DynProg.cpp

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/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 1999-2007 Soeren Sonnenburg
 * Written (W) 1999-2007 Gunnar Raetsch
 * Written (W) 2008-2009 Jonas Behr
 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#include <shogun/structure/DynProg.h>
#include <shogun/mathematics/Math.h>
#include <shogun/io/SGIO.h>
#include <shogun/lib/config.h>
#include <shogun/features/StringFeatures.h>
#include <shogun/features/Alphabet.h>
#include <shogun/structure/Plif.h>
#include <shogun/structure/IntronList.h>

#include <stdlib.h>
#include <stdio.h>
#include <time.h>
#include <ctype.h>

using namespace shogun;

//#define USE_TMP_ARRAYCLASS
//#define DYNPROG_DEBUG

int32_t CDynProg::word_degree_default[4]={3,4,5,6} ;
int32_t CDynProg::cum_num_words_default[5]={0,64,320,1344,5440} ;
int32_t CDynProg::frame_plifs[3]={4,5,6};
int32_t CDynProg::num_words_default[4]=   {64,256,1024,4096} ;
int32_t CDynProg::mod_words_default[32] = {1,1,1,1,1,1,1,1,
                                    1,1,1,1,1,1,1,1,
                                    0,0,0,0,0,0,0,0,
                                    0,0,0,0,0,0,0,0} ;
bool CDynProg::sign_words_default[16] = {true,true,true,true,true,true,true,true,
                                      false,false,false,false,false,false,false,false} ; // whether to use counts or signum of counts
int32_t CDynProg::string_words_default[16] = {0,0,0,0,0,0,0,0,
                                       1,1,1,1,1,1,1,1} ; // which string should be used

CDynProg::CDynProg(int32_t num_svms /*= 8 */)
: CSGObject(), m_transition_matrix_a_id(1,1), m_transition_matrix_a(1,1),
    m_transition_matrix_a_deriv(1,1), m_initial_state_distribution_p(1),
    m_initial_state_distribution_p_deriv(1), m_end_state_distribution_q(1),
    m_end_state_distribution_q_deriv(1),

      // multi svm
      m_num_degrees(4),
      m_num_svms(num_svms),
      m_word_degree(word_degree_default, m_num_degrees, true, true),
      m_cum_num_words(cum_num_words_default, m_num_degrees+1, true, true),
      m_cum_num_words_array(m_cum_num_words.get_array()),
      m_num_words(num_words_default, m_num_degrees, true, true),
      m_num_words_array(m_num_words.get_array()),
      m_mod_words(mod_words_default, m_num_svms, 2, true, true),
      m_mod_words_array(m_mod_words.get_array()),
      m_sign_words(sign_words_default, m_num_svms, true, true),
      m_sign_words_array(m_sign_words.get_array()),
      m_string_words(string_words_default, m_num_svms, true, true),
      m_string_words_array(m_string_words.get_array()),
      //m_svm_pos_start(m_num_degrees),
      m_num_unique_words(m_num_degrees),
      m_svm_arrays_clean(true),

      m_max_a_id(0), m_observation_matrix(1,1,1),
      m_pos(1),
      m_seq_len(0),
      m_orf_info(1,2),
      m_plif_list(1),
      m_PEN(1,1),
      m_genestr(1), m_wordstr(NULL), m_dict_weights(1,1), m_segment_loss(1,1,2),
      m_segment_ids(1),
      m_segment_mask(1),
      m_my_state_seq(1),
      m_my_pos_seq(1),
      m_my_scores(1),
      m_my_losses(1),
      m_scores(1),
      m_states(1,1),
      m_positions(1,1),

      m_seq_sparse1(NULL),
      m_seq_sparse2(NULL),
      m_plif_matrices(NULL),

      m_genestr_stop(1),
      m_intron_list(NULL),
      m_num_intron_plifs(0),
      m_lin_feat(1,1), //by Jonas
      m_raw_intensities(NULL),
      m_probe_pos(NULL),
      m_num_probes_cum(NULL),
      m_num_lin_feat_plifs_cum(NULL),
      m_num_raw_data(0),

      m_long_transitions(true),
      m_long_transition_threshold(1000)
{
    trans_list_forward = NULL ;
    trans_list_forward_cnt = NULL ;
    trans_list_forward_val = NULL ;
    trans_list_forward_id = NULL ;
    trans_list_len = 0 ;

    mem_initialized = true ;

    m_N=1;

    m_raw_intensities = NULL;
    m_probe_pos = NULL;
    m_num_probes_cum = SG_MALLOC(int32_t, 100);
    m_num_probes_cum[0] = 0;
    //m_use_tiling=false;
    m_num_lin_feat_plifs_cum = SG_MALLOC(int32_t, 100);
    m_num_lin_feat_plifs_cum[0] = m_num_svms;
    m_num_raw_data = 0;
#ifdef ARRAY_STATISTICS
    m_word_degree.set_array_name("word_degree");
#endif

    m_transition_matrix_a_id.set_array_name("transition_matrix_a_id");
    m_transition_matrix_a.set_array_name("transition_matrix_a");
    m_transition_matrix_a_deriv.set_array_name("transition_matrix_a_deriv");
    m_mod_words.set_array_name("mod_words");
    m_orf_info.set_array_name("orf_info");
    m_segment_sum_weights.set_array_name("segment_sum_weights");
    m_PEN.set_array_name("PEN");
    m_PEN_state_signals.set_array_name("PEN_state_signals");
    m_dict_weights.set_array_name("dict_weights");
    m_states.set_array_name("states");
    m_positions.set_array_name("positions");
    m_lin_feat.set_array_name("lin_feat");


    m_observation_matrix.set_array_name("m_observation_matrix");
    m_segment_loss.set_array_name("m_segment_loss");
    m_seg_loss_obj = new CSegmentLoss();
}

CDynProg::~CDynProg()
{
    if (trans_list_forward_cnt)
        SG_FREE(trans_list_forward_cnt);
    if (trans_list_forward)
    {
        for (int32_t i=0; i<trans_list_len; i++)
        {
            if (trans_list_forward[i])
                SG_FREE(trans_list_forward[i]);
        }
        SG_FREE(trans_list_forward);
    }
    if (trans_list_forward_val)
    {
        for (int32_t i=0; i<trans_list_len; i++)
        {
            if (trans_list_forward_val[i])
                SG_FREE(trans_list_forward_val[i]);
        }
        SG_FREE(trans_list_forward_val);
    }
    if (trans_list_forward_id)
    {
        for (int32_t i=0; i<trans_list_len; i++)
        {
            if (trans_list_forward_id[i])
                SG_FREE(trans_list_forward_id[i]);
        }
        SG_FREE(trans_list_forward_id);
    }
    if (m_raw_intensities)
        SG_FREE(m_raw_intensities);
    if (m_probe_pos)
        SG_FREE(m_probe_pos);
    if (m_num_probes_cum)
      SG_FREE(m_num_probes_cum);
    if (m_num_lin_feat_plifs_cum)
      SG_FREE(m_num_lin_feat_plifs_cum);

    delete m_intron_list;

    SG_UNREF(m_seq_sparse1);
    SG_UNREF(m_seq_sparse2);
    SG_UNREF(m_plif_matrices);
}

int32_t CDynProg::get_num_svms()
{
    return m_num_svms;
}

void CDynProg::precompute_stop_codons()
{
    int32_t length=m_genestr.get_dim1();

    m_genestr_stop.resize_array(length) ;
    m_genestr_stop.set_const(0) ;
    m_genestr_stop.set_array_name("genestr_stop") ;
    {
        for (int32_t i=0; i<length-2; i++)
            if ((m_genestr[i]=='t' || m_genestr[i]=='T') &&
                    (((m_genestr[i+1]=='a' || m_genestr[i+1]=='A') &&
                      (m_genestr[i+2]=='a' || m_genestr[i+2]=='g' || m_genestr[i+2]=='A' || m_genestr[i+2]=='G')) ||
                     ((m_genestr[i+1]=='g'||m_genestr[i+1]=='G') && (m_genestr[i+2]=='a' || m_genestr[i+2]=='A') )))
            {
                m_genestr_stop.element(i)=true ;
            }
            else
                m_genestr_stop.element(i)=false ;
        m_genestr_stop.element(length-2)=false ;
        m_genestr_stop.element(length-1)=false ;
    }
}

void CDynProg::set_num_states(int32_t p_N)
{
    m_N=p_N ;

    m_transition_matrix_a_id.resize_array(m_N,m_N) ;
    m_transition_matrix_a.resize_array(m_N,m_N) ;
    m_transition_matrix_a_deriv.resize_array(m_N,m_N) ;
    m_initial_state_distribution_p.resize_array(m_N) ;
    m_initial_state_distribution_p_deriv.resize_array(m_N) ;
    m_end_state_distribution_q.resize_array(m_N);
    m_end_state_distribution_q_deriv.resize_array(m_N) ;

    m_orf_info.resize_array(m_N,2) ;
    m_PEN.resize_array(m_N,m_N) ;
}

int32_t CDynProg::get_num_states()
{
    return m_N;
}

void CDynProg::init_tiling_data(
    int32_t* probe_pos, float64_t* intensities, const int32_t num_probes)
{
    m_num_raw_data++;
    m_num_probes_cum[m_num_raw_data] = m_num_probes_cum[m_num_raw_data-1]+num_probes;

    int32_t* tmp_probe_pos = SG_MALLOC(int32_t, m_num_probes_cum[m_num_raw_data]);
    float64_t* tmp_raw_intensities = SG_MALLOC(float64_t, m_num_probes_cum[m_num_raw_data]);


    if (m_num_raw_data==1){
        memcpy(tmp_probe_pos, probe_pos, num_probes*sizeof(int32_t));
        memcpy(tmp_raw_intensities, intensities, num_probes*sizeof(float64_t));
        //SG_PRINT("raw_intens:%f \n",*tmp_raw_intensities+2);
    }else{
        memcpy(tmp_probe_pos, m_probe_pos, m_num_probes_cum[m_num_raw_data-1]*sizeof(int32_t));
        memcpy(tmp_raw_intensities, m_raw_intensities, m_num_probes_cum[m_num_raw_data-1]*sizeof(float64_t));
        memcpy(tmp_probe_pos+m_num_probes_cum[m_num_raw_data-1], probe_pos, num_probes*sizeof(int32_t));
        memcpy(tmp_raw_intensities+m_num_probes_cum[m_num_raw_data-1], intensities, num_probes*sizeof(float64_t));
    }
    SG_FREE(m_probe_pos);
    SG_FREE(m_raw_intensities);
    m_probe_pos = tmp_probe_pos; //SG_MALLOC(int32_t, num_probes);
    m_raw_intensities = tmp_raw_intensities;//SG_MALLOC(float64_t, num_probes);

    //memcpy(m_probe_pos, probe_pos, num_probes*sizeof(int32_t));
    //memcpy(m_raw_intensities, intensities, num_probes*sizeof(float64_t));

}

void CDynProg::init_content_svm_value_array(const int32_t p_num_svms)
{
    m_lin_feat.resize_array(p_num_svms, m_seq_len);

    // initialize array
    for (int s=0; s<p_num_svms; s++)
      for (int p=0; p<m_seq_len; p++)
        m_lin_feat.set_element(0.0, s, p) ;
}

void CDynProg::resize_lin_feat(const int32_t num_new_feat)
{
    int32_t dim1, dim2;
    m_lin_feat.get_array_size(dim1, dim2);
    ASSERT(dim1==m_num_lin_feat_plifs_cum[m_num_raw_data-1]);
    ASSERT(dim2==m_seq_len); // == number of candidate positions



    float64_t* arr = m_lin_feat.get_array();
    float64_t* tmp = SG_MALLOC(float64_t, (dim1+num_new_feat)*dim2);
    memset(tmp, 0, (dim1+num_new_feat)*dim2*sizeof(float64_t)) ;
    for(int32_t j=0;j<m_seq_len;j++)
                for(int32_t k=0;k<m_num_lin_feat_plifs_cum[m_num_raw_data-1];k++)
            tmp[j*(dim1+num_new_feat)+k] = arr[j*dim1+k];

    m_lin_feat.set_array(tmp, dim1+num_new_feat,dim2, true, true);// copy array and free it later
    SG_FREE(tmp);

    /*for(int32_t j=0;j<5;j++)
    {
        for(int32_t k=0;k<m_num_lin_feat_plifs_cum[m_num_raw_data];k++)
        {
            SG_PRINT("(%i,%i)%f ",k,j,m_lin_feat.get_element(k,j));
        }
        SG_PRINT("\n");
    }
    m_lin_feat.get_array_size(dim1,dim2);
    SG_PRINT("resize_lin_feat: dim1:%i, dim2:%i\n",dim1,dim2);*/

    //SG_PRINT("resize_lin_feat: done\n");
}

void CDynProg::precompute_tiling_plifs(
    CPlif** PEN, const int32_t* tiling_plif_ids, const int32_t num_tiling_plifs)
{
    m_num_lin_feat_plifs_cum[m_num_raw_data] = m_num_lin_feat_plifs_cum[m_num_raw_data-1]+ num_tiling_plifs;
    float64_t* tiling_plif = SG_MALLOC(float64_t, num_tiling_plifs);
    float64_t* svm_value = SG_MALLOC(float64_t, m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs);
    for (int32_t i=0; i<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; i++)
        svm_value[i]=0.0;
    int32_t* tiling_rows = SG_MALLOC(int32_t, num_tiling_plifs);
    for (int32_t i=0; i<num_tiling_plifs; i++)
    {
        tiling_plif[i]=0.0;
        CPlif * plif = PEN[tiling_plif_ids[i]];
        tiling_rows[i] = plif->get_use_svm();

        ASSERT(tiling_rows[i]-1==m_num_lin_feat_plifs_cum[m_num_raw_data-1]+i)
    }
    resize_lin_feat(num_tiling_plifs);


    int32_t* p_tiling_pos  = &m_probe_pos[m_num_probes_cum[m_num_raw_data-1]];
    float64_t* p_tiling_data = &m_raw_intensities[m_num_probes_cum[m_num_raw_data-1]];
    int32_t num=m_num_probes_cum[m_num_raw_data-1];

    for (int32_t pos_idx=0;pos_idx<m_seq_len;pos_idx++)
    {
        while (num<m_num_probes_cum[m_num_raw_data]&&*p_tiling_pos<m_pos[pos_idx])
        {
            for (int32_t i=0; i<num_tiling_plifs; i++)
            {
                svm_value[m_num_lin_feat_plifs_cum[m_num_raw_data-1]+i]=*p_tiling_data;
                CPlif * plif = PEN[tiling_plif_ids[i]];
                ASSERT(m_num_lin_feat_plifs_cum[m_num_raw_data-1]+i==plif->get_use_svm()-1);
                plif->set_do_calc(true);
                tiling_plif[i]+=plif->lookup_penalty(0,svm_value);
                plif->set_do_calc(false);
            }
            p_tiling_data++;
            p_tiling_pos++;
            num++;
        }
        for (int32_t i=0; i<num_tiling_plifs; i++)
            m_lin_feat.set_element(tiling_plif[i],tiling_rows[i]-1,pos_idx);
    }
    SG_FREE(svm_value);
    SG_FREE(tiling_plif);
    SG_FREE(tiling_rows);
}

void CDynProg::create_word_string()
{
    SG_FREE(m_wordstr);
    m_wordstr=SG_MALLOC(uint16_t**, 5440);
    int32_t k=0;
    int32_t genestr_len=m_genestr.get_dim1();

    m_wordstr[k]=SG_MALLOC(uint16_t*, m_num_degrees);
    for (int32_t j=0; j<m_num_degrees; j++)
    {
        m_wordstr[k][j]=NULL ;
        {
            m_wordstr[k][j]=SG_MALLOC(uint16_t, genestr_len);
            for (int32_t i=0; i<genestr_len; i++)
                switch (m_genestr[i])
                {
                    case 'A':
                    case 'a': m_wordstr[k][j][i]=0 ; break ;
                    case 'C':
                    case 'c': m_wordstr[k][j][i]=1 ; break ;
                    case 'G':
                    case 'g': m_wordstr[k][j][i]=2 ; break ;
                    case 'T':
                    case 't': m_wordstr[k][j][i]=3 ; break ;
                    default: ASSERT(0) ;
                }
            CAlphabet::translate_from_single_order(m_wordstr[k][j], genestr_len, m_word_degree[j]-1, m_word_degree[j], 2) ;
        }
    }
}

void CDynProg::precompute_content_values()
{
    for (int32_t s=0; s<m_num_svms; s++)
      m_lin_feat.set_element(0.0, s, 0);

    for (int32_t p=0 ; p<m_seq_len-1 ; p++)
    {
        int32_t from_pos = m_pos[p];
        int32_t to_pos = m_pos[p+1];
        float64_t* my_svm_values_unnormalized = SG_MALLOC(float64_t, m_num_svms);
        //SG_PRINT("%i(%i->%i) ",p,from_pos, to_pos);

        ASSERT(from_pos<=m_genestr.get_dim1());
        ASSERT(to_pos<=m_genestr.get_dim1());

        for (int32_t s=0; s<m_num_svms; s++)
            my_svm_values_unnormalized[s]=0.0;//precomputed_svm_values.element(s,p);

        for (int32_t i=from_pos; i<to_pos; i++)
        {
            for (int32_t j=0; j<m_num_degrees; j++)
            {
                uint16_t word = m_wordstr[0][j][i] ;
                for (int32_t s=0; s<m_num_svms; s++)
                {
                    // check if this k-mer should be considered for this SVM
                    if (m_mod_words.get_element(s,0)==3 && i%3!=m_mod_words.get_element(s,1))
                        continue;
                    my_svm_values_unnormalized[s] += m_dict_weights[(word+m_cum_num_words_array[j])+s*m_cum_num_words_array[m_num_degrees]] ;
                }
            }
        }
        for (int32_t s=0; s<m_num_svms; s++)
        {
            float64_t prev = m_lin_feat.get_element(s, p);
            //SG_PRINT("elem (%i, %i, %f)\n", s, p, prev) ;
            if (prev<-1e20 || prev>1e20)
            {
                SG_ERROR("initialization missing (%i, %i, %f)\n", s, p, prev) ;
                prev=0 ;
            }
            m_lin_feat.set_element(prev + my_svm_values_unnormalized[s], s, p+1);
        }
        SG_FREE(my_svm_values_unnormalized);
    }
    //for (int32_t j=0; j<m_num_degrees; j++)
    //  SG_FREE(m_wordstr[0][j]);
    //SG_FREE(m_wordstr[0]);
}

void CDynProg::set_p_vector(SGVector<float64_t> p)
{
    if (!(p.vlen==m_N))
        SG_ERROR("length of start prob vector p (%i) is not equal to the number of states (%i), N: %i\n",p.vlen, m_N);

    m_initial_state_distribution_p.set_array(p.vector, p.vlen, true, true);
}

void CDynProg::set_q_vector(SGVector<float64_t> q)
{
    if (!(q.vlen==m_N))
        SG_ERROR("length of end prob vector q (%i) is not equal to the number of states (%i), N: %i\n",q.vlen, m_N);
    m_end_state_distribution_q.set_array(q.vector, q.vlen, true, true);
}

void CDynProg::set_a(SGMatrix<float64_t> a)
{
    ASSERT(a.num_cols==m_N);
    ASSERT(a.num_rows==m_N);
    m_transition_matrix_a.set_array(a.matrix, m_N, m_N, true, true);
    m_transition_matrix_a_deriv.resize_array(m_N, m_N);
}

void CDynProg::set_a_id(SGMatrix<int32_t> a)
{
    ASSERT(a.num_cols==m_N);
    ASSERT(a.num_rows==m_N);
    m_transition_matrix_a_id.set_array(a.matrix, m_N, m_N, true, true);
    m_max_a_id = 0;
    for (int32_t i=0; i<m_N; i++)
    {
        for (int32_t j=0; j<m_N; j++)
            m_max_a_id=CMath::max(m_max_a_id, m_transition_matrix_a_id.element(i,j));
    }
}

void CDynProg::set_a_trans_matrix(SGMatrix<float64_t> a_trans)
{
    int32_t num_trans=a_trans.num_rows;
    int32_t num_cols=a_trans.num_cols;

    //CMath::display_matrix(a_trans.matrix,num_trans, num_cols,"a_trans");

    if (!((num_cols==3) || (num_cols==4)))
        SG_ERROR("!((num_cols==3) || (num_cols==4)), num_cols: %i\n",num_cols);

    SG_FREE(trans_list_forward);
    SG_FREE(trans_list_forward_cnt);
    SG_FREE(trans_list_forward_val);
    SG_FREE(trans_list_forward_id);

    trans_list_forward = NULL ;
    trans_list_forward_cnt = NULL ;
    trans_list_forward_val = NULL ;
    trans_list_len = 0 ;

    m_transition_matrix_a.set_const(0) ;
    m_transition_matrix_a_id.set_const(0) ;

    mem_initialized = true ;

    trans_list_forward_cnt=NULL ;
    trans_list_len = m_N ;
    trans_list_forward = SG_MALLOC(T_STATES*, m_N);
    trans_list_forward_cnt = SG_MALLOC(T_STATES, m_N);
    trans_list_forward_val = SG_MALLOC(float64_t*, m_N);
    trans_list_forward_id = SG_MALLOC(int32_t*, m_N);

    int32_t start_idx=0;
    for (int32_t j=0; j<m_N; j++)
    {
        int32_t old_start_idx=start_idx;

        while (start_idx<num_trans && a_trans.matrix[start_idx+num_trans]==j)
        {
            start_idx++;

            if (start_idx>1 && start_idx<num_trans)
                ASSERT(a_trans.matrix[start_idx+num_trans-1] <= a_trans.matrix[start_idx+num_trans]);
        }

        if (start_idx>1 && start_idx<num_trans)
            ASSERT(a_trans.matrix[start_idx+num_trans-1] <= a_trans.matrix[start_idx+num_trans]);

        int32_t len=start_idx-old_start_idx;
        ASSERT(len>=0);

        trans_list_forward_cnt[j] = 0 ;

        if (len>0)
        {
            trans_list_forward[j]     = SG_MALLOC(T_STATES, len);
            trans_list_forward_val[j] = SG_MALLOC(float64_t, len);
            trans_list_forward_id[j] = SG_MALLOC(int32_t, len);
        }
        else
        {
            trans_list_forward[j]     = NULL;
            trans_list_forward_val[j] = NULL;
            trans_list_forward_id[j]  = NULL;
        }
    }

    for (int32_t i=0; i<num_trans; i++)
    {
        int32_t from_state   = (int32_t)a_trans.matrix[i] ;
        int32_t to_state = (int32_t)a_trans.matrix[i+num_trans] ;
        float64_t val = a_trans.matrix[i+num_trans*2] ;
        int32_t id = 0 ;
        if (num_cols==4)
            id = (int32_t)a_trans.matrix[i+num_trans*3] ;
        //SG_DEBUG( "id=%i\n", id) ;

        ASSERT(to_state>=0 && to_state<m_N);
        ASSERT(from_state>=0 && from_state<m_N);

        trans_list_forward[to_state][trans_list_forward_cnt[to_state]]=from_state ;
        trans_list_forward_val[to_state][trans_list_forward_cnt[to_state]]=val ;
        trans_list_forward_id[to_state][trans_list_forward_cnt[to_state]]=id ;
        trans_list_forward_cnt[to_state]++ ;
        m_transition_matrix_a.element(from_state, to_state) = val ;
        m_transition_matrix_a_id.element(from_state, to_state) = id ;
        //SG_PRINT("from_state:%i to_state:%i trans_matrix_a_id:%i \n",from_state, to_state,m_transition_matrix_a_id.element(from_state, to_state));
    } ;

    m_max_a_id = 0 ;
    for (int32_t i=0; i<m_N; i++)
        for (int32_t j=0; j<m_N; j++)
        {
            //if (m_transition_matrix_a_id.element(i,j))
            //SG_DEBUG( "(%i,%i)=%i\n", i,j, m_transition_matrix_a_id.element(i,j)) ;
            m_max_a_id = CMath::max(m_max_a_id, m_transition_matrix_a_id.element(i,j)) ;
        }
    //SG_DEBUG( "m_max_a_id=%i\n", m_max_a_id) ;
}


void CDynProg::init_mod_words_array(SGMatrix<int32_t> mod_words_input)
{
    //for (int32_t i=0; i<mod_words_input.num_cols; i++)
    //{
    //  for (int32_t j=0; j<mod_words_input.num_rows; j++)
    //      SG_PRINT("%i ",mod_words_input[i*mod_words_input.num_rows+j]);
    //  SG_PRINT("\n");
    //}
    m_svm_arrays_clean=false ;

    ASSERT(m_num_svms==mod_words_input.num_rows);
    ASSERT(mod_words_input.num_cols==2);

    m_mod_words.set_array(mod_words_input.matrix, mod_words_input.num_rows, 2, true, true) ;
    m_mod_words_array = m_mod_words.get_array() ;

    /*SG_DEBUG( "m_mod_words=[") ;
    for (int32_t i=0; i<mod_words_input.num_rows; i++)
        SG_DEBUG( "%i, ", p_mod_words_array[i]) ;
        SG_DEBUG( "]\n") ;*/
}

bool CDynProg::check_svm_arrays()
{
    //SG_DEBUG( "wd_dim1=%d, m_cum_num_words=%d, m_num_words=%d, m_svm_pos_start=%d, num_uniq_w=%d, mod_words_dims=(%d,%d), sign_w=%d,string_w=%d\n m_num_degrees=%d, m_num_svms=%d, m_num_strings=%d", m_word_degree.get_dim1(), m_cum_num_words.get_dim1(), m_num_words.get_dim1(), m_svm_pos_start.get_dim1(), m_num_unique_words.get_dim1(), m_mod_words.get_dim1(), m_mod_words.get_dim2(), m_sign_words.get_dim1(), m_string_words.get_dim1(), m_num_degrees, m_num_svms, m_num_strings);
    if ((m_word_degree.get_dim1()==m_num_degrees) &&
            (m_cum_num_words.get_dim1()==m_num_degrees+1) &&
            (m_num_words.get_dim1()==m_num_degrees) &&
            //(word_used.get_dim1()==m_num_degrees) &&
            //(word_used.get_dim2()==m_num_words[m_num_degrees-1]) &&
            //(word_used.get_dim3()==m_num_strings) &&
            //      (svm_values_unnormalized.get_dim1()==m_num_degrees) &&
            //      (svm_values_unnormalized.get_dim2()==m_num_svms) &&
            //(m_svm_pos_start.get_dim1()==m_num_degrees) &&
            (m_num_unique_words.get_dim1()==m_num_degrees) &&
            (m_mod_words.get_dim1()==m_num_svms) &&
            (m_mod_words.get_dim2()==2) &&
            (m_sign_words.get_dim1()==m_num_svms) &&
            (m_string_words.get_dim1()==m_num_svms))
    {
        m_svm_arrays_clean=true ;
        return true ;
    }
    else
    {
        if ((m_num_unique_words.get_dim1()==m_num_degrees) &&
            (m_mod_words.get_dim1()==m_num_svms) &&
            (m_mod_words.get_dim2()==2) &&
            (m_sign_words.get_dim1()==m_num_svms) &&
            (m_string_words.get_dim1()==m_num_svms))
            SG_PRINT("OK\n") ;
        else
            SG_PRINT("not OK\n") ;

        if (!(m_word_degree.get_dim1()==m_num_degrees))
            SG_WARNING("SVM array: word_degree.get_dim1()!=m_num_degrees") ;
        if (!(m_cum_num_words.get_dim1()==m_num_degrees+1))
            SG_WARNING("SVM array: m_cum_num_words.get_dim1()!=m_num_degrees+1") ;
        if (!(m_num_words.get_dim1()==m_num_degrees))
            SG_WARNING("SVM array: m_num_words.get_dim1()==m_num_degrees") ;
        //if (!(m_svm_pos_start.get_dim1()==m_num_degrees))
        //  SG_WARNING("SVM array: m_svm_pos_start.get_dim1()!=m_num_degrees") ;
        if (!(m_num_unique_words.get_dim1()==m_num_degrees))
            SG_WARNING("SVM array: m_num_unique_words.get_dim1()!=m_num_degrees") ;
        if (!(m_mod_words.get_dim1()==m_num_svms))
            SG_WARNING("SVM array: m_mod_words.get_dim1()!=num_svms") ;
        if (!(m_mod_words.get_dim2()==2))
            SG_WARNING("SVM array: m_mod_words.get_dim2()!=2") ;
        if (!(m_sign_words.get_dim1()==m_num_svms))
            SG_WARNING("SVM array: m_sign_words.get_dim1()!=num_svms") ;
        if (!(m_string_words.get_dim1()==m_num_svms))
            SG_WARNING("SVM array: m_string_words.get_dim1()!=num_svms") ;

        m_svm_arrays_clean=false ;
        return false ;
    }
}

void CDynProg::set_observation_matrix(SGNDArray<float64_t> seq)
{
    if (seq.num_dims!=3)
        SG_ERROR("Expected 3-dimensional Matrix\n");

    int32_t N=seq.dims[0];
    int32_t cand_pos=seq.dims[1];
    int32_t max_num_features=seq.dims[2];

    if (!m_svm_arrays_clean)
    {
        SG_ERROR( "SVM arrays not clean") ;
        return ;
    } ;

    ASSERT(N==m_N);
    ASSERT(cand_pos==m_seq_len);
    ASSERT(m_initial_state_distribution_p.get_dim1()==N);
    ASSERT(m_end_state_distribution_q.get_dim1()==N);

    m_observation_matrix.set_array(seq.array, N, m_seq_len, max_num_features, true, true) ;
}
int32_t CDynProg::get_num_positions()
{
    return m_seq_len;
}

void CDynProg::set_content_type_array(SGMatrix<float64_t> seg_path)
{
    ASSERT(seg_path.num_rows==2);
    ASSERT(seg_path.num_cols==m_seq_len);

    if (seg_path.matrix!=NULL)
    {
        int32_t *segment_ids = SG_MALLOC(int32_t, m_seq_len);
        float64_t *segment_mask = SG_MALLOC(float64_t, m_seq_len);
        for (int32_t i=0; i<m_seq_len; i++)
        {
                segment_ids[i] = (int32_t)seg_path.matrix[2*i] ;
                segment_mask[i] = seg_path.matrix[2*i+1] ;
        }
        best_path_set_segment_ids_mask(segment_ids, segment_mask, m_seq_len) ;
        SG_FREE(segment_ids);
        SG_FREE(segment_mask);
    }
    else
    {
        int32_t *izeros = SG_MALLOC(int32_t, m_seq_len);
        float64_t *dzeros = SG_MALLOC(float64_t, m_seq_len);
        for (int32_t i=0; i<m_seq_len; i++)
        {
            izeros[i]=0 ;
            dzeros[i]=0.0 ;
        }
        best_path_set_segment_ids_mask(izeros, dzeros, m_seq_len) ;
        SG_FREE(izeros);
        SG_FREE(dzeros);
    }
}

void CDynProg::set_pos(SGVector<int32_t> pos)
{
    m_pos.set_array(pos.vector, pos.vlen, true, true) ;
    m_seq_len = pos.vlen;
}

void CDynProg::set_orf_info(SGMatrix<int32_t> orf_info)
{
    if (orf_info.num_cols!=2)
        SG_ERROR( "orf_info size incorrect %i!=2\n", orf_info.num_cols) ;

    m_orf_info.set_array(orf_info.matrix, orf_info.num_rows, orf_info.num_cols, true, true) ;
    m_orf_info.set_array_name("orf_info") ;
}

void CDynProg::set_sparse_features(CSparseFeatures<float64_t>* seq_sparse1, CSparseFeatures<float64_t>* seq_sparse2)
{
    if ((!seq_sparse1 && seq_sparse2) || (seq_sparse1 && !seq_sparse2))
        SG_ERROR("Sparse features must either both be NULL or both NON-NULL\n");

    SG_UNREF(m_seq_sparse1);
    SG_UNREF(m_seq_sparse2);

    m_seq_sparse1=seq_sparse1;
    m_seq_sparse2=seq_sparse2;
    SG_REF(m_seq_sparse1);
    SG_REF(m_seq_sparse2);
}

void CDynProg::set_plif_matrices(CPlifMatrix* pm)
{
    SG_UNREF(m_plif_matrices);

    m_plif_matrices=pm;

    SG_REF(m_plif_matrices);
}

void CDynProg::set_gene_string(SGVector<char> genestr)
{
    ASSERT(genestr.vector);
    ASSERT(genestr.vlen>0);

    m_genestr.set_array(genestr.vector, genestr.vlen, true, true) ;
}

void CDynProg::set_my_state_seq(int32_t* my_state_seq)
{
    ASSERT(my_state_seq && m_seq_len>0);
    m_my_state_seq.resize_array(m_seq_len);
    for (int32_t i=0; i<m_seq_len; i++)
        m_my_state_seq[i]=my_state_seq[i];
}

void CDynProg::set_my_pos_seq(int32_t* my_pos_seq)
{
    ASSERT(my_pos_seq && m_seq_len>0);
    m_my_pos_seq.resize_array(m_seq_len);
    for (int32_t i=0; i<m_seq_len; i++)
        m_my_pos_seq[i]=my_pos_seq[i];
}

void CDynProg::set_dict_weights(SGMatrix<float64_t> dictionary_weights)
{
    if (m_num_svms!=dictionary_weights.num_cols)
    {
        SG_ERROR( "m_dict_weights array does not match num_svms=%i!=%i\n",
                m_num_svms, dictionary_weights.num_cols) ;
    }

    m_dict_weights.set_array(dictionary_weights.matrix, dictionary_weights.num_rows, m_num_svms, true, true) ;

    // initialize, so it does not bother when not used
    m_segment_loss.resize_array(m_max_a_id+1, m_max_a_id+1, 2) ;
    m_segment_loss.set_const(0) ;
    m_segment_ids.resize_array(m_observation_matrix.get_dim2()) ;
    m_segment_mask.resize_array(m_observation_matrix.get_dim2()) ;
    m_segment_ids.set_const(0) ;
    m_segment_mask.set_const(0) ;
}

void CDynProg::best_path_set_segment_loss(SGMatrix<float64_t> segment_loss)
{
    int32_t m=segment_loss.num_rows;
    int32_t n=segment_loss.num_cols;
    // here we need two matrices. Store it in one: 2N x N
    if (2*m!=n)
        SG_ERROR( "segment_loss should be 2 x quadratic matrix: %i!=%i\n", 2*m, n) ;

    if (m!=m_max_a_id+1)
        SG_ERROR( "segment_loss size should match m_max_a_id: %i!=%i\n", m, m_max_a_id+1) ;

    m_segment_loss.set_array(segment_loss.matrix, m, n/2, 2, true, true) ;
    /*for (int32_t i=0; i<n; i++)
        for (int32_t j=0; j<n; j++)
        SG_DEBUG( "loss(%i,%i)=%f\n", i,j, m_segment_loss.element(0,i,j)) ;*/
}

void CDynProg::best_path_set_segment_ids_mask(
    int32_t* segment_ids, float64_t* segment_mask, int32_t m)
{

    if (m!=m_observation_matrix.get_dim2())
        SG_ERROR("size of segment_ids or segment_mask (%i)  does not match the size of the feature matrix (%i)", m, m_observation_matrix.get_dim2());
    int32_t max_id = 0;
    for (int32_t i=1;i<m;i++)
        max_id = CMath::max(max_id,segment_ids[i]);
    //SG_PRINT("max_id: %i, m:%i\n",max_id, m);
    m_segment_ids.set_array(segment_ids, m, true, true) ;
    m_segment_ids.set_array_name("m_segment_ids");
    m_segment_mask.set_array(segment_mask, m, true, true) ;
    m_segment_mask.set_array_name("m_segment_mask");

    m_seg_loss_obj->set_segment_mask(&m_segment_mask);
    m_seg_loss_obj->set_segment_ids(&m_segment_ids);
    m_seg_loss_obj->compute_loss(m_pos.get_array(), m_seq_len);
}

SGVector<float64_t> CDynProg::get_scores()
{
    SGVector<float64_t> scores(m_scores.get_dim1());
    memcpy(scores.vector,m_scores.get_array(), sizeof(float64_t)*(m_scores.get_dim1()));

    return scores;
}

SGMatrix<int32_t> CDynProg::get_states()
{
    SGMatrix<int32_t> states(m_states.get_dim1(), m_states.get_dim2());

    int32_t sz = sizeof(int32_t)*( m_states.get_dim1() * m_states.get_dim2() );
    memcpy(states.matrix ,m_states.get_array(),sz);

    return states;
}

SGMatrix<int32_t> CDynProg::get_positions()
{
   SGMatrix<int32_t> positions(m_positions.get_dim1(), m_positions.get_dim2());

   int32_t sz = sizeof(int32_t)*(m_positions.get_dim1()*m_positions.get_dim2());
   memcpy(positions.matrix, m_positions.get_array(),sz);

   return positions;
}

void CDynProg::get_path_scores(float64_t** scores, int32_t* seq_len)
{
   ASSERT(scores && seq_len);

   *seq_len=m_my_scores.get_dim1();

   int32_t sz = sizeof(float64_t)*(*seq_len);

   *scores = SG_MALLOC(float64_t, *seq_len);
   ASSERT(*scores);

   memcpy(*scores,m_my_scores.get_array(),sz);
}

void CDynProg::get_path_losses(float64_t** losses, int32_t* seq_len)
{
    ASSERT(losses && seq_len);

    *seq_len=m_my_losses.get_dim1();

   int32_t sz = sizeof(float64_t)*(*seq_len);

   *losses = SG_MALLOC(float64_t, *seq_len);
   ASSERT(*losses);

   memcpy(*losses,m_my_losses.get_array(),sz);
}


bool CDynProg::extend_orf(
    int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos,
    int32_t to)
{
#ifdef DYNPROG_TIMING_DETAIL
    MyTime.start() ;
#endif

    if (start<0)
        start=0 ;
    if (to<0)
        to=0 ;

    int32_t orf_target = orf_to-orf_from ;
    if (orf_target<0) orf_target+=3 ;

    int32_t pos ;
    if (last_pos==to)
        pos = to-orf_to-3 ;
    else
        pos=last_pos ;

    if (pos<0)
    {
#ifdef DYNPROG_TIMING_DETAIL
        MyTime.stop() ;
        orf_time += MyTime.time_diff_sec() ;
#endif
        return true ;
    }

    for (; pos>=start; pos-=3)
        if (m_genestr_stop[pos])
        {
#ifdef DYNPROG_TIMING_DETAIL
            MyTime.stop() ;
            orf_time += MyTime.time_diff_sec() ;
#endif
            return false ;
        }


    last_pos = CMath::min(pos+3,to-orf_to-3) ;

#ifdef DYNPROG_TIMING_DETAIL
    MyTime.stop() ;
    orf_time += MyTime.time_diff_sec() ;
#endif
    return true ;
}

void CDynProg::compute_nbest_paths(int32_t max_num_signals, bool use_orf,
        int16_t nbest, bool with_loss, bool with_multiple_sequences)
    {

    //FIXME we need checks here if all the fields are of right size
    //SG_PRINT("m_seq_len: %i\n", m_seq_len);
    //SG_PRINT("m_pos[0]: %i\n", m_pos[0]);
    //SG_PRINT("\n");

    //FIXME these variables can go away when compute_nbest_paths uses them
    //instead of the local pointers below
    const float64_t* seq_array = m_observation_matrix.get_array();
    m_scores.resize_array(nbest) ;
    m_states.resize_array(nbest, m_observation_matrix.get_dim2()) ;
    m_positions.resize_array(nbest, m_observation_matrix.get_dim2()) ;

    for (int32_t i=0; i<nbest; i++)
    {
        m_scores[i]=-1;
        for (int32_t j=0; j<m_observation_matrix.get_dim2(); j++)
        {
            m_states.element(i,j)=-1;
            m_positions.element(i,j)=-1;
        }
    }
    float64_t* prob_nbest=m_scores.get_array();
    int32_t* my_state_seq=m_states.get_array();
    int32_t* my_pos_seq=m_positions.get_array();

    CPlifBase** Plif_matrix=m_plif_matrices->get_plif_matrix();
    CPlifBase** Plif_state_signals=m_plif_matrices->get_state_signals();
    //END FIXME


#ifdef DYNPROG_TIMING
        segment_init_time = 0.0 ;
        segment_pos_time = 0.0 ;
        segment_extend_time = 0.0 ;
        segment_clean_time = 0.0 ;
        orf_time = 0.0 ;
        svm_init_time = 0.0 ;
        svm_pos_time = 0.0 ;
        svm_clean_time = 0.0 ;
        inner_loop_time = 0.0 ;
        content_svm_values_time = 0.0 ;
        content_plifs_time = 0.0 ;
        inner_loop_max_time = 0.0 ;
        long_transition_time = 0.0 ;

        MyTime2.start() ;
#endif

        if (!m_svm_arrays_clean)
        {
            SG_ERROR( "SVM arrays not clean") ;
            return ;
        }

#ifdef DYNPROG_DEBUG
        m_transition_matrix_a.set_array_name("transition_matrix");
        m_transition_matrix_a.display_array();
        m_mod_words.display_array() ;
        m_sign_words.display_array() ;
        m_string_words.display_array() ;
        //SG_PRINT("use_orf = %i\n", use_orf) ;
#endif

        int32_t max_look_back = 1000 ;
        bool use_svm = false ;

        SG_DEBUG("m_N:%i, m_seq_len:%i, max_num_signals:%i\n",m_N, m_seq_len, max_num_signals) ;

        //for (int32_t i=0;i<m_N*m_seq_len*max_num_signals;i++)
      //   SG_PRINT("(%i)%0.2f ",i,seq_array[i]);

        CDynamicObjectArray PEN((CSGObject**) Plif_matrix, m_N, m_N, false, false) ; // 2d, CPlifBase*
        PEN.set_array_name("PEN");

        CDynamicObjectArray PEN_state_signals((CSGObject**) Plif_state_signals, m_N, max_num_signals, false, false) ; // 2d,  CPlifBase*
        PEN_state_signals.set_array_name("state_signals");

        CDynamicArray<float64_t> seq(m_N, m_seq_len) ; // 2d
        seq.set_array_name("seq") ;
        seq.set_const(0) ;

#ifdef DYNPROG_DEBUG
        SG_PRINT("m_num_raw_data: %i\n",m_num_raw_data);
        SG_PRINT("m_num_intron_plifs: %i\n", m_num_intron_plifs);
        SG_PRINT("m_num_svms: %i\n", m_num_svms);
        SG_PRINT("m_num_lin_feat_plifs_cum: ");
        for (int i=0; i<=m_num_raw_data; i++)
            SG_PRINT(" %i  ",m_num_lin_feat_plifs_cum[i]);
        SG_PRINT("\n");
#endif

        float64_t* svm_value = SG_MALLOC(float64_t , m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs);
        { // initialize svm_svalue
            for (int32_t s=0; s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; s++)
                svm_value[s]=0 ;
        }

        { // convert seq_input to seq
            // this is independent of the svm values

            CDynamicArray<float64_t> *seq_input=NULL ; // 3d
            if (seq_array!=NULL)
            {
                //SG_PRINT("using dense seq_array\n") ;

                seq_input=new CDynamicArray<float64_t>(seq_array, m_N, m_seq_len, max_num_signals) ;
                seq_input->set_array_name("seq_input") ;
                //seq_input.display_array() ;

                ASSERT(m_seq_sparse1==NULL) ;
                ASSERT(m_seq_sparse2==NULL) ;
            } else
            {
                SG_PRINT("using sparse seq_array\n") ;

                ASSERT(m_seq_sparse1!=NULL) ;
                ASSERT(m_seq_sparse2!=NULL) ;
                ASSERT(max_num_signals==2) ;
            }

            for (int32_t i=0; i<m_N; i++)
                for (int32_t j=0; j<m_seq_len; j++)
                    seq.element(i,j) = 0 ;

            for (int32_t i=0; i<m_N; i++)
                for (int32_t j=0; j<m_seq_len; j++)
                    for (int32_t k=0; k<max_num_signals; k++)
                    {
                        if ((PEN_state_signals.element(i,k)==NULL) && (k==0))
                        {
                            // no plif
                            if (seq_input!=NULL)
                                seq.element(i,j) = seq_input->element(i,j,k) ;
                            else
                            {
                                if (k==0)
                                    seq.element(i,j) = m_seq_sparse1->get_feature(i,j) ;
                                if (k==1)
                                    seq.element(i,j) = m_seq_sparse2->get_feature(i,j) ;
                            }
                            break ;
                        }
                        if (PEN_state_signals.element(i,k)!=NULL)
                        {
                            if (seq_input!=NULL)
                            {
                                // just one plif
                                if (CMath::is_finite(seq_input->element(i,j,k)))
                                    seq.element(i,j) += ((CPlifBase*) PEN_state_signals.element(i,k))->lookup_penalty(seq_input->element(i,j,k), svm_value) ;
                                else
                                    // keep infinity values
                                    seq.element(i,j) = seq_input->element(i, j, k) ;
                            }
                            else
                            {
                                if (k==0)
                                {
                                    // just one plif
                                    if (CMath::is_finite(m_seq_sparse1->get_feature(i,j)))
                                        seq.element(i,j) += ((CPlifBase*) PEN_state_signals.element(i,k))->lookup_penalty(m_seq_sparse1->get_feature(i,j), svm_value) ;
                                    else
                                        // keep infinity values
                                        seq.element(i,j) = m_seq_sparse1->get_feature(i, j) ;
                                }
                                if (k==1)
                                {
                                    // just one plif
                                    if (CMath::is_finite(m_seq_sparse2->get_feature(i,j)))
                                        seq.element(i,j) += ((CPlifBase*) PEN_state_signals.element(i,k))->lookup_penalty(m_seq_sparse2->get_feature(i,j), svm_value) ;
                                    else
                                        // keep infinity values
                                        seq.element(i,j) = m_seq_sparse2->get_feature(i, j) ;
                                }
                            }
                        }
                        else
                            break ;
                    }
            delete seq_input;
            SG_FREE(svm_value);
        }

        // allow longer transitions than look_back
        bool long_transitions = m_long_transitions ;
        CDynamicArray<int32_t> long_transition_content_start_position(m_N,m_N) ; // 2d
        long_transition_content_start_position.set_array_name("long_transition_content_start_position");
#ifdef DYNPROG_DEBUG
        CDynamicArray<int32_t> long_transition_content_end_position(m_N,m_N) ; // 2d
        long_transition_content_end_position.set_array_name("long_transition_content_end_position");
#endif
        CDynamicArray<int32_t> long_transition_content_start(m_N,m_N) ; // 2d
        long_transition_content_start.set_array_name("long_transition_content_start");

        CDynamicArray<float64_t> long_transition_content_scores(m_N,m_N) ; // 2d
        long_transition_content_scores.set_array_name("long_transition_content_scores");
#ifdef DYNPROG_DEBUG

        CDynamicArray<float64_t> long_transition_content_scores_pen(m_N,m_N) ; // 2d
        long_transition_content_scores_pen.set_array_name("long_transition_content_scores_pen");

        CDynamicArray<float64_t> long_transition_content_scores_prev(m_N,m_N) ; // 2d
        long_transition_content_scores_prev.set_array_name("long_transition_content_scores_prev");

        CDynamicArray<float64_t> long_transition_content_scores_elem(m_N,m_N) ; // 2d
        long_transition_content_scores_elem.set_array_name("long_transition_content_scores_elem");
#endif
        CDynamicArray<float64_t> long_transition_content_scores_loss(m_N,m_N) ; // 2d
        long_transition_content_scores_loss.set_array_name("long_transition_content_scores_loss");

        if (nbest!=1)
        {
            SG_ERROR("Long transitions are not supported for nbest!=1") ;
            long_transitions = false ;
        }
        long_transition_content_scores.set_const(-CMath::INFTY);
#ifdef DYNPROG_DEBUG
        long_transition_content_scores_pen.set_const(0) ;
        long_transition_content_scores_elem.set_const(0) ;
        long_transition_content_scores_prev.set_const(0) ;
#endif
        if (with_loss)
            long_transition_content_scores_loss.set_const(0) ;
        long_transition_content_start.set_const(0) ;
        long_transition_content_start_position.set_const(0) ;
#ifdef DYNPROG_DEBUG
        long_transition_content_end_position.set_const(0) ;
#endif

        svm_value = SG_MALLOC(float64_t , m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs);
        { // initialize svm_svalue
            for (int32_t s=0; s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; s++)
                svm_value[s]=0 ;
        }

        CDynamicArray<int32_t> look_back(m_N,m_N) ; // 2d
        look_back.set_array_name("look_back");
        //CDynamicArray<int32_t> look_back_orig(m_N,m_N) ;
        //look_back.set_array_name("look_back_orig");


        { // determine maximal length of look-back
            for (int32_t i=0; i<m_N; i++)
                for (int32_t j=0; j<m_N; j++)
                {
                    look_back.set_element(INT_MAX, i, j) ;
                    //look_back_orig.set_element(INT_MAX, i, j) ;
                }

            for (int32_t j=0; j<m_N; j++)
            {
                // only consider transitions that are actually allowed
                const T_STATES num_elem   = trans_list_forward_cnt[j] ;
                const T_STATES *elem_list = trans_list_forward[j] ;

                for (int32_t i=0; i<num_elem; i++)
                {
                    T_STATES ii = elem_list[i] ;

                    CPlifBase *penij=(CPlifBase*) PEN.element(j, ii) ;
                    if (penij==NULL)
                    {
                        if (long_transitions)
                        {
                            look_back.set_element(m_long_transition_threshold, j, ii) ;
                            //look_back_orig.set_element(m_long_transition_max, j, ii) ;
                        }
                        continue ;
                    }

                    /* if the transition is an ORF or we do computation with loss, we have to disable long transitions */
                    if ((m_orf_info.element(ii,0)!=-1) || (m_orf_info.element(j,1)!=-1) || (!long_transitions))
                    {
                        look_back.set_element(CMath::ceil(penij->get_max_value()), j, ii) ;
                        //look_back_orig.set_element(CMath::ceil(penij->get_max_value()), j, ii) ;
                        if (CMath::ceil(penij->get_max_value()) > max_look_back)
                        {
                            SG_DEBUG( "%d %d -> value: %f\n", ii,j,penij->get_max_value());
                            max_look_back = (int32_t) (CMath::ceil(penij->get_max_value()));
                        }
                    }
                    else
                    {
                        look_back.set_element(CMath::min( (int32_t)CMath::ceil(penij->get_max_value()), m_long_transition_threshold ), j, ii) ;
                        //look_back_orig.set_element( (int32_t)CMath::ceil(penij->get_max_value()), j, ii) ;
                    }

                    if (penij->uses_svm_values())
                        use_svm=true ;
                }
            }
            /* make sure max_look_back is at least as long as a long transition */
            if (long_transitions)
                max_look_back = CMath::max(m_long_transition_threshold, max_look_back) ;

            /* make sure max_look_back is not longer than the whole string */
            max_look_back = CMath::min(m_genestr.get_dim1(), max_look_back) ;

            int32_t num_long_transitions = 0 ;
            for (int32_t i=0; i<m_N; i++)
                for (int32_t j=0; j<m_N; j++)
                {
                    if (look_back.get_element(i,j)==m_long_transition_threshold)
                        num_long_transitions++ ;
                    if (look_back.get_element(i,j)==INT_MAX)
                    {
                        if (long_transitions)
                        {
                            look_back.set_element(m_long_transition_threshold, i, j) ;
                            //look_back_orig.set_element(m_long_transition_max, i, j) ;
                        }
                        else
                        {
                            look_back.set_element(max_look_back, i, j) ;
                            //look_back_orig.set_element(m_long_transition_max, i, j) ;
                        }
                    }
                }
            SG_DEBUG("Using %i long transitions\n", num_long_transitions) ;
        }
        //SG_PRINT("max_look_back: %i \n", max_look_back) ;

        //SG_PRINT("use_svm=%i, genestr_len: \n", use_svm, m_genestr.get_dim1()) ;
        SG_DEBUG("use_svm=%i\n", use_svm) ;

        SG_DEBUG("maxlook: %d m_N: %d nbest: %d \n", max_look_back, m_N, nbest);
        const int32_t look_back_buflen = (max_look_back*m_N+1)*nbest ;
        SG_DEBUG("look_back_buflen=%i\n", look_back_buflen) ;
        /*const float64_t mem_use = (float64_t)(m_seq_len*m_N*nbest*(sizeof(T_STATES)+sizeof(int16_t)+sizeof(int32_t))+
          look_back_buflen*(2*sizeof(float64_t)+sizeof(int32_t))+
          m_seq_len*(sizeof(T_STATES)+sizeof(int32_t))+
          m_genestr.get_dim1()*sizeof(bool))/(1024*1024);*/

        //bool is_big = (mem_use>200) || (m_seq_len>5000) ;

        /*if (is_big)
          {
          SG_DEBUG("calling compute_nbest_paths: m_seq_len=%i, m_N=%i, lookback=%i nbest=%i\n",
          m_seq_len, m_N, max_look_back, nbest) ;
          SG_DEBUG("allocating %1.2fMB of memory\n",
          mem_use) ;
          }*/
        ASSERT(nbest<32000) ;

        CDynamicArray<float64_t> delta(m_seq_len, m_N, nbest) ; // 3d
        delta.set_array_name("delta");
        float64_t* delta_array = delta.get_array() ;
        //delta.set_const(0) ;

        CDynamicArray<T_STATES> psi(m_seq_len, m_N, nbest) ; // 3d
        psi.set_array_name("psi");
        //psi.set_const(0) ;

        CDynamicArray<int16_t> ktable(m_seq_len, m_N, nbest) ; // 3d
        ktable.set_array_name("ktable");
        //ktable.set_const(0) ;

        CDynamicArray<int32_t> ptable(m_seq_len, m_N, nbest) ; // 3d
        ptable.set_array_name("ptable");
        //ptable.set_const(0) ;

        CDynamicArray<float64_t> delta_end(nbest) ;
        delta_end.set_array_name("delta_end");
        //delta_end.set_const(0) ;

        CDynamicArray<T_STATES> path_ends(nbest) ;
        path_ends.set_array_name("path_ends");
        //path_ends.set_const(0) ;

        CDynamicArray<int16_t> ktable_end(nbest) ;
        ktable_end.set_array_name("ktable_end");
        //ktable_end.set_const(0) ;

        float64_t * fixedtempvv=SG_MALLOC(float64_t, look_back_buflen);
        memset(fixedtempvv, 0, look_back_buflen*sizeof(float64_t)) ;
        int32_t * fixedtempii=SG_MALLOC(int32_t, look_back_buflen);
        memset(fixedtempii, 0, look_back_buflen*sizeof(int32_t)) ;

        CDynamicArray<float64_t> oldtempvv(look_back_buflen) ;
        oldtempvv.set_array_name("oldtempvv");

        CDynamicArray<float64_t> oldtempvv2(look_back_buflen) ;
        oldtempvv2.set_array_name("oldtempvv2");
        //oldtempvv.set_const(0) ;
        //oldtempvv.display_size() ;

        CDynamicArray<int32_t> oldtempii(look_back_buflen) ;
        oldtempii.set_array_name("oldtempii");

        CDynamicArray<int32_t> oldtempii2(look_back_buflen) ;
        oldtempii2.set_array_name("oldtempii2");
        //oldtempii.set_const(0) ;

        CDynamicArray<T_STATES> state_seq(m_seq_len) ;
        state_seq.set_array_name("state_seq");
        //state_seq.set_const(0) ;

        CDynamicArray<int32_t> pos_seq(m_seq_len) ;
        pos_seq.set_array_name("pos_seq");
        //pos_seq.set_const(0) ;


        m_dict_weights.set_array_name("dict_weights") ;
        m_word_degree.set_array_name("word_degree") ;
        m_cum_num_words.set_array_name("cum_num_words") ;
        m_num_words.set_array_name("num_words") ;
        //word_used.set_array_name("word_used") ;
        //svm_values_unnormalized.set_array_name("svm_values_unnormalized") ;
        //m_svm_pos_start.set_array_name("svm_pos_start") ;
        m_num_unique_words.set_array_name("num_unique_words") ;

        PEN.set_array_name("PEN") ;
        seq.set_array_name("seq") ;

        delta.set_array_name("delta") ;
        psi.set_array_name("psi") ;
        ktable.set_array_name("ktable") ;
        ptable.set_array_name("ptable") ;
        delta_end.set_array_name("delta_end") ;
        path_ends.set_array_name("path_ends") ;
        ktable_end.set_array_name("ktable_end") ;

#ifdef USE_TMP_ARRAYCLASS
        fixedtempvv.set_array_name("fixedtempvv") ;
        fixedtempii.set_array_name("fixedtempvv") ;
#endif

        oldtempvv.set_array_name("oldtempvv") ;
        oldtempvv2.set_array_name("oldtempvv2") ;
        oldtempii.set_array_name("oldtempii") ;
        oldtempii2.set_array_name("oldtempii2") ;



#ifdef DYNPROG_DEBUG
        state_seq.display_size() ;
        pos_seq.display_size() ;

        m_dict_weights.display_size() ;
        m_word_degree.display_array() ;
        m_cum_num_words.display_array() ;
        m_num_words.display_array() ;
        //word_used.display_size() ;
        //svm_values_unnormalized.display_size() ;
        //m_svm_pos_start.display_array() ;
        m_num_unique_words.display_array() ;

        PEN.display_size() ;
        PEN_state_signals.display_size() ;
        seq.display_size() ;
        m_orf_info.display_size() ;

        //m_genestr_stop.display_size() ;
        delta.display_size() ;
        psi.display_size() ;
        ktable.display_size() ;
        ptable.display_size() ;
        delta_end.display_size() ;
        path_ends.display_size() ;
        ktable_end.display_size() ;

#ifdef USE_TMP_ARRAYCLASS
        fixedtempvv.display_size() ;
        fixedtempii.display_size() ;
#endif

        //oldtempvv.display_size() ;
        //oldtempii.display_size() ;

        state_seq.display_size() ;
        pos_seq.display_size() ;

        //seq.set_const(0) ;

#endif //DYNPROG_DEBUG




        {
            for (int32_t s=0; s<m_num_svms; s++)
                ASSERT(m_string_words_array[s]<1)  ;
        }


        //CDynamicArray<int32_t*> trans_matrix_svms(m_N,m_N); // 2d
        //CDynamicArray<int32_t> trans_matrix_num_svms(m_N,m_N); // 2d

        { // initialization

            for (T_STATES i=0; i<m_N; i++)
            {
                //delta.element(0, i, 0) = get_p(i) + seq.element(i,0) ;        // get_p defined in HMM.h to be equiv to initial_state_distribution
                delta.element(delta_array, 0, i, 0, m_seq_len, m_N) = get_p(i) + seq.element(i,0) ;        // get_p defined in HMM.h to be equiv to initial_state_distribution
                psi.element(0,i,0)   = 0 ;
                if (nbest>1)
                    ktable.element(0,i,0)  = 0 ;
                ptable.element(0,i,0)  = 0 ;
                for (int16_t k=1; k<nbest; k++)
                {
                    int32_t dim1, dim2, dim3 ;
                    delta.get_array_size(dim1, dim2, dim3) ;
                    //SG_DEBUG("i=%i, k=%i -- %i, %i, %i\n", i, k, dim1, dim2, dim3) ;
                    //delta.element(0, i, k)    = -CMath::INFTY ;
                    delta.element(delta_array, 0, i, k, m_seq_len, m_N)    = -CMath::INFTY ;
                    psi.element(0,i,0)      = 0 ;                  // <--- what's this for?
                    if (nbest>1)
                        ktable.element(0,i,k)     = 0 ;
                    ptable.element(0,i,k)     = 0 ;
                }
                /*
                   for (T_STATES j=0; j<m_N; j++)
                   {
                   CPlifBase * penalty = PEN.element(i,j) ;
                   int32_t num_current_svms=0;
                   int32_t svm_ids[] = {-8, -7, -6, -5, -4, -3, -2, -1};
                   if (penalty)
                   {
                   SG_PRINT("trans %i -> %i \n",i,j);
                   penalty->get_used_svms(&num_current_svms, svm_ids);
                   trans_matrix_svms.set_element(svm_ids,i,j);
                   for (int32_t l=0;l<num_current_svms;l++)
                   SG_PRINT("svm_ids[%i]: %i \n",l,svm_ids[l]);
                   trans_matrix_num_svms.set_element(num_current_svms,i,j);
                   }
                   }
                   */

            }
        }

        SG_DEBUG("START_RECURSION \n\n");

        // recursion
        for (int32_t t=1; t<m_seq_len; t++)
        {
            //if (is_big && t%(1+(m_seq_len/1000))==1)
            //  SG_PROGRESS(t, 0, m_seq_len);
            //SG_PRINT("%i\n", t) ;

            for (T_STATES j=0; j<m_N; j++)
            {
                if (seq.element(j,t)<=-1e20)
                { // if we cannot observe the symbol here, then we can omit the rest
                    for (int16_t k=0; k<nbest; k++)
                    {
                        delta.element(delta_array, t, j, k, m_seq_len, m_N)    = seq.element(j,t) ;
                        psi.element(t,j,k)         = 0 ;
                        if (nbest>1)
                            ktable.element(t,j,k)  = 0 ;
                        ptable.element(t,j,k)      = 0 ;
                    }
                }
                else
                {
                    const T_STATES num_elem   = trans_list_forward_cnt[j] ;
                    const T_STATES *elem_list = trans_list_forward[j] ;
                    const float64_t *elem_val      = trans_list_forward_val[j] ;
                    const int32_t *elem_id      = trans_list_forward_id[j] ;

                    int32_t fixed_list_len = 0 ;
                    float64_t fixedtempvv_ = CMath::INFTY ;
                    int32_t fixedtempii_ = 0 ;
                    bool fixedtemplong = false ;

                    for (int32_t i=0; i<num_elem; i++)
                    {
                        T_STATES ii = elem_list[i] ;

                        const CPlifBase* penalty = (CPlifBase*) PEN.element(j,ii) ;

                        /*int32_t look_back = max_look_back ;
                          if (0)
                          { // find lookback length
                          CPlifBase *pen = (CPlifBase*) penalty ;
                          if (pen!=NULL)
                          look_back=(int32_t) (CMath::ceil(pen->get_max_value()));
                          if (look_back>=1e6)
                          SG_PRINT("%i,%i -> %d from %ld\n", j, ii, look_back, (long)pen) ;
                          ASSERT(look_back<1e6);
                          } */

                        int32_t look_back_ = look_back.element(j, ii) ;

                        int32_t orf_from = m_orf_info.element(ii,0) ;
                        int32_t orf_to   = m_orf_info.element(j,1) ;
                        if((orf_from!=-1)!=(orf_to!=-1))
                            SG_DEBUG("j=%i  ii=%i  orf_from=%i orf_to=%i p=%1.2f\n", j, ii, orf_from, orf_to, elem_val[i]) ;
                        ASSERT((orf_from!=-1)==(orf_to!=-1)) ;

                        int32_t orf_target = -1 ;
                        if (orf_from!=-1)
                        {
                            orf_target=orf_to-orf_from ;
                            if (orf_target<0)
                                orf_target+=3 ;
                            ASSERT(orf_target>=0 && orf_target<3) ;
                        }

                        int32_t orf_last_pos = m_pos[t] ;
#ifdef DYNPROG_TIMING
                        MyTime3.start() ;
#endif
                        int32_t num_ok_pos = 0 ;

                        for (int32_t ts=t-1; ts>=0 && m_pos[t]-m_pos[ts]<=look_back_; ts--)
                        {
                            bool ok ;
                            //int32_t plen=t-ts;

                            /*for (int32_t s=0; s<m_num_svms; s++)
                              if ((fabs(svs.svm_values[s*svs.seqlen+plen]-svs2.svm_values[s*svs.seqlen+plen])>1e-6) ||
                              (fabs(svs.svm_values[s*svs.seqlen+plen]-svs3.svm_values[s*svs.seqlen+plen])>1e-6))
                              {
                              SG_DEBUG( "s=%i, t=%i, ts=%i, %1.5e, %1.5e, %1.5e\n", s, t, ts, svs.svm_values[s*svs.seqlen+plen], svs2.svm_values[s*svs.seqlen+plen], svs3.svm_values[s*svs.seqlen+plen]);
                              }*/

                            if (orf_target==-1)
                                ok=true ;
                            else if (m_pos[ts]!=-1 && (m_pos[t]-m_pos[ts])%3==orf_target)
                                ok=(!use_orf) || extend_orf(orf_from, orf_to, m_pos[ts], orf_last_pos, m_pos[t]) ;
                            else
                                ok=false ;

                            if (ok)
                            {

                                float64_t segment_loss = 0.0 ;
                                if (with_loss)
                                {
                                    segment_loss = m_seg_loss_obj->get_segment_loss(ts, t, elem_id[i]);
                                    //if (segment_loss!=segment_loss2)
                                        //SG_PRINT("segment_loss:%f segment_loss2:%f\n", segment_loss, segment_loss2);
                                }
                                // BEST_PATH_TRANS

                                int32_t frame = orf_from;//m_orf_info.element(ii,0);
                                lookup_content_svm_values(ts, t, m_pos[ts], m_pos[t], svm_value, frame);

                                float64_t pen_val = 0.0 ;
                                if (penalty)
                                {
#ifdef DYNPROG_TIMING_DETAIL
                                    MyTime.start() ;
#endif
                                    pen_val = penalty->lookup_penalty(m_pos[t]-m_pos[ts], svm_value) ;

#ifdef DYNPROG_TIMING_DETAIL
                                    MyTime.stop() ;
                                    content_plifs_time += MyTime.time_diff_sec() ;
#endif
                                }

#ifdef DYNPROG_TIMING_DETAIL
                                MyTime.start() ;
#endif
                                num_ok_pos++ ;

                                if (nbest==1)
                                {
                                    float64_t  val        = elem_val[i] + pen_val ;
                                    if (with_loss)
                                        val              += segment_loss ;

                                    float64_t mval = -(val + delta.element(delta_array, ts, ii, 0, m_seq_len, m_N)) ;

                                    if (mval<fixedtempvv_)
                                    {
                                        fixedtempvv_ = mval ;
                                        fixedtempii_ = ii + ts*m_N;
                                        fixed_list_len = 1 ;
                                        fixedtemplong = false ;
                                    }
                                }
                                else
                                {
                                    for (int16_t diff=0; diff<nbest; diff++)
                                    {
                                        float64_t  val        = elem_val[i]  ;
                                        val                  += pen_val ;
                                        if (with_loss)
                                            val              += segment_loss ;

                                        float64_t mval = -(val + delta.element(delta_array, ts, ii, diff, m_seq_len, m_N)) ;

                                        /* only place -val in fixedtempvv if it is one of the nbest lowest values in there */
                                        /* fixedtempvv[i], i=0:nbest-1, is sorted so that fixedtempvv[0] <= fixedtempvv[1] <= ...*/
                                        /* fixed_list_len has the number of elements in fixedtempvv */

                                        if ((fixed_list_len < nbest) || ((0==fixed_list_len) || (mval < fixedtempvv[fixed_list_len-1])))
                                        {
                                            if ( (fixed_list_len<nbest) && ((0==fixed_list_len) || (mval>fixedtempvv[fixed_list_len-1])) )
                                            {
                                                fixedtempvv[fixed_list_len] = mval ;
                                                fixedtempii[fixed_list_len] = ii + diff*m_N + ts*m_N*nbest;
                                                fixed_list_len++ ;
                                            }
                                            else  // must have mval < fixedtempvv[fixed_list_len-1]
                                            {
                                                int32_t addhere = fixed_list_len;
                                                while ((addhere > 0) && (mval < fixedtempvv[addhere-1]))
                                                    addhere--;

                                                // move everything from addhere+1 one forward
                                                for (int32_t jj=fixed_list_len-1; jj>addhere; jj--)
                                                {
                                                    fixedtempvv[jj] = fixedtempvv[jj-1];
                                                    fixedtempii[jj] = fixedtempii[jj-1];
                                                }

                                                fixedtempvv[addhere] = mval;
                                                fixedtempii[addhere] = ii + diff*m_N + ts*m_N*nbest;

                                                if (fixed_list_len < nbest)
                                                    fixed_list_len++;
                                            }
                                        }
                                    }
                                }
#ifdef DYNPROG_TIMING_DETAIL
                                MyTime.stop() ;
                                inner_loop_max_time += MyTime.time_diff_sec() ;
#endif
                            }
                        }
#ifdef DYNPROG_TIMING
                        MyTime3.stop() ;
                        inner_loop_time += MyTime3.time_diff_sec() ;
#endif
                    }
                    for (int32_t i=0; i<num_elem; i++)
                    {
                        T_STATES ii = elem_list[i] ;

                        const CPlifBase* penalty = (CPlifBase*) PEN.element(j,ii) ;

                        /*int32_t look_back = max_look_back ;
                          if (0)
                          { // find lookback length
                          CPlifBase *pen = (CPlifBase*) penalty ;
                          if (pen!=NULL)
                          look_back=(int32_t) (CMath::ceil(pen->get_max_value()));
                          if (look_back>=1e6)
                          SG_PRINT("%i,%i -> %d from %ld\n", j, ii, look_back, (long)pen) ;
                          ASSERT(look_back<1e6);
                          } */

                        int32_t look_back_ = look_back.element(j, ii) ;
                        //int32_t look_back_orig_ = look_back_orig.element(j, ii) ;

                        int32_t orf_from = m_orf_info.element(ii,0) ;
                        int32_t orf_to   = m_orf_info.element(j,1) ;
                        if((orf_from!=-1)!=(orf_to!=-1))
                            SG_DEBUG("j=%i  ii=%i  orf_from=%i orf_to=%i p=%1.2f\n", j, ii, orf_from, orf_to, elem_val[i]) ;
                        ASSERT((orf_from!=-1)==(orf_to!=-1)) ;

                        int32_t orf_target = -1 ;
                        if (orf_from!=-1)
                        {
                            orf_target=orf_to-orf_from ;
                            if (orf_target<0)
                                orf_target+=3 ;
                            ASSERT(orf_target>=0 && orf_target<3) ;
                        }

                        //int32_t loss_last_pos = t ;
                        //float64_t last_loss = 0.0 ;

#ifdef DYNPROG_TIMING
                        MyTime3.start() ;
#endif

                        /* long transition stuff */
                        /* only do this, if
                         * this feature is enabled
                         * this is not a transition with ORF restrictions
                         * the loss is switched off
                         * nbest=1
                         */
#ifdef DYNPROG_TIMING
                        MyTime3.start() ;
#endif
                        // long transitions, only when not considering ORFs
                        if ( long_transitions && orf_target==-1 && look_back_ == m_long_transition_threshold )
                        {

                            // update table for 5' part  of the long segment

                            int32_t start = long_transition_content_start.get_element(ii, j) ;
                            int32_t end_5p_part = start ;
                            for (int32_t start_5p_part=start; m_pos[t]-m_pos[start_5p_part] > m_long_transition_threshold ; start_5p_part++)
                            {
                                // find end_5p_part, which is greater than start_5p_part and at least m_long_transition_threshold away
                                while (end_5p_part<=t && m_pos[end_5p_part+1]-m_pos[start_5p_part]<=m_long_transition_threshold)
                                    end_5p_part++ ;

                                ASSERT(m_pos[end_5p_part+1]-m_pos[start_5p_part] > m_long_transition_threshold || end_5p_part==t) ;
                                ASSERT(m_pos[end_5p_part]-m_pos[start_5p_part] <= m_long_transition_threshold) ;

                                float64_t pen_val = 0.0;
                                /* recompute penalty, if necessary */
                                if (penalty)
                                {
                                    int32_t frame = m_orf_info.element(ii,0);
                                    lookup_content_svm_values(start_5p_part, end_5p_part, m_pos[start_5p_part], m_pos[end_5p_part], svm_value, frame); // * t -> end_5p_part
                                    pen_val = penalty->lookup_penalty(m_pos[end_5p_part]-m_pos[start_5p_part], svm_value) ;
                                }

                                /*if (m_pos[start_5p_part]==1003)
                                  {
                                  SG_PRINT("Part1: %i - %i   vs  %i - %i\n", m_pos[t], m_pos[ts], m_pos[end_5p_part], m_pos[start_5p_part]) ;
                                  SG_PRINT("Part1: ts=%i  t=%i  start_5p_part=%i  m_seq_len=%i\n", m_pos[ts], m_pos[t], m_pos[start_5p_part], m_seq_len) ;
                                  }*/

                                float64_t mval_trans = -( elem_val[i] + pen_val*0.5 + delta.element(delta_array, start_5p_part, ii, 0, m_seq_len, m_N) ) ;
                                //float64_t mval_trans = -( elem_val[i] + delta.element(delta_array, ts, ii, 0, m_seq_len, m_N) ) ; // enable this for the incomplete extra check

                                float64_t segment_loss_part1=0.0 ;
                                if (with_loss)
                                {  // this is the loss from the start of the long segment (5' part + middle section)

                                    segment_loss_part1 = m_seg_loss_obj->get_segment_loss(start_5p_part /*long_transition_content_start_position.get_element(ii,j)*/, end_5p_part, elem_id[i]); // * unsure

                                    mval_trans -= segment_loss_part1 ;
                                }


                                if (0)//m_pos[end_5p_part] - m_pos[long_transition_content_start_position.get_element(ii, j)] > look_back_orig_/*m_long_transition_max*/)
                                {
                                    // this restricts the maximal length of segments,
                                    // but the current implementation is not valid since the
                                    // long transition is discarded without loocking if there
                                    // is a second best long transition in between
                                    long_transition_content_scores.set_element(-CMath::INFTY, ii, j) ;
                                    long_transition_content_start_position.set_element(0, ii, j) ;
                                    if (with_loss)
                                        long_transition_content_scores_loss.set_element(0.0, ii, j) ;
#ifdef DYNPROG_DEBUG
                                    long_transition_content_scores_pen.set_element(0.0, ii, j) ;
                                    long_transition_content_scores_elem.set_element(0.0, ii, j) ;
                                    long_transition_content_scores_prev.set_element(0.0, ii, j) ;
                                    long_transition_content_end_position.set_element(0, ii, j) ;
#endif
                                }
                                if (with_loss)
                                {
                                    float64_t old_loss = long_transition_content_scores_loss.get_element(ii, j) ;
                                    float64_t new_loss = m_seg_loss_obj->get_segment_loss(long_transition_content_start_position.get_element(ii,j), end_5p_part, elem_id[i]);
                                    float64_t score = long_transition_content_scores.get_element(ii, j) - old_loss + new_loss ;
                                    long_transition_content_scores.set_element(score, ii, j) ;
                                    long_transition_content_scores_loss.set_element(new_loss, ii, j) ;
#ifdef DYNPROG_DEBUG
                                    long_transition_content_end_position.set_element(end_5p_part, ii, j) ;
#endif

                                }
                                if (-long_transition_content_scores.get_element(ii, j) > mval_trans )
                                {
                                    /* then the old long transition is either too far away or worse than the current one */
                                    long_transition_content_scores.set_element(-mval_trans, ii, j) ;
                                    long_transition_content_start_position.set_element(start_5p_part, ii, j) ;
                                    if (with_loss)
                                        long_transition_content_scores_loss.set_element(segment_loss_part1, ii, j) ;
#ifdef DYNPROG_DEBUG
                                    long_transition_content_scores_pen.set_element(pen_val*0.5, ii, j) ;
                                    long_transition_content_scores_elem.set_element(elem_val[i], ii, j) ;
                                    long_transition_content_scores_prev.set_element(delta.element(delta_array, start_5p_part, ii, 0, m_seq_len, m_N), ii, j) ;
                                    /*ASSERT(fabs(long_transition_content_scores.get_element(ii, j)-(long_transition_content_scores_pen.get_element(ii, j) +
                                      long_transition_content_scores_elem.get_element(ii, j) +
                                      long_transition_content_scores_prev.get_element(ii, j)))<1e-6) ;*/
                                    long_transition_content_end_position.set_element(end_5p_part, ii, j) ;
#endif
                                }
                                //
                                // this sets the position where the search for better 5'parts is started the next time
                                // whithout this the prediction takes ages
                                //
                                long_transition_content_start.set_element(start_5p_part, ii, j) ;
                            }

                            // consider the 3' part at the end of the long segment:
                            // * with length = m_long_transition_threshold
                            // * content prediction and loss only for this part

                            // find ts > 0 with distance from m_pos[t] greater m_long_transition_threshold
                            // precompute: only depends on t
                            int ts = t;
                            while (ts>0 && m_pos[t]-m_pos[ts-1] <= m_long_transition_threshold)
                                ts-- ;

                            if (ts>0)
                            {
                                ASSERT((m_pos[t]-m_pos[ts-1] > m_long_transition_threshold) && (m_pos[t]-m_pos[ts] <= m_long_transition_threshold)) ;


                                /* only consider this transition, if the right position was found */
                                float pen_val_3p = 0.0 ;
                                if (penalty)
                                {
                                    int32_t frame = orf_from ; //m_orf_info.element(ii, 0);
                                    lookup_content_svm_values(ts, t, m_pos[ts], m_pos[t], svm_value, frame);
                                    pen_val_3p = penalty->lookup_penalty(m_pos[t]-m_pos[ts], svm_value) ;
                                }

                                float64_t mval = -(long_transition_content_scores.get_element(ii, j) + pen_val_3p*0.5) ;

                                {
#ifdef DYNPROG_DEBUG
                                    float64_t segment_loss_part2=0.0 ;
                                    float64_t segment_loss_part1=0.0 ;
#endif
                                    float64_t segment_loss_total=0.0 ;

                                    if (with_loss)
                                    {   // this is the loss for the 3' end fragment of the segment
                                        // (the 5' end and the middle section loss is already contained in mval)

#ifdef DYNPROG_DEBUG
                                        // this is an alternative, which should be identical, if the loss is additive
                                        segment_loss_part2 = m_seg_loss_obj->get_segment_loss_extend(long_transition_content_end_position.get_element(ii,j), t, elem_id[i]);
                                        //mval -= segment_loss_part2 ;
                                        segment_loss_part1 = m_seg_loss_obj->get_segment_loss(long_transition_content_start_position.get_element(ii,j), long_transition_content_end_position.get_element(ii,j), elem_id[i]);
#endif
                                        segment_loss_total = m_seg_loss_obj->get_segment_loss(long_transition_content_start_position.get_element(ii,j), t, elem_id[i]);
                                        mval -= (segment_loss_total-long_transition_content_scores_loss.get_element(ii, j)) ;
                                    }

#ifdef DYNPROG_DEBUG
                                    if (m_pos[t]==10108 ||m_pos[t]==12802 ||m_pos[t]== 12561)
                                    {
                                        SG_PRINT("Part2: %i,%i,%i: val=%1.6f  pen_val_3p*0.5=%1.6f (t=%i, ts=%i, ts-1=%i, ts+1=%i); scores=%1.6f (pen=%1.6f,prev=%1.6f,elem=%1.6f,loss=%1.1f), positions=%i,%i,%i,  loss=%1.1f/%1.1f (%i,%i)\n",
                                                 m_pos[t], j, ii, -mval, 0.5*pen_val_3p, m_pos[t], m_pos[ts], m_pos[ts-1], m_pos[ts+1],
                                                 long_transition_content_scores.get_element(ii, j),
                                                 long_transition_content_scores_pen.get_element(ii, j),
                                                 long_transition_content_scores_prev.get_element(ii, j),
                                                 long_transition_content_scores_elem.get_element(ii, j),
                                                 long_transition_content_scores_loss.get_element(ii, j),
                                                 m_pos[long_transition_content_start_position.get_element(ii,j)],
                                                 m_pos[long_transition_content_end_position.get_element(ii,j)],
                                                 m_pos[long_transition_content_start.get_element(ii,j)], segment_loss_part2, segment_loss_total, long_transition_content_start_position.get_element(ii,j), t) ;
                                        SG_PRINT("fixedtempvv_: %1.6f, from_state:%i from_pos:%i\n ",-fixedtempvv_, (fixedtempii_%m_N), m_pos[(fixedtempii_-(fixedtempii_%(m_N*nbest)))/(m_N*nbest)] );
                                    }

                                    if (fabs(segment_loss_part2+long_transition_content_scores_loss.get_element(ii, j) - segment_loss_total)>1e-3)
                                    {
                                        SG_ERROR("LOSS: total=%1.1f (%i-%i)  part1=%1.1f/%1.1f (%i-%i)  part2=%1.1f (%i-%i)  sum=%1.1f  diff=%1.1f\n",
                                                 segment_loss_total, m_pos[long_transition_content_start_position.get_element(ii,j)], m_pos[t],
                                                 long_transition_content_scores_loss.get_element(ii, j), segment_loss_part1, m_pos[long_transition_content_start_position.get_element(ii,j)], m_pos[long_transition_content_end_position.get_element(ii,j)],
                                                 segment_loss_part2, m_pos[long_transition_content_end_position.get_element(ii,j)], m_pos[t],
                                                 segment_loss_part2+long_transition_content_scores_loss.get_element(ii, j),
                                                 segment_loss_part2+long_transition_content_scores_loss.get_element(ii, j) - segment_loss_total) ;
                                    }
#endif
                                }

                                // prefer simpler version to guarantee optimality
                                //
                                // original:
                                /* if ((mval < fixedtempvv_) &&
                                    (m_pos[t] - m_pos[long_transition_content_start_position.get_element(ii, j)])<=look_back_orig_) */
                                if (mval < fixedtempvv_)
                                {
                                    /* then the long transition is better than the short one => replace it */
                                    int32_t fromtjk =  fixedtempii_ ;
                                    /*SG_PRINT("%i,%i: Long transition (%1.5f=-(%1.5f+%1.5f+%1.5f+%1.5f), %i) to m_pos %i better than short transition (%1.5f,%i) to m_pos %i \n",
                                      m_pos[t], j,
                                      mval, pen_val_3p*0.5, long_transition_content_scores_pen.get_element(ii, j), long_transition_content_scores_elem.get_element(ii, j), long_transition_content_scores_prev.get_element(ii, j), ii,
                                      m_pos[long_transition_content_position.get_element(ii, j)],
                                      fixedtempvv_, (fromtjk%m_N), m_pos[(fromtjk-(fromtjk%(m_N*nbest)))/(m_N*nbest)]) ;*/
                                    ASSERT((fromtjk-(fromtjk%(m_N*nbest)))/(m_N*nbest)==0 || m_pos[(fromtjk-(fromtjk%(m_N*nbest)))/(m_N*nbest)]>=m_pos[long_transition_content_start_position.get_element(ii, j)] || fixedtemplong) ;

                                    fixedtempvv_ = mval ;
                                    fixedtempii_ = ii + m_N*long_transition_content_start_position.get_element(ii, j) ;
                                    fixed_list_len = 1 ;
                                    fixedtemplong = true ;
                                }
                            }
                        }
                    }
#ifdef DYNPROG_TIMING
                    MyTime3.stop() ;
                    long_transition_time += MyTime3.time_diff_sec() ;
#endif


                    int32_t numEnt = fixed_list_len;

                    float64_t minusscore;
                    int64_t fromtjk;

                    for (int16_t k=0; k<nbest; k++)
                    {
                        if (k<numEnt)
                        {
                            if (nbest==1)
                            {
                                minusscore = fixedtempvv_ ;
                                fromtjk = fixedtempii_ ;
                            }
                            else
                            {
                                minusscore = fixedtempvv[k];
                                fromtjk = fixedtempii[k];
                            }

                            delta.element(delta_array, t, j, k, m_seq_len, m_N)    = -minusscore + seq.element(j,t);
                            psi.element(t,j,k)      = (fromtjk%m_N) ;
                            if (nbest>1)
                                ktable.element(t,j,k)   = (fromtjk%(m_N*nbest)-psi.element(t,j,k))/m_N ;
                            ptable.element(t,j,k)   = (fromtjk-(fromtjk%(m_N*nbest)))/(m_N*nbest) ;
                        }
                        else
                        {
                            delta.element(delta_array, t, j, k, m_seq_len, m_N)    = -CMath::INFTY ;
                            psi.element(t,j,k)      = 0 ;
                            if (nbest>1)
                                ktable.element(t,j,k)     = 0 ;
                            ptable.element(t,j,k)     = 0 ;
                        }
                    }
                }
            }
        }
        { //termination
            int32_t list_len = 0 ;
            for (int16_t diff=0; diff<nbest; diff++)
            {
                for (T_STATES i=0; i<m_N; i++)
                {
                    oldtempvv[list_len] = -(delta.element(delta_array, (m_seq_len-1), i, diff, m_seq_len, m_N)+get_q(i)) ;
                    oldtempii[list_len] = i + diff*m_N ;
                    list_len++ ;
                }
            }

            CMath::nmin(oldtempvv.get_array(), oldtempii.get_array(), list_len, nbest) ;

            for (int16_t k=0; k<nbest; k++)
            {
                delta_end.element(k) = -oldtempvv[k] ;
                path_ends.element(k) = (oldtempii[k]%m_N) ;
                if (nbest>1)
                    ktable_end.element(k) = (oldtempii[k]-path_ends.element(k))/m_N ;
            }


        }

        { //state sequence backtracking
            for (int16_t k=0; k<nbest; k++)
            {
                prob_nbest[k]= delta_end.element(k) ;

                int32_t i         = 0 ;
                state_seq[i]  = path_ends.element(k) ;
                int16_t q   = 0 ;
                if (nbest>1)
                    q=ktable_end.element(k) ;
                pos_seq[i]    = m_seq_len-1 ;

                while (pos_seq[i]>0)
                {
                    ASSERT(i+1<m_seq_len);
                    //SG_DEBUG("s=%i p=%i q=%i\n", state_seq[i], pos_seq[i], q) ;
                    state_seq[i+1] = psi.element(pos_seq[i], state_seq[i], q);
                    pos_seq[i+1]   = ptable.element(pos_seq[i], state_seq[i], q) ;
                    if (nbest>1)
                        q              = ktable.element(pos_seq[i], state_seq[i], q) ;
                    i++ ;
                }
                //SG_DEBUG("s=%i p=%i q=%i\n", state_seq[i], pos_seq[i], q) ;
                int32_t num_states = i+1 ;
                for (i=0; i<num_states;i++)
                {
                    my_state_seq[i+k*m_seq_len] = state_seq[num_states-i-1] ;
                    my_pos_seq[i+k*m_seq_len]   = pos_seq[num_states-i-1] ;
                }
                if (num_states<m_seq_len)
                {
                    my_state_seq[num_states+k*m_seq_len]=-1 ;
                    my_pos_seq[num_states+k*m_seq_len]=-1 ;
                }
            }
        }

        //if (is_big)
        //  SG_PRINT( "DONE.     \n") ;


#ifdef DYNPROG_TIMING
        MyTime2.stop() ;

        //if (is_big)
        SG_PRINT("Timing:  orf=%1.2f s \n Segment_init=%1.2f s Segment_pos=%1.2f s  Segment_extend=%1.2f s Segment_clean=%1.2f s\nsvm_init=%1.2f s  svm_pos=%1.2f  svm_clean=%1.2f\n  content_svm_values_time=%1.2f  content_plifs_time=%1.2f\ninner_loop_max_time=%1.2f inner_loop=%1.2f long_transition_time=%1.2f\n total=%1.2f\n", orf_time, segment_init_time, segment_pos_time, segment_extend_time, segment_clean_time, svm_init_time, svm_pos_time, svm_clean_time, content_svm_values_time, content_plifs_time, inner_loop_max_time, inner_loop_time, long_transition_time, MyTime2.time_diff_sec()) ;
#endif

        SG_FREE(fixedtempvv);
        SG_FREE(fixedtempii);
    }


void CDynProg::best_path_trans_deriv(
    int32_t *my_state_seq, int32_t *my_pos_seq,
    int32_t my_seq_len, const float64_t *seq_array, int32_t max_num_signals)
{
    m_initial_state_distribution_p_deriv.resize_array(m_N) ;
    m_end_state_distribution_q_deriv.resize_array(m_N) ;
    m_transition_matrix_a_deriv.resize_array(m_N,m_N) ;
    //m_my_scores.resize_array(m_my_state_seq.get_array_size()) ;
    //m_my_losses.resize_array(m_my_state_seq.get_array_size()) ;
    m_my_scores.resize_array(my_seq_len);
    m_my_losses.resize_array(my_seq_len);
    float64_t* my_scores=m_my_scores.get_array();
    float64_t* my_losses=m_my_losses.get_array();
    CPlifBase** Plif_matrix=m_plif_matrices->get_plif_matrix();
    CPlifBase** Plif_state_signals=m_plif_matrices->get_state_signals();

    if (!m_svm_arrays_clean)
    {
        SG_ERROR( "SVM arrays not clean") ;
        return ;
    } ;
    //SG_PRINT( "genestr_len=%i, genestr_num=%i\n", genestr_len, genestr_num) ;
    //m_mod_words.display() ;
    //m_sign_words.display() ;
    //m_string_words.display() ;

    bool use_svm = false ;

    CDynamicObjectArray PEN((CSGObject**) Plif_matrix, m_N, m_N, false, false) ; // 2d, CPlifBase*
    PEN.set_array_name("PEN");

    CDynamicObjectArray PEN_state_signals((CSGObject**) Plif_state_signals, m_N, max_num_signals, false, false) ; // 2d, CPlifBase*
    PEN_state_signals.set_array_name("PEN_state_signals");

    CDynamicArray<float64_t> seq_input(seq_array, m_N, m_seq_len, max_num_signals) ;
    seq_input.set_array_name("seq_input");

    { // determine whether to use svm outputs and clear derivatives
        for (int32_t i=0; i<m_N; i++)
            for (int32_t j=0; j<m_N; j++)
            {
                CPlifBase* penij=(CPlifBase*) PEN.element(i,j) ;
                if (penij==NULL)
                    continue ;

                if (penij->uses_svm_values())
                    use_svm=true ;
                penij->penalty_clear_derivative() ;
            }
        for (int32_t i=0; i<m_N; i++)
            for (int32_t j=0; j<max_num_signals; j++)
            {
                CPlifBase* penij=(CPlifBase*) PEN_state_signals.element(i,j) ;
                if (penij==NULL)
                    continue ;
                if (penij->uses_svm_values())
                    use_svm=true ;
                penij->penalty_clear_derivative() ;
            }
    }

    { // set derivatives of p, q and a to zero

        for (int32_t i=0; i<m_N; i++)
        {
            m_initial_state_distribution_p_deriv.element(i)=0 ;
            m_end_state_distribution_q_deriv.element(i)=0 ;
            for (int32_t j=0; j<m_N; j++)
                m_transition_matrix_a_deriv.element(i,j)=0 ;
        }
    }

    { // clear score vector
        for (int32_t i=0; i<my_seq_len; i++)
        {
            my_scores[i]=0.0 ;
            my_losses[i]=0.0 ;
        }
    }

    //int32_t total_len = 0 ;

    //m_transition_matrix_a.display_array() ;
    //m_transition_matrix_a_id.display_array() ;

    // compute derivatives for given path
    float64_t* svm_value = SG_MALLOC(float64_t, m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs);
    float64_t* svm_value_part1 = SG_MALLOC(float64_t, m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs);
    float64_t* svm_value_part2 = SG_MALLOC(float64_t, m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs);
    for (int32_t s=0; s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; s++)
    {
        svm_value[s]=0 ;
        svm_value_part1[s]=0 ;
        svm_value_part2[s]=0 ;
    }

    //#ifdef DYNPROG_DEBUG
    float64_t total_score = 0.0 ;
    float64_t total_loss = 0.0 ;
    //#endif

    ASSERT(my_state_seq[0]>=0) ;
    m_initial_state_distribution_p_deriv.element(my_state_seq[0])++ ;
    my_scores[0] += m_initial_state_distribution_p.element(my_state_seq[0]) ;

    ASSERT(my_state_seq[my_seq_len-1]>=0) ;
    m_end_state_distribution_q_deriv.element(my_state_seq[my_seq_len-1])++ ;
    my_scores[my_seq_len-1] += m_end_state_distribution_q.element(my_state_seq[my_seq_len-1]);

    //#ifdef DYNPROG_DEBUG
    total_score += my_scores[0] + my_scores[my_seq_len-1] ;
    //#endif

    SG_DEBUG( "m_seq_len=%i\n", my_seq_len) ;
    for (int32_t i=0; i<my_seq_len-1; i++)
    {
        if (my_state_seq[i+1]==-1)
            break ;
        int32_t from_state = my_state_seq[i] ;
        int32_t to_state   = my_state_seq[i+1] ;
        int32_t from_pos   = my_pos_seq[i] ;
        int32_t to_pos     = my_pos_seq[i+1] ;

        int32_t elem_id = m_transition_matrix_a_id.element(from_state, to_state) ;
        my_losses[i] = m_seg_loss_obj->get_segment_loss(from_pos, to_pos, elem_id);

#ifdef DYNPROG_DEBUG


        if (i>0)// test if segment loss is additive
        {
            float32_t loss1 = m_seg_loss_obj->get_segment_loss(my_pos_seq[i-1], my_pos_seq[i], elem_id);
            float32_t loss2 = m_seg_loss_obj->get_segment_loss(my_pos_seq[i], my_pos_seq[i+1], elem_id);
            float32_t loss3 = m_seg_loss_obj->get_segment_loss(my_pos_seq[i-1], my_pos_seq[i+1], elem_id);
            SG_PRINT("loss1:%f loss2:%f loss3:%f, diff:%f\n", loss1, loss2, loss3, loss1+loss2-loss3);
            if (CMath::abs(loss1+loss2-loss3)>0)
            {
                SG_PRINT( "%i. segment loss %f (id=%i): from=%i(%i), to=%i(%i)\n", i, my_losses[i], elem_id, from_pos, from_state, to_pos, to_state) ;
            }
        }
        io->set_loglevel(M_DEBUG) ;
        SG_DEBUG( "%i. segment loss %f (id=%i): from=%i(%i), to=%i(%i)\n", i, my_losses[i], elem_id, from_pos, from_state, to_pos, to_state) ;
#endif
        // increase usage of this transition
        m_transition_matrix_a_deriv.element(from_state, to_state)++ ;
        my_scores[i] += m_transition_matrix_a.element(from_state, to_state) ;
        //SG_PRINT("m_transition_matrix_a.element(%i, %i),%f \n",from_state, to_state, m_transition_matrix_a.element(from_state, to_state));
#ifdef DYNPROG_DEBUG
        SG_DEBUG( "%i. scores[i]=%f\n", i, my_scores[i]) ;
#endif

        /*int32_t last_svm_pos[m_num_degrees] ;
          for (int32_t qq=0; qq<m_num_degrees; qq++)
          last_svm_pos[qq]=-1 ;*/

        bool is_long_transition = false ;
        if (m_long_transitions)
        {
            if (m_pos[to_pos]-m_pos[from_pos]>m_long_transition_threshold)
                is_long_transition = true ;
            if (m_orf_info.element(from_state,0)!=-1)
                is_long_transition = false ;
        }

        int32_t from_pos_thresh = from_pos ;
        int32_t to_pos_thresh = to_pos ;

        if (use_svm)
        {
            if (is_long_transition)
            {

                while (from_pos_thresh<to_pos && m_pos[from_pos_thresh+1] - m_pos[from_pos] <= m_long_transition_threshold) // *
                    from_pos_thresh++ ;
                ASSERT(from_pos_thresh<to_pos) ;
                ASSERT(m_pos[from_pos_thresh] - m_pos[from_pos] <= m_long_transition_threshold); // *
                ASSERT(m_pos[from_pos_thresh+1] - m_pos[from_pos] > m_long_transition_threshold);// *

                int32_t frame = m_orf_info.element(from_state,0);
                lookup_content_svm_values(from_pos, from_pos_thresh, m_pos[from_pos], m_pos[from_pos_thresh], svm_value_part1, frame);

#ifdef DYNPROG_DEBUG
                SG_PRINT("part1: pos1: %i  pos2: %i   pos3: %i  \nsvm_value_part1: ", m_pos[from_pos], m_pos[from_pos_thresh], m_pos[from_pos_thresh+1]) ;
                for (int32_t s=0; s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; s++)
                    SG_PRINT("%1.4f  ", svm_value_part1[s]);
                SG_PRINT("\n");
#endif

                while (to_pos_thresh>0 && m_pos[to_pos] - m_pos[to_pos_thresh-1] <= m_long_transition_threshold) // *
                    to_pos_thresh-- ;
                ASSERT(to_pos_thresh>0) ;
                ASSERT(m_pos[to_pos] - m_pos[to_pos_thresh] <= m_long_transition_threshold) ; // *
                ASSERT(m_pos[to_pos] - m_pos[to_pos_thresh-1] > m_long_transition_threshold) ; // *

                lookup_content_svm_values(to_pos_thresh, to_pos, m_pos[to_pos_thresh], m_pos[to_pos], svm_value_part2, frame);

#ifdef DYNPROG_DEBUG
                SG_PRINT("part2: pos1: %i  pos2: %i   pos3: %i  \nsvm_value_part2: ", m_pos[to_pos], m_pos[to_pos_thresh], m_pos[to_pos_thresh+1]) ;
                for (int32_t s=0; s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; s++)
                    SG_PRINT("%1.4f  ", svm_value_part2[s]);
                SG_PRINT("\n");
#endif
            }
            else
            {
                /* normal case */

                //SG_PRINT("from_pos: %i; to_pos: %i; m_pos[to_pos]-m_pos[from_pos]: %i \n",from_pos, to_pos, m_pos[to_pos]-m_pos[from_pos]);
                int32_t frame = m_orf_info.element(from_state,0);
                if (false)//(frame>=0)
                {
                    int32_t num_current_svms=0;
                    int32_t svm_ids[] = {-8, -7, -6, -5, -4, -3, -2, -1};
                    SG_PRINT("penalties(%i, %i), frame:%i  ", from_state, to_state, frame);
                    ((CPlifBase*) PEN.element(to_state, from_state))->get_used_svms(&num_current_svms, svm_ids);
                    SG_PRINT("\n");
                }

                lookup_content_svm_values(from_pos, to_pos, m_pos[from_pos],m_pos[to_pos], svm_value, frame);
#ifdef DYNPROG_DEBUG
                SG_PRINT("part2: pos1: %i  pos2: %i   \nsvm_values: ", m_pos[from_pos], m_pos[to_pos]) ;
                for (int32_t s=0; s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs; s++)
                    SG_PRINT("%1.4f  ", svm_value[s]);
                SG_PRINT("\n");
#endif
            }
        }

        if (PEN.element(to_state, from_state)!=NULL)
        {
            float64_t nscore = 0 ;
            if (is_long_transition)
            {
                float64_t pen_value_part1 = ((CPlifBase*) PEN.element(to_state, from_state))->lookup_penalty(m_pos[from_pos_thresh]-m_pos[from_pos], svm_value_part1) ;
                float64_t pen_value_part2 = ((CPlifBase*) PEN.element(to_state, from_state))->lookup_penalty(m_pos[to_pos]-m_pos[to_pos_thresh], svm_value_part2) ;
                nscore= 0.5*pen_value_part1 + 0.5*pen_value_part2 ;
            }
            else
                nscore = ((CPlifBase*) PEN.element(to_state, from_state))->lookup_penalty(m_pos[to_pos]-m_pos[from_pos], svm_value) ;

            if (false)//(nscore<-1e9)
                    SG_PRINT("is_long_transition=%i  (from_pos=%i (%i), to_pos=%i (%i)=> %1.5f\n",
                        is_long_transition, m_pos[from_pos], from_state, m_pos[to_pos], to_state, nscore) ;

            my_scores[i] += nscore ;

            for (int32_t s=m_num_svms;s<m_num_lin_feat_plifs_cum[m_num_raw_data]; s++)/*set tiling plif values to neutral values (that do not influence derivative calculation)*/
            {
                svm_value[s]=-CMath::INFTY;
                svm_value_part1[s]=-CMath::INFTY;
                svm_value_part2[s]=-CMath::INFTY;
            }

#ifdef DYNPROG_DEBUG
            //SG_DEBUG( "%i. transition penalty: from_state=%i to_state=%i from_pos=%i [%i] to_pos=%i [%i] value=%i\n", i, from_state, to_state, from_pos, m_pos[from_pos], to_pos, m_pos[to_pos], m_pos[to_pos]-m_pos[from_pos]) ;
#endif
            if (is_long_transition)
            {
#ifdef DYNPROG_DEBUG
                float64_t sum_score = 0.0 ;

                for (int kk=0; kk<i; kk++)
                    sum_score += my_scores[i] ;

                SG_PRINT("is_long_transition=%i  (from_pos=%i (%i), to_pos=%i (%i)=> %1.5f, %1.5f --- 1: %1.6f (%i-%i)  2: %1.6f (%i-%i) \n",
                        is_long_transition, m_pos[from_pos], from_state, m_pos[to_pos], to_state,
                        nscore, sum_score,
                        PEN.element(to_state, from_state)->lookup_penalty(m_pos[from_pos_thresh]-m_pos[from_pos], svm_value_part1)*0.5, m_pos[from_pos], m_pos[from_pos_thresh],
                        PEN.element(to_state, from_state)->lookup_penalty(m_pos[to_pos]-m_pos[to_pos_thresh], svm_value_part2)*0.5, m_pos[to_pos_thresh], m_pos[to_pos]) ;
#endif
            }

            if (is_long_transition)
            {
                ((CPlifBase*) PEN.element(to_state, from_state))->penalty_add_derivative(m_pos[from_pos_thresh]-m_pos[from_pos], svm_value_part1, 0.5) ;
                ((CPlifBase*) PEN.element(to_state, from_state))->penalty_add_derivative(m_pos[to_pos]-m_pos[to_pos_thresh], svm_value_part2, 0.5) ;
            }
            else
                ((CPlifBase*) PEN.element(to_state, from_state))->penalty_add_derivative(m_pos[to_pos]-m_pos[from_pos], svm_value, 1) ;

            //SG_PRINT("m_num_raw_data = %i \n", m_num_raw_data) ;

            // for tiling array and rna-seq data every single measurement must be added to the derivative
            // in contrast to the content svm predictions where we have a single value per transition;
            // content svm predictions have already been added to the derivative, thus we start with d=1
            // instead of d=0
            if (is_long_transition)
            {
                for (int32_t d=1; d<=m_num_raw_data; d++)
                {
                    for (int32_t s=0;s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs;s++)
                        svm_value[s]=-CMath::INFTY;
                    float64_t* intensities = SG_MALLOC(float64_t, m_num_probes_cum[d]);
                    int32_t num_intensities = raw_intensities_interval_query(m_pos[from_pos], m_pos[from_pos_thresh],intensities, d);
                    for (int32_t k=0;k<num_intensities;k++)
                    {
                        for (int32_t j=m_num_lin_feat_plifs_cum[d-1];j<m_num_lin_feat_plifs_cum[d];j++)
                            svm_value[j]=intensities[k];

                        ((CPlifBase*) PEN.element(to_state, from_state))->penalty_add_derivative(-CMath::INFTY, svm_value, 0.5) ;

                    }
                    num_intensities = raw_intensities_interval_query(m_pos[to_pos_thresh], m_pos[to_pos],intensities, d);
                    for (int32_t k=0;k<num_intensities;k++)
                    {
                        for (int32_t j=m_num_lin_feat_plifs_cum[d-1];j<m_num_lin_feat_plifs_cum[d];j++)
                            svm_value[j]=intensities[k];

                        ((CPlifBase*) PEN.element(to_state, from_state))->penalty_add_derivative(-CMath::INFTY, svm_value, 0.5) ;

                    }
                    SG_FREE(intensities);

                }
            }
            else
            {
                for (int32_t d=1; d<=m_num_raw_data; d++)
                {
                    for (int32_t s=0;s<m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs;s++)
                        svm_value[s]=-CMath::INFTY;
                    float64_t* intensities = SG_MALLOC(float64_t, m_num_probes_cum[d]);
                    int32_t num_intensities = raw_intensities_interval_query(m_pos[from_pos], m_pos[to_pos],intensities, d);
                    //SG_PRINT("m_pos[from_pos]:%i, m_pos[to_pos]:%i, num_intensities:%i\n",m_pos[from_pos],m_pos[to_pos], num_intensities);
                    for (int32_t k=0;k<num_intensities;k++)
                    {
                        for (int32_t j=m_num_lin_feat_plifs_cum[d-1];j<m_num_lin_feat_plifs_cum[d];j++)
                            svm_value[j]=intensities[k];

                        ((CPlifBase*) PEN.element(to_state, from_state))->penalty_add_derivative(-CMath::INFTY, svm_value, 1) ;

                    }
                    SG_FREE(intensities);
                }
            }

        }
#ifdef DYNPROG_DEBUG
        SG_DEBUG( "%i. scores[i]=%f\n", i, my_scores[i]) ;
#endif

        //SG_DEBUG( "emmission penalty skipped: to_state=%i to_pos=%i value=%1.2f score=%1.2f\n", to_state, to_pos, seq_input.element(to_state, to_pos), 0.0) ;
        for (int32_t k=0; k<max_num_signals; k++)
        {
            if ((PEN_state_signals.element(to_state,k)==NULL)&&(k==0))
            {
#ifdef DYNPROG_DEBUG
                SG_DEBUG( "%i. emmission penalty: to_state=%i to_pos=%i score=%1.2f (no signal plif)\n", i, to_state, to_pos, seq_input.element(to_state, to_pos, k)) ;
#endif
                my_scores[i] += seq_input.element(to_state, to_pos, k) ;
                //if (seq_input.element(to_state, to_pos, k) !=0)
                //  SG_PRINT("features(%i,%i): %f\n",to_state,to_pos,seq_input.element(to_state, to_pos, k));
                break ;
            }
            if (PEN_state_signals.element(to_state, k)!=NULL)
            {
                float64_t nscore = ((CPlifBase*) PEN_state_signals.element(to_state,k))->lookup_penalty(seq_input.element(to_state, to_pos, k), svm_value) ; // this should be ok for long_transitions (svm_value does not matter)
                my_scores[i] += nscore ;
#ifdef DYNPROG_DEBUG
                if (false)//(nscore<-1e9)
                {
                    SG_PRINT("is_long_transition=%i  (from_pos=%i (%i), from_state=%i, to_pos=%i (%i) to_state=%i=> %1.5f, dim3:%i, seq_input.element(to_state, to_pos, k): %1.4f\n",
                        is_long_transition, m_pos[from_pos], from_pos, from_state, m_pos[to_pos], to_pos, to_state, nscore, k, seq_input.element(to_state, to_pos, k)) ;
                    for (int x=0; x<23; x++)
                    {
                        for (int i=-10; i<10; i++)
                            SG_PRINT("%1.4f\t", seq_input.element(x, to_pos+i, k));
                        SG_PRINT("\n");
                    }

                }
#endif
                //break ;
                //int32_t num_current_svms=0;
                //int32_t svm_ids[] = {-8, -7, -6, -5, -4, -3, -2, -1};
                //SG_PRINT("PEN_state_signals->id: ");
                //PEN_state_signals.element(to_state, k)->get_used_svms(&num_current_svms, svm_ids);
                //SG_PRINT("\n");
                //if (nscore != 0)
                //SG_PRINT( "%i. emmission penalty: to_state=%i to_pos=%i value=%1.2f score=%1.2f k=%i\n", i, to_state, to_pos, seq_input.element(to_state, to_pos, k), nscore, k) ;
#ifdef DYNPROG_DEBUG
                SG_DEBUG( "%i. emmission penalty: to_state=%i to_pos=%i value=%1.2f score=%1.2f k=%i\n", i, to_state, to_pos, seq_input.element(to_state, to_pos, k), nscore, k) ;
#endif
                ((CPlifBase*) PEN_state_signals.element(to_state,k))->penalty_add_derivative(seq_input.element(to_state, to_pos, k), svm_value, 1) ; // this should be ok for long_transitions (svm_value does not matter)
            } else
                break ;
        }

        //#ifdef DYNPROG_DEBUG
        //SG_PRINT( "scores[%i]=%f (final) \n", i, my_scores[i]) ;
        //SG_PRINT( "losses[%i]=%f (final) , total_loss: %f \n", i, my_losses[i], total_loss) ;
        total_score += my_scores[i] ;
        total_loss += my_losses[i] ;
        //#endif
    }
    //#ifdef DYNPROG_DEBUG
    //SG_PRINT( "total score = %f \n", total_score) ;
    //SG_PRINT( "total loss = %f \n", total_loss) ;
    //#endif
    SG_FREE(svm_value);
    SG_FREE(svm_value_part1);
    SG_FREE(svm_value_part2);
}

int32_t CDynProg::raw_intensities_interval_query(const int32_t from_pos, const int32_t to_pos, float64_t* intensities, int32_t type)
{
    ASSERT(from_pos<to_pos);
    int32_t num_intensities = 0;
    int32_t* p_tiling_pos  = &m_probe_pos[m_num_probes_cum[type-1]];
    float64_t* p_tiling_data = &m_raw_intensities[m_num_probes_cum[type-1]];
    int32_t last_pos;
    int32_t num = m_num_probes_cum[type-1];
    while (*p_tiling_pos<to_pos)
    {
        if (*p_tiling_pos>=from_pos)
        {
            intensities[num_intensities] = *p_tiling_data;
            num_intensities++;
        }
        num++;
        if (num>=m_num_probes_cum[type])
            break;
        last_pos = *p_tiling_pos;
        p_tiling_pos++;
        p_tiling_data++;
        ASSERT(last_pos<*p_tiling_pos);
    }
    return num_intensities;
}

void CDynProg::lookup_content_svm_values(const int32_t from_state, const int32_t to_state, const int32_t from_pos, const int32_t to_pos, float64_t* svm_values, int32_t frame)
{
#ifdef DYNPROG_TIMING_DETAIL
    MyTime.start() ;
#endif
//  ASSERT(from_state<to_state);
//  if (!(from_pos<to_pos))
//      SG_ERROR("from_pos!<to_pos, from_pos: %i to_pos: %i \n",from_pos,to_pos);
    for (int32_t i=0;i<m_num_svms;i++)
    {
        float64_t to_val   = m_lin_feat.get_element(i, to_state);
        float64_t from_val = m_lin_feat.get_element(i, from_state);
        svm_values[i] = (to_val-from_val)/(to_pos-from_pos);
    }
    for (int32_t i=m_num_svms;i<m_num_lin_feat_plifs_cum[m_num_raw_data];i++)
    {
        float64_t to_val   = m_lin_feat.get_element(i, to_state);
        float64_t from_val = m_lin_feat.get_element(i, from_state);
        svm_values[i] = to_val-from_val ;
    }
    if (m_intron_list)
    {
        int32_t* support = SG_MALLOC(int32_t, m_num_intron_plifs);
        m_intron_list->get_intron_support(support, from_state, to_state);
        int32_t intron_list_start = m_num_lin_feat_plifs_cum[m_num_raw_data];
        int32_t intron_list_end = m_num_lin_feat_plifs_cum[m_num_raw_data]+m_num_intron_plifs;
        int32_t cnt = 0;
        for (int32_t i=intron_list_start; i<intron_list_end;i++)
        {
            svm_values[i] = (float64_t) (support[cnt]);
            cnt++;
        }
        //if (to_pos>3990 && to_pos<4010)
        //  SG_PRINT("from_state:%i to_state:%i support[0]:%i support[1]:%i\n",from_state, to_state, support[0], support[1]);
        SG_FREE(support);
    }
    // find the correct row with precomputed frame predictions
    if (frame!=-1)
    {
        svm_values[frame_plifs[0]] = 1e10;
        svm_values[frame_plifs[1]] = 1e10;
        svm_values[frame_plifs[2]] = 1e10;
        int32_t global_frame = from_pos%3;
        int32_t row = ((global_frame+frame)%3)+4;
        float64_t to_val   = m_lin_feat.get_element(row, to_state);
        float64_t from_val = m_lin_feat.get_element(row, from_state);
        svm_values[frame+frame_plifs[0]] = (to_val-from_val)/(to_pos-from_pos);
    }
#ifdef DYNPROG_TIMING_DETAIL
    MyTime.stop() ;
    content_svm_values_time += MyTime.time_diff_sec() ;
#endif
}
void CDynProg::set_intron_list(CIntronList* intron_list, int32_t num_plifs)
{
    m_intron_list = intron_list;
    m_num_intron_plifs = num_plifs;
}