int aln_compare ( int argc, char *argv[])
{
int a, b, c,f;
-
+
+ int ik =0;
Alignment *A, *B;
Sequence *SA, *SB, *TOT_SEQ=NULL;
Sequence *defined_residueA;
/*LIST VARIABLES*/
Constraint_list *CL_A;
Constraint_list *CL_B;
- CLIST_TYPE *clist_entry;
+
int pos_in_clist;
Sequence *CLS;
int **posB;
int **seq_cache;
int is_same;
- int n;
+ int *correct_column;
/*RESULTS_VARIABLES*/
int **tot_count;
int **pos_count;
CL_A=aln2constraint_list (A,CL_A, "sim");
CL_B=aln2constraint_list (B,CL_B, "sim");
- clist_entry=vcalloc ( CL_A->entry_len, CL_A->el_size);
+
glob=vcalloc ( A->nseq+1, sizeof (int));
pw_glob=declare_int ( A->nseq+1, A->nseq+1);
if ( strm( compare_mode, "sp"))
{
- for ( b=0,a=0; a<CL_A->ne; a++)
- {
- s1=vread_clist(CL_A, a, SEQ1);
- s2=vread_clist(CL_A, a, SEQ2);
- clist_entry=extract_entry ( clist_entry, a, CL_A);
-
- glob[0]++;
- glob[s1+1]++;
- glob[s2+1]++;
- pw_glob[s1][s2]++;
- pw_glob[s2][s1]++;
-
- clist_entry=extract_entry ( clist_entry, a, CL_A);
-
- if ((main_search_in_list_constraint (clist_entry,&pos_in_clist,4,CL_B))!=NULL)
- {
- vwrite_clist ( CL_A, a, MISC, 1);
- b++;
- }
- else
- {
- vwrite_clist ( CL_A, a, MISC, 0);
- }
+ int *entry;
+ while (entry=extract_entry (CL_A))
+ {
+ s1=entry[SEQ1];
+ s2=entry[SEQ2];
+ glob[0]++;
+ glob[s1+1]++;
+ glob[s2+1]++;
+ pw_glob[s1][s2]++;
+ pw_glob[s2][s1]++;
+ entry[MISC]=1;
+
+ if ((main_search_in_list_constraint (entry,&pos_in_clist,4,CL_B))!=NULL)
+ add_entry2list (entry,CL_A);
+
}
}
- else if ( strm( compare_mode, "column"))
+ else if ( strm( compare_mode, "column") )
{
- posA=aln2pos_simple_2(A);
- posB=aln2pos_simple_2(B);
- seq_cache=declare_int ( A->nseq, A->len_aln+1);
- for ( n=0,a=0; a< A->len_aln; a++)
+ int *entry;
+ posA=aln2pos_simple_2(A);
+ posB=aln2pos_simple_2(B);
+ seq_cache=declare_int ( A->nseq, A->len_aln+1);
+ for ( a=0; a< A->len_aln; a++)
for ( b=0; b<B->len_aln; b++)
+ {
+ is_same=compare_pos_column(posA, a, posB, b, A->nseq);
+ if(is_same)
{
- is_same=compare_pos_column(posA, a, posB, b, A->nseq);
-
- n+=is_same;
- if (is_same)
- {
- for (c=0; c< A->nseq;c++)if ( posA[c][a]>0)seq_cache[c][posA[c][a]]=1;
- }
+ for (c=0; c< A->nseq;c++)
+ {
+ if(posA[c][a]>0)
+ {
+ seq_cache[c][posA[c][a]]=1;
+ }
+ }
}
-
- for ( a=0,b=0; a< CL_A->ne; a++)
- {
- s1=vread_clist(CL_A, a, SEQ1);
- s2=vread_clist(CL_A, a, SEQ2);
- glob[0]++;
- glob[s1+1]++;
- glob[s2+1]++;
- pw_glob[s1][s2]++;
- pw_glob[s2][s1]++;
- r1=vread_clist(CL_A, a, R1);
- if (seq_cache[s1][r1]){b++;vwrite_clist ( CL_A, a, MISC, 1);}
+ }
+
+ while (entry=extract_entry (CL_A))
+ {
+ s1=entry[SEQ1];
+ s2=entry[SEQ2];
+ r1=entry[R1];
+ entry[MISC]=0;
+ glob[0]++;
+ glob[s1+1]++;
+ glob[s2+1]++;
+ pw_glob[s1][s2]++;
+ pw_glob[s2][s1]++;
+
+ if (seq_cache[s1][r1])
+ {
+ entry[MISC]=1;
+ add_entry2list (entry, CL_A);
+ }
}
- free_int (posA, -1);
- free_int (posB, -1);
- free_int (seq_cache, -1);
-
- }
-
+ free_int (posA, -1);
+ free_int (posB, -1);
+ free_int (seq_cache, -1);
+ }
+ else if ( strm( compare_mode, "tc") )
+ {
+ correct_column = vcalloc(A->len_aln+1, sizeof (int));
+ posA=aln2pos_simple_2(A);
+ posB=aln2pos_simple_2(B);
+ for ( a=0; a< A->len_aln; a++)
+ for ( b=0; b<B->len_aln; b++)
+ {
+ is_same = compare_pos_column(posA, a, posB, b, A->nseq);
+ if(is_same)
+ correct_column[a] = is_same;
+ }
+ free_int (posB, -1);
+ }
+
for ( a=0; a< n_structure; a++)
{
ST=read_structure (struct_file[a],struct_format[a], A,B,ST,n_symbol[a], symbol_list[a]);
pw_pos_count=vcalloc ( A->nseq, sizeof (int**));
for ( a=0; a< A->nseq; a++)pw_pos_count[a]=declare_int ( A->nseq, n_categories);
+
+ /*COMPARISON MODULE*/
+ if (strm( compare_mode, "tc") )
+ {
+ int column_is_structure;
+ int pair_is_structure;
- /*COMPARISON MODULE*/
- for ( a=0; a< n_categories; a++)
- {
- for (b=0; b<CL_A->ne; b++)
+ for ( a=0; a< n_categories; a++)
+ {
+ for(b = 0; b < A->len_aln; b++)
+ {
+ column_is_structure = 1;
+ pair_is_structure = 0;
+ for (s1=0; s1< A->nseq-1; s1++)
{
- s1=vread_clist(CL_A, b, SEQ1);
- s2=vread_clist(CL_A, b, SEQ2);
-
- r1=vread_clist(CL_A, b, R1);
- r2=vread_clist(CL_A, b, R2);
-
- c=vread_clist(CL_A, b, MISC);
-
- if ( is_in_struct_category ( s1, s2, r1, r2, ST, category[a], n_sub_categories[a]))
+ for(s2=s1+1; s2 < A->nseq; s2++)
+ {
+ if ((posA[s1][b]>0) && (posA[s2][b]>0))
+ {
+ pair_is_structure=is_in_struct_category(s1,s2,posA[s1][b],posA[s2][b],ST,category[a], n_sub_categories[a]);
+ column_is_structure = (column_is_structure && pair_is_structure);
+ if(pair_is_structure)
+ {
+ tot_count[a][s1+1]++;
+ tot_count[a][s2+1]++;
+ pw_tot_count[s1][s2][a]++;
+ pw_tot_count[s2][s1][a]++;
+ if (correct_column[b])
+ {
+ pw_pos_count[s1][s2][a]++;
+ pw_pos_count[s2][s1][a]++;
+ pos_count[a][s1+1]++;
+ pos_count[a][s2+1]++;
+ }
+ }
+ }
+ }
+ }
+ if(column_is_structure && pair_is_structure)
+ {
+ tot_count[a][0]++;
+ if(correct_column[b])
+ {
+ pos_count[a][0]++;
+ }
+ }
+ }
+ }
+ free_int (posA, -1);
+ }
+ else
+ {
+ /*COMPARISON MODULE*/
+ int *entry;
+ for ( a=0; a< n_categories; a++)
+ {
+ while (entry=extract_entry (CL_A))
+ {
+ s1=entry[SEQ1];
+ s2=entry[SEQ2];
+ r1=entry[R1];
+ r2=entry[R2];
+ c= entry[MISC];
+ if ( is_in_struct_category ( s1, s2, r1, r2, ST, category[a], n_sub_categories[a]))
{
-
- tot_count[a][0]++;
- tot_count[a][s1+1]++;
- tot_count[a][s2+1]++;
- pw_tot_count[s1][s2][a]++;
- pw_tot_count[s2][s1][a]++;
- if ( c==1)
- {
- pw_pos_count[s1][s2][a]++;
- pw_pos_count[s2][s1][a]++;
- pos_count[a][0]++;
- pos_count[a][s1+1]++;
- pos_count[a][s2+1]++;
- }
+ tot_count[a][0]++;
+ tot_count[a][s1+1]++;
+ tot_count[a][s2+1]++;
+ pw_tot_count[s1][s2][a]++;
+ pw_tot_count[s2][s1][a]++;
+ if ( c==1)
+ {
+ pw_pos_count[s1][s2][a]++;
+ pw_pos_count[s2][s1][a]++;
+ pos_count[a][0]++;
+ pos_count[a][s1+1]++;
+ pos_count[a][s2+1]++;
+ }
+ }
}
-
- }
- }
-
-
-
-
-
+ }
+ }
+// printf("pos=%d,tot=%d\n", pos_count[0][0], tot_count[0][0]);
/*Measure of Aligned Sequences Similarity*/
sim=get_aln_compare_sim ((strcmp (sim_aln, "al1")==0)?A:B, ST,sim_category[0], sim_n_sub_categories[0], sim_matrix);
sim_param=analyse_sim ((strcmp (sim_aln, "al1")==0)?A:B, sim);
-
/*Fill the Result_structure*/
R=vcalloc ( 1, sizeof (Result));
/*Rewriting of Alignment A*/
if ( output_aln)
{
+ int *entry;
A->residue_case=2;
aln_output_tot =declare_int ( A->nseq, A->len_aln+1);
aln_output_count=declare_int ( A->nseq, A->len_aln+1);
- for ( a=0; a< CL_A->ne; a++)
+ while (entry=extract_entry (CL_A))
{
- clist_entry=extract_entry ( clist_entry, a, CL_A);
- aln_output_tot[clist_entry[SEQ1]][clist_entry[R1]]++;
- aln_output_tot[clist_entry[SEQ2]][clist_entry[R2]]++;
+ aln_output_tot[entry[SEQ1]][entry[R1]]++;
+ aln_output_tot[entry[SEQ2]][entry[R2]]++;
- aln_output_count[clist_entry[SEQ1]][clist_entry[R1]]+=clist_entry[MISC];
- aln_output_count[clist_entry[SEQ2]][clist_entry[R2]]+=clist_entry[MISC];
+ aln_output_count[entry[SEQ1]][entry[R1]]+=entry[MISC];
+ aln_output_count[entry[SEQ2]][entry[R2]]+=entry[MISC];
}
+
for ( a=0; a< A->nseq; a++)
{
}
/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
+/*� Centro de Regulacio Genomica */
/*and */
/*Cedric Notredame */
/*Tue Jul 1 10:00:54 WEST 2008. */
/**/
/* */
/*********************************COPYRIGHT NOTICE**********************************/
-/*********************************COPYRIGHT NOTICE**********************************/
+/******************************COPYRIGHT NOTICE*******************************/
/*© Centro de Regulacio Genomica */
/*and */
/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
/*All rights reserved.*/
/*This file is part of T-COFFEE.*/
/**/
/**/
/**/
/* */
-/*********************************COPYRIGHT NOTICE**********************************/
+/******************************COPYRIGHT NOTICE*******************************/
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