125     int leni;      in calculate_shatter_FiveStateProtein()  local
141     leni = mat->leni;      in calculate_shatter_FiveStateProtein()
154     if( endi > mat->leni )     in calculate_shatter_FiveStateProtein()
155       endi = mat->leni;    in calculate_shatter_FiveStateProtein()
619 …if((mat->basematrix = BaseMatrix_alloc_matrix_and_specials(2,(mat->leni + 1) * 5,2,2)) == NULL)  {…  in score_only_FiveStateProtein()
620 …only matrix for FiveStateProtein cannot be allocated, (asking for 1  by %d  cells)",mat->leni*5);    in score_only_FiveStateProtein()
629       for(i=(-1);i<mat->leni;i++)    {    in score_only_FiveStateProtein()
644       for(i=0;i<mat->leni;i++)   { /*for all query positions*/   in score_only_FiveStateProtein()
982     out->leni = query->len;    in allocate_FiveStateProtein_only()
1012         if( dpri->cache->maxleni >= (out->lenj+1)*5 && dpri->cache->maxlenj >= (out->leni+1))      in allocate_Expl_FiveStateProtein()
1019 …if( (out->basematrix = BaseMatrix_alloc_matrix_and_specials((out->lenj+1)*5,(out->leni+1),2,out->l…  in allocate_Expl_FiveStateProtein()
1020 …rix FiveStateProtein cannot be allocated, (asking for %d by %d main cells)",out->leni,out->lenj);    in allocate_Expl_FiveStateProtein()
1257 …DC_OPT_SHADOW_MATRIX(thismatrix,i,j,state) (score_pointers[(((j+1)% 1) * (leni+1) * 5) + ((i+1) * …
1258 …OW_MATRIX_SP(thismatrix,i,j,state,shadow) (shadow_pointers[(((j+1)% 1) * (leni+1) * 40) + ((i+1) *…
1282 …  out->basematrix = BaseMatrix_alloc_matrix_and_specials(16,(out->leni + 1) * 5,16,out->lenj+1);     in allocate_Small_FiveStateProtein()
1284 …shadow matrix FiveStateProtein cannot be allocated, (asking for 2 by %d main cells)",out->leni+2);   in allocate_Small_FiveStateProtein()
3393     int leni;      in dc_optimised_start_end_calc_FiveStateProtein()  local
3401     leni = mat->query->len;    in dc_optimised_start_end_calc_FiveStateProtein()
3403     total = leni * lenj;   in dc_optimised_start_end_calc_FiveStateProtein()
3406     score_pointers = (int *) calloc (1 * (leni + 1) * 5,sizeof(int));      in dc_optimised_start_end_calc_FiveStateProtein()
3407     shadow_pointers = (int *) calloc (1 * (leni + 1) * 5 * 8,sizeof(int));     in dc_optimised_start_end_calc_FiveStateProtein()
3411       for(i=0;i<leni;i++)    { /*for each i position in strip*/   in dc_optimised_start_end_calc_FiveStateProtein()
4741     int leni;      in calculate_FiveStateProtein()  local
4753     leni = mat->leni;      in calculate_FiveStateProtein()
4755     tot = leni * lenj;     in calculate_FiveStateProtein()
4763       for(i=0;i<leni;i++)    {    in calculate_FiveStateProtein()
5021     if( endi > mat->leni )     in calculate_dpenv_FiveStateProtein()
5022       endi = mat->leni;    in calculate_dpenv_FiveStateProtein()
5031       for(i=1;i<mat->leni;i++)   {    in calculate_dpenv_FiveStateProtein()
5321     out->leni = 0;     in FiveStateProtein_alloc()