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kalign2_hirschberg_dna.c

/*
      kalign2_hirschberg_dna.c
      
      Released under GPL - see the 'COPYING' file   
      
      Copyright (C) 2006 Timo Lassmann <timolassmann@gmail.com>
      
      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
      any later version.

      This program is distributed in the hope that it will be useful,
      but WITHOUT ANY WARRANTY; without even the implied warranty of
      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      GNU General Public License for more details.

      You should have received a copy of the GNU General Public License
      along with this program; if not, write to the Free Software
      Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
    
      Please send bug reports, comments etc. to:
      timolassmann@gmail.com
*/


#include "kalign2.h"
#include "kalign2_hirschberg_dna.h"
#define MAX(a, b) (a > b ? a : b)
#define MAX3(a,b,c) MAX(MAX(a,b),c)


int** dna_alignment(struct alignment* aln,int* tree,float**submatrix, int** map)
{
      struct hirsch_mem* hm = 0;
      int i,j,g,a,b,c;
      int len_a;
      int len_b;
      float** profile = 0;

      profile = malloc(sizeof(float*)*numprofiles);
      for ( i = 0;i< numprofiles;i++){
            profile[i] = 0;
      }

      map = malloc(sizeof(int*)*numprofiles);
      for ( i = 0;i < numprofiles;i++){
            map[i] = 0;
      }
      
      hm = hirsch_mem_alloc(hm,1024);
      fprintf(stderr,"\nAlignment:\n");
      for (i = 0; i < (numseq-1);i++){
            a = tree[i*3];
            b = tree[i*3+1];
            c = tree[i*3+2];
            fprintf(stderr,"\r%8.0f percent done",(float)(i) /(float)numseq * 100);
            //fprintf(stderr,"Aligning:%d %d->%d      done:%0.2f\n",a,b,c,((float)(i+1)/(float)numseq)*100);
            len_a = aln->sl[a];
            len_b = aln->sl[b];

            
            g = (len_a > len_b)? len_a:len_b;
            map[c] = malloc(sizeof(int) * (g+2));
            if(g > hm->size){
                  hm = hirsch_mem_realloc(hm,g);
            }

            for (j = 0; j < (g+2);j++){
                  map[c][j] = -1;
            }

            if (a < numseq){
                  profile[a] = dna_make_profile(profile[a],aln->s[a],len_a,submatrix);
            }
            if (b < numseq){
                  profile[b] = dna_make_profile(profile[b],aln->s[b],len_b,submatrix);
            }
            
      
            dna_set_gap_penalties(profile[a],len_a,aln->nsip[b]);
            dna_set_gap_penalties(profile[b],len_b,aln->nsip[a]);

            hm->starta = 0;
            hm->startb = 0;
            hm->enda = len_a;
            hm->endb = len_b;
            hm->len_a = len_a;
            hm->len_b = len_b;
            
            hm->f[0].a = 0.0;
            hm->f[0].ga =  -FLOATINFTY;
            hm->f[0].gb = -FLOATINFTY;
            hm->b[0].a = 0.0;
            hm->b[0].ga =  -FLOATINFTY;
            hm->b[0].gb =  -FLOATINFTY;
      //    fprintf(stderr,"LENA:%d LENB:%d     numseq:%d\n",len_a,len_b,numseq);
            if(a < numseq){
                  if(b < numseq){
                        map[c] = hirsch_dna_ss_dyn(submatrix,aln->s[a],aln->s[b],hm,map[c]);
                  }else{
                        hm->enda = len_b;
                        hm->endb = len_a;
                        hm->len_a = len_b;
                        hm->len_b = len_a;
                        map[c] = hirsch_dna_ps_dyn(profile[b],aln->s[a],hm,map[c],aln->nsip[b]);
                        map[c] = mirror_hirsch_path(map[c],len_a,len_b);
                  }
            }else{
                  if(b < numseq){
                        map[c] = hirsch_dna_ps_dyn(profile[a],aln->s[b],hm,map[c],aln->nsip[a]);
                  }else{
                        if(len_a < len_b){
                              map[c] = hirsch_dna_pp_dyn(profile[a],profile[b],hm,map[c]);
                        }else{
                              hm->enda = len_b;
                              hm->endb = len_a;
                              hm->len_a = len_b;
                              hm->len_b = len_a;
                              map[c] = hirsch_dna_pp_dyn(profile[b],profile[a],hm,map[c]);
                              map[c] = mirror_hirsch_path(map[c],len_a,len_b);
                        }
                  }
            }

            
            map[c] = add_gap_info_to_hirsch_path(map[c],len_a,len_b);

            if(i != numseq-2){
                  profile[c] = malloc(sizeof(float)*22*(map[c][0]+2));
                  profile[c] = dna_update(profile[a],profile[b],profile[c],map[c],aln->nsip[a],aln->nsip[b]);
            }
                  
            aln->sl[c] = map[c][0];
      
            aln->nsip[c] = aln->nsip[a] + aln->nsip[b];
            aln->sip[c] = malloc(sizeof(int)*(aln->nsip[a] + aln->nsip[b]));
            g =0;
            for (j = aln->nsip[a];j--;){
                  aln->sip[c][g] = aln->sip[a][j];
                  g++;
            }
            for (j = aln->nsip[b];j--;){
                  aln->sip[c][g] = aln->sip[b][j];
                  g++;
            }

            free(profile[a]);
            free(profile[b]);
      }
      
      fprintf(stderr,"\r%8.0f percent done\n",100.0);
      //free(profile[numprofiles-1]);
      free(profile);
      hirsch_mem_free(hm);
      for (i = 32;i--;){
            free(submatrix[i]);
      }
      free(submatrix);
      return map;
}


int* hirsch_dna_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path)
{
      int mid = ((hm->enda - hm->starta) / 2)+ hm->starta;
      float input_states[6] = {hm->f[0].a,hm->f[0].ga,hm->f[0].gb,hm->b[0].a,hm->b[0].ga,hm->b[0].gb};
      int old_cor[5] = {hm->starta,hm->enda,hm->startb,hm->endb,mid};

      if(hm->starta  >= hm->enda){
            return hirsch_path;
      }
      if(hm->startb  >= hm->endb){
            return hirsch_path;
      }


      hm->enda = mid;

      //fprintf(stderr,"Forward:%d-%d     %d-%d\n",hm->starta,hm->enda,hm->startb,hm->endb);
      hm->f = foward_hirsch_dna_ss_dyn(subm,seq1,seq2,hm);

      hm->starta = mid;
      hm->enda = old_cor[1];
      //fprintf(stderr,"Backward:%d-%d    %d-%d\n",hm->starta,hm->enda,hm->startb,hm->endb);
      hm->b = backward_hirsch_dna_ss_dyn(subm,seq1,seq2,hm);


      hirsch_path = hirsch_align_two_dna_ss_vector(subm,seq1,seq2,hm,hirsch_path,input_states,old_cor);
      return hirsch_path;
}

int* hirsch_align_two_dna_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[])
{
      struct states* f = hm->f;
      struct states* b = hm->b;
      int i,j,c;
      int transition = -1;
      
      
      //code:
      // a -> a = 1
      // a -> ga = 2
      // a -> gb = 3
      // ga ->ga = 4
      // ga -> a = 5
      //gb->gb = 6;
      //gb->a = 7;
      
      //int max = -INFTY;
      float max = -INFTY;     
      float middle =  (hm->endb - hm->startb)/2 + hm->startb;
      float sub = 0.0;
      
      i = hm->startb;
      c = -1;
      for(i = hm->startb; i < hm->endb;i++){
            sub = abs(middle -i);
            sub /= 1000; 
      //    fprintf(stderr,"%d-%d   %f\n",hm->startb,hm->endb,sub);
            if(f[i].a+b[i].a-sub > max){
                  max = f[i].a+b[i].a-sub;
      //          fprintf(stderr,"aligned->aligned:%d + %d = %d\n",f[i].a,b[i].a,f[i].a+b[i].a);
                  transition = 1;
                  c = i;
            }
            if(f[i].a+b[i].ga-gpo-sub > max){
                  max = f[i].a+b[i].ga-gpo-sub;
      //          fprintf(stderr,"aligned->gap_a:%d + %d +%d = %d\n",f[i].a,b[i].ga,prof1[27],f[i].a+b[i].ga+prof2[27]);
                  transition = 2;
                  c = i;
            }
            if(f[i].a+b[i].gb -gpo-sub > max){
                  max = f[i].a+b[i].gb - gpo-sub;
      //          fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
                  transition = 3;
                  c = i;
            }
            if(f[i].ga+b[i].a - gpo-sub > max){
                  max = f[i].ga+b[i].a - gpo-sub;
      //          fprintf(stderr,"gap_a->aligned:%d + %d + %d(gpo) = %d\n",f[i].ga,b[i].a,prof2[27],f[i].ga+b[i].a+prof2[27]);
                  transition = 5;
                  c = i;
            }


            if(hm->startb == 0){
                  if(f[i].gb+b[i].gb - tgpe-sub > max){
                        max = f[i].gb+b[i].gb -tgpe-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                        transition = 6;
                        c = i;
                  }
            }else{
                  if(f[i].gb+b[i].gb - gpe -sub> max){
                        max = f[i].gb+b[i].gb - gpe-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                        transition = 6;
                        c = i;
                  }
            }
            if(f[i].gb+b[i].a - gpo-sub > max){
                  max = f[i].gb+b[i].a - gpo-sub;
      //          fprintf(stderr,"gap_b->aligned:%d + %d + %d(gpo) = %d\n",f[i].gb,b[i].a,prof1[27],f[i].gb+b[i].a+prof1[27]);
                  transition = 7;
                  c = i;
            }
      }
      i = hm->endb;
      sub = abs(middle -i);
      sub /= 1000; 
      
      if(f[i].a+b[i].gb-gpo-sub > max){
            max = f[i].a+b[i].gb - gpo-sub;
      //          fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
            transition = 3;
            c = i;
      }
      if(hm->endb == hm->len_b){
            if(f[i].gb+b[i].gb -tgpe-sub > max){
                  max = f[i].gb+b[i].gb - tgpe-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                  transition = 6;
                  c = i;
            }     
      }else{
            if(f[i].gb+b[i].gb - gpe-sub > max){
                  max = f[i].gb+b[i].gb - tgpe-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                  transition = 6;
                  c = i;
            }
      }
      
      
      //fprintf(stderr,"Transition:%d     at:%d\n",transition,c);
      
      j = hirsch_path[0];
      switch(transition){
            case 1: //a -> a = 1
                  
                  hirsch_path[old_cor[4]] = c;
                  hirsch_path[old_cor[4]+1] = c+1;
                  
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
      //          fprintf(stderr,"Using this for start:%d   %d    %d\n",hm->f[0].a,hm->f[0].ga,hm->f[0].gb);
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d  what:%d-%d      %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  break;
            case 2:// a -> ga = 2
                  
                  hirsch_path[old_cor[4]] = c;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  

                  //backward:
                  hm->starta = old_cor[4];
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = 0.0;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d  what:%d-%d      %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  break;
            case 3:// a -> gb = 3
                  
                  hirsch_path[old_cor[4]] = c;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = 0.0;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  break;
            case 5://ga -> a = 5
                  hirsch_path[old_cor[4]+1] = c+1;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);

                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = 0.0;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4];
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  break;
            case 6://gb->gb = 6;
                  
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = 0.0;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  hm->startb = old_cor[2];
                  hm->endb = c;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = 0.0;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  break;
            case 7://gb->a = 7;
                  
                  hirsch_path[old_cor[4]+1] = c+1;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = 0.0;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  hm->startb = old_cor[2];
                  hm->endb = c;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
                  break;
      }
            
      return hirsch_path;
}



struct states* foward_hirsch_dna_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm)
{
      struct states* s = hm->f;
      float *subp = 0;
      const int starta = hm->starta;
      const int enda = hm->enda;
      const int startb = hm->startb;
      const int endb = hm->endb;
      
      register float pa = 0;
      register float pga = 0;
      register float pgb = 0;
      register float ca = 0;
      register int i = 0;
      register int j = 0;
      

      s[startb].a = s[0].a;
      s[startb].ga = s[0].ga;
      s[startb].gb = s[0].gb;
      if(startb == 0){
            for (j = startb+1; j < endb;j++){

                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j-1].ga,s[j-1].a)-tgpe;
                  
                  s[j].gb = -FLOATINFTY;
            }           
      }else{

            for (j = startb+1; j < endb;j++){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j-1].ga - gpe,s[j-1].a-gpo);
                  s[j].gb = -FLOATINFTY;
            }
      }
      s[endb].a = -FLOATINFTY;
      s[endb].ga = -FLOATINFTY;
      s[endb].gb = -FLOATINFTY;
      seq2--;

      for (i = starta;i < enda;i++){
            subp = subm[seq1[i]];

            pa = s[startb].a;
            pga = s[startb].ga;
            pgb = s[startb].gb;
            s[startb].a = -FLOATINFTY;
            s[startb].ga = -FLOATINFTY;
            if(startb == 0){
                  s[startb].gb = MAX(pgb,pa) - tgpe;
            }else{
                  s[startb].gb = MAX(pgb - gpe,pa - gpo);
            }
            for (j = startb+1; j < endb;j++){
                  ca = s[j].a;
                  pa = MAX3(pa,pga-gpo,pgb-gpo);      
                  pa += subp[seq2[j]];
                  
                  s[j].a = pa;
                  
                  pga = s[j].ga;
                  
                  s[j].ga = MAX(s[j-1].ga-gpe,s[j-1].a-gpo);
                  
                  pgb = s[j].gb;
                  
                  s[j].gb = MAX(pgb-gpe ,ca-gpo);
                  
                  pa = ca;
            }
            ca = s[j].a;
            pa = MAX3(pa,pga-gpo,pgb-gpo);
            pa += subp[seq2[j]];
                  
            s[j].a = pa;
                  
            s[j].ga = -FLOATINFTY;//MAX(s[j-1].ga-gpe,s[j-1].a-gpo);
            if (endb != hm->len_b){
                  s[j].gb = MAX(s[j].gb-gpe ,ca-gpo);
            }else{
                  s[j].gb = MAX(s[j].gb,ca)-tgpe;
            }
      }
      return s;
}

struct states* backward_hirsch_dna_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm)
{

      struct states* s = hm->b;
      float *subp = 0;
      const int starta = hm->starta;
      const int enda = hm->enda;
      const int startb = hm->startb;
      const int endb = hm->endb;
      register float pa = 0;
      register float pga = 0;
      register float pgb = 0;
      register float ca = 0;
      register int i = 0;
      register int j = 0;

      s[endb].a = s[0].a ;
      s[endb].ga = s[0].ga;
      s[endb].gb = s[0].gb;
      
      
      //init of first row;
      
      //j = endb-startb;
      if(endb == hm->len_b){
            for(j = endb-1;j > startb;j--){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j+1].ga,s[j+1].a)-tgpe;
                  s[j].gb = -FLOATINFTY;
            }
      }else{
            for(j = endb-1;j > startb;j--){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j+1].ga-gpe,s[j+1].a-gpo);      
                  s[j].gb = -FLOATINFTY;
            }
      }

      
      s[startb].a = -FLOATINFTY;
      s[startb].ga = -FLOATINFTY;
      s[startb].gb = -FLOATINFTY;

      i = enda-starta;
      seq1+= starta;
      while(i--){
            subp = subm[seq1[i]];
            pa = s[endb].a;
            pga = s[endb].ga;
            pgb = s[endb].gb;
            s[endb].a = -FLOATINFTY;
            s[endb].ga = -FLOATINFTY;

            if(endb == hm->len_b){
                  s[endb].gb = MAX(pgb,pa)-tgpe;
            }else{
                  s[endb].gb = MAX(pgb-gpe,pa-gpo);
            }

            for(j = endb-1;j > startb;j--){

                  ca = s[j].a;
                  pa = MAX3(pa,pga - gpo,pgb-gpo);
                  
                  pa += subp[seq2[j]];

                  s[j].a = pa;
                  
                  pga = s[j].ga;
                  
                  s[j].ga = MAX(s[j+1].ga-gpe,s[j+1].a-gpo);
                  
                  pgb = s[j].gb;

                  s[j].gb = MAX(pgb-gpe,ca-gpo);
                  
                  pa = ca;
            }
            ca = s[j].a;

            pa = MAX3(pa,pga - gpo,pgb-gpo);
                  
            pa += subp[seq2[j]];

            s[j].a = pa;
            
            s[j].ga = -FLOATINFTY;//MAX(s[j+1].ga-gpe,s[j+1].a-gpo);
            
            if(startb){
                  s[j].gb = MAX(s[j].gb-gpe,ca-gpo);
            }else{
                  s[j].gb = MAX(s[j].gb,ca)-tgpe;
            }
      }           
      return s;
}


int* hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path,int sip)
{
      int mid = ((hm->enda - hm->starta) / 2)+ hm->starta;
      float input_states[6] = {hm->f[0].a,hm->f[0].ga,hm->f[0].gb,hm->b[0].a,hm->b[0].ga,hm->b[0].gb};
      int old_cor[5] = {hm->starta,hm->enda,hm->startb,hm->endb,mid};


      if(hm->starta  >= hm->enda){
            return hirsch_path;
      }
      if(hm->startb  >= hm->endb){
            return hirsch_path;
      }

      hm->enda = mid;
      hm->f = foward_hirsch_dna_ps_dyn(prof1,seq2,hm,sip);
      
      /*int i;
      fprintf(stderr,"FOWARD\n");
      for (i = hm->startb; i <= hm->endb;i++){
            fprintf(stderr,"%d      %d    %d\n",hm->f[i].a,hm->f[i].ga,hm->f[i].gb);
      }*/

      hm->starta = mid;
      hm->enda = old_cor[1];
      hm->b = backward_hirsch_dna_ps_dyn(prof1,seq2,hm,sip);
      
      /*fprintf(stderr,"BaCKWARD\n");
      for (i = hm->startb; i <= hm->endb;i++){
            fprintf(stderr,"%d      %d    %d\n",hm->b[i].a,hm->b[i].ga,hm->b[i].gb);
      }*/

      hirsch_path = hirsch_align_two_dna_ps_vector(prof1,seq2,hm,hirsch_path,input_states,old_cor,sip);
      return hirsch_path;
}



int* hirsch_align_two_dna_ps_vector(const float* prof1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip)
{
      struct states* f = hm->f;
      struct states* b = hm->b;
      int i,j,c;
      int transition = -1;
      
      const int open = gpo * sip;
      
      
      //code:
      // a -> a = 1
      // a -> ga = 2
      // a -> gb = 3
      // ga ->ga = 4
      // ga -> a = 5
      //gb->gb = 6;
      //gb->a = 7;
      
      //int max = -INFTY;
      float max = -INFTY;     
      float middle =  (hm->endb - hm->startb)/2 + hm->startb;
      float sub = 0.0;
      
      
      prof1+= (22 * (old_cor[4]+1));
      
      i = hm->startb;
      c = -1;
      for(i = hm->startb; i < hm->endb;i++){
            sub = abs(middle -i);
            sub /= 1000; 
            if(f[i].a+b[i].a-sub> max){
                  max = f[i].a+b[i].a-sub;
      //          fprintf(stderr,"aligned->aligned:%d + %d = %d\n",f[i].a,b[i].a,f[i].a+b[i].a);
                  transition = 1;
                  c = i;
            }
            if(f[i].a+b[i].ga-open-sub > max){
                  max = f[i].a+b[i].ga-open-sub;
      //          fprintf(stderr,"aligned->gap_a:%d + %d +%d = %d\n",f[i].a,b[i].ga,prof1[27],f[i].a+b[i].ga+prof2[27]);
                  transition = 2;
                  c = i;
            }
            if(f[i].a+b[i].gb+prof1[8]-sub > max){
                  max = f[i].a+b[i].gb+prof1[8]-sub;
      //          fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
                  transition = 3;
                  c = i;
            }
            if(f[i].ga+b[i].a-open-sub > max){
                  max = f[i].ga+b[i].a-open-sub;
      //          fprintf(stderr,"gap_a->aligned:%d + %d + %d(gpo) = %d\n",f[i].ga,b[i].a,prof2[27],f[i].ga+b[i].a+prof2[27]);
                  transition = 5;
                  c = i;
            }


            if(hm->startb == 0){
                  if(f[i].gb+b[i].gb+prof1[10]-sub > max){
                        max = f[i].gb+b[i].gb+prof1[10]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                        transition = 6;
                        c = i;
                  }
            }else{
                  if(f[i].gb+b[i].gb+prof1[9]-sub > max){
                        max = f[i].gb+b[i].gb+prof1[9]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                        transition = 6;
                        c = i;
                  }
            }
            if(f[i].gb+b[i].a+prof1[8-22]-sub > max){
                  max = f[i].gb+b[i].a+prof1[8-22]-sub;
      //          fprintf(stderr,"gap_b->aligned:%d + %d + %d(gpo) = %d\n",f[i].gb,b[i].a,prof1[27],f[i].gb+b[i].a+prof1[27]);
                  transition = 7;
                  c = i;
            }
      }
      i = hm->endb;
      sub = abs(middle -i);
      sub /= 1000; 
      if(f[i].a+b[i].gb+prof1[8]-sub > max){
            max = f[i].a+b[i].gb+prof1[8]-sub;
      //          fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
            transition = 3;
            c = i;
      }
      if(hm->endb == hm->len_b){
            if(f[i].gb+b[i].gb+prof1[10]-sub > max){
                  max = f[i].gb+b[i].gb+prof1[10]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                  transition = 6;
                  c = i;
            }     
      }else{
            if(f[i].gb+b[i].gb+prof1[9]-sub > max){
                  max = f[i].gb+b[i].gb+prof1[0]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                  transition = 6;
                  c = i;
            }
      }
      
      
      
      prof1-= (22 * (old_cor[4]+1));
      
      //fprintf(stderr,"Transition:%d     at:%d\n",transition,c);
      
      j = hirsch_path[0];
      switch(transition){
            case 1: //a -> a = 1
                  
                  hirsch_path[old_cor[4]] = c;
                  hirsch_path[old_cor[4]+1] = c+1;
                  
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
      //          fprintf(stderr,"Using this for start:%d   %d    %d\n",hm->f[0].a,hm->f[0].ga,hm->f[0].gb);
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d  what:%d-%d      %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);
                  break;
            case 2:// a -> ga = 2
                  
                  hirsch_path[old_cor[4]] = c;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);

                  //backward:
                  hm->starta = old_cor[4];
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = 0.0;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d  what:%d-%d      %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);
                  break;
            case 3:// a -> gb = 3
                  
                  hirsch_path[old_cor[4]] = c;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = 0.0;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);
                  break;
            case 5://ga -> a = 5
                  hirsch_path[old_cor[4]+1] = c+1;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);

                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = 0.0;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4];
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);
                  break;
            case 6://gb->gb = 6;
                  
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = 0.0;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  hm->startb = old_cor[2];
                  hm->endb = c;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);               


                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = 0.0;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);
                  break;
            case 7://gb->a = 7;
                  
                  hirsch_path[old_cor[4]+1] = c+1;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = 0.0;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  hm->startb = old_cor[2];
                  hm->endb = c;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_ps_dyn(prof1,seq2,hm,hirsch_path,sip);
                  break;
      }
            
      return hirsch_path;
}

struct states* foward_hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip)
{
      //unsigned int freq[26];
      struct states* s = hm->f;
      const int starta = hm->starta;
      const int enda = hm->enda;
      const int startb = hm->startb;
      const int endb = hm->endb;
      
      register float pa = 0;
      register float pga = 0;
      register float pgb = 0;
      register float ca = 0;
      register int i = 0;
      register int j = 0;
      
      const float open = gpo * sip;
      const float ext = gpe *sip;
      const float text = tgpe * sip;
      
      
      
      prof1 += (starta) * 22;
      s[startb].a = s[0].a;
      s[startb].ga = s[0].ga;
      s[startb].gb = s[0].gb;
      if(startb == 0){
            for (j = startb+1; j < endb;j++){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j-1].ga,s[j-1].a) - text;
                  s[j].gb = -FLOATINFTY;
            }     
      }else{
            for (j = startb+1; j < endb;j++){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j-1].ga-ext,s[j-1].a-open);     
                  s[j].gb = -FLOATINFTY;
            }
      }
      
      
      s[endb].a = -FLOATINFTY;
      s[endb].ga = -FLOATINFTY;
      s[endb].gb = -FLOATINFTY;
      seq2--;

      for (i = starta;i < enda;i++){
            prof1 += 22;
            pa = s[startb].a;
            pga = s[startb].ga;
            pgb = s[startb].gb;
            s[startb].a = -FLOATINFTY;
            s[startb].ga = -FLOATINFTY;
            if(startb == 0){
                  s[startb].gb = MAX(pgb,pa)+prof1[10];
            }else{
                  s[startb].gb = MAX(pgb+prof1[9],pa+prof1[8]);
            }
            for (j = startb+1; j < endb;j++){
                  ca = s[j].a;
                  pa = MAX3(pa,pga -open,pgb + prof1[-14]);
                  pa += prof1[11 + seq2[j]];


                  s[j].a = pa;
                  
                  pga = s[j].ga;
                  
                  s[j].ga = MAX(s[j-1].ga-ext,s[j-1].a-open);
                  
                  pgb = s[j].gb;

                  s[j].gb = MAX(pgb+prof1[9],ca+prof1[8]);

                  pa = ca;
            }     
            ca = s[j].a;

            pa = MAX3(pa,pga -open,pgb + prof1[-14]);
                  
            pa += prof1[11 + seq2[j]];


            s[j].a = pa;

            s[j].ga = -FLOATINFTY;//MAX(s[j-1].ga-ext,s[j-1].a-open);
                        
            if (hm->endb != hm->len_b){
                  s[j].gb = MAX(s[j].gb+prof1[9] ,ca+prof1[8]);
            }else{
                  s[j].gb = MAX(s[j].gb,ca)+ prof1[10];
            }
      }
      prof1 -= 22 * (enda);
      return s;
}

struct states* backward_hirsch_dna_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip)
{
      //unsigned int freq[26];
      struct states* s = hm->b;
      const int starta = hm->starta;
      const int enda = hm->enda;
      const int startb = hm->startb;
      const int endb = hm->endb;
      
      register float pa = 0;
      register float pga = 0;
      register float pgb = 0;
      register float ca = 0;
      register int i = 0;
      register int j = 0;
      
      const float open = gpo * sip;
      const float ext = gpe *sip;
      const float text = tgpe * sip;
      

      prof1 += (enda+1) * 22;

      s[endb].a = s[0].a;
      s[endb].ga = s[0].ga;
      s[endb].gb = s[0].gb;
      
      
      //init of first row;
      //j = endb-startb;
      if(endb == hm->len_b){
            for(j = endb-1;j > startb;j--){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j+1].ga,s[j+1].a)-text;   
                  s[j].gb = -FLOATINFTY;
            }
      }else{
            for(j = endb-1;j > startb;j--){
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j+1].ga-ext,s[j+1].a-open);
                  s[j].gb = -FLOATINFTY;
            }
      }
      
      s[startb].a = -FLOATINFTY;
      s[startb].ga = -FLOATINFTY;
      s[startb].gb = -FLOATINFTY;

      i = enda-starta;
      while(i--){
            prof1 -= 22;

            pa = s[endb].a;
            pga = s[endb].ga;
            pgb = s[endb].gb;
            s[endb].a = -FLOATINFTY;
            s[endb].ga = -FLOATINFTY;

            if(endb == hm->len_b){
                  s[endb].gb = MAX(pgb,pa) +prof1[10];
            }else{
                  s[endb].gb = MAX(pgb+prof1[9],pa+prof1[8]);
            }

            for(j = endb-1;j > startb;j--){
                  ca = s[j].a;
                  pa = MAX3(pa,pga - open,pgb +prof1[30]);
                  pa += prof1[11 + seq2[j]];

                  s[j].a = pa;
                  
                  pga = s[j].ga;
                  
                  s[j].ga = MAX(s[j+1].ga-ext,s[j+1].a-open);

                  pgb = s[j].gb;

                  s[j].gb = MAX(pgb+prof1[9],ca+prof1[8]);
                  
                  pa = ca;
            }
            ca = s[j].a;

            pa = MAX3(pa,pga - open,pgb +prof1[30]);
            pa += prof1[11 + seq2[j]];

            s[j].a = pa;
                  

            s[j].ga = -FLOATINFTY;//MAX(s[j+1].ga-ext,s[j+1].a-open);
            if(hm->startb){
                  s[j].gb = MAX(s[j].gb+prof1[9], ca+prof1[8]);
            }else{
                  s[j].gb = MAX(s[j].gb,ca)+prof1[10];
            }
      }           
      return s;
}




int* hirsch_dna_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path)
{
      int mid = ((hm->enda - hm->starta) / 2)+ hm->starta;
      float input_states[6] = {hm->f[0].a,hm->f[0].ga,hm->f[0].gb,hm->b[0].a,hm->b[0].ga,hm->b[0].gb};
      int old_cor[5] = {hm->starta,hm->enda,hm->startb,hm->endb,mid};

      
      //fprintf(stderr,"starta:%d enda:%d startb:%d endb:%d mid:%d\n",hm->starta,hm->enda,hm->startb,hm->endb,mid);
      
      
      if(hm->starta  >= hm->enda){
            return hirsch_path;
      }
      if(hm->startb  >= hm->endb){
            return hirsch_path;
      }

      hm->enda = mid;
      hm->f = foward_hirsch_dna_pp_dyn(prof1,prof2,hm);
      /*int i;
      fprintf(stderr,"FOWARD\n");
      for (i = hm->startb; i <= hm->endb;i++){
            fprintf(stderr,"%d      %d    %d\n",hm->f[i].a,hm->f[i].ga,hm->f[i].gb);
      }*/

      hm->starta = mid;
      hm->enda = old_cor[1];
      hm->b = backward_hirsch_dna_pp_dyn(prof1,prof2,hm);
      /*fprintf(stderr,"BaCKWARD\n");

      for (i = hm->startb; i <= hm->endb;i++){
            fprintf(stderr,"%d      %d    %d\n",hm->b[i].a,hm->b[i].ga,hm->b[i].gb);
      }*/

      hirsch_path = hirsch_align_two_dna_pp_vector(prof1,prof2,hm,hirsch_path,input_states,old_cor);
      return hirsch_path;
}



int* hirsch_align_two_dna_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path, float input_states[],int old_cor[])
{
      struct states* f = hm->f;
      struct states* b = hm->b;
      int i,j,c;
      int transition = -1;
      
      
      //code:
      // a -> a = 1
      // a -> ga = 2
      // a -> gb = 3
      // ga ->ga = 4
      // ga -> a = 5
      //gb->gb = 6;
      //gb->a = 7;
      
      //int max = -INFTY;
      float max = -INFTY;     
      float middle =  (hm->endb - hm->startb)/2 + hm->startb;
      float sub = 0.0;
      
      
      prof1+= (22 * (old_cor[4]+1));
      prof2 += (22 * (hm->startb));
      
      i = hm->startb;
      c = -1;
      for(i = hm->startb; i < hm->endb;i++){
            sub = abs(middle -i);
            sub /= 1000; 
            prof2 += 22;
            if(f[i].a+b[i].a-sub > max){
                  max = f[i].a+b[i].a-sub;
      //          fprintf(stderr,"aligned->aligned:%d + %d = %d\n",f[i].a,b[i].a,f[i].a+b[i].a);
                  transition = 1;
                  c = i;
            }
            if(f[i].a+b[i].ga+prof2[8]-sub > max){
                  max = f[i].a+b[i].ga+prof2[8]-sub;
      //          fprintf(stderr,"aligned->gap_a:%d + %d +%d = %d\n",f[i].a,b[i].ga,prof1[27],f[i].a+b[i].ga+prof2[27]);
                  transition = 2;
                  c = i;
            }
            if(f[i].a+b[i].gb+prof1[8]-sub > max){
                  max = f[i].a+b[i].gb+prof1[8]-sub;
      //          fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
                  transition = 3;
                  c = i;
            }
            if(f[i].ga+b[i].a+prof2[-14]-sub > max){
                  max = f[i].ga+b[i].a+prof2[-14]-sub;
      //          fprintf(stderr,"gap_a->aligned:%d + %d + %d(gpo) = %d\n",f[i].ga,b[i].a,prof2[27],f[i].ga+b[i].a+prof2[27]);
                  transition = 5;
                  c = i;
            }


            if(hm->startb == 0){
                  if(f[i].gb+b[i].gb+prof1[10]-sub > max){
                        max = f[i].gb+b[i].gb+prof1[10]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                        transition = 6;
                        c = i;
                  }
            }else{
                  if(f[i].gb+b[i].gb+prof1[9]-sub > max){
                        max = f[i].gb+b[i].gb+prof1[9]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                        transition = 6;
                        c = i;
                  }
            }
            if(f[i].gb+b[i].a+prof1[-14]-sub > max){
                  max = f[i].gb+b[i].a+prof1[-14]-sub;
      //          fprintf(stderr,"gap_b->aligned:%d + %d + %d(gpo) = %d\n",f[i].gb,b[i].a,prof1[27],f[i].gb+b[i].a+prof1[27]);
                  transition = 7;
                  c = i;
            }
      }
      i = hm->endb;
      sub = abs(middle -i);
      sub /= 1000; 
      if(f[i].a+b[i].gb+prof1[8]-sub > max){
            max = f[i].a+b[i].gb+prof1[8]-sub;
      //          fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
            transition = 3;
            c = i;
      }
      if(hm->endb == hm->len_b){
            if(f[i].gb+b[i].gb+prof1[10]-sub > max){
                  max = f[i].gb+b[i].gb+prof1[10]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                  transition = 6;
                  c = i;
            }     
      }else{
            if(f[i].gb+b[i].gb+prof1[9]-sub > max){
                  max = f[i].gb+b[i].gb+prof1[9]-sub;
      //                fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
                  transition = 6;
                  c = i;
            }
      }
      
      
      
      prof1-= (22 * (old_cor[4]+1));
      prof2 -= (hm->endb *22);
      
      //fprintf(stderr,"Transition:%d     at:%d\n",transition,c);
      
      j = hirsch_path[0];
      switch(transition){
            case 1: //a -> a = 1
                  
                  hirsch_path[old_cor[4]] = c;
                  hirsch_path[old_cor[4]+1] = c+1;
                  
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
      //          fprintf(stderr,"Using this for start:%d   %d    %d\n",hm->f[0].a,hm->f[0].ga,hm->f[0].gb);
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d  what:%d-%d      %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);
                  break;
            case 2:// a -> ga = 2
                  
                  hirsch_path[old_cor[4]] = c;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4];
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = 0.0;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d  what:%d-%d      %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);
                  break;
            case 3:// a -> gb = 3
                  
                  hirsch_path[old_cor[4]] = c;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = 0.0;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = 0.0;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);
                  break;
            case 5://ga -> a = 5
                  hirsch_path[old_cor[4]+1] = c+1;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);

                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = 0.0;
                  hm->b[0].gb = -FLOATINFTY;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4];
                  
                  hm->startb = old_cor[2];
                  hm->endb = c-1;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);
                  break;
            case 6://gb->gb = 6;
                  
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = 0.0;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  hm->startb = old_cor[2];
                  hm->endb = c;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c;
                  hm->endb = old_cor[3];
                  hm->f[0].a = -FLOATINFTY;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = 0.0;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);
                  break;
            case 7://gb->a = 7;
                  
                  hirsch_path[old_cor[4]+1] = c+1;
      //          fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
                  //foward:
                  hm->f[0].a = input_states[0];
                  hm->f[0].ga = input_states[1];
                  hm->f[0].gb = input_states[2];
                  hm->b[0].a = -FLOATINFTY;
                  hm->b[0].ga = -FLOATINFTY;
                  hm->b[0].gb = 0.0;
                  
                  hm->starta = old_cor[0];
                  hm->enda = old_cor[4]-1;
                  hm->startb = old_cor[2];
                  hm->endb = c;
                  //fprintf(stderr,"Following first: %d  what:%d-%d     %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);

                  //backward:
                  hm->starta = old_cor[4]+1;
                  hm->enda = old_cor[1];
                  hm->startb = c+1;
                  hm->endb = old_cor[3];
                  hm->f[0].a = 0.0;
                  hm->f[0].ga = -FLOATINFTY;
                  hm->f[0].gb = -FLOATINFTY;
                  hm->b[0].a = input_states[3];
                  hm->b[0].ga = input_states[4];
                  hm->b[0].gb = input_states[5];
      
                  //fprintf(stderr,"Following last: %d\n",c+1);
                  hirsch_path = hirsch_dna_pp_dyn(prof1,prof2,hm,hirsch_path);
                  break;
      }
            
      return hirsch_path;
}

struct states* foward_hirsch_dna_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)
{
      struct states* s = hm->f;

      register float pa = 0;
      register float pga = 0;
      register float pgb = 0;
      register float ca = 0;
      register int i = 0;
      register int j = 0;
      
      
      
      prof1 += (hm->starta) * 22;
      prof2 +=  (hm->startb) * 22;
      s[hm->startb].a = s[0].a;
      s[hm->startb].ga = s[0].ga;
      s[hm->startb].gb = s[0].gb;
      if(hm->startb == 0){
            for (j = hm->startb+1; j < hm->endb;j++){
                  prof2+=22;
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j-1].ga,s[j-1].a)+prof2[10];
                  s[j].gb = -FLOATINFTY;
            }     
            prof2 += 22;      
      }else{

            for (j = hm->startb+1; j < hm->endb;j++){
                  prof2+=22;
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j-1].ga+prof2[9],s[j-1].a+prof2[8]);
                  s[j].gb = -FLOATINFTY;
            }
            prof2 += 22;
      }
      
      prof2 -= (hm->endb-hm->startb) * 22;
      
      s[hm->endb].a = -FLOATINFTY;
      s[hm->endb].ga = -FLOATINFTY;
      s[hm->endb].gb = -FLOATINFTY;


      for (i = hm->starta;i < hm->enda;i++){
            prof1 += 22;

            pa = s[hm->startb].a;
            pga = s[hm->startb].ga;
            pgb = s[hm->startb].gb;
            s[hm->startb].a = -FLOATINFTY;
            s[hm->startb].ga = -FLOATINFTY;
            if(hm->startb == 0){
                  s[hm->startb].gb = MAX(pgb,pa)+ prof1[10];
            }else{
                  s[hm->startb].gb = MAX(pgb+prof1[9],pa+prof1[8]);
            }
            for (j = hm->startb+1; j < hm->endb;j++){
                  prof2 += 22;
                  ca = s[j].a;
                  pa = MAX3(pa,pga + prof2[-14],pgb + prof1[-14]);

                  prof2 += 11;

                  pa += prof1[0]*prof2[0];
                  pa += prof1[1]*prof2[1];
                  pa += prof1[2]*prof2[2];
                  pa += prof1[3]*prof2[3];
                  pa += prof1[4]*prof2[4];
                  pa += prof1[5]*prof2[5];
                  pa += prof1[6]*prof2[6];
                  pa += prof1[7]*prof2[7];
                  
                  
                  prof2 -= 11;      

                  s[j].a = pa;
                  
                  pga = s[j].ga;
                  
                  s[j].ga = MAX(s[j-1].ga+prof2[9],s[j-1].a+prof2[8]);
                  
                  pgb = s[j].gb;

                  s[j].gb = MAX(pgb+prof1[9] ,ca+prof1[8]);

                  pa = ca;
            }
            prof2 += 22;
            ca = s[j].a;
                  
            pa = MAX3(pa,pga + prof2[-14],pgb + prof1[-14]);
            prof2 += 11;

            pa += prof1[0]*prof2[0];
            pa += prof1[1]*prof2[1];
            pa += prof1[2]*prof2[2];
            pa += prof1[3]*prof2[3];
            pa += prof1[4]*prof2[4];
            pa += prof1[5]*prof2[5];
            pa += prof1[6]*prof2[6];
            pa += prof1[7]*prof2[7];
            
            prof2 -= 11;      

            s[j].a = pa;

            s[j].ga = -FLOATINFTY;

            if (hm->endb != hm->len_b){
                  s[j].gb = MAX(s[j].gb+prof1[9] ,ca+prof1[8]);
            }else{
                  s[j].gb = MAX(s[j].gb,ca)+ prof1[10];
            }
            
            
            prof2 -= (hm->endb-hm->startb) * 22;
            
      }
      prof1 -= 22 * (hm->enda);
      return s;
}

struct states* backward_hirsch_dna_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm)
{
      struct states* s = hm->b;
      register float pa = 0;
      register float pga = 0;
      register float pgb = 0;
      register float ca = 0;
      register int i = 0;
      register int j = 0;

      prof1 += (hm->enda+1) * 22;
      prof2 += (hm->endb+1) * 22;
      s[hm->endb].a = s[0].a;
      s[hm->endb].ga = s[0].ga;
      s[hm->endb].gb = s[0].gb;
      
      
      //init of first row;
      //j = endb-startb;
      if(hm->endb == hm->len_b){
            
            for(j = hm->endb-1;j > hm->startb;j--){
                  prof2 -= 22;
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j+1].ga,s[j+1].a)+prof2[10];
                  s[j].gb = -FLOATINFTY;
            }
            prof2 -= 22;
      }else{
            for(j = hm->endb-1;j > hm->startb;j--){
                  prof2 -= 22;
                  s[j].a = -FLOATINFTY;
                  s[j].ga = MAX(s[j+1].ga+prof2[9],s[j+1].a+prof2[8]);
                  s[j].gb = -FLOATINFTY;
            }
            prof2 -= 22;
      }
      
      s[hm->startb].a = -FLOATINFTY;
      s[hm->startb].ga = -FLOATINFTY;
      s[hm->startb].gb = -FLOATINFTY;

      i = hm->enda-hm->starta;
      while(i--){
            prof1 -= 22;

            pa = s[hm->endb].a;
            pga = s[hm->endb].ga;
            pgb = s[hm->endb].gb;
            s[hm->endb].a = -FLOATINFTY;
            s[hm->endb].ga = -FLOATINFTY;

            if(hm->endb == hm->len_b){
                  s[hm->endb].gb = MAX(pgb,pa)+prof1[10];
            }else{
                  s[hm->endb].gb = MAX(pgb+prof1[9] ,pa+prof1[8]);
            }
            //j = endb-startb;
            prof2 += (hm->endb-hm->startb) *22;
            //while(j--){
            for(j = hm->endb-1;j > hm->startb;j--){
                  prof2 -= 22;
                  ca = s[j].a;

                  pa = MAX3(pa,pga + prof2[30],pgb + prof1[30]);

                  prof2 += 11;
                  pa += prof1[0]*prof2[0];
                  pa += prof1[1]*prof2[1];
                  pa += prof1[2]*prof2[2];
                  pa += prof1[3]*prof2[3];
                  pa += prof1[4]*prof2[4];
                  pa += prof1[5]*prof2[5];
                  pa += prof1[6]*prof2[6];
                  pa += prof1[7]*prof2[7];
                  prof2 -= 11;

                  s[j].a = pa;
                  
                  pga = s[j].ga;
                  
                  s[j].ga = MAX(s[j+1].ga+prof2[9], s[j+1].a+prof2[8]);
                  
                  pgb = s[j].gb;

                  s[j].gb = MAX(pgb+prof1[9], ca+prof1[8]);

                  pa = ca;
            }
            prof2 -= 22;
            ca = s[j].a;

            pa = MAX3(pa,pga + prof2[30],pgb + prof1[30]);
            
            prof2 += 11;
            pa += prof1[0]*prof2[0];
            pa += prof1[1]*prof2[1];
            pa += prof1[2]*prof2[2];
            pa += prof1[3]*prof2[3];
            pa += prof1[4]*prof2[4];
            pa += prof1[5]*prof2[5];
            pa += prof1[6]*prof2[6];
            pa += prof1[7]*prof2[7];
            prof2 -= 11;

            s[j].a = pa;
            
            //pga = s[j].ga;
            s[j].ga = -FLOATINFTY;//MAX(s[j+1].ga+prof2[28], s[j+1].a+prof2[27]);

            //pgb = s[j].gb;
            if(hm->startb){
                  s[j].gb = MAX(s[j].gb+prof1[9], ca+prof1[8]);
            }else{
                  s[j].gb = MAX(s[j].gb,ca)+prof1[10];
            }
      }           
      return s;
}

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