0;
    int32_t len=0;

    if (ktype==K_COMBINED)
    {
        int32_t num_weights=0;
        const float64_t* weights=
            ((CCombinedKernel*) kernel)->get_subkernel_weights(num_weights);

        set_vector(weights, num_weights);
        return true;
    }

    float64_t* weights=NULL;
    if (ktype==K_WEIGHTEDDEGREE)
        weights=((CWeightedDegreeStringKernel*) kernel)->
            get_degree_weights(degree, len);
    else if (ktype==K_WEIGHTEDDEGREEPOS)
        weights=((CWeightedDegreePositionStringKernel*) kernel)->
            get_degree_weights(degree, len);
    else
        SG_ERROR("Only works for Weighted Degree (Position) kernels.\n");

    if (len==0)
        len=1;

    set_matrix(weights, degree, len);

    return true;
}

bool CSGInterface::cmd_compute_by_subkernels()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");
    if (!kernel->get_rhs())
        SG_ERROR("No rhs.\n");

    int32_t num_vec=kernel->get_rhs()->get_num_vectors();
    int32_t degree=0;
    int32_t len=0;
    EKernelType ktype=kernel->get_kernel_type();

    // it would be nice to have a common base class for the WD kernels
    if (ktype==K_WEIGHTEDDEGREE)
    {
        CWeightedDegreeStringKernel* k=(CWeightedDegreeStringKernel*) kernel;
        k->get_degree_weights(degree, len);
        if (!k->is_tree_initialized())
            SG_ERROR("Kernel optimization not initialized.\n");
    }
    else if (ktype==K_WEIGHTEDDEGREEPOS)
    {
        CWeightedDegreePositionStringKernel* k=
            (CWeightedDegreePositionStringKernel*) kernel;
        k->get_degree_weights(degree, len);
        if (!k->is_tree_initialized())
            SG_ERROR("Kernel optimization not initialized.\n");
    }
    else
        SG_ERROR("Only works for Weighted Degree (Position) kernels.\n");

    if (len==0)
        len=1;

    int32_t num_feat=degree*len;
    int32_t num=num_feat*num_vec;
    float64_t* result=SG_MALLOC(float64_t, num);

    for (int32_t i=0; i<num; i++)
        result[i]=0;

    if (ktype==K_WEIGHTEDDEGREE)
    {
        CWeightedDegreeStringKernel* k=(CWeightedDegreeStringKernel*) kernel;
        for (int32_t i=0; i<num_vec; i++)
            k->compute_by_tree(i, &result[i*num_feat]);
    }
    else
    {
        CWeightedDegreePositionStringKernel* k=
            (CWeightedDegreePositionStringKernel*) kernel;
        for (int32_t i=0; i<num_vec; i++)
            k->compute_by_tree(i, &result[i*num_feat]);
    }

    set_matrix(result, num_feat, num_vec);
    SG_FREE(result);

    return true;
}

bool CSGInterface::cmd_init_kernel_optimization()
{
    if (m_nrhs<1 || !create_return_values(0))
        return false;

    return ui_kernel->init_kernel_optimization();
}

bool CSGInterface::cmd_get_kernel_optimization()
{
    if (m_nrhs<1 || !create_return_values(1))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel defined.\n");

    switch (kernel->get_kernel_type())
    {
        case K_WEIGHTEDDEGREEPOS:
        {
            if (m_nrhs!=2)
                SG_ERROR("parameter missing\n");

            int32_t max_order=get_int();
            if ((max_order<1) || (max_order>12))
            {
                SG_WARNING( "max_order out of range 1..12 (%d). setting to 1\n", max_order);
                max_order=1;
            }

            CWeightedDegreePositionStringKernel* k=(CWeightedDegreePositionStringKernel*) kernel;
            CSVM* svm=(CSVM*) ui_classifier->get_classifier();
            if (!svm)
                SG_ERROR("No SVM defined.\n");

            int32_t num_suppvec=svm->get_num_support_vectors();
            int32_t* sv_idx=SG_MALLOC(int32_t, num_suppvec);
            float64_t* sv_weight=SG_MALLOC(float64_t, num_suppvec);
            int32_t num_feat=0;
            int32_t num_sym=0;

            for (int32_t i=0; i<num_suppvec; i++)
            {
                sv_idx[i]=svm->get_support_vector(i);
                sv_weight[i]=svm->get_alpha(i);
            }

            float64_t* position_weights=k->extract_w(max_order, num_feat,
                num_sym, NULL, num_suppvec, sv_idx, sv_weight);
            SG_FREE(sv_idx);
            SG_FREE(sv_weight);

            set_matrix(position_weights, num_sym, num_feat);
            SG_FREE(position_weights);

            return true;
        }

        case K_COMMWORDSTRING:
        case K_WEIGHTEDCOMMWORDSTRING:
        {
            CCommWordStringKernel* k=(CCommWordStringKernel*) kernel;
            int32_t len=0;
            float64_t* weights;
            k->get_dictionary(len, weights);

            set_vector(weights, len);
            return true;
        }
        case K_LINEAR:
        {
            CLinearKernel* k=(CLinearKernel*) kernel;
            int32_t len=0;
            const float64_t* weights=k->get_normal(len);

            set_vector(weights, len);
            return true;
        }
        default:
            SG_ERROR("Unsupported kernel %s.\n", kernel->get_name());
    }

    return true;
}

bool CSGInterface::cmd_delete_kernel_optimization()
{
    if (m_nrhs<1 || !create_return_values(0))
        return false;

    return ui_kernel->delete_kernel_optimization();
}

bool CSGInterface::cmd_use_diagonal_speedup()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    bool speedup=get_bool();

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel defined.\n");

    if (kernel->get_kernel_type()==K_COMBINED)
    {
        SG_DEBUG("Identified combined kernel.\n");
        kernel=((CCombinedKernel*) kernel)->get_last_kernel();
        if (!kernel)
            SG_ERROR("No last kernel defined.\n");
    }

    if (kernel->get_kernel_type()!=K_COMMWORDSTRING)
        SG_ERROR("Currently only commwordstring kernel supports diagonal speedup\n");

    ((CCommWordStringKernel*) kernel)->set_use_dict_diagonal_optimization(speedup);

    SG_INFO("Diagonal speedup %s.\n", speedup ? "enabled" : "disabled");

    return true;
}

bool CSGInterface::cmd_set_kernel_optimization_type()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* opt_type=get_str_from_str_or_direct(len);

    bool success=ui_kernel->set_optimization_type(opt_type);

    SG_FREE(opt_type);
    return success;
}

bool CSGInterface::cmd_set_solver()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* solver=get_str_from_str_or_direct(len);

    bool success=ui_classifier->set_solver(solver);

    SG_FREE(solver);
    return success;
}

bool CSGInterface::cmd_set_constraint_generator()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* cg=get_str_from_str_or_direct(len);

    bool success=ui_classifier->set_constraint_generator(cg);

    SG_FREE(cg);
    return success;
}

bool CSGInterface::cmd_set_prior_probs()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    CSalzbergWordStringKernel* kernel=
        (CSalzbergWordStringKernel*) ui_kernel->get_kernel();
    if (kernel->get_kernel_type()!=K_SALZBERG)
        SG_ERROR("SalzbergWordStringKernel required for setting prior probs!\n");

    float64_t pos_probs=get_real_from_real_or_str();
    float64_t neg_probs=get_real_from_real_or_str();

    kernel->set_prior_probs(pos_probs, neg_probs);

    return true;
}

bool CSGInterface::cmd_set_prior_probs_from_labels()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    CSalzbergWordStringKernel* kernel=
        (CSalzbergWordStringKernel*) ui_kernel->get_kernel();
    if (kernel->get_kernel_type()!=K_SALZBERG)
    SG_ERROR("SalzbergWordStringKernel required for setting prior probs!\n");

    float64_t* lab=NULL;
    int32_t len=0;
    get_vector(lab, len);

    CLabels* labels=new CLabels(len);
    for (int32_t i=0; i<len; i++)
    {
        if (!labels->set_label(i, lab[i]))
            SG_ERROR("Couldn't set label %d (of %d): %f.\n", i, len, lab[i]);
    }
    SG_FREE(lab);

    kernel->set_prior_probs_from_labels(labels);

    SG_UNREF(labels);
    return true;
}

#ifdef USE_SVMLIGHT
bool CSGInterface::cmd_resize_kernel_cache()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t size=get_int_from_int_or_str();
    return ui_kernel->resize_kernel_cache(size);
}
#endif //USE_SVMLIGHT


bool CSGInterface::cmd_set_distance()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    CDistance* distance=NULL;
    int32_t len=0;
    char* type=get_str_from_str_or_direct(len);
    char* dtype=get_str_from_str_or_direct(len);

    if (strmatch(type, "MINKOWSKI") && m_nrhs==4)
    {
        float64_t k=get_real_from_real_or_str();
        distance=ui_distance->create_minkowski(k);
    }
    else if (strmatch(type, "MANHATTAN"))
    {
        if (strmatch(dtype, "REAL"))
            distance=ui_distance->create_generic(D_MANHATTAN);
        else if (strmatch(dtype, "WORD"))
            distance=ui_distance->create_generic(D_MANHATTANWORD);
    }
    else if (strmatch(type, "HAMMING") && strmatch(dtype, "WORD"))
    {
        bool use_sign=false;
        if (m_nrhs==4)
            use_sign=get_bool_from_bool_or_str(); // optional

        distance=ui_distance->create_hammingword(use_sign);
    }
    else if (strmatch(type, "CANBERRA"))
    {
        if (strmatch(dtype, "REAL"))
            distance=ui_distance->create_generic(D_CANBERRA);
        else if (strmatch(dtype, "WORD"))
            distance=ui_distance->create_generic(D_CANBERRAWORD);
    }
    else if (strmatch(type, "CHEBYSHEW") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_CHEBYSHEW);
    }
    else if (strmatch(type, "GEODESIC") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_GEODESIC);
    }
    else if (strmatch(type, "JENSEN") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_JENSEN);
    }
    else if (strmatch(type, "CHISQUARE") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_CHISQUARE);
    }
    else if (strmatch(type, "TANIMOTO") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_TANIMOTO);
    }
    else if (strmatch(type, "COSINE") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_COSINE);
    }
    else if (strmatch(type, "BRAYCURTIS") && strmatch(dtype, "REAL"))
    {
        distance=ui_distance->create_generic(D_BRAYCURTIS);
    }
    else if (strmatch(type, "EUCLIDIAN"))
    {
        if (strmatch(dtype, "REAL"))
            distance=ui_distance->create_generic(D_EUCLIDIAN);
        else if (strmatch(dtype, "SPARSEREAL"))
            distance=ui_distance->create_generic(D_SPARSEEUCLIDIAN);
    }
    else
        SG_NOTIMPLEMENTED;

    SG_FREE(type);
    SG_FREE(dtype);
    return ui_distance->set_distance(distance);
}

bool CSGInterface::cmd_init_distance()
{
    SG_DEPRECATED;
    return true;
}

bool CSGInterface::cmd_get_distance_matrix()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t len=0;
    char* target=get_string(len);

    bool success=ui_distance->init_distance(target);

    if (success)
    {
        CDistance* distance=ui_distance->get_distance();
        if (!distance || !distance->has_features())
            SG_ERROR("No distance defined or not initialized.\n");

        int32_t num_vec_lhs=0;
        int32_t num_vec_rhs=0;
        float64_t* dmatrix=NULL;
        dmatrix=distance->get_distance_matrix_real(num_vec_lhs, num_vec_rhs, dmatrix);

        set_matrix(dmatrix, num_vec_lhs, num_vec_rhs);
        SG_FREE(dmatrix);
    }

    return success;
}


/* POIM */

bool CSGInterface::cmd_get_SPEC_consensus()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");
    if (kernel->get_kernel_type()!=K_COMMWORDSTRING)
        SG_ERROR("Only works for CommWordString kernels.\n");

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    ASSERT(svm);
    int32_t num_suppvec=svm->get_num_support_vectors();
    int32_t* sv_idx=SG_MALLOC(int32_t, num_suppvec);
    float64_t* sv_weight=SG_MALLOC(float64_t, num_suppvec);
    int32_t num_feat=0;

    for (int32_t i=0; i<num_suppvec; i++)
    {
        sv_idx[i]=svm->get_support_vector(i);
        sv_weight[i]=svm->get_alpha(i);
    }

    char* consensus=((CCommWordStringKernel*) kernel)->compute_consensus(
        num_feat, num_suppvec, sv_idx, sv_weight);
    SG_FREE(sv_idx);
    SG_FREE(sv_weight);

    set_vector(consensus, num_feat);
    SG_FREE(consensus);

    return true;
}

bool CSGInterface::cmd_get_SPEC_scoring()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t max_order=get_int();
    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");

    EKernelType ktype=kernel->get_kernel_type();
    if (ktype!=K_COMMWORDSTRING && ktype!=K_WEIGHTEDCOMMWORDSTRING)
        SG_ERROR("Only works for (Weighted) CommWordString kernels.\n");

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    ASSERT(svm);
    int32_t num_suppvec=svm->get_num_support_vectors();
    int32_t* sv_idx=SG_MALLOC(int32_t, num_suppvec);
    float64_t* sv_weight=SG_MALLOC(float64_t, num_suppvec);
    int32_t num_feat=0;
    int32_t num_sym=0;

    for (int32_t i=0; i<num_suppvec; i++)
    {
        sv_idx[i]=svm->get_support_vector(i);
        sv_weight[i]=svm->get_alpha(i);
    }

    if ((max_order<1) || (max_order>8))
    {
        SG_WARNING( "max_order out of range 1..8 (%d). setting to 1\n", max_order);
        max_order=1;
    }

    float64_t* position_weights=NULL;
    if (ktype==K_COMMWORDSTRING)
        position_weights=((CCommWordStringKernel*) kernel)->compute_scoring(
            max_order, num_feat, num_sym, NULL,
            num_suppvec, sv_idx, sv_weight);
    else
        position_weights=((CWeightedCommWordStringKernel*) kernel)->compute_scoring(
            max_order, num_feat, num_sym, NULL,
            num_suppvec, sv_idx, sv_weight);
    SG_FREE(sv_idx);
    SG_FREE(sv_weight);

    set_matrix(position_weights, num_sym, num_feat);
    SG_FREE(position_weights);

    return true;
}

bool CSGInterface::cmd_get_WD_consensus()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel.\n");
    if (kernel->get_kernel_type()!=K_WEIGHTEDDEGREEPOS)
        SG_ERROR("Only works for Weighted Degree Position kernels.\n");

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    ASSERT(svm);
    int32_t num_suppvec=svm->get_num_support_vectors();
    int32_t* sv_idx=SG_MALLOC(int32_t, num_suppvec);
    float64_t* sv_weight=SG_MALLOC(float64_t, num_suppvec);
    int32_t num_feat=0;

    for (int32_t i=0; i<num_suppvec; i++)
    {
        sv_idx[i]=svm->get_support_vector(i);
        sv_weight[i]=svm->get_alpha(i);
    }

    char* consensus=((CWeightedDegreePositionStringKernel*) kernel)->compute_consensus(
            num_feat, num_suppvec, sv_idx, sv_weight);
    SG_FREE(sv_idx);
    SG_FREE(sv_weight);

    set_vector(consensus, num_feat);
    SG_FREE(consensus);

    return true;
}

bool CSGInterface::cmd_compute_POIM_WD()
{
    if (m_nrhs!=3 || !create_return_values(1))
        return false;

    int32_t max_order=get_int();
    float64_t* distribution=NULL;
    int32_t num_dfeat=0;
    int32_t num_dvec=0;
    get_matrix(distribution, num_dfeat, num_dvec);

    if (!distribution)
        SG_ERROR("Wrong distribution.\n");

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No Kernel.\n");
    if (kernel->get_kernel_type()!=K_WEIGHTEDDEGREEPOS)
        SG_ERROR("Only works for Weighted Degree Position kernels.\n");

    int32_t seqlen=0;
    int32_t num_sym=0;
    CStringFeatures<char>* sfeat=(CStringFeatures<char>*)
        (((CWeightedDegreePositionStringKernel*) kernel)->get_lhs());
    ASSERT(sfeat);
    seqlen=sfeat->get_max_vector_length();
    num_sym=(int32_t) sfeat->get_num_symbols();

    if (num_dvec!=seqlen || num_dfeat!=num_sym)
    {
        SG_ERROR("distribution should have (seqlen x num_sym) elements"
                "(seqlen: %d vs. %d symbols: %d vs. %d)\n", seqlen,
                num_dvec, num_sym, num_dfeat);
    }

        CSVM* svm=(CSVM*) ui_classifier->get_classifier();
        ASSERT(svm);
        int32_t num_suppvec=svm->get_num_support_vectors();
        int32_t* sv_idx=SG_MALLOC(int32_t, num_suppvec);
        float64_t* sv_weight=SG_MALLOC(float64_t, num_suppvec);

        for (int32_t i=0; i<num_suppvec; i++)
        {
            sv_idx[i]=svm->get_support_vector(i);
            sv_weight[i]=svm->get_alpha(i);
        }

        /*
        if ((max_order < 1) || (max_order > 12))
        {
            SG_WARNING( "max_order out of range 1..12 (%d). setting to 1.\n", max_order);
            max_order=1;
        }
        */

        float64_t* position_weights;
        position_weights=((CWeightedDegreePositionStringKernel*) kernel)->compute_POIM(
                max_order, seqlen, num_sym, NULL,
                num_suppvec, sv_idx, sv_weight, distribution);
        SG_FREE(sv_idx);
        SG_FREE(sv_weight);

        set_matrix(position_weights, num_sym, seqlen);
        SG_FREE(position_weights);

        return true;
    }

    bool CSGInterface::cmd_get_WD_scoring()
    {
        if (m_nrhs!=2 || !create_return_values(1))
            return false;

        int32_t max_order=get_int();

        CKernel* kernel=ui_kernel->get_kernel();
        if (!kernel)
            SG_ERROR("No kernel.\n");
        if (kernel->get_kernel_type()!=K_WEIGHTEDDEGREEPOS)
            SG_ERROR("Only works for Weighted Degree Position kernels.\n");

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    ASSERT(svm);
    int32_t num_suppvec=svm->get_num_support_vectors();
    int32_t* sv_idx=SG_MALLOC(int32_t, num_suppvec);
    float64_t* sv_weight=SG_MALLOC(float64_t, num_suppvec);
    int32_t num_feat=0;
    int32_t num_sym=0;

    for (int32_t i=0; i<num_suppvec; i++)
    {
        sv_idx[i]=svm->get_support_vector(i);
        sv_weight[i]=svm->get_alpha(i);
    }

    if ((max_order<1) || (max_order>12))
    {
        SG_WARNING("max_order out of range 1..12 (%d). setting to 1\n", max_order);
        max_order=1;
    }

    float64_t* position_weights=
        ((CWeightedDegreePositionStringKernel*) kernel)->compute_scoring(
            max_order, num_feat, num_sym, NULL, num_suppvec, sv_idx, sv_weight);
    SG_FREE(sv_idx);
    SG_FREE(sv_weight);

    set_matrix(position_weights, num_sym, num_feat);
    SG_FREE(position_weights);

    return true;
}


/* Classifier */

bool CSGInterface::cmd_classify()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    if (!ui_kernel->get_kernel() ||
            !ui_kernel->get_kernel()->get_kernel_type()==K_CUSTOM)
    {
        CFeatures* feat=ui_features->get_test_features();
        if (!feat)
            SG_ERROR("No features found.\n");
    }

    CLabels* labels=ui_classifier->classify();
    if (!labels)
        SG_ERROR("Classify failed\n");

    int32_t num_vec=labels->get_num_labels();
    float64_t* result=SG_MALLOC(float64_t, num_vec);
    for (int32_t i=0; i<num_vec; i++)
        result[i]=labels->get_label(i);
    SG_UNREF(labels);

    set_vector(result, num_vec);
    SG_FREE(result);

    return true;
}

bool CSGInterface::cmd_classify_example()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t idx=get_int();
    float64_t result=0;

    if (!ui_classifier->classify_example(idx, result))
        SG_ERROR("Classify_example failed.\n");

    set_real(result);

    return true;
}

bool CSGInterface::cmd_get_classifier()
{
    if (m_nrhs<1 || m_nrhs>2 || !create_return_values(2))
        return false;

    int32_t idx=-1;
    if (m_nrhs==2)
        idx=get_int();

    float64_t* bias=NULL;
    float64_t* weights=NULL;
    int32_t rows=0;
    int32_t cols=0;
    int32_t brows=0;
    int32_t bcols=0;

    if (!ui_classifier->get_trained_classifier(
        weights, rows, cols, bias, brows, bcols, idx))
        return false;

    //SG_PRINT("brows %d, bcols %d\n", brows, bcols);
    //CMath::display_matrix(bias, brows, bcols);
    set_matrix(bias, brows, bcols);
    SG_FREE(bias);

    //SG_PRINT("rows %d, cols %d\n", rows, cols);
    //CMath::display_matrix(weights, rows, cols);
    set_matrix(weights, rows, cols);
    SG_FREE(weights);

    return true;
}

bool CSGInterface::cmd_new_classifier()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* name=get_str_from_str_or_direct(len);
    int32_t d=6;
    int32_t from_d=40;

    if (m_nrhs>2)
    {
        d=get_int_from_int_or_str();

        if (m_nrhs>3)
            from_d=get_int_from_int_or_str();
    }

    bool success=ui_classifier->new_classifier(name, d, from_d);

    SG_FREE(name);
    return success;
}

bool CSGInterface::cmd_save_classifier()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool success=ui_classifier->save(filename);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_load_classifier()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);
    char* type=get_str_from_str_or_direct(len);

    bool success=ui_classifier->load(filename, type);

    SG_FREE(filename);
    SG_FREE(type);
    return success;
}


bool CSGInterface::cmd_get_num_svms()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    set_int(ui_classifier->get_num_svms());

    return true;
}


bool CSGInterface::cmd_get_svm()
{
    return cmd_get_classifier();
}

bool CSGInterface::cmd_set_svm()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    float64_t bias=get_real();

    float64_t* alphas=NULL;
    int32_t num_feat_alphas=0;
    int32_t num_vec_alphas=0;
    get_matrix(alphas, num_feat_alphas, num_vec_alphas);

    if (!alphas)
        SG_ERROR("No proper alphas given.\n");
    if (num_vec_alphas!=2)
        SG_ERROR("Not 2 vectors in alphas.\n");

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    if (!svm)
        SG_ERROR("No SVM object available.\n");

    svm->create_new_model(num_feat_alphas);
    svm->set_bias(bias);

    int32_t num_support_vectors=svm->get_num_support_vectors();
    for (int32_t i=0; i<num_support_vectors; i++)
    {
        svm->set_alpha(i, alphas[i]);
        svm->set_support_vector(i, (int32_t) alphas[i+num_support_vectors]);
    }
    SG_FREE(alphas);

    return true;
}

bool CSGInterface::cmd_set_linear_classifier()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    float64_t bias=get_real();

    float64_t* w=NULL;
    int32_t len=0;
    get_vector(w, len);

    if (!len)
        SG_ERROR("No proper weight vector given.\n");

    CLinearMachine* c=(CLinearMachine*) ui_classifier->get_classifier();
    if (!c)
        SG_ERROR("No Linear Classifier object available.\n");

    c->set_w(SGVector<float64_t>(w, len));
    c->set_bias(bias);

    SG_FREE(w);

    return true;
}

bool CSGInterface::cmd_get_svm_objective()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    if (!svm)
        SG_ERROR("No SVM set.\n");

    set_real(svm->get_objective());

    return true;
}

bool CSGInterface::cmd_compute_svm_primal_objective()
{
    return do_compute_objective(SVM_PRIMAL);
}

bool CSGInterface::cmd_compute_svm_dual_objective()
{
    return do_compute_objective(SVM_DUAL);
}

bool CSGInterface::cmd_compute_mkl_dual_objective()
{
    return do_compute_objective(MKL_DUAL);
}

bool CSGInterface::cmd_compute_relative_mkl_duality_gap()
{
    return do_compute_objective(MKL_RELATIVE_DUALITY_GAP);
}

bool CSGInterface::cmd_compute_absolute_mkl_duality_gap()
{
    return do_compute_objective(MKL_ABSOLUTE_DUALITY_GAP);
}

bool CSGInterface::do_compute_objective(E_WHICH_OBJ obj)
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    float64_t result=23.5;

    CSVM* svm=(CSVM*) ui_classifier->get_classifier();
    if (!svm)
        SG_ERROR("No SVM set.\n");

    CLabels* trainlabels=NULL;
    trainlabels=ui_labels->get_train_labels();

    if (!trainlabels)
        SG_ERROR("No trainlabels available.\n");

    CKernel* kernel=ui_kernel->get_kernel();
    if (!kernel)
        SG_ERROR("No kernel available.\n");

    if (!ui_kernel->is_initialized() || !kernel->has_features())
        SG_ERROR("Kernel not initialized.\n");

    ((CKernelMachine*) svm)->set_labels(trainlabels);
    ((CKernelMachine*) svm)->set_kernel(kernel);


    switch (obj)
    {
        case  SVM_PRIMAL:
            result=svm->compute_svm_primal_objective();
            break;
        case  SVM_DUAL:
            result=svm->compute_svm_dual_objective();
            break;
        case  MKL_PRIMAL:
            ASSERT( svm->get_classifier_type() == CT_MKLCLASSIFICATION );
            result=((CMKL*) svm)->compute_mkl_primal_objective();
            break;
        case  MKL_DUAL:
            ASSERT( svm->get_classifier_type() == CT_MKLCLASSIFICATION );
            result=((CMKL*) svm)->compute_mkl_dual_objective();
            break;
        case  MKL_RELATIVE_DUALITY_GAP:
            {
                ASSERT( svm->get_classifier_type() == CT_MKLCLASSIFICATION );
                float64_t primal=((CMKL*) svm)->compute_mkl_dual_objective();
                float64_t dual=((CMKL*) svm)->compute_mkl_primal_objective();
                result=(primal-dual)/dual;
            }
            break;
        case  MKL_ABSOLUTE_DUALITY_GAP:
            {
                ASSERT( svm->get_classifier_type() == CT_MKLCLASSIFICATION );
                float64_t primal=((CMKL*) svm)->compute_mkl_dual_objective();
                float64_t dual=((CMKL*) svm)->compute_mkl_primal_objective();
                result=dual-primal;
            }
            break;
        default:
            SG_SERROR("Error calling do_compute_objective\n");
            return false;
    };

    set_real(result);
    return true;
}

bool CSGInterface::cmd_train_classifier()
{
    if (m_nrhs<1 || !create_return_values(0))
        return false;

    CMachine* classifier=ui_classifier->get_classifier();
    if (!classifier)
        SG_ERROR("No classifier available.\n");

    EClassifierType type=classifier->get_classifier_type();
    switch (type)
    {
        case CT_LIGHT:
        case CT_LIGHTONECLASS:
        case CT_LIBSVM:
        case CT_SCATTERSVM:
        case CT_MPD:
        case CT_GPBT:
        case CT_CPLEXSVM:
        case CT_GMNPSVM:
        case CT_GNPPSVM:
        case CT_KERNELPERCEPTRON:
        case CT_LIBSVR:
        case CT_LIBSVMMULTICLASS:
        case CT_LIBSVMONECLASS:
        case CT_SVRLIGHT:
        case CT_LARANK:
            return ui_classifier->train_svm();
        case CT_MKLMULTICLASS:
            return ui_classifier->train_mkl_multiclass();
        case CT_MKLCLASSIFICATION:
        case CT_MKLREGRESSION:
        case CT_MKLONECLASS:
            return ui_classifier->train_mkl();

        case CT_KRR:
            return ui_classifier->train_krr();

        case CT_KNN:
        {
            if (m_nrhs<2)
                return false;

            int32_t k=get_int_from_int_or_str();

            return ui_classifier->train_knn(k);
        }

        case CT_KMEANS:
        {
            if (m_nrhs<3)
                return false;

            int32_t k=get_int_from_int_or_str();
            int32_t max_iter=get_int_from_int_or_str();

            return ui_classifier->train_clustering(k, max_iter);
        }

        case CT_HIERARCHICAL:
        {
            if (m_nrhs<2)
                return false;

            int32_t merges=get_int_from_int_or_str();

            return ui_classifier->train_clustering(merges);
        }

        case CT_LDA:
        {
            float64_t gamma=0;
            if (m_nrhs==2)
                gamma=get_real_from_real_or_str();

            return ui_classifier->train_linear(gamma);
        }

        case CT_PERCEPTRON:
        case CT_SVMLIN:
        case CT_SVMPERF:
        case CT_SUBGRADIENTSVM:
        case CT_SVMOCAS:
        case CT_SVMSGD:
        case CT_LPM:
        case CT_LPBOOST:
        case CT_SUBGRADIENTLPM:
        case CT_LIBLINEAR:
            return ui_classifier->train_linear();

        case CT_WDSVMOCAS:
            return ui_classifier->train_wdocas();

        default:
            SG_ERROR("Unknown classifier type %d.\n", type);
    }

    return false;
}

bool CSGInterface::cmd_do_auc_maximization()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    bool do_auc=get_bool_from_bool_or_str();

    return ui_classifier->set_do_auc_maximization(do_auc);
}

bool CSGInterface::cmd_set_perceptron_parameters()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    float64_t lernrate=get_real_from_real_or_str();
    int32_t maxiter=get_int_from_int_or_str();

    return ui_classifier->set_perceptron_parameters(lernrate, maxiter);
}

bool CSGInterface::cmd_set_svm_qpsize()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    int32_t qpsize=get_int_from_int_or_str();

    return ui_classifier->set_svm_qpsize(qpsize);
}

bool CSGInterface::cmd_set_svm_max_qpsize()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    int32_t max_qpsize=get_int_from_int_or_str();

    return ui_classifier->set_svm_max_qpsize(max_qpsize);
}

bool CSGInterface::cmd_set_svm_bufsize()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    int32_t bufsize=get_int_from_int_or_str();

    return ui_classifier->set_svm_bufsize(bufsize);
}

bool CSGInterface::cmd_set_svm_C()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    float64_t C1=get_real_from_real_or_str();
    float64_t C2=C1;

    if (m_nrhs==3)
        C2=get_real_from_real_or_str();

    return ui_classifier->set_svm_C(C1, C2);
}

bool CSGInterface::cmd_set_svm_epsilon()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t epsilon=get_real_from_real_or_str();

    return ui_classifier->set_svm_epsilon(epsilon);
}

bool CSGInterface::cmd_set_svr_tube_epsilon()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t tube_epsilon=get_real_from_real_or_str();

    return ui_classifier->set_svr_tube_epsilon(tube_epsilon);
}

bool CSGInterface::cmd_set_svm_nu()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t nu=get_real_from_real_or_str();

    return ui_classifier->set_svm_nu(nu);
}

bool CSGInterface::cmd_set_svm_mkl_parameters()
{
    if (m_nrhs<3 || m_nrhs>4 || !create_return_values(0))
        return false;

    float64_t weight_epsilon=get_real_from_real_or_str();
    float64_t C_mkl=get_real_from_real_or_str();
    float64_t mkl_norm=1.0;
    
    if (m_nrhs==4)
        mkl_norm=get_real_from_real_or_str();

    return ui_classifier->set_svm_mkl_parameters(weight_epsilon, C_mkl, mkl_norm);
}

bool CSGInterface::cmd_set_elasticnet_lambda()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;
    float64_t lambda=get_real_from_real_or_str();
    return ui_classifier->set_elasticnet_lambda(lambda);
}

bool CSGInterface::cmd_set_mkl_block_norm()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;
    float64_t bnorm=get_real_from_real_or_str();
    return ui_classifier->set_mkl_block_norm(bnorm);
}


bool CSGInterface::cmd_set_max_train_time()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t max_train_time=get_real_from_real_or_str();

    return ui_classifier->set_max_train_time(max_train_time);
}

bool CSGInterface::cmd_set_svm_shrinking_enabled()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    bool shrinking_enabled=get_bool_from_bool_or_str();

    return ui_classifier->set_svm_shrinking_enabled(shrinking_enabled);
}

bool CSGInterface::cmd_set_svm_batch_computation_enabled()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    bool batch_computation_enabled=get_bool_from_bool_or_str();

    return ui_classifier->set_svm_batch_computation_enabled(
        batch_computation_enabled);
}

bool CSGInterface::cmd_set_svm_linadd_enabled()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    bool linadd_enabled=get_bool_from_bool_or_str();

    return ui_classifier->set_svm_linadd_enabled(linadd_enabled);
}

bool CSGInterface::cmd_set_svm_bias_enabled()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    bool bias_enabled=get_bool_from_bool_or_str();

    return ui_classifier->set_svm_bias_enabled(bias_enabled);
}

bool CSGInterface::cmd_set_mkl_interleaved_enabled()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    bool interleaved_enabled=get_bool_from_bool_or_str();

    return ui_classifier->set_mkl_interleaved_enabled(interleaved_enabled);
}

bool CSGInterface::cmd_set_krr_tau()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t tau=get_real_from_real_or_str();

    return ui_classifier->set_krr_tau(tau);
}


/* Preproc */

bool CSGInterface::cmd_add_preproc()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* type=get_str_from_str_or_direct(len);
    CPreprocessor* preproc=NULL;

    if (strmatch(type, "NORMONE"))
        preproc=ui_preproc->create_generic(P_NORMONE);
    else if (strmatch(type, "LOGPLUSONE"))
        preproc=ui_preproc->create_generic(P_LOGPLUSONE);
    else if (strmatch(type, "SORTWORDSTRING"))
        preproc=ui_preproc->create_generic(P_SORTWORDSTRING);
    else if (strmatch(type, "SORTULONGSTRING"))
        preproc=ui_preproc->create_generic(P_SORTULONGSTRING);
    else if (strmatch(type, "DECOMPRESSCHARSTRING"))
        preproc=ui_preproc->create_generic(P_DECOMPRESSCHARSTRING);
    else if (strmatch(type, "SORTWORD"))
        preproc=ui_preproc->create_generic(P_SORTWORD);

    else if (strmatch(type, "PRUNEVARSUBMEAN"))
    {
        bool divide_by_std=false;
        if (m_nrhs==3)
            divide_by_std=get_bool_from_bool_or_str();

        preproc=ui_preproc->create_prunevarsubmean(divide_by_std);
    }

#ifdef HAVE_LAPACK
    else if (strmatch(type, "PCA") && m_nrhs==4)
    {
        bool do_whitening=get_bool_from_bool_or_str();
        float64_t threshold=get_real_from_real_or_str();

        preproc=ui_preproc->create_pca(do_whitening, threshold);
    }
#endif

    else
        SG_NOTIMPLEMENTED;

    SG_FREE(type);
    return ui_preproc->add_preproc(preproc);
}

bool CSGInterface::cmd_del_preproc()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_preproc->del_preproc();
}

bool CSGInterface::cmd_attach_preproc()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);

    bool do_force=false;
    if (m_nrhs==3)
        do_force=get_bool_from_bool_or_str();

    bool success=ui_preproc->attach_preproc(target, do_force);

    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_clean_preproc()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_preproc->clean_preproc();
}


/* HMM */

bool CSGInterface::cmd_new_plugin_estimator()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    float64_t pos_pseudo=get_real_from_real_or_str();
    float64_t neg_pseudo=get_real_from_real_or_str();

    return ui_pluginestimate->new_estimator(pos_pseudo, neg_pseudo);
}

bool CSGInterface::cmd_train_estimator()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_pluginestimate->train();
}

bool CSGInterface::cmd_plugin_estimate_classify_example()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t idx=get_int();
    float64_t result=ui_pluginestimate->apply(idx);

    set_vector(&result, 1);
    return true;
}

bool CSGInterface::cmd_plugin_estimate_classify()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CFeatures* feat=ui_features->get_test_features();
    if (!feat)
        SG_ERROR("No features found.\n");

    int32_t num_vec=feat->get_num_vectors();
    float64_t* result=SG_MALLOC(float64_t, num_vec);
    CLabels* labels=ui_pluginestimate->apply();
    for (int32_t i=0; i<num_vec; i++)
        result[i]=labels->get_label(i);
    SG_UNREF(labels);

    set_vector(result, num_vec);
    SG_FREE(result);

    return true;
}

bool CSGInterface::cmd_set_plugin_estimate()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    float64_t* emission_probs=NULL;
    int32_t num_probs=0;
    int32_t num_vec=0;
    get_matrix(emission_probs, num_probs, num_vec);

    if (num_vec!=2)
        SG_ERROR("Need at least 1 set of positive and 1 set of negative params.\n");

    float64_t* pos_params=emission_probs;
    float64_t* neg_params=&(emission_probs[num_probs]);

    float64_t* model_sizes=NULL;
    int32_t len=0;
    get_vector(model_sizes, len);

    int32_t seq_length=(int32_t) model_sizes[0];
    int32_t num_symbols=(int32_t) model_sizes[1];
    if (num_probs!=seq_length*num_symbols)
        SG_ERROR("Mismatch in number of emission probs and sequence length * number of symbols.\n");

    ui_pluginestimate->get_estimator()->set_model_params(
        pos_params, neg_params, seq_length, num_symbols);

    return true;
}

bool CSGInterface::cmd_get_plugin_estimate()
{
    if (m_nrhs!=1 || !create_return_values(2))
        return false;

    float64_t* pos_params=NULL;
    float64_t* neg_params=NULL;
    int32_t num_params=0;
    int32_t seq_length=0;
    int32_t num_symbols=0;

    if (!ui_pluginestimate->get_estimator()->get_model_params(
        pos_params, neg_params, seq_length, num_symbols))
        return false;

    num_params=seq_length*num_symbols;

    float64_t* result=SG_MALLOC(float64_t, num_params*2);
    for (int32_t i=0; i<num_params; i++)
        result[i]=pos_params[i];
    for (int32_t i=0; i<num_params; i++)
        result[i+num_params]=neg_params[i];

    set_matrix(result, num_params, 2);
    SG_FREE(result);

    float64_t model_sizes[2];
    model_sizes[0]=(float64_t) seq_length;
    model_sizes[1]=(float64_t) num_symbols;
    set_vector(model_sizes, 2);

    return true;
}

bool CSGInterface::cmd_convergence_criteria()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    int32_t num_iterations=get_int_from_int_or_str();
    float64_t epsilon=get_real_from_real_or_str();

    return ui_hmm->convergence_criteria(num_iterations, epsilon);
}

bool CSGInterface::cmd_normalize()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    bool keep_dead_states=get_bool_from_bool_or_str();

    return ui_hmm->normalize(keep_dead_states);
}

bool CSGInterface::cmd_add_states()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    int32_t num_states=get_int_from_int_or_str();
    float64_t value=get_real_from_real_or_str();

    return ui_hmm->add_states(num_states, value);
}

bool CSGInterface::cmd_permutation_entropy()
{
    if (m_nrhs<3 || !create_return_values(0))
        return false;

    int32_t width=get_int_from_int_or_str();
    int32_t seq_num=get_int_from_int_or_str();

    return ui_hmm->permutation_entropy(width, seq_num);
}

bool CSGInterface::cmd_relative_entropy()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    float64_t* entropy=NULL;
    int32_t len=0;
    bool success=ui_hmm->relative_entropy(entropy, len);
    if (!success)
        return false;

    set_vector(entropy, len);

    SG_FREE(entropy);
    return true;
}

bool CSGInterface::cmd_entropy()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    float64_t* entropy=NULL;
    int32_t len=0;
    bool success=ui_hmm->entropy(entropy, len);
    if (!success)
        return false;

    set_vector(entropy, len);

    SG_FREE(entropy);
    return true;
}

bool CSGInterface::cmd_hmm_classify()
{
    return do_hmm_classify(false, false);
}

bool CSGInterface::cmd_one_class_hmm_classify()
{
    return do_hmm_classify(false, true);
}

bool CSGInterface::cmd_one_class_linear_hmm_classify()
{
    return do_hmm_classify(true, true);
}

bool CSGInterface::do_hmm_classify(bool linear, bool one_class)
{
    if (m_nrhs>1 || !create_return_values(1))
        return false;

    CFeatures* feat=ui_features->get_test_features();
    if (!feat)
        return false;

    int32_t num_vec=feat->get_num_vectors();
    CLabels* labels=NULL;

    if (linear) // must be one_class as well
    {
        labels=ui_hmm->linear_one_class_classify();
    }
    else
    {
        if (one_class)
            labels=ui_hmm->one_class_classify();
        else
            labels=ui_hmm->classify();
    }
    if (!labels)
        return false;

    float64_t* result=SG_MALLOC(float64_t, num_vec);
    for (int32_t i=0; i<num_vec; i++)
        result[i]=labels->get_label(i);
    SG_UNREF(labels);

    set_vector(result, num_vec);
    SG_FREE(result);

    return true;
}

bool CSGInterface::cmd_one_class_hmm_classify_example()
{
    return do_hmm_classify_example(true);
}

bool CSGInterface::cmd_hmm_classify_example()
{
    return do_hmm_classify_example(false);
}

bool CSGInterface::do_hmm_classify_example(bool one_class)
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t idx=get_int();
    float64_t result=0;

    if (one_class)
        result=ui_hmm->one_class_classify_example(idx);
    else
        result=ui_hmm->classify_example(idx);

    set_real(result);

    return true;
}

bool CSGInterface::cmd_output_hmm()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->output_hmm();
}

bool CSGInterface::cmd_output_hmm_defined()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->output_hmm_defined();
}

bool CSGInterface::cmd_hmm_likelihood()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    CHMM* h=ui_hmm->get_current();
    if (!h)
        SG_ERROR("No HMM.\n");

    float64_t likelihood=h->model_probability();
    set_real(likelihood);

    return true;
}

bool CSGInterface::cmd_likelihood()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->likelihood();
}

bool CSGInterface::cmd_save_likelihood()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool is_binary=false;
    if (m_nrhs==3)
        is_binary=get_bool_from_bool_or_str();

    bool success=ui_hmm->save_likelihood(filename, is_binary);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_get_viterbi_path()
{
    if (m_nrhs!=2 || !create_return_values(2))
        return false;

    int32_t dim=get_int();
    SG_DEBUG("dim: %f\n", dim);

    CHMM* h=ui_hmm->get_current();
    if (!h)
        return false;

    CFeatures* feat=ui_features->get_test_features();
    if (!feat || (feat->get_feature_class()!=C_STRING) ||
            (feat->get_feature_type()!=F_WORD))
        return false;

    h->set_observations((CStringFeatures<uint16_t>*) feat);

    int32_t num_feat=0;
    bool free_vec;
    uint16_t* vec=((CStringFeatures<uint16_t>*) feat)->get_feature_vector(dim, num_feat, free_vec);
    if (!vec || num_feat<=0)
    {
        ((CStringFeatures<uint16_t>*) feat)->free_feature_vector(vec, dim, free_vec);
        return false;
    }
    ((CStringFeatures<uint16_t>*) feat)->free_feature_vector(vec, dim, free_vec);

    SG_DEBUG( "computing viterbi path for vector %d (length %d)\n", dim, num_feat);
    float64_t likelihood=0;
    T_STATES* path=h->get_path(dim, likelihood);

    set_vector(path, num_feat);
    SG_FREE(path);
    set_real(likelihood);

    return true;
}

bool CSGInterface::cmd_viterbi_train()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->viterbi_train();
}

bool CSGInterface::cmd_viterbi_train_defined()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->viterbi_train_defined();
}

bool CSGInterface::cmd_baum_welch_train()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->baum_welch_train();
}

bool CSGInterface::cmd_baum_welch_train_defined()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->baum_welch_train_defined();
}


bool CSGInterface::cmd_baum_welch_trans_train()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_hmm->baum_welch_trans_train();
}

bool CSGInterface::cmd_linear_train()
{
    if (m_nrhs<1 || !create_return_values(0))
        return false;

    if (m_nrhs==2)
    {
        int32_t len=0;
        char* align=get_str_from_str_or_direct(len);

        bool success=ui_hmm->linear_train(align[0]);

        SG_FREE(align);
        return success;
    }
    else
        return ui_hmm->linear_train();
}

bool CSGInterface::cmd_save_path()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool is_binary=false;
    if (m_nrhs==3)
        is_binary=get_bool_from_bool_or_str();

    bool success=ui_hmm->save_path(filename, is_binary);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_append_hmm()
{
    if (m_nrhs!=5 || !create_return_values(0))
        return false;

    CHMM* old_h=ui_hmm->get_current();
    if (!old_h)
        SG_ERROR("No current HMM set.\n");

    float64_t* p=NULL;
    int32_t N_p=0;
    get_vector(p, N_p);

    float64_t* q=NULL;
    int32_t N_q=0;
    get_vector(q, N_q);

    float64_t* a=NULL;
    int32_t M_a=0;
    int32_t N_a=0;
    get_matrix(a, M_a, N_a);
    int32_t N=N_a;

    float64_t* b=NULL;
    int32_t M_b=0;
    int32_t N_b=0;
    get_matrix(b, M_b, N_b);
    int32_t M=N_b;

    if (N_p!=N || N_q!=N || N_a!=N || M_a!=N || N_b!=M || M_b!=N)
    {
        SG_ERROR("Model matrices not matching in size.\n"
                "p:(%d) q:(%d) a:(%d,%d) b(%d,%d)\n",
                N_p, N_q, N_a, M_a, N_b, M_b);
    }

    CHMM* h=new CHMM(N, M, NULL, ui_hmm->get_pseudo());
    int32_t i,j;

    for (i=0; i<N; i++)
    {
        h->set_p(i, p[i]);
        h->set_q(i, q[i]);
    }

    for (i=0; i<N; i++)
        for (j=0; j<N; j++)
            h->set_a(i,j, a[i+j*N]);

    for (i=0; i<N; i++)
        for (j=0; j<M; j++)
            h->set_b(i,j, b[i+j*N]);

    old_h->append_model(h);
    SG_UNREF(h);

    return true;
}

bool CSGInterface::cmd_append_model()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;
    if (m_nrhs>2 && m_nrhs!=4)
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);
    int32_t base1=-1;
    int32_t base2=-1;
    if (m_nrhs>2)
    {
        base1=get_int_from_int_or_str();
        base2=get_int_from_int_or_str();
    }

    bool success=ui_hmm->append_model(filename, base1, base2);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_new_hmm()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    int32_t n=get_int_from_int_or_str();
    int32_t m=get_int_from_int_or_str();

    return ui_hmm->new_hmm(n, m);
}

bool CSGInterface::cmd_load_hmm()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool success=ui_hmm->load(filename);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_save_hmm()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool is_binary=false;
    if (m_nrhs==3)
        is_binary=get_bool_from_bool_or_str();

    bool success=ui_hmm->save(filename, is_binary);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_set_hmm()
{
    if (m_nrhs!=5 || !create_return_values(0))
        return false;

    float64_t* p=NULL;
    int32_t N_p=0;
    get_vector(p, N_p);

    float64_t* q=NULL;
    int32_t N_q=0;
    get_vector(q, N_q);

    float64_t* a=NULL;
    int32_t M_a=0;
    int32_t N_a=0;
    get_matrix(a, M_a, N_a);
    int32_t N=N_a;

    float64_t* b=NULL;
    int32_t M_b=0;
    int32_t N_b=0;
    get_matrix(b, M_b, N_b);
    int32_t M=N_b;

    if (N_p!=N || N_q!=N || N_a!=N || M_a!=N || N_b!=M || M_b!=N)
    {
        SG_ERROR("Model matrices not matching in size.\n"
                "p:(%d) q:(%d) a:(%d,%d) b(%d,%d)\n",
                N_p, N_q, N_a, M_a, N_b, M_b);
    }

    CHMM* current=ui_hmm->get_current();
    if (!current)
        SG_ERROR("Need a previously created HMM.\n");

    int32_t i,j;

    for (i=0; i<N; i++)
    {
        current->set_p(i, p[i]);
        current->set_q(i, q[i]);
    }

    for (i=0; i<N; i++)
        for (j=0; j<N; j++)
            current->set_a(i,j, a[i+j*N]);

    for (i=0; i<N; i++)
        for (j=0; j<M; j++)
            current->set_b(i,j, b[i+j*N]);

    CStringFeatures<uint16_t>* sf = ((CStringFeatures<uint16_t>*) (ui_features->get_train_features()));
    current->set_observations(sf);

    return true;
}

bool CSGInterface::cmd_set_hmm_as()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* target=get_str_from_str_or_direct(len);

    bool success=ui_hmm->set_hmm_as(target);

    SG_FREE(target);
    return success;
}

bool CSGInterface::cmd_set_chop()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t value=get_real_from_real_or_str();
    return ui_hmm->chop(value);
}

bool CSGInterface::cmd_set_pseudo()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t value=get_real_from_real_or_str();
    return ui_hmm->set_pseudo(value);
}

bool CSGInterface::cmd_load_definitions()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    bool do_init=false;
    if (m_nrhs==3)
        do_init=get_bool_from_bool_or_str();

    bool success=ui_hmm->load_definitions(filename, do_init);

    SG_FREE(filename);
    return success;
}

bool CSGInterface::cmd_get_hmm()
{
    if (m_nrhs!=1 || !create_return_values(4))
        return false;

    CHMM* h=ui_hmm->get_current();
    if (!h)
        return false;

    int32_t N=h->get_N();
    int32_t M=h->get_M();
    int32_t i=0;
    int32_t j=0;
    float64_t* p=SG_MALLOC(float64_t, N);
    float64_t* q=SG_MALLOC(float64_t, N);

    for (i=0; i<N; i++)
    {
        p[i]=h->get_p(i);
        q[i]=h->get_q(i);
    }

    set_vector(p, N);
    SG_FREE(p);
    set_vector(q, N);
    SG_FREE(q);

    float64_t* a=SG_MALLOC(float64_t, N*N);
    for (i=0; i<N; i++)
        for (j=0; j<N; j++)
            a[i+j*N]=h->get_a(i, j);
    set_matrix(a, N, N);
    SG_FREE(a);

    float64_t* b=SG_MALLOC(float64_t, N*M);
    for (i=0; i<N; i++)
        for (j=0; j<M; j++)
            b[i+j*N]=h->get_b(i, j);
    set_matrix(b, N, M);
    SG_FREE(b);

    return true;
}

bool CSGInterface::cmd_best_path()
{
    if (m_nrhs!=3 || !create_return_values(0))
        return false;

    int32_t from=get_int_from_int_or_str();
    int32_t to=get_int_from_int_or_str();

    return ui_hmm->best_path(from, to);
}

bool CSGInterface::cmd_best_path_2struct()
{
    if (m_nrhs!=12 || !create_return_values(3))
        return false;

    SG_ERROR("Sorry, this parameter list is awful!\n");

    return true;
}

void CSGInterface::get_vector(bool*& vector, int32_t& len)
{
    int32_t* int_vector;
    get_vector(int_vector, len);

    ASSERT(len>0);
    vector= SG_MALLOC(bool, len);

    for (int32_t i=0; i<len; i++)
        vector[i]= (int_vector[i]!=0);

    SG_FREE(int_vector);
}

void CSGInterface::set_vector(const bool* vector, int32_t len)
{
    int32_t* int_vector = SG_MALLOC(int32_t, len);
    for (int32_t i=0;i<len;i++)
    {
        if (vector[i])
            int_vector[i]=1;
        else
            int_vector[i]=0;
    }
    set_vector(int_vector,len);
    SG_FREE(int_vector);
}

bool CSGInterface::cmd_set_plif_struct()
{
    // ARG 2 
    int32_t Nid=0;
    int32_t* ids;
    get_vector(ids,Nid);

    // ARG 3
    int32_t Nname=0;
    int32_t Mname=0;
    SGString<char>* names;
    get_string_list(names, Nname,Mname);

    // ARG 4
    int32_t Nlimits=0;
    int32_t Mlimits=0;
    float64_t* all_limits;
    get_matrix(all_limits, Mlimits, Nlimits);

    // ARG 5
    int32_t Npenalties=0;
    int32_t Mpenalties=0;
    float64_t* all_penalties;
    get_matrix(all_penalties, Mpenalties, Npenalties);

    // ARG 6
    int32_t Ntransform=0;
    int32_t Mtransform=0;
    SGString<char>* all_transform;
    get_string_list(all_transform, Ntransform, Mtransform);

    // ARG 7
    int32_t Nmin=0;
    float64_t* min_values;
    get_vector(min_values,Nmin);

    // ARG 8
    int32_t Nmax=0;
    float64_t* max_values;
    get_vector(max_values,Nmax);

    // ARG 9
    int32_t Ncache=0;
    bool* all_use_cache;
    get_vector(all_use_cache,Ncache);

    // ARG 10
    int32_t Nsvm=0;
    int32_t* all_use_svm;
    get_vector(all_use_svm,Nsvm);

    // ARG 11
    int32_t Ncalc=0;
    bool* all_do_calc;
    get_vector(all_do_calc,Ncalc);

    if (Ncalc!=Nsvm)
        SG_ERROR("Ncalc!=Nsvm, Ncalc:%i, Nsvm:%i\n",Ncalc,Nsvm);
    if (Ncalc!=Ncache)
        SG_ERROR("Ncalc!=Ncache, Ncalc:%i, Ncache:%i\n",Ncalc,Ncache);
    if (Ncalc!=Ntransform)
        SG_ERROR("Ncalc!=Ntransform, Ncalc:%i, Ntransform:%i\n",Ncalc,Ntransform);
    if (Ncalc!=Nmin)
        SG_ERROR("Ncalc!=Nmin, Ncalc:%i, Nmin:%i\n",Ncalc,Nmin);
    if (Ncalc!=Nmax)
        SG_ERROR("Ncalc!=Nmax, Ncalc:%i, Nmax:%i\n",Ncalc,Nmax);
    if (Ncalc!=Npenalties)
        SG_ERROR("Ncalc!=Npenalties, Ncalc:%i, Npenalties:%i\n",Ncalc,Npenalties);
    if (Ncalc!=Nlimits)
        SG_ERROR("Ncalc!=Nlimits, Ncalc:%i, Nlimits:%i\n",Ncalc,Nlimits);
    if (Ncalc!=Nname)
        SG_ERROR("Ncalc!=Nname, Ncalc:%i, Nname:%i\n",Ncalc,Nname);
    if (Ncalc!=Nid)
        SG_ERROR("Ncalc!=Nid, Ncalc:%i, Nid:%i\n",Ncalc,Nid);
    if (Mlimits!=Mpenalties)
        SG_ERROR("Mlimits!=Mpenalties, Mlimits:%i, Mpenalties:%i\n",Mlimits,Mpenalties);

    int32_t N = Ncalc;
    int32_t M = Mlimits;    
    CPlifMatrix* pm=ui_structure->get_plif_matrix();
    pm->create_plifs(N, M);
    pm->set_plif_ids(SGVector<int32_t>(ids, N));
    pm->set_plif_min_values(SGVector<float64_t>(min_values, N));
    pm->set_plif_max_values(SGVector<float64_t>(max_values, N));
    pm->set_plif_use_cache(SGVector<bool>(all_use_cache, N));
    pm->set_plif_use_svm(SGVector<int32_t>(all_use_svm, N));
    pm->set_plif_limits(SGMatrix<float64_t>(all_limits, N, M));
    pm->set_plif_penalties(SGMatrix<float64_t>(all_penalties, N, M));
    pm->set_plif_names(names, N);
    pm->set_plif_transform_type(all_transform, N);

    SG_FREE(all_limits);
    SG_FREE(all_penalties);
    SG_FREE(names);
    SG_FREE(all_transform);
    SG_FREE(min_values);
    SG_FREE(max_values); 
    SG_FREE(all_use_cache); 
    SG_FREE(all_use_svm);
    SG_FREE(all_do_calc);

    return true;
}

bool CSGInterface::cmd_get_plif_struct()
{
    CPlifMatrix* pm=ui_structure->get_plif_matrix();
    CPlif** PEN = pm->get_PEN();
    int32_t N = pm->get_num_plifs();
    int32_t M = pm->get_num_limits();

    
    int32_t* ids = SG_MALLOC(int32_t, N);
    float64_t* max_values = SG_MALLOC(float64_t, N);
    float64_t* min_values = SG_MALLOC(float64_t, N);
    SGString<char>* names = SG_MALLOC(SGString<char>, N);
    SGString<char>* all_transform = SG_MALLOC(SGString<char>, N);
    float64_t* all_limits = SG_MALLOC(float64_t, N*M);
    float64_t* all_penalties = SG_MALLOC(float64_t, N*M);
    bool* all_use_cache = SG_MALLOC(bool, N);
    int32_t* all_use_svm = SG_MALLOC(int32_t, N);
    bool* all_do_calc = SG_MALLOC(bool, N);
    for (int32_t i=0;i<N;i++)
    {
        ids[i]=PEN[i]->get_id();
        names[i].string = PEN[i]->get_plif_name();
        names[i].slen = strlen(PEN[i]->get_plif_name());
        float64_t* limits = PEN[i]->get_plif_limits();
        float64_t* penalties = PEN[i]->get_plif_penalties();
        for (int32_t j=0;j<M;j++)
        {
            all_limits[i*M+j]=limits[j];
            all_penalties[i*M+j]=penalties[j];
        }
        all_transform[i].string = (char*) PEN[i]->get_transform_type();
        all_transform[i].slen = strlen(PEN[i]->get_transform_type());
        min_values[i]=PEN[i]->get_min_value();
        max_values[i]=PEN[i]->get_max_value();
        all_use_cache[i]=PEN[i]->get_use_cache();
        all_use_svm[i]=PEN[i]->get_use_svm();
        all_do_calc[i]=PEN[i]->get_do_calc();
        
    }
    set_vector(ids,N);
    set_string_list(names, N);
    set_matrix(all_limits, M, N);
    set_matrix(all_penalties, M, N);
    set_string_list(all_transform, N);
    set_vector(min_values,N);
    set_vector(max_values,N);
    set_vector(all_use_cache,N);
    set_vector(all_use_svm,N);
    set_vector(all_do_calc,N);

    SG_FREE(ids);
    SG_FREE(max_values);    
    SG_FREE(min_values);
    SG_FREE(names);
    SG_FREE(all_transform);
    SG_FREE(all_limits);
    SG_FREE(all_penalties);
    SG_FREE(all_use_cache);
    SG_FREE(all_use_svm);
    SG_FREE(all_do_calc);

    return true;
}
/*bool CSGInterface::cmd_signals_set_model()
{
    // ARG 1
    int32_t len=0;
    char* filename;
    filename = get_string(len);

    CTrainPredMaster* tpm = new CTrainPredMaster(ui_kernel);

    tpm->read_models_from_file(filename);

    return true;
    }*/
bool CSGInterface::cmd_signals_set_positions()
{
    return true;
}
bool CSGInterface::cmd_signals_set_labels()
{
    return true;
}
bool CSGInterface::cmd_signals_set_split()
{
    return true;
}
bool CSGInterface::cmd_signals_set_train_mask()
{
    return true;
}
bool CSGInterface::cmd_signals_add_feature()
{
    return true;
}
bool CSGInterface::cmd_signals_add_kernel()
{
    return true;
}
bool CSGInterface::cmd_signals_run()
{
    return true;
}

bool CSGInterface::cmd_init_dyn_prog()
{
    //ARG 1
    int32_t num_svms=get_int();

    CDynProg* h=new CDynProg(num_svms);
    ui_structure->set_dyn_prog(h);
    return true;
}

bool CSGInterface::cmd_clean_up_dyn_prog()
{
    return ui_structure->cleanup();
}

bool CSGInterface::cmd_set_model()
{
    
    CPlifMatrix* pm=ui_structure->get_plif_matrix();
    
    CDynProg* h = ui_structure->get_dyn_prog();
    int32_t num_svms = h->get_num_svms();
    //CDynProg* h=new CDynProg(Nweights/* = num_svms */);

    //ARG 1
    // transition pointers 
    // link transitions to length, content, frame (and tiling)
    // plifs (#states x #states x 3 or 4)
    int32_t numDim=0;
    int32_t* Dim=0;
    float64_t* penalties_array=NULL;
    get_ndarray(penalties_array,Dim,numDim);
    ASSERT(numDim==3);
    ASSERT(Dim[0]==Dim[1]);

    if (!pm->compute_plif_matrix(SGNDArray<float64_t>(penalties_array, Dim, numDim)))
        SG_ERROR("error computing plif  matrix\n");
    ui_structure->set_num_states(Dim[0]);
    SG_FREE(penalties_array);

    // ARG 2
    // bool-> determines if orf information should be used
    bool use_orf = get_bool();
    ui_structure->set_use_orf(use_orf);

    // ARG 3
    // determines for which contents which orf should be used (#contents x 2)
    int32_t Nmod=0;
    int32_t Mmod=0;
    int32_t* mod_words;
    get_matrix(mod_words, Nmod,Mmod);
    if (Nmod != num_svms)
        SG_ERROR("should be equal: Nmod: %i, num_svms: %i\n",Nmod,num_svms);
    ASSERT(Mmod == 2)
    h->init_mod_words_array(SGMatrix<int32_t>(mod_words, Nmod, Mmod));
    SG_FREE(mod_words);

    // ARG 4
    // links: states -> signal plifs (#states x 2)
    int32_t num_states=0;
    int32_t feat_dim3=0;
    int32_t* state_signals;
    get_matrix(state_signals,num_states,feat_dim3);
    ASSERT(num_states==Dim[0]);
    pm->compute_signal_plifs(SGMatrix<int32_t>(state_signals, feat_dim3, num_states));
    SG_FREE(state_signals);


    // ARG 5
    // ORF info (#states x 2)
    int32_t Norf=0;
    int32_t Morf=0;
    int32_t* orf_info;
    get_matrix(orf_info,Norf,Morf);
    ASSERT(Norf==num_states)
    ASSERT(Morf==2)

    ui_structure->set_orf_info(orf_info, Norf, Morf);
    h->set_orf_info(SGMatrix<int32_t>(orf_info, Norf, Morf));
    SG_FREE(orf_info);

    h->set_num_states(num_states) ;
    
    return true;
}

bool CSGInterface::cmd_precompute_content_svms()
{

    // ARG 1
    int32_t seq_len=0;
    char* seq;
    seq = get_string(seq_len);

    // ARG 2
    // all feature positions
    int32_t Npos=0;
    int32_t* all_pos;
    get_vector(all_pos, Npos);

    //ARG 3
    // content svm weights
    int32_t Nweights=0;
    int32_t num_svms=0;
    float64_t* weights;
    get_matrix(weights, Nweights, num_svms);
    if (Nweights!=5440)
      SG_PRINT("Dimension mismatch: got %i, expect %i\n", Nweights, 5440) ;
    ui_structure->set_content_svm_weights(weights, Nweights, num_svms);

    CDynProg* h = ui_structure->get_dyn_prog();
    if (!h)
        SG_ERROR("no DynProg object found, use init_dyn_prog first\n");


    //float64_t* weights = ui_structure->get_content_svm_weights();
    //int32_t Mweights = h->get_num_svms();
    //int32_t Nweights = ui_structure->get_num_svm_weights();
    h->set_pos(SGVector<int32_t>(all_pos, Npos));
    h->set_gene_string(SGVector<char>(seq, seq_len));
    SG_FREE(seq);
    h->create_word_string();
    h->precompute_stop_codons();
    h->init_content_svm_value_array(num_svms);
    h->set_dict_weights(SGMatrix<float64_t>(weights, Nweights, num_svms));
    SG_FREE(weights);
    h->precompute_content_values();
    SG_DEBUG("precompute_content_svms done\n");
    return true;
}

bool CSGInterface::cmd_get_lin_feat()
{
    CDynProg* h = ui_structure->get_dyn_prog();
    if (!h)
        SG_ERROR("no DynProg object found, use set_model first\n");


    int32_t dim1, dim2 = 0;
    float64_t* lin_feat = h->get_lin_feat(dim1, dim2);

    set_matrix(lin_feat, dim1, dim2);

    return true;
}
bool CSGInterface::cmd_set_lin_feat()
{
    // ARG 1
    int32_t Nseq=0;
    char* seq;
    seq = get_string(Nseq);

    // ARG 2
    // all feature positions
    int32_t Npos=0;
    int32_t* all_pos;
    get_vector(all_pos, Npos);

    //ARG 3 
    //
    int32_t num_svms, seq_len;
    float64_t* lin_feat=NULL;
    get_matrix(lin_feat, num_svms, seq_len);

        if (Npos!=seq_len)
      {
        SG_ERROR("Dimension mismatch: got %i positions and (%ix%i) values\n", Npos, num_svms, seq_len) ;

        SG_FREE(lin_feat);
        SG_FREE(seq);
        SG_FREE(all_pos);
        
        return false ;
      }

    CDynProg* h = ui_structure->get_dyn_prog();
    if (!h)
        SG_ERROR("no DynProg object found, use set_model first\n");

    h->set_pos(SGVector<int32_t>(all_pos, Npos));
    h->set_gene_string(SGVector<char>(seq, Nseq));
    h->precompute_stop_codons();
    h->init_content_svm_value_array(num_svms);
    h->set_lin_feat(lin_feat, num_svms, seq_len);

    SG_FREE(lin_feat);
    SG_FREE(seq);
    SG_FREE(all_pos);

    return true;
}
bool CSGInterface::cmd_long_transition_settings()
{
    bool use_long_transitions = get_bool();
    int32_t threshold = get_int();
    int32_t max_len = get_int();

    CDynProg* h = ui_structure->get_dyn_prog();
        if (!h) 
                SG_ERROR("no DynProg object found, use set_model first\n");

    h->long_transition_settings(use_long_transitions, threshold, max_len);

    return true;
}
bool CSGInterface::cmd_set_feature_matrix()
{
    int32_t num_states = ui_structure->get_num_states();

    //ARG 1
    // feature matrix (#states x #feature_positions x max_num_signals)
    int32_t* Dims=0;
    int32_t numDims=0;
    float64_t* features = NULL;
    get_ndarray(features, Dims, numDims);
    
    if (numDims!=3)
        SG_ERROR("expected a 3 dimensional array, got %i dimensions\n", numDims);
    if (Dims[0]!=num_states)
        SG_ERROR("number of rows (%i) not equal number of states (%i)\n",Dims[0], num_states);
    ASSERT(ui_structure->set_feature_matrix(features, Dims));

    ASSERT(ui_structure->set_feature_dims(Dims));

    SG_FREE(features);
    SG_FREE(Dims);

    return true;
}
bool CSGInterface::cmd_set_feature_matrix_sparse()
{
    int32_t num_pos = ui_structure->get_num_positions();
    int32_t num_states = ui_structure->get_num_states();

    //ARG 1
    // feature matrix (#states x #feature_positions x max_num_signals)
    int32_t dim11, dim12 ;
    SGSparseVector<float64_t> *features1=NULL ;
    get_sparse_matrix(features1, dim11, dim12);
    
    int32_t dim21, dim22 ;
    SGSparseVector<float64_t> *features2=NULL ;
    get_sparse_matrix(features2, dim21, dim22);

    ASSERT(dim11==dim21) ;
    ASSERT(dim12==dim22) ;

    int32_t *Dims = SG_MALLOC(int32_t, 3);
    Dims[0]=dim11 ;
    Dims[1]=dim12 ;
    Dims[2]=2 ;

    ASSERT(Dims[0]==num_states)
    ASSERT(Dims[1]==num_pos)

    ASSERT(ui_structure->set_feature_matrix_sparse(features1, features2, Dims));
    ASSERT(ui_structure->set_feature_dims(Dims));

    SG_FREE(features1);
    SG_FREE(features2);
    SG_FREE(Dims);
    
    return true;
}
bool CSGInterface::cmd_init_intron_list()
{
    //ARG1 start_positions
    int32_t Nstart_positions;
    int32_t* start_positions;
    get_vector(start_positions, Nstart_positions);
        //SG_PRINT("Nstart_positions:%i\n",Nstart_positions);
    
    //ARG2 end_positions
    int32_t Nend_positions;
    int32_t* end_positions;
    get_vector(end_positions, Nend_positions);
        //SG_PRINT("Nend_positions:%i\n",Nend_positions);

    //ARG3 quality  
    int32_t Nquality;
        int32_t* quality;
        get_vector(quality, Nquality);
        //SG_PRINT("Nquality:%i\n",Nquality);

    //ARG4 all candidate positions
    int32_t Nall_pos;
        int32_t* all_pos;
        get_vector(all_pos, Nall_pos);
        //SG_PRINT("Nall_pos:%i\n",Nall_pos);

    ASSERT(Nquality==Nend_positions);
    ASSERT(Nend_positions==Nstart_positions);

    CIntronList* intron_list = new CIntronList();

    intron_list->init_list(all_pos, Nall_pos);

    intron_list->read_introns(start_positions, end_positions, quality, Nstart_positions);

    SG_FREE(start_positions);
    SG_FREE(end_positions);
    SG_FREE(quality);
    SG_FREE(all_pos);

    //int32_t test;
    //int32_t testq;
    //intron_list->get_coverage(&test, &testq, 15 ,16);

    //SG_PRINT("coverage: %i, quality: %i\n",test, testq);
    
    CDynProg* h = ui_structure->get_dyn_prog();
    if (!h)
        SG_ERROR("no DynProg object found, use set_model first\n");

    h->set_intron_list(intron_list, 2);

    return true;
}
bool CSGInterface::cmd_precompute_tiling_features()
{
    CPlifMatrix* pm=ui_structure->get_plif_matrix();
    CPlif** PEN  = pm->get_PEN();
    CDynProg* h  = ui_structure->get_dyn_prog();

    int32_t Nintensities=0;
    float64_t* intensities;
    get_vector(intensities, Nintensities);

    int32_t Nprobe_pos=0;
    int32_t* probe_pos;
    get_vector(probe_pos, Nprobe_pos);
    ASSERT(Nprobe_pos==Nintensities);

    int32_t Ntiling_plif_ids=0;
    int32_t* tiling_plif_ids;
    get_vector(tiling_plif_ids, Ntiling_plif_ids);

    h->init_tiling_data(probe_pos,intensities, Nprobe_pos);
    h->precompute_tiling_plifs(PEN, tiling_plif_ids, Ntiling_plif_ids);
    return true;
}

bool CSGInterface::cmd_best_path_trans()
{
    CDynProg* h = ui_structure->get_dyn_prog();

    CSegmentLoss* seg_loss_obj = h->get_segment_loss_object();  

    CPlifMatrix* pm=ui_structure->get_plif_matrix();

    int32_t num_states = h->get_num_states();
    int32_t* feat_dims = ui_structure->get_feature_dims();
    float64_t* features = (ui_structure->get_feature_matrix(false));
    CSparseFeatures<float64_t>* features_sparse1 = (ui_structure->get_feature_matrix_sparse(0));
    CSparseFeatures<float64_t>* features_sparse2 = (ui_structure->get_feature_matrix_sparse(1));
    int32_t* orf_info = ui_structure->get_orf_info();
    bool use_orf = ui_structure->get_use_orf();
    int32_t Nplif = pm->get_num_plifs();

    // ARG 1
    // transitions from initial state (#states x 1)
    int32_t Np=0;
    float64_t* p;
    get_vector(p, Np);
    if (Np!=num_states)
        SG_ERROR("# transitions from initial state (%i) does not match # states (%i)\n", Np, num_states);

    // ARG 2
    // transitions to end state (#states x 1)
    int32_t Nq=0;
    float64_t* q;
    get_vector(q, Nq);
    if (Nq!=num_states)
        SG_ERROR("# transitions to end state (%i) does not match # states (%i)\n", Nq, num_states);

    // ARG 3
    // number of best paths
    int32_t Nnbest=0;
    int32_t* all_nbest;
    get_vector(all_nbest, Nnbest);
    int32_t nbest;
    int32_t nother = 0;
    if (Nnbest==2)
    {
        nbest =all_nbest[0];    
        nother=all_nbest[1];    
    }
    else
        nbest =all_nbest[0];    
    SG_FREE(all_nbest);

    // ARG 4
    // segment path (2 x #feature_positions)
    // masking/weighting of loss for specific 
    // regions of the true path
    int32_t Nseg_path=0;
    int32_t Mseg_path=0;
    float64_t* seg_path;
    get_matrix(seg_path, Nseg_path, Mseg_path);

    // ARG 5
    // links for transitions (#transitions x 4)
    int32_t Na_trans=0;
    int32_t num_a_trans=0;
    float64_t* a_trans;
    get_matrix(a_trans, num_a_trans, Na_trans);

    // ARG 6
    // loss matrix (#segment x 2*#segments)
    // one (#segment x #segments)-matrix for segment loss 
    // and one for nucleotide loss
    int32_t Nloss=0;
    int32_t Mloss=0;
    float64_t* loss;
    get_matrix(loss, Nloss,Mloss);
    
    int32_t M = h->get_num_positions();
    
    // check input
    ASSERT(num_states==Nq); 

    CPlif** PEN=pm->get_PEN();
    ASSERT(PEN);
    
    h->set_p_vector(SGVector<float64_t>(p, num_states));
    SG_FREE(p); p=NULL ;
    h->set_q_vector(SGVector<float64_t>(q, num_states));
    SG_FREE(q); q=NULL ;

    if (seg_path!=NULL)
    {
        h->set_a_trans_matrix(SGMatrix<float64_t>(a_trans, num_a_trans, Na_trans)) ;
    }
    else
    {
        h->set_a_trans_matrix(SGMatrix<float64_t>(a_trans, num_a_trans, 3)) ; // segment_id = 0 
    }
    SG_FREE(a_trans);
    a_trans=NULL ;

    if (!h->check_svm_arrays())
    {
        SG_ERROR( "svm arrays inconsistent\n") ;
        CPlif::delete_penalty_struct(PEN, Nplif) ;
        return false ;
    }
    
    SG_DEBUG("best_path_trans: M: %i, Mseg_path: %i\n", M, Mseg_path);
    
    h->set_observation_matrix(SGNDArray<float64_t>(features, feat_dims, 3));

    if (seg_path!=NULL)
    {
        h->best_path_set_segment_loss(SGMatrix<float64_t>(loss, Nloss, Mloss)) ;
        seg_loss_obj->set_segment_loss(loss, Nloss, Mloss);
    }
    else
    {
        float64_t zero2[2] = {0.0, 0.0} ;
        h->best_path_set_segment_loss(SGMatrix<float64_t>(zero2, 2, 1)) ;
        seg_loss_obj->set_segment_loss(zero2, 2, 1);
    }
    h->set_content_type_array(SGMatrix<float64_t>(seg_path,Nseg_path,Mseg_path));
    SG_FREE(seg_path);
    
    bool segment_loss_non_zero=false;
    for (int32_t i=0; i<Nloss*Mloss; i++)
    {
        if (loss[i]>1e-3)
            segment_loss_non_zero=true;
    }

    SG_FREE(loss);
    loss=NULL;

    h->set_orf_info(SGMatrix<int32_t>(orf_info, num_states, 2));
    h->set_sparse_features(features_sparse1, features_sparse2);
    h->set_plif_matrices(pm);

    if (segment_loss_non_zero)
    {
            SG_DEBUG("Using version with segment_loss\n") ;
            if (nbest==1)
                h->compute_nbest_paths(feat_dims[2], use_orf, 1,true,false);
            else
                h->compute_nbest_paths(feat_dims[2], use_orf, 2,true,false);
    }
    else
    {
            SG_DEBUG("Using version without segment_loss\n") ;
            if (nbest==1)
                h->compute_nbest_paths(feat_dims[2], use_orf, 1,false,false);
            else
                h->compute_nbest_paths(feat_dims[2], use_orf, 2,false,false);
    }

    SGVector<float64_t> p_prob=h->get_scores();

    SGMatrix<int32_t> states=h->get_states();

    SGMatrix<int32_t> my_pos=h->get_positions();

    // transcribe result
    float64_t* d_my_path= SG_MALLOC(float64_t, (nbest+nother)*M);
    float64_t* d_my_pos= SG_MALLOC(float64_t, (nbest+nother)*M);
    
    for (int32_t k=0; k<(nbest+nother); k++)
    {
        for (int32_t i=0; i<M; i++)
        {
            d_my_path[i*(nbest+nother)+k] = states.matrix[i+k*M] ;
            d_my_pos[i*(nbest+nother)+k] = my_pos.matrix[i+k*M] ;
        }
    }
    SG_FREE(states.matrix);
    SG_FREE(my_pos.matrix);

    set_vector(p_prob.vector,nbest+nother);
    set_vector(d_my_path, (nbest+nother)*M);
    set_vector(d_my_pos, (nbest+nother)*M);

    SG_FREE(d_my_path);
    SG_FREE(d_my_pos);

    return true;

}

bool CSGInterface::cmd_best_path_trans_deriv()
{
    int32_t num_states = ui_structure->get_num_states();
    int32_t* feat_dims = ui_structure->get_feature_dims();
    float64_t* features = (ui_structure->get_feature_matrix(false));

    CPlifMatrix* pm=ui_structure->get_plif_matrix();
    int32_t Nplif = pm->get_num_plifs();
    CPlif** PEN = pm->get_PEN();

    // ARG 1
    // transitions from initial state (#states x 1)
    int32_t Np=0;
    float64_t* p=NULL;
    get_vector(p, Np);
    if (Np!=num_states)
        SG_ERROR("Np!=num_states; Np:%i num_states:%i",Np,num_states);

    // ARG 2
    // transitions to end state (#states x 1)
    int32_t Nq=0;
    float64_t* q=NULL;
    get_vector(q, Nq);
    if (Nq!=num_states)
        SG_ERROR("Nq!=num_states; Nq:%i num_states:%i",Nq,num_states);


    // ARG 3
    // segment path (2 x #feature_positions)
    // masking/weighting of loss for specific 
    // regions of the true path
    int32_t Nseg_path=0;
    int32_t Mseg_path=0;
    float64_t* seg_path;
    get_matrix(seg_path,Nseg_path,Mseg_path);

    // ARG 4
    // links for transitions (#transitions x 4)
    int32_t Na_trans=0;
    int32_t num_a_trans=0;
    float64_t* a_trans=NULL;
    get_matrix(a_trans, num_a_trans, Na_trans);

    // ARG 5
    // loss matrix (#segment x 2*#segments)
    // one (#segment x #segments)-matrix for segment loss 
    // and one for nucleotide loss
    int32_t Nloss=0;
    int32_t Mloss=0;
    float64_t* loss=NULL;
    get_matrix(loss, Nloss,Mloss);

    // ARG 6
    // path to calc derivative for 
    int32_t Nmystate_seq=0;
    int32_t* mystate_seq=NULL;
    get_vector(mystate_seq, Nmystate_seq);

    // ARG 7
    // positions of the path
    int32_t Nmypos_seq=0;
    int32_t* mypos_seq=NULL;
    get_vector(mypos_seq, Nmypos_seq);


    //a => a_trans

    int32_t max_plif_id = 0 ;
    int32_t max_plif_len = 1 ;
    for (int32_t i=0; i<Nplif; i++)
    {
        if (i>0 && PEN[i]->get_id()!=i)
            SG_ERROR("PEN[i]->get_id()!=i; PEN[%i]->get_id():%i  ,\n",i, PEN[i]->get_id());
        if (i>max_plif_id)
            max_plif_id=i ;
        if (PEN[i]->get_plif_len()>max_plif_len)
            max_plif_len=PEN[i]->get_plif_len() ;
    } ;


    CDynProg* h = ui_structure->get_dyn_prog();
    CSegmentLoss* seg_loss_obj = h->get_segment_loss_object();
    h->set_num_states(num_states) ;
    h->set_p_vector(SGVector<float64_t>(p, num_states)) ;
    h->set_q_vector(SGVector<float64_t>(q, num_states)) ;

    if (seg_path!=NULL) 
        h->set_a_trans_matrix(SGMatrix<float64_t>(a_trans, num_a_trans, Na_trans)) ;
    else
        h->set_a_trans_matrix(SGMatrix<float64_t>(a_trans, num_a_trans, 3)) ;

    if (!h->check_svm_arrays())
        SG_ERROR( "svm arrays inconsistent\n") ;

    int32_t *my_path = SG_MALLOC(int32_t, Nmypos_seq+1);
    memset(my_path, -1, Nmypos_seq*sizeof(int32_t)) ;
    int32_t *my_pos = SG_MALLOC(int32_t, Nmypos_seq+1);
    memset(my_pos, -1, Nmypos_seq*sizeof(int32_t)) ;

    h->set_observation_matrix(SGNDArray<float64_t>(features, feat_dims, 3));
    for (int32_t i=0; i<Nmypos_seq; i++)
    {
        my_path[i] = mystate_seq[i] ;
        my_pos[i]  = mypos_seq[i] ;
    }

    if (seg_path!=NULL)
    {
        h->best_path_set_segment_loss(SGMatrix<float64_t>(loss, Nloss, Mloss)) ;
        seg_loss_obj->set_segment_loss(loss, Nloss, Mloss);
    }
    else
    {
        float64_t zero2[2] = {0.0, 0.0} ;
        h->best_path_set_segment_loss(SGMatrix<float64_t>(zero2, 2, 1)) ;
        seg_loss_obj->set_segment_loss(zero2, 2, 1);
    }
    h->set_content_type_array(SGMatrix<float64_t>(seg_path,Nseg_path,Mseg_path));

    float64_t* p_Plif_deriv = SG_MALLOC(float64_t, (max_plif_id+1)*max_plif_len);
    CArray2<float64_t> a_Plif_deriv(p_Plif_deriv, max_plif_id+1, max_plif_len, false, false) ;

    float64_t* p_A_deriv   = SG_MALLOC(float64_t, num_states*num_states);
    float64_t* p_p_deriv   = SG_MALLOC(float64_t, num_states);
    float64_t* p_q_deriv   = SG_MALLOC(float64_t, num_states);

    h->set_plif_matrices(pm);
    h->best_path_trans_deriv(my_path, my_pos, Nmypos_seq, features, feat_dims[2]);

    float64_t* p_my_scores;
    int32_t n_scores;
    h->get_path_scores(&p_my_scores, &n_scores);

    float64_t* p_my_losses;
    int32_t n_losses;
    h->get_path_losses(&p_my_losses, &n_losses);

    for (int32_t i=0; i<num_states; i++)
    {
        for (int32_t j=0; j<num_states; j++)
            p_A_deriv[i+j*num_states] = h->get_a_deriv(i, j) ;

        p_p_deriv[i]=h->get_p_deriv(i) ;
        p_q_deriv[i]=h->get_q_deriv(i) ;
    }

    for (int32_t id=0; id<=max_plif_id; id++)
    {
        int32_t len=0 ;
        const float64_t * deriv = PEN[id]->get_cum_derivative(len) ;
        ASSERT(len<=max_plif_len) ;
        for (int32_t j=0; j<max_plif_len; j++)
            a_Plif_deriv.element(id, j)= deriv[j] ;
    }

    set_vector(p_p_deriv, num_states);
    set_vector(p_q_deriv, num_states);
    set_matrix(p_A_deriv, num_states, num_states);
    set_matrix(p_Plif_deriv, (max_plif_id+1), max_plif_len);
    set_vector(p_my_scores, Nmypos_seq);
    set_vector(p_my_losses, Nmypos_seq);

    SG_FREE(p_A_deriv);
    SG_FREE(p_p_deriv);
    SG_FREE(p_q_deriv);
    SG_FREE(p_Plif_deriv);
    free(p_my_scores);
    free(p_my_losses);

    SG_FREE(my_path);
    SG_FREE(my_pos);

    SG_FREE(p);
    SG_FREE(q);
    SG_FREE(seg_path);
    SG_FREE(a_trans);
    SG_FREE(loss);
    SG_FREE(mystate_seq);
    SG_FREE(mypos_seq);

    return true ;
}

bool CSGInterface::cmd_precompute_subkernels()
{
    if (m_nrhs!=1 || !create_return_values(0))
        return false;

    return ui_kernel->precompute_subkernels();
}
bool CSGInterface::cmd_crc()
{
    if (m_nrhs!=2 || !create_return_values(1))
        return false;

    int32_t slen=0;
    char* string=get_string(slen);
    ASSERT(string);
    uint8_t* bstring=SG_MALLOC(uint8_t, slen);

    for (int32_t i=0; i<slen; i++)
        bstring[i]=string[i];
    SG_FREE(string);

    int32_t val=CHash::crc32(bstring, slen);
    SG_FREE(bstring);
    set_int(val);

    return true;
}

bool CSGInterface::cmd_system()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* command=SG_MALLOC(char, 10000);
    memset(command, 0, sizeof(char)*10000);
    char* cmd=get_str_from_str_or_direct(len);
    strncat(command, cmd, 10000);
    SG_FREE(cmd);

    while (m_rhs_counter<m_nrhs)
    {
        strncat(command, " ", 10000);
        char* arg=get_str_from_str_or_direct(len);
        strncat(command, arg, 10000);
        SG_FREE(arg);
    }

    int32_t success=system(command);

    return (success==0);
}

bool CSGInterface::cmd_exit()
{
    exit(0);
    return 0; //never reached but necessary to keep sun compiler happy
}

bool CSGInterface::cmd_exec()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);
    FILE* file=fopen(filename, "r");
    if (!file)
    {
        SG_FREE(filename);
        SG_ERROR("Error opening file: %s.\n", filename);
    }

    while (!feof(file))
    {
        // FIXME: interpret lines as input
        break;
    }

    fclose(file);
    return true;
}

bool CSGInterface::cmd_set_output()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* filename=get_str_from_str_or_direct(len);

    if (file_out)
        fclose(file_out);
    file_out=NULL;

    SG_INFO("Setting output file to: %s.\n", filename);

    if (strmatch(filename, "STDERR"))
        io->set_target(stderr);
    else if (strmatch(filename, "STDOUT"))
        io->set_target(stdout);
    else
    {
        file_out=fopen(filename, "w");
        if (!file_out)
            SG_ERROR("Error opening output file %s.\n", filename);
        io->set_target(file_out);
    }

    return true;
}

bool CSGInterface::cmd_set_threshold()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    float64_t value=get_real_from_real_or_str();

    ui_math->set_threshold(value);
    return true;
}

bool CSGInterface::cmd_init_random()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    uint32_t initseed=(uint32_t) get_int_from_int_or_str();
    ui_math->init_random(initseed);

    return true;
}

bool CSGInterface::cmd_set_num_threads()
{
    if (m_nrhs!=2 || !create_return_values(0))
        return false;

    int32_t num_threads=get_int_from_int_or_str();

    parallel->set_num_threads(num_threads);
    SG_INFO("Set number of threads to %d.\n", num_threads);

    return true;
}

bool CSGInterface::cmd_translate_string()
{
    if (m_nrhs!=4 || !create_return_values(1))
        return false;

    float64_t* string=NULL;
    int32_t len;
    get_vector(string, len);

    int32_t order=get_int();
    int32_t start=get_int();

    const int32_t max_val=2; /* DNA->2bits */
    int32_t i,j;
    uint16_t* obs=SG_MALLOC(uint16_t, len);

    for (i=0; i<len; i++)
    {
        switch ((char) string[i])
        {
            case 'A': obs[i]=0; break;
            case 'C': obs[i]=1; break;
            case 'G': obs[i]=2; break;
            case 'T': obs[i]=3; break;
            case 'a': obs[i]=0; break;
            case 'c': obs[i]=1; break;
            case 'g': obs[i]=2; break;
            case 't': obs[i]=3; break;
            default: SG_ERROR("Wrong letter in string.\n");
        }
    }

    //convert interval of size T
    for (i=len-1; i>=order-1; i--)
    {
        uint16_t value=0;
        for (j=i; j>=i-order+1; j--)
            value=(value>>max_val) | ((obs[j])<<(max_val*(order-1)));
        
        obs[i]=(uint16_t) value;
    }
    
    for (i=order-2;i>=0;i--)
    {
        uint16_t value=0;
        for (j=i; j>=i-order+1; j--)
        {
            value= (value >> max_val);
            if (j>=0)
                value|=(obs[j]) << (max_val * (order-1));
        }
        obs[i]=value;
    }

    float64_t* real_obs=SG_MALLOC(float64_t, len);
    for (i=start; i<len; i++)
        real_obs[i-start]=(float64_t) obs[i];
    SG_FREE(obs);

    set_vector(real_obs, len);
    SG_FREE(real_obs);

    return true;
}

bool CSGInterface::cmd_clear()
{
    // reset guilib
    SG_UNREF(ui_classifier);
    ui_classifier=new CGUIClassifier(this);
    SG_UNREF(ui_distance);
    ui_distance=new CGUIDistance(this);
    SG_UNREF(ui_features);
    ui_features=new CGUIFeatures(this);
    SG_UNREF(ui_hmm);
    ui_hmm=new CGUIHMM(this);
    SG_UNREF(ui_kernel);
    ui_kernel=new CGUIKernel(this);
    SG_UNREF(ui_labels);
    ui_labels=new CGUILabels(this);
    SG_UNREF(ui_math);
    ui_math=new CGUIMath(this);
    SG_UNREF(ui_pluginestimate);
    ui_pluginestimate=new CGUIPluginEstimate(this);
    SG_UNREF(ui_preproc);
    ui_preproc=new CGUIPreprocessor(this);
    SG_UNREF(ui_time);
    ui_time=new CGUITime(this);

    return true;
}

bool CSGInterface::cmd_tic()
{
    ui_time->start();
    return true;
}

bool CSGInterface::cmd_toc()
{
    ui_time->stop();
    return true;
}

bool CSGInterface::cmd_print()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* msg=get_str_from_str_or_direct(len);

    SG_PRINT("%s\n", msg);

    SG_FREE(msg);
    return true;
}

bool CSGInterface::cmd_echo()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* level=get_str_from_str_or_direct(len);

    if (strmatch(level, "OFF"))
    {
        echo=false;
        SG_INFO("Echo is off.\n");
    }
    else
    {
        echo=true;
        SG_INFO("Echo is on.\n");
    }

    SG_FREE(level);
    return true;
}

bool CSGInterface::cmd_loglevel()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* level=get_str_from_str_or_direct(len);

    if (strmatch(level, "ALL") || strmatch(level, "GCDEBUG"))
        io->set_loglevel(MSG_GCDEBUG);
    else if (strmatch(level, "DEBUG"))
        io->set_loglevel(MSG_DEBUG);
    else if (strmatch(level, "INFO"))
        io->set_loglevel(MSG_INFO);
    else if (strmatch(level, "NOTICE"))
        io->set_loglevel(MSG_NOTICE);
    else if (strmatch(level, "WARN"))
        io->set_loglevel(MSG_WARN);
    else if (strmatch(level, "ERROR"))
        io->set_loglevel(MSG_ERROR);
    else if (strmatch(level, "CRITICAL"))
        io->set_loglevel(MSG_CRITICAL);
    else if (strmatch(level, "ALERT"))
        io->set_loglevel(MSG_ALERT);
    else if (strmatch(level, "EMERGENCY"))
        io->set_loglevel(MSG_EMERGENCY);
    else
        SG_ERROR("Unknown loglevel '%s'.\n", level);

    SG_INFO("Loglevel set to %s.\n", level);

    SG_FREE(level);
    return true;
}

bool CSGInterface::cmd_syntax_highlight()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* hili=get_str_from_str_or_direct(len);

    if (strmatch(hili, "ON"))
    {
        hilight.set_ansi_syntax_hilighting();
        io->enable_syntax_highlighting();
    }
    else if (strmatch(hili, "OFF"))
    {
        hilight.disable_syntax_hilighting();
        io->disable_syntax_highlighting();
    }
    else
        SG_ERROR("arguments to " N_SYNTAX_HIGHLIGHT " are ON|OFF - found '%s'.\n", hili);

    SG_INFO("Syntax hilighting set to %s.\n", hili);

    SG_FREE(hili);
    return true;
}

bool CSGInterface::cmd_progress()
{
    if (m_nrhs<2 || !create_return_values(0))
        return false;

    int32_t len=0;
    char* progress=get_str_from_str_or_direct(len);

    if (strmatch(progress, "ON"))
        io->enable_progress();
    else if (strmatch(progress, "OFF"))
        io->disable_progress();
    else
        SG_ERROR("arguments to progress are ON|OFF - found '%s'.\n", progress);

    SG_INFO("Progress set to %s.\n", progress);

    SG_FREE(progress);
    return true;
}

bool CSGInterface::cmd_get_version()
{
    if (m_nrhs!=1 || !create_return_values(1))
        return false;

    set_int(version->get_version_revision());

    return true;
}

bool CSGInterface::cmd_help()
{
    if ((m_nrhs!=1 && m_nrhs!=2) || !create_return_values(0))
        return false;

    int32_t i=0;

    SG_PRINT("\n");
    if (m_nrhs==1) // unspecified help
    {
        SG_PRINT("Help is available for the following topics.\n"
                 "-------------------------------------------\n\n");
        while (sg_methods[i].command)
        {
            bool is_group_item=false;
            if (!sg_methods[i].method && !sg_methods[i].usage_prefix)
                is_group_item=true;

            if (is_group_item)
            {
                SG_PRINT("%s%s%s\n",
                        hilight.get_command_prefix(),
                        sg_methods[i].command,
                        hilight.get_command_suffix());
            }

            i++;
        }
        SG_PRINT("\nUse sg('%shelp%s', '%s<topic>%s')"
                " to see the list of commands in this group, e.g.\n\n"
                "\tsg('%shelp%s', '%sFeatures%s')\n\n"
                "to see the list of commands for the 'Features' group.\n"
                "\nOr use sg('%shelp%s', '%sall%s')"
                " to see a brief listing of all commands.\n\nTo disable syntax"
                " highlighting (useful e.g. in the matlab GUI) use\n\n"
                "\tsg('syntax_highlight','OFF')\n",
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix());
    }
    else // m_nrhs == 2 -> all commands, single command or group help
    {
        bool found=false;
        bool in_group=false;
        int32_t clen=0;
        char* command=get_string(clen);

        if (strmatch("doxygen", command) || strmatch("DOXYGEN", command))
        {
            found=true;
            while (sg_methods[i].command)
            {
                if (sg_methods[i].usage_prefix) // display group item
                {
                    SG_PRINT("\\arg \\b %s \\verbatim %s%s%s \\endverbatim\n",
                            sg_methods[i].command,
                            sg_methods[i].usage_prefix,
                            sg_methods[i].command,
                            sg_methods[i].usage_suffix);
                }
                else if (!sg_methods[i].method) // display group
                {
                    SG_PRINT("\n\\section %s_sec %s\n", 
                            sg_methods[i].command, sg_methods[i].command);
                }
                i++;
            }
        }
        if (strmatch("all", command) || strmatch("ALL", command))
        {
            found=true;
            while (sg_methods[i].command)
            {
                if (sg_methods[i].usage_prefix) // display group item
                {
                    SG_PRINT("\t%s%s%s%s%s\n", sg_methods[i].usage_prefix, 
                            hilight.get_command_prefix(),
                            sg_methods[i].command,
                            hilight.get_command_suffix(),
                            sg_methods[i].usage_suffix);
                }
                else if (!sg_methods[i].method) // display group
                {
                    SG_PRINT("\nCommands in group %s%s%s\n", 
                            hilight.get_command_prefix(),
                            sg_methods[i].command,
                            hilight.get_command_suffix());
                }
                i++;
            }
        }
        else
        {
            while (sg_methods[i].command)
            {
                if (in_group)
                {
                    if (sg_methods[i].usage_prefix) // display group item
                        SG_PRINT("\t%s%s%s\n",
                            hilight.get_command_prefix(),
                            sg_methods[i].command,
                            hilight.get_command_suffix());
                    else // next group reached -> end
                        break;
                }
                else
                {
                    found=strmatch(sg_methods[i].command, command);
                    if (found)
                    {
                        if (sg_methods[i].usage_prefix) // found item
                        {
                            SG_PRINT("Usage for %s%s%s\n\n\t%s%s%s%s%s\n",
                                    hilight.get_command_prefix(),
                                    sg_methods[i].command,
                                    hilight.get_command_suffix(),
                                    sg_methods[i].usage_prefix,
                                    hilight.get_command_prefix(),
                                    sg_methods[i].command,
                                    hilight.get_command_suffix(),
                                    sg_methods[i].usage_suffix);
                            break;
                        }
                        else // found group item
                        {
                            SG_PRINT("Commands in group %s%s%s\n\n",
                                    hilight.get_command_prefix(),
                                    sg_methods[i].command,
                                    hilight.get_command_suffix());
                            in_group=true;
                        }
                    }
                }

                i++;
            }
        }

        if (!found)
            SG_PRINT("Could not find help for command %s.\n", command);
        else if (in_group)
        {
            SG_PRINT("\n\nUse sg('%shelp%s', '%s<command>%s')"
                    " to see the usage pattern of a single command, e.g.\n\n"
                    "\tsg('%shelp%s', '%sclassify%s')\n\n"
                    " to see the usage pattern of the command 'classify'.\n",
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix(),
                    hilight.get_command_prefix(), hilight.get_command_suffix());
        }

        SG_FREE(command);
    }


    SG_PRINT("\n");

    return true;
}
#ifdef TRACE_MEMORY_ALLOCS
    extern CSet<MemoryBlock>* sg_mallocs;
#endif

bool CSGInterface::cmd_whos()
{
    if ((m_nrhs!=1) || !create_return_values(0))
        return false;

#ifdef TRACE_MEMORY_ALLOCS
    SG_PRINT("Blocks allocated by shogun\n");
    list_memory_allocs();
    SG_PRINT("\n");
    return true;
#else
    SG_PRINT("Requires shogun to be compiled with --enable-trace-mallocs\n");
    return false;
#endif
}

bool CSGInterface::cmd_send_command()
{
    SG_DEPRECATED;

    int32_t len=0;
    char* arg=get_string(len);
    //SG_DEBUG("legacy: arg == %s\n", arg);
    m_legacy_strptr=arg;

    char* command=get_str_from_str(len);
    int32_t i=0;
    bool success=false;

    while (sg_methods[i].command)
    {
        if (strmatch(command, sg_methods[i].command))
        {
            SG_DEBUG("legacy: found command %s\n", sg_methods[i].command);
            // fix-up m_nrhs; +1 to include command
            m_nrhs=get_num_args_in_str()+1;

            if (!(interface->*(sg_methods[i].method))())
            {
                SG_ERROR("Usage: %s%s%s\n\n\t%s%s%s%s%s\n",
                        hilight.get_command_prefix(),
                        sg_methods[i].command,
                        hilight.get_command_suffix(),
                        sg_methods[i].usage_prefix,
                        hilight.get_command_prefix(),
                        sg_methods[i].command,
                        hilight.get_command_suffix(),
                        sg_methods[i].usage_suffix);
            }
            else
            {
                success=true;
                break;
            }
        }

        i++;
    }

    if (!success)
        SG_ERROR("Non-supported legacy command %s.\n", command);

    SG_FREE(command);
    SG_FREE(arg);
    return success;
}

bool CSGInterface::cmd_run_python()
{
    SG_ERROR("Only available in the elwms interface\n");
    return false;
}

bool CSGInterface::cmd_run_octave()
{
    SG_ERROR("Only available in the elwms interface\n");
    return false;
}

bool CSGInterface::cmd_run_r()
{
    SG_ERROR("Only available in the elwms interface\n");
    return false;
}

bool CSGInterface::cmd_pr_loqo()
{
    if (m_nrhs!=7 || !create_return_values(2))
        return false;

    float64_t* c=NULL;
    int32_t lenc=0;
    get_vector(c, lenc);

    int32_t n = lenc;

    float64_t* H=NULL;
    int32_t nH=0;
    int32_t mH=0;
    get_matrix(H, nH, mH);
    ASSERT(nH==n && mH==n);

    float64_t* A=NULL;
    int32_t nA=0;
    int32_t mA=0;
    get_matrix(A, nA, mA);
    ASSERT(mA==n);
    int32_t m=nA;

    float64_t* b=NULL;
    int32_t lenb=0;
    get_vector(b, lenb);
    ASSERT(lenb==m);

    float64_t* l=NULL;
    int32_t lenl=0;
    get_vector(l, lenl);
    ASSERT(lenl==n);

    float64_t* u=NULL;
    int32_t lenu=0;
    get_vector(u, lenu);
    ASSERT(lenu==n);

    float64_t* x=SG_MALLOC(float64_t, 3*n);
    CMath::fill_vector(x, 3*n, 0.0);

    float64_t* y=SG_MALLOC(float64_t, m+2*n);
    CMath::fill_vector(y, m+2*n, 0.0);

    pr_loqo(n,m, c, H, A, b, l, u, x, y, 0, 5, 50, 0.05, 100, 0);

    set_vector(x, n);
    set_vector(y, m);

    SG_FREE(c);
    SG_FREE(H);
    SG_FREE(A);
    SG_FREE(b);
    SG_FREE(l);
    SG_FREE(u);
    SG_FREE(x);
    SG_FREE(y);
    return true;
}

void CSGInterface::print_prompt()
{
    SG_PRINT("%sshogun%s >> ",
            hilight.get_prompt_prefix(),
            hilight.get_prompt_suffix());
}

// legacy-related methods

char* CSGInterface::get_str_from_str_or_direct(int32_t& len)
{
    if (m_legacy_strptr)
        return get_str_from_str(len);
    else
        return get_string(len);
}

int32_t CSGInterface::get_int_from_int_or_str()
{
    if (m_legacy_strptr)
    {
        int32_t len=0;
        char* str=get_str_from_str(len);
        int32_t val=strtol(str, NULL, 10);

        SG_FREE(str);
        return val;
    }
    else
        return get_int();
}

float64_t CSGInterface::get_real_from_real_or_str()
{
    if (m_legacy_strptr)
    {
        int32_t len=0;
        char* str=get_str_from_str(len);
        float64_t val=strtod(str, NULL);

        SG_FREE(str);
        return val;
    }
    else
        return get_real();
}

bool CSGInterface::get_bool_from_bool_or_str()
{
    if (m_legacy_strptr)
    {
        int32_t len=0;
        char* str=get_str_from_str(len);
        bool val=strtol(str, NULL, 10)!=0;

        SG_FREE(str);
        return val;
    }
    else
        return get_bool();
}

void CSGInterface::get_vector_from_int_vector_or_str(int32_t*& vector, int32_t& len)
{
    if (m_legacy_strptr)
    {
        len=get_vector_len_from_str(len);
        if (len==0)
        {
            vector=NULL;
            return;
        }

        vector=SG_MALLOC(int32_t, len);
        char* str=NULL;
        int32_t slen=0;
        for (int32_t i=0; i<len; i++)
        {
            str=get_str_from_str(slen);
            vector[i]=strtol(str, NULL, 10);
            //SG_DEBUG("vec[%d]: %d\n", i, vector[i]);
            SG_FREE(str);
        }
    }
    else
        get_vector(vector, len);
}

void CSGInterface::get_vector_from_real_vector_or_str(
    float64_t*& vector, int32_t& len)
{
    if (m_legacy_strptr)
    {
        len=get_vector_len_from_str(len);
        if (len==0)
        {
            vector=NULL;
            return;
        }

        vector=SG_MALLOC(float64_t, len);
        char* str=NULL;
        int32_t slen=0;
        for (int32_t i=0; i<len; i++)
        {
            str=get_str_from_str(slen);
            vector[i]=strtod(str, NULL);
            //SG_DEBUG("vec[%d]: %f\n", i, vector[i]);
            SG_FREE(str);
        }
    }
    else
        get_vector(vector, len);
}

int32_t CSGInterface::get_vector_len_from_str(int32_t expected_len)
{
    int32_t num_args=get_num_args_in_str();

    if (expected_len==0 || num_args==expected_len)
        return num_args;
    else if (num_args==2*expected_len)
    {
        // special case for position_weights; a bit shaky...
        return expected_len;
    }
    else
        SG_ERROR("Expected vector length %d does not match actual length %d.\n", expected_len, num_args);

    return 0;
}

char* CSGInterface::get_str_from_str(int32_t& len)
{
    if (!m_legacy_strptr)
        return NULL;

    int32_t i=0;
    while (m_legacy_strptr[i]!='\0' && !isspace(m_legacy_strptr[i]))
        i++;

    len=i;
    char* str=SG_MALLOC(char, len+1);
    for (i=0; i<len; i++)
        str[i]=m_legacy_strptr[i];
    str[len]='\0';

    // move legacy strptr
    if (m_legacy_strptr[len]=='\0')
        m_legacy_strptr=NULL;
    else
    {
        m_legacy_strptr=m_legacy_strptr+len;
        m_legacy_strptr=SGIO::skip_spaces(m_legacy_strptr);
    }

    return str;
}

int32_t CSGInterface::get_num_args_in_str()
{
    if (!m_legacy_strptr)
        return 0;

    int32_t count=0;
    int32_t i=0;
    bool in_arg=false;
    while (m_legacy_strptr[i]!='\0')
    {
        if (!isspace(m_legacy_strptr[i]) && !in_arg)
        {
            count++;
            in_arg=true;
        }
        else if (isspace(m_legacy_strptr[i]) && in_arg)
            in_arg=false;

        i++;
    }

    return count;
}

// handler

bool CSGInterface::handle()
{
    int32_t len=0;
    bool success=false;

#ifndef WIN32
    CSignal::set_handler();
#endif

    char* command=NULL;
    command=interface->get_command(len);

    SG_DEBUG("command: %s, nrhs %d\n", command, m_nrhs);
    int32_t i=0;
    while (sg_methods[i].command)
    {
        if (strmatch(command, sg_methods[i].command))
        {
            SG_DEBUG("found command %s%s%s\n",
                    hilight.get_command_prefix(),
                    sg_methods[i].command,
                    hilight.get_command_suffix());

            if (!(interface->*(sg_methods[i].method))())
            {
                if (sg_methods[i].usage_prefix)
                {
                    SG_ERROR("Usage: %s%s%s\n\n\t%s%s%s%s%s\n",
                            hilight.get_command_prefix(),
                            sg_methods[i].command,
                            hilight.get_command_suffix(),
                            sg_methods[i].usage_prefix,
                            hilight.get_command_prefix(),
                            sg_methods[i].command,
                            hilight.get_command_suffix(),
                            sg_methods[i].usage_suffix);
                }
                else
                    SG_ERROR("Non-supported command %s%s%s.\n",
                            hilight.get_command_prefix(),
                            sg_methods[i].command,
                            hilight.get_command_suffix());
            }
            else
            {
                success=true;
                break;
            }
        }
        i++;
    }

#ifndef WIN32
    CSignal::unset_handler();
#endif

    if (!success)
        SG_ERROR("Unknown command %s%s%s.\n",
                hilight.get_command_prefix(),
                command,
                hilight.get_command_suffix());

    SG_FREE(command);
    return success;
}