61 PackAln * PackAln_read_Shatter_GeneWise6(GeneWise6 * mat)   in PackAln_read_Shatter_GeneWise6()
86 int GeneWise6_shatter_access_main(GeneWise6 * mat,int i,int j,int state)   in GeneWise6_shatter_access_main()
104 int GeneWise6_shatter_access_special(GeneWise6 * mat,int i,int j,int state)   in GeneWise6_shatter_access_special()
121 boolean calculate_shatter_GeneWise6(GeneWise6 * mat,DPEnvelope * dpenv)   in calculate_shatter_GeneWise6()
861     GeneWise6 * mat;       in score_only_GeneWise6()
1180     GeneWise6 * mat;   in PackAln_bestmemory_GeneWise6()
1261 GeneWise6 * allocate_GeneWise6_only(GeneWiseScore* query,ComplexSequence* target ,GeneParser4Score …  in allocate_GeneWise6_only()
1263     GeneWise6 * out;       in allocate_GeneWise6_only()
1296 GeneWise6 * allocate_Expl_GeneWise6(GeneWiseScore* query,ComplexSequence* target ,GeneParser4Score …  in allocate_Expl_GeneWise6()
1298     GeneWise6 * out;   in allocate_Expl_GeneWise6()
1336 void init_GeneWise6(GeneWise6 * mat)   in init_GeneWise6()
1382 void recalculate_PackAln_GeneWise6(PackAln * pal,GeneWise6 * mat)   in recalculate_PackAln_GeneWise6()
1602 GeneWise6 * allocate_Small_GeneWise6(GeneWiseScore* query,ComplexSequence* target ,GeneParser4Score…  in allocate_Small_GeneWise6()
1604     GeneWise6 * out;   in allocate_Small_GeneWise6()
1639 PackAln * PackAln_calculate_Small_GeneWise6(GeneWise6 * mat,DPEnvelope * dpenv)   in PackAln_calculate_Small_GeneWise6()
1733 AlnRangeSet * AlnRangeSet_calculate_Small_GeneWise6(GeneWise6 * mat)   in AlnRangeSet_calculate_Small_GeneWise6()
1763 AlnRangeSet * AlnRangeSet_from_GeneWise6(GeneWise6 * mat)   in AlnRangeSet_from_GeneWise6()
1804 AlnRange * AlnRange_build_GeneWise6(GeneWise6 * mat,int stopj,int stopspecstate,int * startj,int * …  in AlnRange_build_GeneWise6()
1870 boolean read_hidden_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,int st…  in read_hidden_GeneWise6()
1944 int max_hidden_GeneWise6(GeneWise6 * mat,int hiddenj,int i,int j,int state,boolean isspecial,int * …  in max_hidden_GeneWise6()
2336 boolean read_special_strip_GeneWise6(GeneWise6 * mat,int stopi,int stopj,int stopstate,int * startj…  in read_special_strip_GeneWise6()
2416 int max_special_strip_GeneWise6(GeneWise6 * mat,int i,int j,int state,boolean isspecial,int * reti,…  in max_special_strip_GeneWise6()
2467 int max_matrix_to_special_GeneWise6(GeneWise6 * mat,int i,int j,int state,int cscore,int * reti,int…  in max_matrix_to_special_GeneWise6()
2584 void calculate_hidden_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,int …  in calculate_hidden_GeneWise6()
2823 void init_hidden_GeneWise6(GeneWise6 * mat,int starti,int startj,int stopi,int stopj)   in init_hidden_GeneWise6()
2881 boolean full_dc_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,int stopj,…  in full_dc_GeneWise6()
2959 boolean do_dc_single_pass_GeneWise6(GeneWise6 * mat,int starti,int startj,int startstate,int stopi,…  in do_dc_single_pass_GeneWise6()
2988 void push_dc_at_merge_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int * stopj,DPEnvel…  in push_dc_at_merge_GeneWise6()
3645 void follow_on_dc_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * …  in follow_on_dc_GeneWise6()
3965 void run_up_dc_GeneWise6(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,DPEnvelope * dpe…  in run_up_dc_GeneWise6()
4197 void init_dc_GeneWise6(GeneWise6 * mat)   in init_dc_GeneWise6()
4239 int start_end_find_end_GeneWise6(GeneWise6 * mat,int * endj)   in start_end_find_end_GeneWise6()
4276 boolean dc_optimised_start_end_calc_GeneWise6(GeneWise6 *mat,DPEnvelope * dpenv)   in dc_optimised_start_end_calc_GeneWise6()
4705 void init_start_end_linear_GeneWise6(GeneWise6 * mat)   in init_start_end_linear_GeneWise6()
5088 PackAln * PackAln_read_Expl_GeneWise6(GeneWise6 * mat)   in PackAln_read_Expl_GeneWise6()
5111 int GeneWise6_explicit_access_main(GeneWise6 * mat,int i,int j,int state)   in GeneWise6_explicit_access_main()
5129 int GeneWise6_explicit_access_special(GeneWise6 * mat,int i,int j,int state)   in GeneWise6_explicit_access_special()
5146 PackAln * PackAln_read_generic_GeneWise6(GeneWise6 * mat,GeneWise6_access_func_holder h)   in PackAln_read_generic_GeneWise6()
5232 int find_end_GeneWise6(GeneWise6 * mat,int * ri,int * rj,int * state,boolean * isspecial,GeneWise6_…  in find_end_GeneWise6()
5276 void GeneWise6_debug_show_matrix(GeneWise6 * mat,int starti,int stopi,int startj,int stopj,FILE * o…  in GeneWise6_debug_show_matrix()
5318 int max_calc_GeneWise6(GeneWise6 * mat,int i,int j,int state,boolean isspecial,int * reti,int * ret…  in max_calc_GeneWise6()
5744 int max_calc_special_GeneWise6(GeneWise6 * mat,int i,int j,int state,boolean isspecial,int * reti,i…  in max_calc_special_GeneWise6()
5823 boolean calculate_GeneWise6(GeneWise6 * mat)   in calculate_GeneWise6()
6119 boolean calculate_dpenv_GeneWise6(GeneWise6 * mat,DPEnvelope * dpenv)   in calculate_dpenv_GeneWise6()
6473 GeneWise6 * GeneWise6_alloc(void)   in GeneWise6_alloc()
6475     GeneWise6 * out;/* out is exported at end of function */   in GeneWise6_alloc()
6479     if((out=(GeneWise6 *) ckalloc (sizeof(GeneWise6))) == NULL)  {    in GeneWise6_alloc()
6508 GeneWise6 * free_GeneWise6(GeneWise6 * obj)   in free_GeneWise6()