--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <stdarg.h>
+#include <string.h>
+#include <ctype.h>
+#include "io_lib_header.h"
+#include "util_lib_header.h"
+#include "define_header.h"
+
+#include "dp_lib_header.h"
+float compute_lambda (int **matrix,char *alphabet);
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR EVALUATING THE CONSISTENCY BETWEEN ALN AND CL */
+/* */
+/*********************************************************************************************/
+
+/*Fast: score= extended_res/max_extended_residue_for the whole aln
+ slow: score= extended_res/sum all extended score for that residue
+ non_extended score= non_ext /sum all non extended score for that residue
+ heuristic score= extended /sum of extended score of all pairs in the library
+ (i.e. Not ALL the possible pairs)
+*/
+Alignment * main_coffee_evaluate_output2 ( Alignment *IN,Constraint_list *CL, const char *mode );
+int sub_aln2ecl_raw_score (Alignment *A, Constraint_list *CL, int ns, int *ls)
+{
+ int **pos;
+ int p1,r1, r2, s1, s2;
+ int score=0;
+
+ if ( !A) return 0;
+ A=reorder_aln (A, (CL->S)->name,(CL->S)->nseq);
+ pos=aln2pos_simple ( A,A->nseq);
+
+
+
+ for (p1=0; p1<A->len_aln; p1++)
+ {
+ for (s1=0; s1<ns-1; s1++)
+ {
+ for (s2=s1+1; s2<ns; s2++)
+ {
+
+ r1=pos[ls[s1]][p1];
+ r2=pos[ls[s2]][p1];
+ if (r1>0 && r2>0)
+ {
+ score+= residue_pair_extended_list_pc (CL,ls[s1], r1, ls[s2], r2)*SCORE_K;
+ }
+ }
+ }
+ }
+ free_int (pos, -1);
+ return score;
+ return (score/(((ns*ns)-ns)/2))/A->len_aln;
+}
+int aln2ecl_raw_score (Alignment *A, Constraint_list *CL)
+{
+ int **pos;
+ int p1,r1, r2, s1, s2;
+ int score=0;
+ if ( !A) return 0;
+ A=reorder_aln (A, (CL->S)->name,(CL->S)->nseq);
+ pos=aln2pos_simple ( A,A->nseq);
+
+
+
+ for (p1=0; p1<A->len_aln; p1++)
+ {
+ for (s1=0; s1<A->nseq-1; s1++)
+ {
+ for (s2=s1+1; s2<A->nseq; s2++)
+ {
+
+ r1=pos[s1][p1];
+ r2=pos[s2][p1];
+ if (r1>0 && r2>0)score+= residue_pair_extended_list_pc (CL,s1, r1, s2, r2);
+ }
+ }
+ }
+ free_int (pos, -1);
+ return score;
+ return (score/(((A->nseq*A->nseq)-A->nseq)/2))/A->len_aln;
+}
+int node2sub_aln_score (Alignment *A,Constraint_list *CL, char *mode, NT_node T)
+{
+ if ( !T || !T->right ||!T->left)return 0;
+ else
+ {
+ int *ns;
+ int **ls;
+ ns=vcalloc (2, sizeof (int));
+ ls=vcalloc (2, sizeof (int*));
+ ns[0]= (T->left)->nseq;
+ ns[1]=(T->right)->nseq;
+ ls[0]= (T->left)->lseq;
+ ls[1]=(T->right)->lseq;
+
+ return sub_aln2sub_aln_score (A, CL, mode, ns, ls);
+ }
+ return -1;
+}
+int sub_aln2sub_aln_score ( Alignment *A,Constraint_list *CL, const char *mode, int *ns, int **ls)
+{
+ /*Warning: Does Not Take Gaps into account*/
+
+ int **pos;
+ int a;
+ float score=0;
+
+ /*Make sure evaluation functions update their cache if needed*/
+ A=update_aln_random_tag (A);
+ pos=aln2pos_simple ( A, -1, ns, ls);
+ for (a=0; a< A->len_aln; a++)
+ score+=CL->get_dp_cost (A, pos, ns[0], ls[0], a, pos, ns[1],ls[1], a, CL);
+ free_int (pos, -1);
+
+ score=(int)(((float)score)/(A->len_aln*SCORE_K));
+ score=(int)(CL->residue_index && CL->normalise)?((score*MAXID)/(CL->normalise)):(score);
+ return (int)score;
+}
+int sub_aln2sub_aln_raw_score ( Alignment *A,Constraint_list *CL, const char *mode, int *ns, int **ls)
+{
+ /*Warning: Does Not Take Gaps into account*/
+
+ int **pos;
+ int a;
+ float score=0;
+
+ /*Make sure evaluation functions update their cache if needed*/
+ A=update_aln_random_tag (A);
+ pos=aln2pos_simple ( A, -1, ns, ls);
+ for (a=0; a< A->len_aln; a++)
+ score+=CL->get_dp_cost (A, pos, ns[0], ls[0], a, pos, ns[1],ls[1], a, CL);
+ free_int (pos, -1);
+ return (int) score;
+}
+
+Alignment* main_coffee_evaluate_output_sub_aln ( Alignment *A,Constraint_list *CL, const char *mode, int *n_s, int **l_s)
+{
+ Alignment *SUB1, *SUB2, *SUB3;
+ int a, b, c,*list_seq;
+
+
+ if (strm ( CL->evaluate_mode, "no"))return NULL;
+ else
+ {
+ list_seq=vcalloc (n_s[0]+n_s[1], sizeof (int));
+ for (b=0, a=0; a< 2; a++){for (c=0;c< n_s[a]; c++)list_seq[b++]=l_s[a][c];}
+
+
+ SUB1=copy_aln (A, NULL);
+ SUB2=extract_sub_aln (SUB1,n_s[0]+n_s[1],list_seq);
+ SUB3=main_coffee_evaluate_output (SUB2,CL,CL->evaluate_mode);
+ free_aln (SUB1);
+ free_aln (SUB2);
+ vfree (list_seq);
+
+ return SUB3;
+ }
+}
+Alignment * overlay_alignment_evaluation ( Alignment *I, Alignment *O)
+{
+ int a, b, c, r, i;
+ int *buf;
+
+ if ( !I || !O) return O;
+ if ( I->len_aln!=O->len_aln)printf_exit (EXIT_FAILURE, stderr, "ERROR: Incompatible alignments in overlay_alignment_evaluation");
+
+ buf=vcalloc ( MAX(I->len_aln, O->len_aln), sizeof (int));
+
+ for (a=0; a<O->nseq; a++)
+ {
+ if (!strm (I->name[a], O->name[a]))printf_exit (EXIT_FAILURE, stderr, "ERROR: Incompatible alignments in overlay_alignment_evaluation");
+ for (b=0; b<O->len_aln; b++)
+ {
+ r=I->seq_al[a][b];
+ if ( islower(r))O->seq_al[a][b]=0;
+ else if (r<=9 || (r>='0' && r<='9'))O->seq_al[a][b]=I->seq_al[a][b];
+ }
+ }
+ return O;
+}
+
+Alignment * main_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL, const char *mode )
+{
+
+ Alignment *TopS=NULL, *LastS=NULL, *CurrentS=NULL;
+
+
+ if ( IN->A)IN=IN->A;
+ while (IN)
+ {
+
+ CurrentS= main_coffee_evaluate_output2(IN, CL, mode);
+ if (!TopS)LastS=TopS=CurrentS;
+ else
+ {
+ LastS->A=CurrentS;
+ LastS=CurrentS;
+ }
+ IN=IN->A;
+ }
+ return TopS;
+}
+
+Alignment * main_coffee_evaluate_output2 ( Alignment *IN,Constraint_list *CL, const char *mode )
+{
+
+ /*Make sure evaluation functions update their cache if needed*/
+ IN=update_aln_random_tag (IN);
+
+ if ( CL->evaluate_residue_pair==evaluate_matrix_score || CL->ne==0 ||strm ( mode , "categories") || strm ( mode , "matrix")|| strm(mode, "sar")|| strstr (mode, "boxshade") )
+ {
+
+ if ( strm ( mode , "categories")) return categories_evaluate_output (IN, CL);
+ else if ( strm ( mode , "matrix"))return matrix_evaluate_output (IN, CL);
+ else if ( strm ( mode, "sar"))return sar_evaluate_output (IN, CL);
+ else if ( strstr ( mode, "boxshade"))return boxshade_evaluate_output (IN, CL, atoi (strstr(mode, "_")+1));
+
+ else if ( CL->evaluate_residue_pair==evaluate_matrix_score) return matrix_evaluate_output (IN, CL);
+ else if ( CL->ne==0) return matrix_evaluate_output (IN, CL);
+ }
+ else if ( strm (mode, "no"))return NULL;
+ else if ( strstr( mode, "triplet"))
+ {
+ return triplet_coffee_evaluate_output ( IN,CL);
+ }
+ else if ( strstr ( mode, "fast"))
+ {
+ return fast_coffee_evaluate_output ( IN,CL);
+ }
+ else if ( strstr ( mode, "slow"))
+ {
+ return slow_coffee_evaluate_output ( IN,CL);
+ }
+
+ else if ( strstr ( mode, "non_extended"))
+ {
+ return non_extended_t_coffee_evaluate_output ( IN,CL);
+ }
+
+ else if ( strm (mode, "sequences"))
+ {
+ return coffee_seq_evaluate_output ( IN,CL);
+ }
+ else
+ {
+ fprintf ( stderr, "\nUNKNOWN MODE FOR ALIGNMENT EVALUATION: *%s* [FATAL:%s]",mode, PROGRAM);
+ crash ("");
+ return NULL;
+ }
+ return IN;
+}
+
+
+
+Alignment * coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ fprintf ( stderr, "\n[WARNING:%s]THE FUNCTION coffee_evaluate_output IS NOT ANYMORE SUPPORTED\n", PROGRAM);
+ fprintf ( stderr, "\n[WARNING]fast_coffee_evaluate_output WILL BE USED INSTEAD\n");
+
+ return fast_coffee_evaluate_output (IN,CL);
+ }
+Alignment * matrix_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ int a,b, c,r, s, r1, r2;
+ Alignment *OUT=NULL;
+
+ double **tot_res;
+ double **max_res;
+
+ double **tot_seq;
+ double **max_seq;
+
+ double **tot_col;
+ double **max_col;
+
+ double max_aln=0;
+ double tot_aln=0;
+
+
+ /*
+ Residue x: sum of observed extended X.. /sum of possible X..
+ */
+
+
+ if ( !CL->M)CL->M=read_matrice ("blosum62mt");
+
+ OUT=copy_aln (IN, OUT);
+
+
+ tot_res=declare_double ( IN->nseq, IN->len_aln);
+ max_res=declare_double ( IN->nseq, IN->len_aln);
+
+ tot_seq=declare_double ( IN->nseq, 1);
+ max_seq=declare_double ( IN->nseq, 1);
+ tot_col=declare_double ( IN->len_aln,1);
+ max_col=declare_double ( IN->len_aln,1);
+
+ max_aln=tot_aln=0;
+
+ for (a=0; a< IN->len_aln; a++)
+ {
+ for ( b=0; b< IN->nseq; b++)
+ {
+ r1=tolower(IN->seq_al[b][a]);
+ if ( is_gap(r1))continue;
+ r= CL->M[r1-'A'][r1-'A'];
+ r= 1;
+ for ( c=0; c<IN->nseq; c++)
+ {
+ r2=tolower(IN->seq_al[c][a]);
+ if (b==c || is_gap (r2))continue;
+
+ s=CL->M[r2-'A'][r1-'A'];
+ s=(s<=0)?0:1;
+
+ tot_res[b][a]+=s;
+ max_res[b][a]+=r;
+
+ tot_col[a][0]+=s;
+ max_col[a][0]+=r;
+
+ tot_seq[b][0]+=s;
+ max_seq[b][0]+=r;
+
+ tot_aln+=s;
+ max_aln+=r;
+ }
+ }
+ }
+
+
+ for ( a=0; a< IN->nseq; a++)
+ {
+ if ( !max_seq[a][0])continue;
+
+ OUT->score_seq[a]=(tot_seq[a][0]*100)/max_seq[a][0];
+ for (b=0; b< IN->len_aln; b++)
+ {
+ r1=IN->seq_al[a][b];
+ if ( is_gap(r1) || !max_res[a][b])continue;
+
+ r1=(tot_res[a][b]*10)/max_res[a][b];
+ r1=(r1>=10)?9:r1;
+ r1=r1<0?0:r1;
+ (OUT)->seq_al[a][b]=r1+'0';
+ }
+ }
+
+ for ( a=0; a< IN->len_aln; a++)
+ {
+ r1=(max_col[a][0]==0)?0:((tot_col[a][0]*10)/max_col[a][0]);
+ r1=(r1>=10)?9:r1;
+ (OUT)->seq_al[OUT->nseq][a]=r1+'0';
+ }
+ sprintf ( OUT->name[IN->nseq], "cons");
+ if (max_aln)OUT->score_seq[OUT->nseq]=OUT->score_aln=(100*tot_aln)/max_aln;
+
+
+ free_double (tot_res,-1);
+ free_double (max_res,-1);
+
+ free_double (tot_seq,-1);
+ free_double (max_seq,-1);
+
+ return OUT;
+ }
+
+Alignment * sar_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ int a,b, c,r, s, r1, r2;
+ Alignment *OUT=NULL;
+
+ double **tot_res;
+ double **max_res;
+
+ double **tot_seq;
+ double **max_seq;
+
+ double **tot_col;
+ double **max_col;
+
+ double max_aln=0;
+ double tot_aln=0;
+
+
+ /*
+ Residue x: sum of observed extended X.. /sum of possible X..
+ */
+
+
+ if ( !CL->M)CL->M=read_matrice ("blosum62mt");
+
+ OUT=copy_aln (IN, OUT);
+
+
+ tot_res=declare_double ( IN->nseq, IN->len_aln);
+ max_res=declare_double ( IN->nseq, IN->len_aln);
+
+ tot_seq=declare_double ( IN->nseq, 1);
+ max_seq=declare_double ( IN->nseq, 1);
+ tot_col=declare_double ( IN->len_aln,1);
+ max_col=declare_double ( IN->len_aln,1);
+
+ max_aln=tot_aln=0;
+
+ for (a=0; a< IN->len_aln; a++)
+ {
+ for (b=0; b< IN->nseq; b++)
+ {
+ r1=tolower(IN->seq_al[b][a]);
+ for (c=0; c<IN->nseq; c++)
+ {
+ r2=tolower(IN->seq_al[c][a]);
+ if (b==c)continue;
+
+ if ( is_gap(r1) && is_gap(r2))s=0;
+ else s=(r1==r2)?1:0;
+
+ r=1;
+
+
+ tot_res[b][a]+=s;
+ max_res[b][a]+=r;
+
+ tot_col[a][0]+=s;
+ max_col[a][0]+=r;
+
+ tot_seq[b][0]+=s;
+ max_seq[b][0]+=r;
+
+ tot_aln+=s;
+ max_aln+=r;
+ }
+ }
+ }
+
+ for ( a=0; a< IN->nseq; a++)
+ {
+ if ( !max_seq[a][0])continue;
+ OUT->score_seq[a]=(max_seq[a][0]*100)/max_seq[a][0];
+ for (b=0; b< IN->len_aln; b++)
+ {
+ r1=IN->seq_al[a][b];
+ if ( is_gap(r1) || !max_res[a][b])continue;
+ r1=(tot_res[a][b]*10)/max_res[a][b];
+ r1=(r1>=10)?9:r1;
+ r1=r1<0?0:r1;
+ (OUT)->seq_al[a][b]=r1+'0';
+ }
+ }
+
+ for ( a=0; a< IN->len_aln; a++)
+ {
+ r1=(max_col[a][0]==0)?0:((tot_col[a][0]*10)/max_col[a][0]);
+ r1=(r1>=10)?9:r1;
+ (OUT)->seq_al[OUT->nseq][a]=r1+'0';
+ }
+ sprintf ( OUT->name[IN->nseq], "cons");
+ if (max_aln)OUT->score_aln=(100*tot_aln)/max_aln;
+
+
+ free_double (tot_res,-1);
+ free_double (max_res,-1);
+
+ free_double (tot_seq,-1);
+ free_double (max_seq,-1);
+
+ return OUT;
+ }
+Alignment * boxshade_evaluate_output ( Alignment *IN,Constraint_list *CL, int T)
+ {
+ Alignment *OUT=NULL;
+ int **aa;
+ int r,br, bs, a, b;
+ float f;
+
+
+ /*
+ Residue x: sum of observed extended X.. /sum of possible X..
+ */
+
+
+ OUT=copy_aln (IN, OUT);
+ aa=declare_int (26, 2);
+
+ for ( a=0; a< OUT->len_aln; a++)
+ {
+ for ( b=0; b< 26; b++){aa[b][1]=0;aa[b][0]='a'+b;}
+ for ( b=0; b< OUT->nseq; b++)
+ {
+ r=tolower(OUT->seq_al[b][a]);
+ if ( !is_gap(r))aa[r-'a'][1]++;
+ }
+ sort_int ( aa, 2, 1, 0,25);
+ f=(aa[25][1]*100)/OUT->nseq;
+
+ if (f<T);
+ else
+ {
+ bs=((f-T)*10)/(100-T);
+ br=aa[25][0];
+
+ if (bs==10)bs--;bs+='0';
+ for ( b=0; b< OUT->nseq; b++)
+ {
+ r=tolower(OUT->seq_al[b][a]);
+ if (r==br && bs>'1')OUT->seq_al[b][a]=bs;
+ }
+ OUT->seq_al[b][a]=bs;
+ }
+ }
+ sprintf ( OUT->name[IN->nseq], "cons");
+
+ return OUT;
+ }
+
+Alignment * categories_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+
+ Alignment *OUT=NULL;
+ int a, b, r;
+ int *aa;
+ float score, nseq2, tot_aln;
+ float n;
+ /*
+ Residue x: sum of observed extended X.. /sum of possible X..
+ */
+ OUT=copy_aln (IN, OUT);
+ aa=vcalloc ( 26, sizeof (int));
+ nseq2=IN->nseq*IN->nseq;
+
+ for (tot_aln=0, a=0; a< IN->len_aln; a++)
+ {
+ for (n=0,b=0; b< IN->nseq; b++)
+ {
+ r=IN->seq_al[b][a];
+
+ if ( is_gap(r))n++;
+ else
+ {
+ aa[tolower(r)-'a']++;
+ n++;
+ }
+ }
+ n=n*n;
+ for ( score=0,b=0; b< 26; b++){score+=aa[b]*aa[b];aa[b]=0;}
+ /*score/=nseq2;*/
+ score=(n==0)?0:score/n;
+ tot_aln+=score;
+ r=score*10;
+ r=(r>=10)?9:r;
+ (OUT)->seq_al[OUT->nseq][a]='0'+r;
+ }
+ OUT->score_aln=(tot_aln/OUT->len_aln)*100;
+ sprintf ( OUT->name[IN->nseq], "cons");
+ vfree(aa);
+ return OUT;
+ }
+
+Alignment * categories_evaluate_output_old ( Alignment *IN,Constraint_list *CL)
+ {
+
+ Alignment *OUT=NULL;
+ int nc,a, b, r;
+ int *aa, ng;
+ float score, nseq2, tot_aln, min=0;
+
+ /*
+ Residue x: sum of observed extended X.. /sum of possible X..
+ */
+ OUT=copy_aln (IN, OUT);
+ aa=vcalloc ( 26, sizeof (int));
+ nseq2=IN->nseq*IN->nseq;
+
+ for (tot_aln=0, a=0; a< IN->len_aln; a++)
+ {
+ for (ng=0,b=0; b< IN->nseq; b++)
+ {
+ r=IN->seq_al[b][a];
+
+ if ( is_gap(r))ng++;
+ else
+ {
+ aa[tolower(r)-'a']++;
+ }
+ }
+ for (nc=0, b=0; b<26; b++)
+ {
+ if ( aa[b])nc++;
+ aa[b]=0;
+ }
+ if (nc>9)score=0;
+ else score=9-nc;
+
+ score=(2*min)/IN->nseq;
+
+ tot_aln+=score;
+ r=score*10;
+ r=(r>=10)?9:r;
+ (OUT)->seq_al[OUT->nseq][a]='0'+r;
+ }
+
+ OUT->score_aln=(tot_aln/OUT->len_aln)*100;
+ sprintf ( OUT->name[IN->nseq], "cons");
+ vfree(aa);
+ return OUT;
+ }
+Alignment * fork_triplet_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * nfork_triplet_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * triplet_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+{
+
+ if (!IN || !CL || !CL->residue_index) return IN;
+
+
+ if ( get_nproc()==1)return nfork_triplet_coffee_evaluate_output (IN,CL);
+ else if (strstr ( CL->multi_thread, "evaluate"))return fork_triplet_coffee_evaluate_output (IN,CL);
+ else return nfork_triplet_coffee_evaluate_output (IN,CL);
+}
+Alignment * fork_triplet_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ Alignment *OUT=NULL;
+ int **pos;
+
+ double score_col=0, score_aln=0, score_res=0, score=0;
+ double max_col=0, max_aln=0, max_res=0;
+ double *max_seq, *score_seq;
+
+ int a,b, x, y,res;
+ int s1,r1,s2,r2,w2,s3,r3,w3;
+ int **lu;
+
+ //multi-threading
+ FILE *fp;
+ char **pid_tmpfile;
+ int sjobs, njobs;
+ int **sl;
+ int j;
+
+ OUT=copy_aln (IN, OUT);
+ pos=aln2pos_simple(IN, IN->nseq);
+ sprintf ( OUT->name[IN->nseq], "cons");
+
+ max_seq=vcalloc ( IN->nseq, sizeof (double));
+ score_seq=vcalloc ( IN->nseq, sizeof (double));
+ lu=declare_int (IN->nseq, IN->len_aln+1);
+
+ //multi Threading stuff
+ njobs=get_nproc();
+ sl=n2splits (njobs,IN->len_aln);
+ pid_tmpfile=vcalloc (njobs, sizeof (char*));
+
+ for (sjobs=0,j=0; sjobs<njobs; j++)
+ {
+ pid_tmpfile[j]=vtmpnam(NULL);
+ if (vvfork (NULL)==0)
+ {
+ initiate_vtmpnam(NULL);
+ fp=vfopen (pid_tmpfile[j], "w");
+ score_aln=max_aln=0;
+ for (a=sl[j][0]; a<sl[j][1]; a++)
+ {
+ if (j==0)output_completion (stderr,a,sl[0][1],1, "Final Evaluation");
+ score_col=max_col=0;
+ for (b=0; b<IN->nseq; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1>=0)lu[s1][r1]=1;
+ }
+ for (b=0; b<IN->nseq; b++)
+ {
+ score_res=max_res=NORM_F;
+ res=NO_COLOR_RESIDUE;
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1<=0)
+ {
+ fprintf (fp, "%d ", res);
+ continue;
+ }
+
+ for (x=1;x<CL->residue_index[s1][r1][0];x+=ICHUNK)
+ {
+ s2=CL->residue_index[s1][r1][x+SEQ2];
+ r2=CL->residue_index[s1][r1][x+R2];
+ w2=CL->residue_index[s1][r1][x+WE];
+ for (y=1; y<CL->residue_index[s2][r2][0];y+=ICHUNK)
+ {
+ s3=CL->residue_index[s2][r2][y+SEQ2];
+ r3=CL->residue_index[s2][r2][y+R2];
+ w3=CL->residue_index[s2][r2][y+WE];
+
+ score=MIN(w2,w3);
+
+ max_res+=score;
+ max_col+=score;
+ max_seq[b]+=score;
+ max_aln+=score;
+
+ if (lu[s3][r3])
+ {
+ score_res+=score;
+ score_col+=score;
+ score_seq[b]+=score;
+ score_aln+=score;
+ }
+ }
+ }
+ res=(max_res==0)?NO_COLOR_RESIDUE:((score_res*10)/max_res);
+ res=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+ fprintf ( fp, "%d ", res);
+ }
+ for (b=0; b<IN->nseq; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1>0)lu[s1][r1]=0;
+ }
+
+ res=(max_col==0)?NO_COLOR_RESIDUE:((score_col*10)/max_col);
+ res=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+ fprintf (fp, "%d ", res);
+ for (b=0; b<IN->nseq; b++)fprintf (fp, "%f %f ", score_seq[b], max_seq[b]);
+ }
+ fprintf (fp, "%f %f ", score_aln, max_aln);
+ vfclose (fp);
+ myexit (EXIT_SUCCESS);
+ }
+ else
+ {
+ sjobs++;
+ }
+ }
+
+ while (sjobs>=0){vwait(NULL); sjobs--;}//wait for all jobs to complete
+
+ for (j=0; j<njobs; j++)
+ {
+ float sseq, mseq;
+ fp=vfopen (pid_tmpfile[j], "r");
+ for (a=sl[j][0];a<sl[j][1]; a++)
+ {
+ for (b=0; b<=IN->nseq; b++)//don't forget the consensus
+ {
+ fscanf (fp, "%d ", &res);
+ OUT->seq_al[b][a]=res;
+ }
+ for (b=0; b<IN->nseq; b++)
+ {
+ fscanf (fp, "%f %f", &sseq, &mseq);
+ score_seq[b]+=sseq;
+ max_seq[b]+=mseq;
+ }
+ }
+ fscanf (fp, "%f %f", &sseq, &mseq);
+ score_aln+=sseq;
+ max_aln+=mseq;
+ vfclose (fp);
+ remove (pid_tmpfile[j]);
+ }
+ fprintf ( stderr, "\n");
+
+ IN->score_aln=OUT->score_aln=(max_aln==0)?0:((score_aln*100)/max_aln);
+ for ( a=0; a< OUT->nseq; a++)
+ {
+ OUT->score_seq[a]=(max_seq[a]==0)?0:((score_seq[a]*100)/max_seq[a]);
+ }
+
+ free_int (lu,-1);
+ free_int (pos , -1);
+ vfree (pid_tmpfile);
+ free_int (sl, -1);
+ vfree ( score_seq);
+ vfree ( max_seq);
+ return OUT;
+ }
+
+Alignment * nfork_triplet_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ Alignment *OUT=NULL;
+ int **pos;
+
+ double score_col=0, score_aln=0, score_res=0, score=0;
+ double max_col=0, max_aln=0, max_res=0;
+ double *max_seq, *score_seq;
+
+ int a,b, x, y,res;
+ int s1,r1,s2,r2,w2,s3,r3,w3;
+ int **lu;
+
+
+
+ OUT=copy_aln (IN, OUT);
+ pos=aln2pos_simple(IN, IN->nseq);
+ sprintf ( OUT->name[IN->nseq], "cons");
+
+ max_seq=vcalloc ( IN->nseq, sizeof (double));
+ score_seq=vcalloc ( IN->nseq, sizeof (double));
+ lu=declare_int (IN->nseq, IN->len_aln+1);
+
+
+
+
+ score_aln=max_aln=0;
+ for (a=0; a<IN->len_aln; a++)
+ {
+ output_completion (stderr,a,IN->len_aln,1, "Final Evaluation");
+ score_col=max_col=0;
+ for (b=0; b<IN->nseq; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1>=0)lu[s1][r1]=1;
+ }
+ for (b=0; b<IN->nseq; b++)
+ {
+ score_res=max_res=NORM_F;
+ OUT->seq_al[b][a]=NO_COLOR_RESIDUE;
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1<=0)continue;
+ for (x=1;x<CL->residue_index[s1][r1][0];x+=ICHUNK)
+ {
+ s2=CL->residue_index[s1][r1][x+SEQ2];
+ r2=CL->residue_index[s1][r1][x+R2];
+ w2=CL->residue_index[s1][r1][x+WE];
+ for (y=1; y<CL->residue_index[s2][r2][0];y+=ICHUNK)
+ {
+ s3=CL->residue_index[s2][r2][y+SEQ2];
+ r3=CL->residue_index[s2][r2][y+R2];
+ w3=CL->residue_index[s2][r2][y+WE];
+
+ score=MIN(w2,w3);
+
+ max_res+=score;
+ max_col+=score;
+ max_seq[b]+=score;
+ max_aln+=score;
+
+ if (lu[s3][r3])
+ {
+ score_res+=score;
+ score_col+=score;
+ score_seq[b]+=score;
+ score_aln+=score;
+ }
+ }
+ }
+ res=(max_res==0)?NO_COLOR_RESIDUE:((score_res*10)/max_res);
+ res=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+ OUT->seq_al[b][a]=res;
+ }
+ for (b=0; b<IN->nseq; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1>0)lu[s1][r1]=0;
+ }
+
+ res=(max_col==0)?NO_COLOR_RESIDUE:((score_col*10)/max_col);
+ res=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+ OUT->seq_al[IN->nseq][a]=res;
+ }
+ fprintf ( stderr, "\n");
+
+ IN->score_aln=OUT->score_aln=(max_aln==0)?0:((score_aln*100)/max_aln);
+ for ( a=0; a< OUT->nseq; a++)
+ {
+ OUT->score_seq[a]=(max_seq[a]==0)?0:((score_seq[a]*100)/max_seq[a]);
+ }
+
+ free_int (lu,-1);
+ free_int (pos , -1);
+ vfree ( score_seq);
+ vfree ( max_seq);
+ return OUT;
+ }
+Alignment * fast_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ int a,b, c, m,res, s, s1, s2, r1, r2;
+ Alignment *OUT=NULL;
+ int **pos, **pos2;
+
+ double score_col=0, score_aln=0, score_res=0;
+ double max_col, max_aln;
+ double *max_seq, *score_seq;
+ int local_m;
+ int local_nseq;
+
+
+ /*NORMALIZE: with the highest scoring pair found in the multiple alignment*/
+
+
+ if ( !CL->evaluate_residue_pair){fprintf ( stderr, "\nWARNING: CL->evaluate_residue_pair Not set\nSet to: extend_residue_pair\n");CL->evaluate_residue_pair= extend_residue_pair; }
+
+ OUT=copy_aln (IN, OUT);
+ pos=aln2pos_simple(IN, IN->nseq);
+ pos2=aln2defined_residues (IN, CL);
+
+ max_seq=vcalloc ( IN->nseq, sizeof (double));
+ score_seq=vcalloc ( IN->nseq, sizeof (double));
+
+
+
+ /*1: Identify the highest scoring pair within the alignment*/
+
+ for ( m=0, a=0; a< IN->len_aln; a++)
+ {
+ for ( b=0; b< IN->nseq; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+
+
+ for ( c=0; c< IN->nseq; c++)
+ {
+ s2=IN->order[c][0];
+ r2=pos[c][a];
+ if ( s1==s2 && !CL->do_self)continue;
+
+ if ( s1< s2)s=(CL->evaluate_residue_pair)( CL, s1, r1, s2, r2);
+ else s=(CL->evaluate_residue_pair)( CL, s2, r2, s1, r1);
+
+ s=(s!=UNDEFINED)?s:0;
+ m=MAX(m, s);
+ }
+ }
+ }
+
+ local_m=m;
+
+ sprintf ( OUT->name[IN->nseq], "cons");
+ for ( max_aln=0,score_aln=0,a=0; a< IN->len_aln; a++)
+ {
+ OUT->seq_al[IN->nseq][a]=NO_COLOR_RESIDUE;
+ for ( local_nseq=0,b=0; b<IN->nseq; b++){local_nseq+=(pos[b][a]>0 && pos2[b][a])?1:0;}
+ local_m=m*(local_nseq-1);
+
+ for ( max_col=0, score_col=0,b=0; b< IN->nseq; b++)
+ {
+ OUT->seq_al[b][a]=NO_COLOR_RESIDUE;
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+
+ if (r1<=0 || !pos2[b][a])
+ {
+ continue;
+ }
+
+ for ( score_res=0,c=0; c< IN->nseq; c++)
+ {
+ s2=IN->order[c][0];
+ r2=pos[c][a];
+
+ if ((s1==s2 && !CL->do_self) || r2<=0 || !pos2[c][a]){continue;}
+ max_col +=m;
+ max_seq[b]+=m;
+ max_aln +=m;
+
+ if ( s1< s2)s=(CL->evaluate_residue_pair)( CL, s1, r1, s2, r2);
+ else s=(CL->evaluate_residue_pair)( CL, s2, r2, s1, r1);
+ s=(s!=UNDEFINED)?s:0;
+
+ score_res+=s;
+ score_col+=s;
+ score_seq[b]+=s;
+ score_aln+=s;
+ }
+
+ res=(local_m==0)?NO_COLOR_RESIDUE:((score_res*10)/local_m);
+ (OUT)->seq_al[b][a]=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+
+
+ }
+
+ res=(max_col==0)?NO_COLOR_RESIDUE:((score_col*10)/max_col);
+ OUT->seq_al[IN->nseq][a]=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+
+ }
+
+ IN->score_aln=OUT->score_aln=(max_aln==0)?0:((score_aln*100)/max_aln);
+ for ( a=0; a< OUT->nseq; a++)
+ {
+ OUT->score_seq[a]=(max_seq[a]==0)?0:((score_seq[a]*100)/max_seq[a]);
+ }
+
+ free_int (pos , -1);
+ free_int (pos2, -1);
+
+ vfree ( score_seq);
+ vfree ( max_seq);
+ return OUT;
+ }
+
+Alignment * slow_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ int a,b, c,res, s, s1, s2, r1, r2;
+ Alignment *OUT=NULL;
+ int **pos, **pos2;
+ double max_score_r, score_r, max;
+ double score_col=0, score_aln=0;
+ double max_score_col, max_score_aln;
+ double *max_score_seq, *score_seq;
+ int ***res_extended_weight;
+ int n_res_in_col;
+
+
+ /*
+ Residue x: sum of observed extended X.. /sum of possible X..
+ */
+
+
+
+
+ if ( !CL->evaluate_residue_pair){fprintf ( stderr, "\nWARNING: CL->evaluate_residue_pair Not set\nSet to: extend_residue_pair\n");CL->evaluate_residue_pair= extend_residue_pair; }
+
+
+ OUT=copy_aln (IN, OUT);
+ pos=aln2pos_simple(IN, IN->nseq);
+ pos2=aln2defined_residues (IN, CL);
+
+ max_score_seq=vcalloc ( IN->nseq, sizeof (double));
+ score_seq=vcalloc ( IN->nseq, sizeof (double));
+ res_extended_weight=declare_arrayN(3,sizeof(int), (CL->S)->nseq, (CL->S)->max_len+1, 2);
+ max=(CL->normalise)?(100*CL->normalise)*SCORE_K:100;
+
+ for (a=0; a< IN->len_aln; a++)
+ {
+ for ( b=0; b< IN->nseq-1; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ for ( c=b+1; c< IN->nseq; c++)
+ {
+ s2=IN->order[c][0];
+ r2=pos[c][a];
+ if ( s1==s2 && !CL->do_self)continue;
+ else if ( r1<=0 || r2<=0) continue;
+ else
+ {
+ s=(CL->evaluate_residue_pair)( CL, s1, r1, s2, r2);
+ res_extended_weight[s1][r1][0]+=s*100;
+ res_extended_weight[s2][r2][0]+=s*100;
+ res_extended_weight[s1][r1][1]+=max;
+ res_extended_weight[s2][r2][1]+=max;
+ }
+ }
+ }
+ }
+
+
+ sprintf ( OUT->name[IN->nseq], "cons");
+ for ( max_score_aln=0,score_aln=0,a=0; a< IN->len_aln; a++)
+ {
+ OUT->seq_al[IN->nseq][a]=NO_COLOR_RESIDUE;
+ for ( n_res_in_col=0,b=0; b<IN->nseq; b++){n_res_in_col+=(pos[b][a]>0 && pos2[b][a]>0)?1:0;}
+ for ( max_score_col=0, score_col=0,b=0; b< IN->nseq; b++)
+ {
+ OUT->seq_al[b][a]=NO_COLOR_RESIDUE;
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1<=0 || pos2[b][a]<1)continue;
+ else
+ {
+ max_score_r =res_extended_weight[s1][r1][1];
+ score_r =res_extended_weight[s1][r1][0];
+ if ( max_score_r==0 && n_res_in_col>1)res=0;
+ else if ( n_res_in_col==1)res=NO_COLOR_RESIDUE;
+ else res=((score_r*10)/max_score_r);
+
+
+ (OUT)->seq_al[b][a]=(res==NO_COLOR_RESIDUE)?res:(MIN(res, 9));
+ max_score_col+=max_score_r;
+ score_col+=score_r;
+ max_score_seq[b]+=max_score_r;
+ score_seq[b]+=score_r;
+ max_score_aln+=max_score_r;
+ score_aln+=score_r;
+ }
+ if ( max_score_col==0 && n_res_in_col>1)res=0;
+ else if ( n_res_in_col<2)res=NO_COLOR_RESIDUE;
+ else res=((score_col*10)/max_score_col);
+
+ OUT->seq_al[IN->nseq][a]=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+ }
+ }
+ IN->score_aln=OUT->score_aln=(max_score_aln==0)?0:((score_aln*100)/max_score_aln);
+ for ( a=0; a< OUT->nseq; a++)
+ {
+ OUT->score_seq[a]=(max_score_seq[a]==0)?0:((score_seq[a]*100)/max_score_seq[a]);
+ }
+
+
+ vfree ( score_seq);
+ vfree ( max_score_seq);
+ free_arrayN((void*)res_extended_weight, 3);
+
+
+ free_int (pos, -1);
+ free_int (pos2, -1);
+ return OUT;
+ }
+
+double genepred2sd (Sequence *S);
+double genepred2avg (Sequence *S);
+double genepred2zsum2 (Sequence *S);
+int * genepred2orf_len (Sequence *S);
+double genepred2acc (Sequence *S, Sequence *PS);
+double seq_genepred2acc (Sequence *S, Sequence *PS, char *name);
+Alignment *coffee_seq_evaluate_output ( Alignment *IN, Constraint_list *CL)
+{
+ int **w, a,b,c,l,i;
+ int avg, min_avg, best_cycle;
+ char **pred_list,**weight_list;
+ FILE *fp;
+ Sequence *S, *PS;
+ int ncycle=20;
+ float nsd, best_score,score, acc;
+ int min_ne;
+ Alignment *A;
+ float *count;
+ min_ne=CL->ne/10; //avoid side effects due to very relaxed libraries
+ w=NULL;
+ pred_list=declare_char (ncycle, 100);
+ weight_list=declare_char(ncycle,100);
+ S=CL->S;
+ fprintf ( stderr, "\nSCORE_MODE: %s\n", CL->genepred_score);
+ for (a=0; a<ncycle && CL->ne>min_ne; a++)
+ {
+ if (w);free_int (w, -1);
+ w=list2residue_total_weight (CL);
+ PS=dnaseq2geneseq (S, w);
+ nsd=(float)(genepred2sd(PS)/genepred2avg(PS));
+ if ( strm (CL->genepred_score, "nsd"))score=nsd;
+ else score=1-seq_genepred2acc (S, PS, CL->genepred_score);
+ fprintf ( stderr, "Cycle: %2d LIB: %6d AVG LENGTH: %6.2f NSD: %8.2f SCORE: %.2f ",a+1,CL->ne,(float) genepred2avg(PS),nsd,score);
+
+ vfree (display_accuracy (genepred_seq2accuracy_counts (S, PS, NULL),stderr));
+ pred_list[a]=vtmpnam(NULL);
+ weight_list[a]=vtmpnam(NULL);
+ output_fasta_seqS(pred_list[a],PS);
+ output_array_int (weight_list[a],w);
+ free_sequence (PS, -1);
+
+ if (a==0 || score<best_score)
+ {
+ best_score=score;
+ best_cycle=a;
+ }
+ CL=relax_constraint_list_4gp(CL);
+ }
+ if (w)free_int(w,-1);
+ S=get_fasta_sequence (pred_list[best_cycle], NULL);
+
+ fprintf ( stderr, "\nSelected Cycle: %d (SCORE=%.4f)----> ", best_cycle+1, best_score);
+ vfree (display_accuracy (genepred_seq2accuracy_counts ((CL->S), S, NULL),stderr));
+
+ genepred_seq2accuracy_counts4all((CL->S), S);
+
+ IN=seq2aln (S,NULL, 1);
+ IN->score_res=input_array_int (weight_list[best_cycle]);
+ return IN;
+}
+
+double seq_genepred2acc (Sequence *S, Sequence *PS, char *name)
+{
+ float *count;
+ float *acc;
+ float r;
+ int ref, target;
+
+ if ( strm (name, "best"))return genepred2acc (S, PS);
+
+ ref=name_is_in_list (name, S->name, S->nseq, 100);
+ target=name_is_in_list (name, PS->name, PS->nseq, 100);
+
+ if ( target==-1 || ref==-1)
+ {
+ printf_exit (EXIT_FAILURE,stderr, "\nERROR: %s is not a valid sequence", name);
+ }
+ count=genepred2accuracy_counts (S->seq[ref],PS->seq[target],NULL);
+ acc=counts2accuracy (count);
+
+ r=acc[3];
+ vfree (acc);
+ vfree (count);
+ return r;
+}
+
+
+
+double genepred2acc (Sequence *S, Sequence *PS)
+{
+ float *count;
+ float *acc;
+ float r;
+ count=genepred_seq2accuracy_counts (S, PS, NULL);
+ acc=counts2accuracy (count);
+
+ r=acc[3];
+ vfree (acc);
+ vfree (count);
+ return r;
+}
+
+double genepred2sd (Sequence *S)
+{
+ double sum=0, sum2=0;
+ int a, b;
+ int *len;
+ len=genepred2orf_len (S);
+
+ for (a=0; a<S->nseq; a++)
+ {
+ sum+=(double)len[a];
+ sum2+=(double)len[a]*(double)len[a];
+ }
+ sum/=(double)S->nseq;
+ sum2/=S->nseq;
+ vfree (len);
+ return sqrt (sum2-(sum*sum));
+}
+double genepred2avg (Sequence *S)
+{
+ int a, b;
+ double avg=0;
+ int *len;
+ len=genepred2orf_len (S);
+
+ for (a=0; a<S->nseq; a++)avg+=len[a];
+ vfree (len);
+ return avg/(double)S->nseq;
+}
+double genepred2zsum2 (Sequence *S)
+{
+ double sum=0, sum2=0, zscore=0, zsum2=0;
+ int a, b;
+ int *len;
+ double sd, avg;
+ sd=genepred2sd(S);
+ avg=genepred2avg (S);
+
+ len=genepred2orf_len (S);
+ for (a=0; a<S->nseq; a++)
+ {
+ zscore=((double)len[a]-avg)/sd;
+ zsum2+=FABS(zscore);
+ }
+ zsum2/=(float)S->nseq;
+ vfree (len);
+ return zsum2;
+}
+int *genepred2orf_len (Sequence *S)
+{
+ int a,b, *len;
+ len=vcalloc (S->nseq, sizeof (int));
+ for (a=0; a<S->nseq; a++)
+ for (b=0; b<S->len[a]; b++)
+ len[a]+=(isupper(S->seq[a][b]));
+ return len;
+}
+
+Alignment *coffee_seq_evaluate_output_old2 ( Alignment *IN, Constraint_list *CL)
+{
+ int **w, a,b,c,l,i;
+ int avg, min_avg, best_cycle;
+ char **pred_list; FILE *fp;
+ Sequence *S, *PS;
+ int ncycle=100;
+ w=NULL;
+ pred_list=declare_char (ncycle, 100);
+ S=CL->S;
+
+ //CL=expand_constraint_list_4gp(CL);
+ min_avg=constraint_list2avg(CL);
+
+ for (a=1; a<ncycle && CL->ne>0; a++)
+ {
+ int t;
+ if (w);free_int (w, -1);
+ w=list2residue_total_weight (CL);
+ CL=relax_constraint_list_4gp (CL);
+ fprintf (stderr,"\nRELAX CYCLE: %2d AVG: %5d [%10d] ", a, avg=constraint_list2avg(CL), CL->ne);
+ for (b=0; b<S->nseq; b++)for (c=0; c<S->len[b]; c++)w[b][c]-=1;
+
+ //rescale nuclotide coding weights
+
+ PS=dnaseq2geneseq (S, w);
+ vfree (display_accuracy (genepred_seq2accuracy_counts (S, PS, NULL),stderr));
+
+
+ free_sequence (PS, PS->nseq);
+ if ( avg<min_avg)
+ {
+ min_avg=avg;
+ best_cycle=a;
+ }
+ }
+
+ S=get_fasta_sequence (pred_list[best_cycle], NULL);
+ vfree (display_accuracy (genepred_seq2accuracy_counts ((CL->S), S, NULL),stderr));myexit (0);
+ for (a=0; a<S->nseq; a++)
+ HERE (">%s\n%s", S->name[a], S->seq[a]);
+ myexit (0);
+ return seq2aln (S,NULL, 1);
+}
+
+
+
+Alignment * non_extended_t_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL)
+ {
+ int a,b, c,res, s1, s2, r1, r2;
+ Alignment *OUT=NULL;
+ int **pos;
+ int max_score_r, score_r;
+ double score_col=0, score_aln=0;
+ int max_score_col, max_score_aln;
+ double *max_score_seq, *score_seq;
+ int local_nseq;
+ int **tot_non_extended_weight;
+ int **res_non_extended_weight;
+ int *l;
+ CLIST_TYPE *entry=NULL;
+ int p;
+ int max_score=0;
+
+ entry=vcalloc (CL->entry_len+1, CL->el_size);
+ if ( !CL->evaluate_residue_pair){fprintf ( stderr, "\nWARNING: CL->evaluate_residue_pair Not set\nSet to: extend_residue_pair\n");CL->evaluate_residue_pair= extend_residue_pair; }
+
+ OUT=copy_aln (IN, OUT);
+ pos=aln2pos_simple(IN, IN->nseq);
+
+
+ max_score_seq=vcalloc ( IN->nseq, sizeof (double));
+ score_seq=vcalloc ( IN->nseq, sizeof (double));
+
+ tot_non_extended_weight=list2residue_total_weight(CL);
+ res_non_extended_weight=declare_int ((CL->S)->nseq, (CL->S)->max_len+1);
+
+ for (a=0; a< IN->len_aln; a++)
+ {
+ for ( b=0; b< IN->nseq-1; b++)
+ {
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ for ( c=b+1; c< IN->nseq; c++)
+ {
+ s2=IN->order[c][0];
+ r2=pos[c][a];
+ if ( s1==s2 && !CL->do_self)continue;
+ else if ( r1<=0 || r2<=0) continue;
+ else
+ {
+ entry[SEQ1]=s1;
+ entry[SEQ2]=s2;
+ entry[R1]=r1;
+ entry[R2]=r2;
+ if ((l=main_search_in_list_constraint (entry,&p,4,CL))!=NULL)
+ {
+ res_non_extended_weight[s1][r1]+=l[WE];
+ res_non_extended_weight[s2][r2]+=l[WE];
+ }
+ entry[SEQ1]=s2;
+ entry[SEQ2]=s1;
+ entry[R1]=r2;
+ entry[R2]=r1;
+ if ((l=main_search_in_list_constraint (entry,&p,4,CL))!=NULL)
+ {
+ res_non_extended_weight[s1][r1]+=l[WE];
+ res_non_extended_weight[s2][r2]+=l[WE];
+ }
+ max_score=MAX(max_score,res_non_extended_weight[s1][r1]);
+ max_score=MAX(max_score,res_non_extended_weight[s2][r2]);
+
+ }
+ }
+ }
+ }
+
+ sprintf ( OUT->name[IN->nseq], "cons");
+ for ( max_score_aln=0,score_aln=0,a=0; a< IN->len_aln; a++)
+ {
+ OUT->seq_al[IN->nseq][a]=NO_COLOR_RESIDUE;
+ for ( local_nseq=0,b=0; b<IN->nseq; b++){local_nseq+=(pos[b][a]>0)?1:0;}
+
+ for ( max_score_col=0, score_col=0,b=0; b< IN->nseq; b++)
+ {
+ OUT->seq_al[b][a]=NO_COLOR_RESIDUE;
+ s1=IN->order[b][0];
+ r1=pos[b][a];
+ if (r1<=0)continue;
+ else
+ {
+ max_score_r =max_score;/*tot_non_extended_weight[s1][r1];*/
+ score_r=res_non_extended_weight[s1][r1];
+ res=(max_score_r==0 || local_nseq<2 )?NO_COLOR_RESIDUE:((score_r*10)/max_score_r);
+
+ (OUT)->seq_al[b][a]=(res==NO_COLOR_RESIDUE)?res:(MIN(res, 9));
+ max_score_col+=max_score_r;
+ score_col+=score_r;
+ max_score_seq[b]+=max_score_r;
+ score_seq[b]+=score_r;
+ max_score_aln+=max_score_r;
+ score_aln+=score_r;
+ }
+ res=(max_score_col==0 || local_nseq<2)?NO_COLOR_RESIDUE:((score_col*10)/max_score_col);
+ OUT->seq_al[IN->nseq][a]=(res==NO_COLOR_RESIDUE)?res:(MIN(res,9));
+ }
+ }
+ IN->score_aln=OUT->score_aln=(max_score_aln==0)?0:((score_aln*100)/max_score_aln);
+ for ( a=0; a< OUT->nseq; a++)
+ {
+ OUT->score_seq[a]=(max_score_seq[a]==0)?0:((score_seq[a]*100)/max_score_seq[a]);
+ OUT->score_seq[a]=(OUT->score_seq[a]>100)?100:OUT->score_seq[a];
+ }
+ OUT->score_aln=(OUT->score_aln>100)?100:OUT->score_aln;
+
+ vfree ( score_seq);
+ vfree ( max_score_seq);
+
+ free_int (tot_non_extended_weight, -1);
+ free_int (res_non_extended_weight, -1);
+ vfree(entry);
+ free_int (pos, -1);
+
+ return OUT;
+ }
+
+
+/*********************************************************************************************/
+/* */
+/* PROFILE/PRofile Functions */
+/* */
+/*********************************************************************************************/
+int channel_profile_profile (int *prf1, int *prf2, Constraint_list *CL);
+
+Profile_cost_func get_profile_mode_function (char *name, Profile_cost_func func)
+{
+ int a;
+ static int nfunc;
+ static Profile_cost_func *flist;
+ static char **nlist;
+
+
+
+ /*The first time: initialize the list of pairwse functions*/
+ /*If func==NULL:REturns a pointer to the function associated with a name*/
+ /*If name is empty:Prints the name of the function associated with name*/
+
+ if ( nfunc==0)
+ {
+ flist=vcalloc ( 100, sizeof (Pwfunc));
+ nlist=declare_char (100, 100);
+
+ flist[nfunc]=cw_profile_profile;
+ sprintf (nlist[nfunc], "cw_profile_profile");
+ nfunc++;
+
+ flist[nfunc]=muscle_profile_profile;
+ sprintf (nlist[nfunc], "muscle_profile_profile");
+ nfunc++;
+
+ flist[nfunc]=channel_profile_profile;
+ sprintf (nlist[nfunc], "channel_profile_profile");
+ nfunc++;
+ }
+
+ for ( a=0; a<nfunc; a++)
+ {
+ if ( (name && strm (nlist[a],name)) || flist[a]==func)
+ {
+ if (name)sprintf (name,"%s", nlist[a]);
+ return flist[a];
+ }
+ }
+ fprintf ( stderr, "\n[%s] is an unknown profile_profile function[FATAL:%s]\n",name, PROGRAM);
+ crash ( "\n");
+ return NULL;
+ }
+
+int generic_evaluate_profile_score (Constraint_list *CL,Alignment *Profile1,int s1, int r1, Alignment *Profile2,int s2, int r2, Profile_cost_func prf_prf)
+ {
+ int *prf1, *prf2;
+ static int *dummy;
+ int score;
+
+
+ /*Generic profile function*/
+ if( !dummy)
+ {
+ dummy=vcalloc (10, sizeof(int));
+ dummy[0]=1;/*Number of Amino acid types on colum*/
+ dummy[1]=5;/*Length of Dummy*/
+ dummy[3]='\0';/*Amino acid*/
+ dummy[4]=1; /*Number of occurences*/
+ dummy[5]=100; /*Frequency in the MSA column*/
+
+ }
+
+ if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+
+ prf1=(Profile1)?(Profile1->P)->count2[r1]:NULL;
+ prf2=(Profile2)?(Profile2->P)->count2[r2]:NULL;
+
+ if (!prf1) {prf1=dummy; prf1[3]=(CL->S)->seq[s1][r1];}
+ else if (!prf2){prf2=dummy; prf2[3]=(CL->S)->seq[s2][r2];}
+
+ score=((prf_prf==NULL)?cw_profile_profile:prf_prf) (prf1, prf2, CL);
+ return score;
+ }
+ else
+ return 0;
+ }
+
+int cw_profile_profile_count (int *prf1, int *prf2, Constraint_list *CL)
+ {
+ /*see function aln2count2 for prf structure*/
+ int a, b, n;
+ int res1, res2;
+ double score=0;
+
+
+ for ( n=0,a=3; a<prf1[1]; a+=3)
+ for ( b=3; b<prf2[1]; b+=3)
+ {
+
+ res1=prf1[a];
+ res2=prf2[b];
+
+ score+=prf1[a+1]*prf2[b+1]*CL->M[res1-'A'][res2-'A'];
+ n+=prf1[a+1]*prf2[b+1];
+ }
+
+
+ score=(score*SCORE_K)/n;
+ return score;
+ }
+int muscle_profile_profile (int *prf1, int *prf2, Constraint_list *CL)
+ {
+ /*see function aln2count2 for prf structure*/
+ int a, b;
+ int res1, res2;
+ double score=0, fg1, fg2, fi, fj, m;
+ static double *exp_lu;
+ if (exp_lu==NULL)
+ {
+ exp_lu=vcalloc ( 10000, sizeof (double));
+ exp_lu+=2000;
+ for ( a=-1000; a<1000; a++)
+ exp_lu[a]=exp((double)a);
+ }
+
+
+
+ for (a=3; a<prf1[1]; a+=3)
+ {
+ res1=prf1[a];
+ fi=(double)prf1[a+2]/100;
+
+ for ( b=3; b<prf2[1]; b+=3)
+ {
+ res2=prf2[b];
+ fj=(double)prf2[b+2]/100;
+ /*m=exp((double)CL->M[res1-'A'][res2-'A']);*/
+ m=exp_lu[CL->M[res1-'A'][res2-'A']];
+ score+=m*fi*fj;
+ }
+ }
+
+ fg1=(double)prf1[2]/100;
+ fg2=(double)prf2[2]/100;
+ score=(score==0)?0:log(score)*(1-fg1)*(1-fg2);
+ score=(score*SCORE_K);
+ /*if ( score<-100)fprintf ( stderr, "\nSCORE %d %d", (int)score, cw_profile_profile(prf1, prf2, CL));*/
+
+ return (int)score;
+ }
+int cw_profile_profile (int *prf1, int *prf2, Constraint_list *CL)
+ {
+ /*see function aln2count2 for prf structure*/
+ int a, b, n,p;
+ int res1, res2;
+ double score=0;
+
+
+ for ( n=0,a=3; a<prf1[1]; a+=3)
+ for ( b=3; b<prf2[1]; b+=3)
+ {
+
+ res1=prf1[a];
+ res2=prf2[b];
+ p=prf1[a+1]*prf2[b+1];
+
+ n+=p;
+ score+=p*CL->M[res1-'A'][res2-'A'];
+ }
+ score=(score*SCORE_K)/((double)(n==0)?1:n);
+ return score;
+ }
+int cw_profile_profile_old (int *prf1, int *prf2, Constraint_list *CL)
+ {
+ /*see function aln2count2 for prf structure*/
+ int a, b, n,p;
+ int res1, res2;
+ double score=0;
+
+
+
+ for ( n=0,a=3; a<prf1[1]; a+=3)
+ for ( b=3; b<prf2[1]; b+=3)
+ {
+
+ res1=prf1[a];
+ res2=prf2[b];
+ p=prf1[a+1]*prf2[b+1];
+
+ n+=p;
+ score+=p*CL->M[res1-'A'][res2-'A'];
+ }
+ score=(score*SCORE_K)/((double)(n==0)?1:n);
+ return score;
+ }
+int channel_profile_profile ( int *prf1, int *prf2, Constraint_list *CL)
+{
+
+ int score=0;
+
+ prf1+=prf1[1];
+ prf2+=prf2[1];
+
+
+ if (prf1[0]!=prf1[0]){fprintf ( stderr, "\nERROR: Inconsistent number of channels [channel_profile_profile::FATAL%s]", PROGRAM);}
+ else
+ {
+ int a, n;
+ for (a=1, n=0; a<=prf1[0]; a++)
+ {
+ if (prf1[a]>0 && prf2[a]>0)
+ {
+ n++;score+=CL->M[prf1[a]-'A'][prf2[a]-'A'];
+
+ }
+ }
+
+ if ( n==0)return 0;
+
+ score=(n==0)?0:(score*SCORE_K)/n;
+
+ }
+ return score;
+}
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR GETING THE COST : (Sequences) ->evaluate_residue_pair */
+/* */
+/*********************************************************************************************/
+int initialize_scoring_scheme (Constraint_list *CL)
+{
+ if (!CL) return 0;
+ else if (!CL->evaluate_residue_pair)return 0;
+ else if ( !CL->S) return 0;
+ else if ( (CL->S)->nseq<2) return 0;
+ else if ( strlen ((CL->S)->seq[0])==0)return 0;
+ else if ( strlen ((CL->S)->seq[1])==0)return 0;
+ else
+ {
+ //CL->evaluate_residue_pair (CL,13,1,16,1);
+ CL->evaluate_residue_pair (CL,0,1,1,1);
+
+ }
+ return 1;
+}
+
+int evaluate_blast_profile_score (Constraint_list *CL, int s1, int r1, int s2, int r2)
+{
+ Alignment *PRF1;
+ Alignment *PRF2;
+
+
+ PRF1=(Alignment*)atop(seq2T_value (CL->S, s1, "A", "_RB_"));
+ PRF2=(Alignment*)atop(seq2T_value (CL->S, s2, "A", "_RB_"));
+
+ return generic_evaluate_profile_score (CL,PRF1,s1, r1, PRF2,s2, r2, CL->profile_mode);
+}
+
+int evaluate_aln_profile_score (Constraint_list *CL, int s1, int r1, int s2, int r2)
+{
+
+ return generic_evaluate_profile_score (CL,seq2R_template_profile((CL->S),s1),s1, r1, seq2R_template_profile(CL->S,s2),s2, r2, CL->profile_mode);
+}
+
+
+int evaluate_profile_score (Constraint_list *CL,Alignment *Prf1, int s1, int r1, Alignment *Prf2,int s2, int r2)
+{
+
+ return generic_evaluate_profile_score (CL, Prf1, s1,r1,Prf2, s2,r2,CL->profile_mode);
+}
+
+int evaluate_cdna_matrix_score (Constraint_list *CL, int s1, int r1, int s2, int r2)
+ {
+ char a1, a2;
+
+ if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+
+ a1=translate_dna_codon((CL->S)->seq[s1]+r1,'x');
+ a2=translate_dna_codon((CL->S)->seq[s2]+r2,'x');
+
+
+
+ if (a1=='x' || a2=='x')return 0;
+ else return CL->M[a1-'A'][a2-'A']*SCORE_K;
+ }
+ else
+ {
+ return 0;
+ }
+ }
+int evaluate_physico_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+{
+ int a, b, p;
+ double tot;
+ static float **prop_table;
+ static int n_prop;
+ static double max;
+ if (r1<0 || r2<0)return 0;
+ if ( !prop_table)
+ {
+ prop_table= initialise_aa_physico_chemical_property_table(&n_prop);
+ for (p=0; p< n_prop; p++)max+=100;
+ max=sqrt(max);
+ }
+ a=tolower (( CL->S)->seq[s1][r1]);
+ b=tolower (( CL->S)->seq[s2][r2]);
+
+ for (tot=0,p=0; p< n_prop; p++)
+ {
+ tot+=(double)(prop_table[p][a]-prop_table[p][b])*(prop_table[p][a]-prop_table[p][b]);
+ }
+
+ tot=(sqrt(tot)/max)*10;
+
+ return (int) tot*SCORE_K;
+}
+
+
+
+int evaluate_diaa_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+ {
+
+ static int ****m;
+ static int *alp;
+
+ if (m==NULL)
+ {
+ FILE *fp;
+ char k1[2], k2[2];
+ int v1, v2, c;
+ char *buf=NULL;
+ int a;
+
+ m=declare_arrayN(4, sizeof (int), 26, 26, 26, 26);
+ fp=vfopen ("diaa_mat.mat", "r");
+ while ((c=fgetc (fp))!=EOF)
+ {
+
+ ungetc (c, fp);
+ buf=vfgets(buf, fp);
+
+ if (c=='#');
+ else
+ {
+ sscanf (buf, "%s %s %d %d", k1, k2, &v1, &v2);
+
+ m[k1[0]-'a'][k1[1]-'a'][k2[0]-'a'][k2[1]-'a']=v1;
+ m[k2[0]-'a'][k2[1]-'a'][k1[0]-'a'][k1[1]-'a']=v1;
+ }
+ }
+ vfclose (fp);
+ alp=vcalloc (256, sizeof (int));
+ for (a=0; a<26; a++)alp[a+'a']=1;
+ alp['b']=0;
+ alp['j']=0;
+ alp['o']=0;
+ alp['u']=0;
+ alp['x']=0;
+ alp['z']=0;
+ }
+
+
+ if (r1>0 && r2>0)
+ {
+ int s=0, n=0;
+ char aa1, aa2, aa3, aa4, u;
+
+ r1--;
+ r2--;
+
+ if (r1>0 && r2>0)
+ {
+ aa1=tolower((CL->S)->seq[s1][r1-1]);
+ aa2=tolower((CL->S)->seq[s1][r1]);
+ aa3=tolower((CL->S)->seq[s2][r2-1]);
+ aa4=tolower((CL->S)->seq[s2][r2]);
+ u=alp[(int)aa1];u+=alp[(int)aa2];u+=alp[(int)aa3];u+=alp[(int)aa4];
+ if (u==4)
+ {
+ s+=m[aa1-'a'][aa2-'a'][aa3-'a'][aa4-'a'];
+ n++;
+ }
+ }
+
+ aa1=tolower((CL->S)->seq[s1][r1]);
+ aa2=tolower((CL->S)->seq[s1][r1+1]);
+ aa3=tolower((CL->S)->seq[s2][r2]);
+ aa4=tolower((CL->S)->seq[s2][r2+1]);
+ u=alp[(int)aa1];u+=alp[(int)aa2];u+=alp[(int)aa3];u+=alp[(int)aa4];
+ if (u==4)
+ {
+ s+=m[aa1-'a'][aa2-'a'][aa3-'a'][aa4-'a'];
+ n++;
+ }
+ if (n)return (s*SCORE_K)/n;
+ else return 0;
+ }
+ return 0;}
+int evaluate_monoaa_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+ {
+
+ static int **m;
+ static int *alp;
+
+ if (m==NULL)
+ {
+ FILE *fp;
+ char k1[2], k2[2];
+ int v1, v2, c;
+ char *buf=NULL;
+ int a;
+
+ m=declare_arrayN(2, sizeof (int), 26, 26);
+ fp=vfopen ("monoaa_mat.mat", "r");
+ while ((c=fgetc (fp))!=EOF)
+ {
+
+ ungetc (c, fp);
+ buf=vfgets(buf, fp);
+
+ if (c=='#');
+ else
+ {
+ sscanf (buf, "%s %s %d %d", k1, k2, &v1, &v2);
+
+ m[k1[0]-'a'][k2[0]-'a']=v1;
+ m[k2[0]-'a'][k1[0]-'a']=v1;
+ }
+ }
+ vfclose (fp);
+ alp=vcalloc (256, sizeof (int));
+ for (a=0; a<26; a++)alp[a+'a']=1;
+ alp['b']=0;
+ alp['j']=0;
+ alp['o']=0;
+ alp['u']=0;
+ alp['x']=0;
+ alp['z']=0;
+ }
+
+
+ if (r1>0 && r2>0)
+ {
+ int s=0, n=0;
+ char aa1, aa3, u;
+
+ r1--;
+ r2--;
+
+ if (r1>0 && r2>0)
+ {
+ aa1=tolower((CL->S)->seq[s1][r1]);
+ aa3=tolower((CL->S)->seq[s2][r2]);
+ u=alp[(int)aa1];u+=alp[(int)aa3];
+ if (u==2)
+ {
+ s+=m[aa1-'a'][aa3-'a'];
+ n++;
+ }
+ }
+
+ if (n)return (s*SCORE_K)/n;
+ else return 0;
+ }
+ return 0;}
+int evaluate_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+ {
+
+ if ( seq2R_template_profile (CL->S,s1) ||seq2R_template_profile (CL->S,s2))
+ {
+ return evaluate_aln_profile_score ( CL, s1,r1, s2, r2);
+ }
+
+ if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+
+ return CL->M[(CL->S)->seq[s1][r1]-'A'][(CL->S)->seq[s2][r2]-'A']*SCORE_K;
+ }
+ else
+ return 0;
+ }
+int *get_curvature ( int s1, Constraint_list *CL);
+int evaluate_curvature_score( Constraint_list *CL, int s1, int r1, int s2, int r2)
+{
+ static int **st;
+ int score;
+ CL->gop=0;
+ CL->gep=0;
+
+ if (!st) st= vcalloc ((CL->S)->nseq, sizeof (char*));
+ if (!st[s1])
+ {
+ st[s1]=get_curvature (s1, CL);
+ }
+ if (!st[s2])
+ {
+ st[s2]=get_curvature (s2, CL);
+ }
+
+ if (r1>0 && r2>0)
+ {
+ char p1, p2;
+
+ r1--;
+ r2--;
+
+ p1=st[s1][r1];
+ p2=st[s2][r2];
+
+ score=p1-p2;
+ score=FABS(score);
+ score=20-score;
+ //HERE ("%d", score);
+ //if (score<0)HERE ("%d", score);
+ return score;
+ }
+ else
+ {
+ return 0;
+ }
+
+}
+int *get_curvature ( int s1, Constraint_list *CL)
+{
+ int *array, n=0, a;
+ char c;
+ FILE *fp;
+ char name [1000], b1[100], b2[100];
+ float f;
+ sprintf ( name, "%s.curvature", (CL->S)->name[s1]);
+ array=vcalloc (strlen ((CL->S)->seq[s1]), sizeof (int));
+ fp=vfopen ( name, "r");
+ while ( fscanf (fp, "%s %d %c %f\n",b1, &a, &c,&f )==4)
+ {
+ if ( c!=(CL->S)->seq[s1][n]){HERE ("ERROR: %c %c", c,(CL->S)->seq[s1][n] );myexit (0);}
+ else array[n++]=(int)(float)100*(float)f;
+ }
+ vfclose (fp);
+ return array;
+}
+int evaluate_tm_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+{
+ static char **st;
+ float F, RF;
+
+ if (!st)
+ {
+ st= vcalloc ((CL->S)->nseq, sizeof (char*));
+ RF=atoigetenv ("TM_FACTOR_4_TCOFFEE");
+ if ( !RF)RF=10;
+ }
+
+ if (!st[s1])st[s1]=seq2T_template_string((CL->S),s1);
+ if (!st[s2])st[s2]=seq2T_template_string((CL->S),s2);
+
+ if (r1<=0 || r2<=0)return 0;
+ else if (st[s1] && st[s2] && (st[s1][r1-1]==st[s2][r2-1]))F=RF;
+ else if (st[s1] && st[s2] && (st[s1][r1-1]!=st[s2][r2-1]))F=0;
+ else F=0;
+
+ return (int)(evaluate_matrix_score (CL, s1, r1, s2, r2))+F;
+}
+int evaluate_ssp_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+{
+ static char **st;
+ float F, RF;
+
+ if (!st)
+ {
+ st= vcalloc ((CL->S)->nseq, sizeof (char*));
+ RF=atoigetenv ("SSP_FACTOR_4_TCOFFEE");
+ if ( !RF)RF=10;
+ }
+
+ if (!st[s1])st[s1]=seq2T_template_string((CL->S),s1);
+ if (!st[s2])st[s2]=seq2T_template_string((CL->S),s2);
+
+ if (r1<=0 || r2<=0)return 0;
+ else if (st[s1] && st[s2] && (st[s1][r1-1]==st[s2][r2-1]))F=RF;
+ else if (st[s1] && st[s2] && (st[s1][r1-1]!=st[s2][r2-1]))F=0;
+ else F=0;
+
+ return (int)(evaluate_matrix_score (CL, s1, r1, s2, r2))+F;
+}
+
+
+int evaluate_combined_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+ {
+ /*
+ function documentation: start
+
+ int evaluate_matrix_score ( Constraint_list *CL, int s1, int s2, int r1, int r2)
+
+ this function evaluates the score for matching residue S1(r1) wit residue S2(r2)
+ using Matrix CL->M;
+
+ function documentation: end
+ */
+
+ if ( seq2R_template_profile (CL->S,s1) ||seq2R_template_profile (CL->S,s2))
+ {
+ return evaluate_aln_profile_score ( CL, s1,r1, s2, r2);
+ }
+
+ if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+ if (r1==0 || r2==0)return CL->M[(CL->S)->seq[s1][r1]-'A'][(CL->S)->seq[s2][r2]-'A']*SCORE_K;
+ else
+ {
+ int A1, A2, B1, B2, a2, b2;
+ int score;
+
+ A1=toupper((CL->S)->seq[s1][r1-1]);
+ A2=toupper((CL->S)->seq[s1][r1]);
+ B1=toupper((CL->S)->seq[s2][r2-1]);
+ B2=toupper((CL->S)->seq[s2][r2]);
+
+ a2=tolower(A2);
+ b2=tolower(B2);
+ A1-='A';A2-='A';B1-='A'; B2-='A';a2-='A';b2-='A';
+
+ score=CL->M[a2][b2]-FABS((CL->M[A1][A2])-(CL->M[B1][B2]));
+ score*=SCORE_K;
+ return score;
+ }
+ }
+ else
+ return 0;
+ }
+
+int residue_pair_non_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+
+ /*
+ This is the generic Function->works with everything
+
+ int residue_pair_non_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2, int field );
+
+ Computes the non extended score for aligning residue seq1(r1) Vs seq2(r2)
+
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+ function documentation: end
+ */
+
+ int p;
+
+
+ static int *entry;
+ int *r;
+ int field;
+
+ field = CL->weight_field;
+
+
+ if ( r1<=0 || r2<=0)return 0;
+ else if ( !CL->extend_jit)
+ {
+ if ( !entry) entry=vcalloc (LIST_N_FIELDS , sizeof (int));
+ entry[SEQ1]=s1;
+ entry[SEQ2]=s2;
+ entry[R1]=r1;
+ entry[R2]=r2;
+ if ( r1==r2 && s1==s2) return UNDEFINED;
+ r=main_search_in_list_constraint( entry,&p,4,CL);
+ if (r==NULL)return 0;
+ else return r[field]*SCORE_K;
+ }
+ else
+ return UNDEFINED;/*ERROR*/
+
+
+ }
+
+
+
+int residue_pair_extended_list_mixt (Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ int score=0;
+
+ score+= residue_pair_extended_list_quadruplet(CL, s1, r1, s2, r2);
+ score+= residue_pair_extended_list (CL, s1, r1, s2, r2);
+
+ return score*SCORE_K;
+ }
+
+int residue_pair_extended_list_quadruplet (Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ double score=0;
+
+ int t_s, t_r, t_w, q_s, q_r, q_w;
+ int a, b;
+ static int **hasch;
+
+ int field;
+ /* This measure the quadruplets cost on a pair of residues*/
+
+
+
+ field=CL->weight_field;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch)
+ {
+ hasch=vcalloc ( (CL->S)->nseq, sizeof (int*));
+ for ( a=0; a< (CL->S)->nseq; a++)hasch[a]=vcalloc ( (CL->S)->len[a]+1, sizeof (int));
+ }
+
+
+ hasch[s1][r1]=100000;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ t_w=CL->residue_index[s1][r1][a+WE];
+ if ( CL->seq_for_quadruplet[t_s])
+ {
+ for ( b=1; b<CL->residue_index[t_s][t_r][0]; b+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][b+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][b+R2];
+ q_w=CL->residue_index[t_s][t_r][b+WE];
+ if (CL-> seq_for_quadruplet[q_s])
+ hasch[q_s][q_r]=MIN(q_w,t_w);
+
+ }
+ }
+ }
+
+
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+ t_w=CL->residue_index[s2][r2][a+WE];
+ if ( CL->seq_for_quadruplet[t_s])
+ {
+ for ( b=1; b<CL->residue_index[t_s][t_r][0]; b+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][b+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][b+R2];
+ q_w=CL->residue_index[t_s][t_r][b+WE];
+ if (hasch[q_s][q_r] && CL->seq_for_quadruplet[q_s])
+ score+=MIN(hasch[q_s][q_r],MIN(q_w,t_w));
+ }
+ }
+ }
+
+ score=(CL->normalise)?((score*CL->normalise)/CL->max_ext_value):score;
+
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ t_w=CL->residue_index[s1][r1][a+WE];
+ if ( CL->seq_for_quadruplet[t_s])
+ {
+ for ( b=1; b<CL->residue_index[t_s][t_r][0]; b+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][b+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][b+R2];
+ hasch[q_s][q_r]=0;
+ }
+ }
+ }
+
+ return (int)(score*SCORE_K);
+ }
+
+
+Constraint_list * R_extension ( Constraint_list *CL, Constraint_list *R);
+int residue_pair_extended_list4rna4 (Constraint_list *CL,int s1, int r1, int s2, int r2 )
+{
+ static int rna_lib;
+
+ if (!rna_lib)
+ {
+ sprintf ( CL->rna_lib, "%s", seq2rna_lib (CL->S, NULL));
+ rna_lib=1;
+ }
+ return residue_pair_extended_list4rna2 (CL, s1, r1, s2,r2);
+}
+int residue_pair_extended_list4rna1 (Constraint_list *CL, int s1, int r1, int s2, int r2 )
+{
+ static Constraint_list *R;
+ if (!R)R=read_rna_lib (CL->S, CL->rna_lib);
+ return residue_pair_extended_list4rna (CL, R, s1, r1, s2, r2);
+}
+
+int residue_pair_extended_list4rna3 (Constraint_list *CL,int s1, int r1, int s2, int r2 )
+{
+ static Constraint_list *R;
+ if (!R)
+ {
+ R=read_rna_lib (CL->S, CL->rna_lib);
+ rna_lib_extension (CL,R);
+ }
+ return residue_pair_extended_list (CL, s1,r1, s2,r2);
+}
+
+int residue_pair_extended_list4rna2 (Constraint_list *CL,int s1, int r1, int s2, int r2 )
+{
+ static Constraint_list *R;
+
+
+ if (!R)
+ {
+
+ R=read_rna_lib (CL->S, CL->rna_lib);
+ rna_lib_extension (CL,R);
+
+ }
+
+ return residue_pair_extended_list4rna (CL, R, s1, r1, s2, r2);
+}
+int residue_pair_extended_list4rna ( Constraint_list *CL,Constraint_list *R, int s1, int r1, int s2, int r2 )
+{
+
+ int a, b, n1, n2;
+ int list1[100];
+ int list2[100];
+ int score=0, score2;
+
+
+
+ if ( r1<0 || r2<0)return 0;
+ n1=n2=0;
+
+ list1[n1++]=r1;
+ for (a=1; a<R->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ list1[n1++]=R->residue_index[s1][r1][a+R2];
+ }
+
+
+ list2[n2++]=r2;
+ for (a=1; a<R->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ list2[n2++]=R->residue_index[s2][r2][a+R2];
+ }
+
+
+ score=residue_pair_extended_list ( CL, s1,list1[0], s2,list2[0]);
+
+ for (score2=0,a=1; a<n1; a++)
+ for ( b=1; b<n2; b++)
+ score2=MAX(residue_pair_extended_list ( CL, s1,list1[a], s2,list2[b]), score2);
+
+ if ( n1==1 || n2==1);
+ else score=MAX(score,score2);
+
+ return score;
+}
+
+
+int residue_pair_extended_list4rna_ref ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+{
+ static Constraint_list *R;
+ int a, b, n1, n2;
+ int list1[100];
+ int list2[100];
+ int score=0, score2;
+
+ if (R==NULL)
+ {
+ char **list;
+ int n,a;
+ list=read_lib_list ( CL->rna_lib, &n);
+
+ R=declare_constraint_list ( CL->S,NULL, NULL, 0,NULL, NULL);
+
+ for (a=0; a< n; a++)
+ {
+ R=read_constraint_list_file (R, list[a]);
+ }
+
+ }
+
+ if ( r1<0 || r2<0)return 0;
+ n1=n2=0;
+
+ list1[n1++]=r1;
+ for (a=1; a<R->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ list1[n1++]=R->residue_index[s1][r1][a+R2];
+ }
+
+
+ list2[n2++]=r2;
+ for (a=1; a<R->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ list2[n2++]=R->residue_index[s2][r2][a+R2];
+ }
+
+
+ score=residue_pair_extended_list ( CL, s1,list1[0], s2,list2[0]);
+
+ for (score2=0,a=1; a<n1; a++)
+ for ( b=1; b<n2; b++)
+ score2=MAX(residue_pair_extended_list ( CL, s1,list1[a], s2,list2[b]), score2);
+
+ if ( n1==1 || n2==1);
+ else score=MAX(score,score2);
+
+ return score;
+}
+
+static int ** clean_residue_pair_hasch (int s1, int r1, int s2, int r2,int **hasch, Constraint_list *CL);
+int residue_pair_extended_list_raw ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ double score=0;
+
+
+
+ int a, t_s, t_r;
+ static int **hasch;
+ static int max_len;
+ int field;
+ double delta;
+ /*
+
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+ field=CL->weight_field;
+ field=WE;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+
+
+ /* Check matches for R1 in the indexed lib*/
+ hasch[s1][r1]=FORBIDEN;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ }
+
+ /*Check Matches for r1 <-> r2 in the indexed lib */
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+
+
+ if (hasch[t_s][t_r])
+ {
+ if (hasch[t_s][t_r]==FORBIDEN)
+ {
+ score+=CL->residue_index[s2][r2][a+field];
+ }
+ else
+ {
+ delta=MIN(hasch[t_s][t_r],CL->residue_index[s2][r2][a+field]);
+ score+=delta;
+ }
+ }
+ }
+
+ clean_residue_pair_hasch ( s1, r1,s2, r2, hasch, CL);
+ return score;
+ }
+int residue_pair_extended_list_4gp ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ double score=0;
+
+
+
+ int a, t_s, t_r;
+ static int **hasch;
+ static int max_len;
+ int field;
+ double delta;
+
+ /*
+
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+ field=CL->weight_field;
+ field=WE;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+
+
+ /* Check matches for R1 in the indexed lib*/
+ hasch[s1][r1]=FORBIDEN;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ }
+
+ /*Check Matches for r1 <-> r2 in the indexed lib */
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+
+
+ if (hasch[t_s][t_r])
+ {
+ if (hasch[t_s][t_r]==FORBIDEN)
+ {
+ score+=((float)CL->residue_index[s2][r2][a+2]/NORM_F);
+ }
+ else
+ {
+ delta=MAX((((float)hasch[t_s][t_r]/NORM_F)),(((float)CL->residue_index[s2][r2][a+field]/NORM_F)));
+ score+=delta;
+ }
+ }
+ }
+
+ clean_residue_pair_hasch ( s1, r1,s2, r2, hasch, CL);
+ score/=(CL->S)->nseq;
+ score *=NORM_F;
+
+ return score;
+ }
+
+int residue_pair_extended_list_pc ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ //old norm does not take into account the number of effective intermediate sequences
+
+ double score=0;
+ int a, t_s, t_r;
+ static int **hasch;
+ int nclean;
+ static int max_len;
+ int field;
+ double delta;
+ float norm1=0;
+ float norm2=0;
+
+ /*
+
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+ field=CL->weight_field;
+ field=WE;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+
+ }
+
+
+ /* Check matches for R1 in the indexed lib*/
+ hasch[s1][r1]=FORBIDEN;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ norm1++;
+
+ }
+
+
+ /*Check Matches for r1 <-> r2 in the indexed lib */
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+ norm2++;
+
+ if (hasch[t_s][t_r])
+ {
+ if (hasch[t_s][t_r]==FORBIDEN)
+ {
+ score+=((float)CL->residue_index[s2][r2][a+field]/NORM_F);
+ }
+ else
+ {
+ delta=MIN((((float)hasch[t_s][t_r]/NORM_F)),(((float)CL->residue_index[s2][r2][a+field]/NORM_F)));
+ score+=delta;
+ }
+ }
+ }
+
+ clean_residue_pair_hasch ( s1, r1,s2, r2, hasch, CL);
+
+ //New Normalization
+ norm1=MIN(norm1,norm2);
+
+ //Old Normailzation: on the number of sequences, useless when not doiang an all against all
+ //norm1=(CL->S)->nseq;
+
+ score=(norm1)?score/norm1:0;
+
+
+ return score*NORM_F;
+ }
+int residue_pair_extended_list_pc_old ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ //old norm does not take into account the number of effective intermediate sequences
+
+ double score=0;
+ int a, t_s, t_r;
+ static int **hasch;
+
+ static int max_len;
+ int field;
+ double delta;
+
+ /*
+
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+ field=CL->weight_field;
+ field=WE;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+
+ /* Check matches for R1 in the indexed lib*/
+ hasch[s1][r1]=FORBIDEN;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ }
+
+
+ /*Check Matches for r1 <-> r2 in the indexed lib */
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+
+
+ if (hasch[t_s][t_r])
+ {
+ if (hasch[t_s][t_r]==FORBIDEN)
+ {
+ score+=((float)CL->residue_index[s2][r2][a+2]/NORM_F);
+ }
+ else
+ {
+ delta=MIN((((float)hasch[t_s][t_r]/NORM_F)),(((float)CL->residue_index[s2][r2][a+field]/NORM_F)));
+ score+=delta;
+ }
+ }
+ }
+
+ clean_residue_pair_hasch ( s1, r1,s2, r2, hasch, CL);
+ score/=(CL->S)->nseq;
+ return score*NORM_F;
+ }
+
+
+int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ double score=0;
+ double max_score=0;
+ double max_val=0;
+
+ int a, t_s, t_r;
+ static int **hasch;
+ static int max_len;
+ int field;
+
+ /*
+ new function: self normalized
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+ field=CL->weight_field;
+ field=WE;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+
+
+ /* Check matches for R1 in the indexed lib*/
+ hasch[s1][r1]=FORBIDEN;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ max_score+=CL->residue_index[s1][r1][a+field];
+ }
+
+ /*Check Matches for r1 <-> r2 in the indexed lib */
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+
+
+ if (hasch[t_s][t_r])
+ {
+ if (hasch[t_s][t_r]==FORBIDEN)
+ {
+ score+=CL->residue_index[s2][r2][a+field];
+ max_score+=CL->residue_index[s2][r2][a+field];
+ }
+ else
+ {
+ double delta;
+ delta=MIN(hasch[t_s][t_r],CL->residue_index[s2][r2][a+field]);
+
+ score+=delta;
+ max_score-=hasch[t_s][t_r];
+ max_score+=delta;
+ max_val=MAX(max_val,delta);
+ }
+ }
+ else
+ {
+ max_score+=CL->residue_index[s2][r2][a+field];
+ }
+ }
+
+ max_score-=hasch[s2][r2];
+ clean_residue_pair_hasch ( s1, r1,s2, r2, hasch, CL);
+
+
+ if ( max_score==0)score=0;
+ else if ( CL->normalise)
+ {
+ score=((score*CL->normalise)/max_score)*SCORE_K;
+ if (max_val> CL->normalise)
+ {
+ score*=max_val/(double)CL->normalise;
+ }
+ }
+ return (int) score;
+ }
+int ** clean_residue_pair_hasch (int s1, int r1, int s2, int r2,int **hasch, Constraint_list *CL)
+ {
+ int a, t_s, t_r;
+ if ( !hasch) return hasch;
+
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=0;
+ }
+ hasch[s1][r1]=hasch[s2][r2]=0;
+ return hasch;
+ }
+
+int residue_pair_test_function ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ double score=0;
+
+ int a, t_s, t_r;
+ static int **hasch;
+ static int max_len;
+ int cons1;
+ int cons2;
+
+ int field;
+ /*
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+
+ CL->weight_field=WE;
+ field=CL->weight_field;
+
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+
+
+ hasch[s1][r1]=1000;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ }
+
+
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+ if (hasch[t_s][t_r])
+ {
+ cons1=hasch[t_s][t_r];
+ cons2=CL->residue_index[s2][r2][a+field];
+ score +=MIN(cons1,cons2);
+ }
+ }
+
+
+ score=(CL->normalise)?((score*CL->normalise)/CL->max_ext_value):score;
+
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=0;
+ }
+ hasch[s1][r1]=hasch[s2][r2]=0;
+
+
+ return (int)(score*SCORE_K);
+ }
+
+int residue_pair_relative_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ int a, t_s, t_r;
+ static int **hasch;
+ static int max_len;
+ int score=0;
+ int total_score=0;
+ int field;
+ /*
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+
+
+ field=CL->weight_field;
+ field=WE;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch || max_len!=(CL->S)->max_len)
+ {
+ max_len=(CL->S)->max_len;
+ if ( hasch) free_int ( hasch, -1);
+ hasch=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+
+
+ hasch[s1][r1]=100000;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ total_score+=CL->residue_index[s1][r1][a+field];
+ }
+
+
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+ total_score+=CL->residue_index[s1][r1][a+field];
+ if (hasch[t_s][t_r])
+ {
+ if (field==WE){score+=2*MIN(hasch[t_s][t_r],CL->residue_index[s2][r2][a+field]);}
+ }
+ }
+
+ score=((CL->normalise*score)/total_score);
+
+
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=0;
+ }
+ hasch[s1][r1]=hasch[s2][r2]=0;
+
+ return score*SCORE_K;
+ }
+int residue_pair_extended_list_g_coffee_quadruplet ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+{
+ int t_s, t_r, t_w, q_s, q_r, q_w;
+ int a, b;
+ static int **hasch;
+ int score=0, s=0;
+
+ int field;
+ /* This measure the quadruplets cost on a pair of residues*/
+
+ field=CL->weight_field;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch)
+ {
+ hasch=vcalloc ( (CL->S)->nseq, sizeof (int*));
+ for ( a=0; a< (CL->S)->nseq; a++)hasch[a]=vcalloc ( (CL->S)->len[a]+1, sizeof (int));
+ }
+
+
+ hasch[s1][r1]=100000;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ t_w=CL->residue_index[s1][r1][a+field];
+ if ( CL->seq_for_quadruplet[t_s])
+ {
+ for ( b=1; b<CL->residue_index[t_s][t_r][0]; b+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][b+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][b+R2];
+ if (CL-> seq_for_quadruplet[q_s])
+ {
+
+ hasch[q_s][q_r]=MIN(CL->residue_index[t_s][t_r][b+2],t_w);
+ }
+ }
+ }
+ }
+
+
+ for (s=0,score=0,a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+ t_w=CL->residue_index[s2][r2][a+field];
+ if ( CL->seq_for_quadruplet[t_s])
+ {
+ for ( b=1; b<CL->residue_index[t_s][t_r][0]; b+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][b+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][b+R2];
+ q_w=CL->residue_index[t_s][t_r][b+field];
+ if (hasch[q_s][q_r] && CL->seq_for_quadruplet[q_s])
+ s=MIN(hasch[q_s][q_r],MIN(CL->residue_index[t_s][t_r][b+2],q_w));
+ score=MAX(score, s);
+ }
+ }
+ }
+
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ t_w=CL->residue_index[s1][r1][a+field];
+ if ( CL->seq_for_quadruplet[t_s])
+ {
+ for ( b=1; b<CL->residue_index[t_s][t_r][0]; b+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][b+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][b+R2];
+ hasch[q_s][q_r]=0;
+ }
+ }
+ }
+
+ return score*SCORE_K;
+ }
+int residue_pair_extended_list_g_coffee ( Constraint_list *CL, int s1, int r1, int s2, int r2 )
+ {
+ int a, t_s, t_r;
+ static int **hasch;
+ int score=0,s;
+
+ int field;
+ /*
+ function documentation: start
+
+ int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+
+ function documentation: end
+ */
+
+ field=CL->weight_field;
+
+ if ( r1<=0 || r2<=0)return 0;
+ if ( !hasch)
+ {
+ hasch=vcalloc ( (CL->S)->nseq, sizeof (int*));
+ for ( a=0; a< (CL->S)->nseq; a++)hasch[a]=vcalloc ( (CL->S)->len[a]+1, sizeof (int));
+ }
+
+
+
+ hasch[s1][r1]=100000;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+field];
+ }
+
+
+ for (s=0, score=0,a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+
+ if (hasch[t_s][t_r])
+ {
+ if (field==WE)
+ {s=MIN(hasch[t_s][t_r],CL->residue_index[s2][r2][a+WE]);
+ score=MAX(s,score);
+ }
+ }
+ }
+
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=0;
+ }
+ hasch[s1][r1]=hasch[s2][r2]=0;
+
+ return score*SCORE_K;
+ }
+
+int extend_residue_pair ( Constraint_list *CL, int s1, int r1, int s2, int r2)
+ {
+ double score=0;
+
+ int a, t_s, t_r, p;
+ static int **hasch;
+
+ static int *entry;
+ int *r;
+ int field;
+
+
+
+ /*
+ This is the generic Function->works with everything
+ should be gradually phased out
+
+
+ int extend_residue_pair ( Constraint_list *CL, int s1, int r1, int s2, int r2, int field )
+
+ Computes the extended score for aligning residue seq1(r1) Vs seq2(r2)
+ Computes: matrix_score
+ non extended score
+ extended score
+
+ The extended score depends on the function index_res_constraint_list.
+ This function can compare a sequence with itself.
+
+ Associated functions: See util constraint list, list extention functions.
+ function documentation: end
+ */
+
+
+ field=CL->weight_field;
+
+ if ( r1<=0 || r2<=0)return 0;
+ else if ( !CL->residue_index && CL->M)
+ {
+ return evaluate_matrix_score (CL, s1,r1, s2, r2);
+ }
+
+ else if ( !CL->extend_jit)
+ {
+ if ( !entry) entry=vcalloc (LIST_N_FIELDS , sizeof (int));
+ entry[SEQ1]=s1;
+ entry[SEQ2]=s2;
+ entry[R1]=r1;
+ entry[R2]=r2;
+ r=main_search_in_list_constraint( entry,&p,4,CL);
+ if (r==NULL)return 0;
+ else return r[field];
+ }
+ else
+ {
+ if ( !hasch)
+ {
+ hasch=vcalloc ( (CL->S)->nseq, sizeof (int*));
+ for ( a=0; a< (CL->S)->nseq; a++)hasch[a]=vcalloc ( (CL->S)->len[a]+1, sizeof (int));
+ }
+
+
+
+ hasch[s1][r1]=100000;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=CL->residue_index[s1][r1][a+WE];
+ }
+
+
+ for (a=1; a< CL->residue_index[s2][r2][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][a+SEQ2];
+ t_r=CL->residue_index[s2][r2][a+R2];
+ if (hasch[t_s][t_r])
+ {
+ if (field==WE)score+=MIN(hasch[t_s][t_r],CL->residue_index[s2][r2][a+WE] );
+
+ }
+ }
+ score=(CL->normalise)?((score*CL->normalise)/CL->max_ext_value):score;
+ for (a=1; a< CL->residue_index[s1][r1][0]; a+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][a+SEQ2];
+ t_r=CL->residue_index[s1][r1][a+R2];
+ hasch[t_s][t_r]=0;
+ }
+ hasch[s1][r1]=hasch[s2][r2]=0;
+
+ return (int)(score*SCORE_K);
+ }
+ }
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR GETTING THE PW COST : CL->get_dp_cost */
+/* */
+/*********************************************************************************************/
+int get_dp_cost_blosum_matrix (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+{
+ int s1, r1, s2, r2;
+ static int **matrix;
+
+ if (!matrix) matrix=read_matrice ("blosum62mt");
+ s1=A->order[list1[0]][0];
+ s2=A->order[list2[0]][0];
+ r1=pos1[list1[0]][col1];
+ r2=pos2[list2[0]][col2];
+
+ /*dp cost function: works only with two sequences*/
+
+ if ( seq2R_template_profile (CL->S,s1) ||seq2R_template_profile (CL->S,s2))
+ return evaluate_aln_profile_score ( CL, s1,r1, s2, r2) -CL->nomatch*SCORE_K;
+ else if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+
+
+ return matrix [(CL->S)->seq[s1][r1]-'A'][(CL->S)->seq[s2][r2]-'A']*SCORE_K -CL->nomatch*SCORE_K;
+
+ }
+ else
+ return -CL->nomatch*SCORE_K ;
+}
+int get_dp_cost_pam_matrix (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+{
+ int s1, r1, s2, r2;
+ static int **matrix;
+
+ if (!matrix) matrix=read_matrice ("pam250mt");
+ s1=A->order[list1[0]][0];
+ s2=A->order[list2[0]][0];
+ r1=pos1[list1[0]][col1];
+ r2=pos2[list2[0]][col2];
+
+ /*dp cost function: works only with two sequences*/
+
+
+ if ( seq2R_template_profile (CL->S,s1) ||seq2R_template_profile (CL->S,s2))
+ return evaluate_aln_profile_score ( CL, s1,r1, s2, r2) -CL->nomatch*SCORE_K;
+ else if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+
+
+ return matrix [(CL->S)->seq[s1][r1]-'A'][(CL->S)->seq[s2][r2]-'A']*SCORE_K -CL->nomatch*SCORE_K;
+
+ }
+ else
+ return -CL->nomatch*SCORE_K ;
+}
+
+int get_dp_cost_pw_matrix (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+{
+ int s1, r1, s2, r2;
+
+ s1=A->order[list1[0]][0];
+ s2=A->order[list2[0]][0];
+ r1=pos1[list1[0]][col1];
+ r2=pos2[list2[0]][col2];
+
+ /*dp cost function: works only with two sequences*/
+ if ( seq2R_template_profile (CL->S,s1) ||seq2R_template_profile (CL->S,s2))
+ return evaluate_aln_profile_score ( CL, s1,r1, s2, r2) -CL->nomatch*SCORE_K;
+ else if (r1>0 && r2>0)
+ {
+ r1--;
+ r2--;
+
+
+ return CL->M[(CL->S)->seq[s1][r1]-'A'][(CL->S)->seq[s2][r2]-'A']*SCORE_K -CL->nomatch*SCORE_K;
+
+ }
+ else
+ return -CL->nomatch*SCORE_K ;
+}
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR GETTING THE COST : CL->get_dp_cost */
+/* */
+/*********************************************************************************************/
+
+
+
+int get_cdna_best_frame_dp_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ int a, b;
+ int n=4;
+ int s;
+ char a1, a2;
+ static int l1, l2;
+ static Alignment *B;
+ static int **score;
+
+ if ( !score)score=declare_int(3, 2);
+
+ if (!A)
+ {
+ free_aln(B);
+ B=NULL;
+ return UNDEFINED;
+ }
+ if (!B)
+ {
+ if (ns1+ns2>2){fprintf ( stderr, "\nERROR: get_cdna_dp_cost mode is only for pair-wise ALN [FATAL]\n");crash("");}
+ free_aln (B);
+ B=copy_aln (A, NULL);
+
+ l1=(int)strlen ( A->seq_al[list1[0]]);
+ for ( b=0; b<l1; b++)
+ B->seq_al[list1[0]][b]=translate_dna_codon (A->seq_al[list1[0]]+b, 'x');
+ l2=(int)strlen ( A->seq_al[list2[0]]);
+ for ( b=0; b<l2; b++)
+ B->seq_al[list2[0]][b]=translate_dna_codon (A->seq_al[list2[0]]+b, 'x');
+ }
+
+/*Set the frame*/
+
+ for ( a=0; a< 3; a++)score[a][0]=score[a][1]=0;
+ for ( a=col1-(n*3),b=col2-(n*3); a<col1+(n*3) ; a++, b++)
+ {
+ if ( a<0 || b<0 || a>=l1 || b>=l2)continue;
+
+ a1=tolower(B->seq_al[list1[0]][a]);
+ a2=tolower(B->seq_al[list2[0]][b]);
+
+ score[a%3][0]+=(a1=='x' || a2=='x')?0:CL->M[a1-'A'][a2-'A'];
+ score[a%3][1]++;
+ }
+
+ for ( a=0; a< 3; a++)score[a][0]=(score[a][1]>0)?(score[a][0]/score[a][1]):0;
+ if ( score[0][0]>score[1][0] && score[0][0]>score[2][0])
+ s=score[0][0];
+ else if ( score[1][0]>score[0][0] && score[1][0]>score[2][0])
+ s=score[1][0];
+ else s=score[2][0];
+
+ return s*SCORE_K;
+
+ }
+
+int get_dp_cost_quadruplet ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ int score;
+
+
+ if ( ns1==1 || ns2==1)
+ score=slow_get_dp_cost ( A, pos1, ns1, list1,col1, pos2, ns2, list2, col2, CL);
+ else
+ score=fast_get_dp_cost_quadruplet ( A, pos1, ns1, list1,col1, pos2, ns2, list2, col2, CL);
+
+ return (score==UNDEFINED)?UNDEFINED:(score-SCORE_K*CL->nomatch);
+ }
+int get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ int MODE=0;
+ int score;
+
+
+
+ if (A==NULL)return 0;
+
+ if (MODE!=2 || MODE==0 || (!CL->residue_index && CL->M) || (!CL->residue_index && CL->T)|| ns1==1 || ns2==1)
+ score=slow_get_dp_cost ( A, pos1, ns1, list1,col1, pos2, ns2, list2, col2, CL);
+ else if (MODE==1 || MODE==2)
+ score=fast_get_dp_cost ( A, pos1, ns1, list1,col1, pos2, ns2, list2, col2, CL);
+ else
+ score=0;
+
+
+
+ return (score==UNDEFINED)?UNDEFINED:(score-SCORE_K*CL->nomatch);
+ }
+int ***make_cw_lu (int **cons, int l, Constraint_list *CL);
+int ***make_cw_lu (int **cons, int l, Constraint_list *CL)
+{
+ int ***lu;
+ int p, a,r;
+
+ lu=declare_arrayN(3, sizeof (int),l,26, 2);
+ for ( p=0; p<l ; p++)
+ {
+ for (r=0; r<26; r++)
+ {
+ for (a=3; a<cons[p][1]; a+=3)
+ {
+ lu[p][r][0]+=cons[p][a+1]*CL->M[r][cons[p][a]-'A'];
+ lu[p][r][1]+=cons[p][a+1];
+ }
+ }
+ }
+ return lu;
+}
+
+int cw_profile_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+{
+ static int last_tag;
+ static int *pr, ***lu;
+ int score;
+ static int *list[2], ns[2], **cons[2], ref;
+ int eva_col,ref_col, a, p, r;
+ float t1, t2;
+
+
+
+
+ if (last_tag!=A->random_tag)
+ {
+ int n1, n2;
+
+ last_tag=A->random_tag;
+ list[0]=list1;ns[0]=ns1;
+ list[1]=list2;ns[1]=ns2;
+ free_int (cons[0],-1);free_int (cons[1],-1);free_arrayN((void*)lu,3);
+ cons[0]=NULL;cons[1]=NULL;lu=NULL;
+
+ n1=sub_aln2nseq_prf (A, ns[0], list[0]);
+ n2=sub_aln2nseq_prf (A, ns[1], list[1]);
+ if ( n1>1 || n2>1)
+ {
+ cons[0]=sub_aln2count_mat2 (A, ns[0], list[0]);
+ cons[1]=sub_aln2count_mat2 (A, ns[1], list[1]);
+ ref=(ns[0]>ns[1])?0:1;
+ lu=make_cw_lu(cons[ref],(int)strlen(A->seq_al[list[ref][0]]), CL);
+ }
+ }
+
+ if (!lu)
+ {
+ char r1, r2;
+ r1=A->seq_al[list1[0]][col1];
+ r2=A->seq_al[list2[0]][col2];
+ if ( r1!='-' && r2!='-')
+ return CL->M[r1-'A'][r2-'A']*SCORE_K -SCORE_K*CL->nomatch;
+ else
+ return -SCORE_K*CL->nomatch;
+ }
+ else
+ {
+ eva_col= (ref==0)?col2:col1;
+ ref_col= (ref==0)?col1:col2;
+ pr=cons[1-ref][eva_col];
+ t1=t2=0;
+ for (a=3; a< pr[1]; a+=3)
+ {
+ r=tolower(pr[a]);
+ p= pr[a+1];
+
+ t1+=lu[ref_col][r-'a'][0]*p;
+ t2+=lu[ref_col][r-'a'][1]*p;
+ }
+ score=(t2==0)?0:(t1*SCORE_K)/t2;
+ score -=SCORE_K*CL->nomatch;
+ return score;
+ }
+}
+int cw_profile_get_dp_cost_old ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+{
+ static int last_tag;
+ static int **cons1, **cons2;
+ int score;
+
+
+ if (last_tag!=A->random_tag)
+ {
+ last_tag=A->random_tag;
+ free_int (cons1,-1);free_int (cons2,-1);
+ cons1=sub_aln2count_mat2 (A, ns1, list1);
+ cons2=sub_aln2count_mat2 (A, ns2, list2);
+ }
+ score=cw_profile_profile (cons1[col1], cons2[col2], CL)-SCORE_K*CL->nomatch;
+ return score;
+}
+
+int cw_profile_get_dp_cost_window ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+{
+ static int last_tag;
+ static int **cons1, **cons2;
+ int a, score, window_size=5, n, p1, p2;
+
+
+ if (last_tag!=A->random_tag)
+ {
+ last_tag=A->random_tag;
+ free_int (cons1,-1);free_int (cons2,-1);
+ cons1=sub_aln2count_mat2 (A, ns1, list1);
+ cons2=sub_aln2count_mat2 (A, ns2, list2);
+ }
+
+ for (n=0,score=0,a=0; a<window_size; a++)
+ {
+ p1=col1-a;
+ p2=col2-a;
+ if ( p1<0 || cons1[p1][0]==END_ARRAY)continue;
+ if ( p2<0 || cons2[p2][0]==END_ARRAY)continue;
+ score+=cw_profile_profile (cons1[col1], cons2[col2], CL)-SCORE_K*CL->nomatch;
+ n++;
+ }
+ if (n>0)score/=n;
+
+ return score;
+ }
+
+int consensus_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ static int last_tag;
+ static char *seq1, *seq2;
+
+
+ /*Works only with matrix*/
+ if (last_tag !=A->random_tag)
+ {
+ int ls1, ls2, lenls1, lenls2;
+
+ last_tag=A->random_tag;
+ vfree (seq1);vfree (seq2);
+ seq1=sub_aln2cons_seq_mat (A, ns1, list1, "blosum62mt");
+ seq2=sub_aln2cons_seq_mat (A, ns2, list2, "blosum62mt");
+ ls1=list1[ns1-1];ls2=list2[ns2-1];
+ lenls1=(int)strlen (A->seq_al[ls1]); lenls2=(int)strlen (A->seq_al[ls2]);
+ }
+
+ return (CL->M[seq1[col1]-'A'][seq2[col2]-'A']*SCORE_K)-SCORE_K*CL->nomatch;
+ }
+
+int fast_get_dp_cost_quadruplet ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ /*WARNING: WORKS ONLY WITH List to Extend*/
+ /*That function does a quruple extension beween two columns by pooling the residues together*/
+
+ double score=0;
+
+ int a,b, c;
+ int n_gap1=0;
+ int n_gap2=0;
+
+ int s1, rs1, r1, t_r, t_s,t_w, q_r, q_s, q_w, s2, rs2, r2;
+ int **buf_pos, buf_ns, *buf_list, buf_col;
+
+ static int **hasch1;
+ static int **hasch2;
+
+ static int **n_hasch1;
+ static int **n_hasch2;
+
+ static int **is_in_col1;
+ static int **is_in_col2;
+
+
+ if (ns2>ns1)
+ {
+ buf_pos=pos1;
+ buf_ns=ns1;
+ buf_list=list1;
+ buf_col=col1;
+
+ pos1=pos2;
+ ns1=ns2;
+ list1=list2;
+ col1=col2;
+
+ pos2=buf_pos;
+ ns2=buf_ns;
+ list2=buf_list;
+ col2=buf_col;
+ }
+
+
+ if ( !hasch1)
+ {
+
+ hasch1=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ hasch2=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ n_hasch1=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ n_hasch2=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ is_in_col1=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ is_in_col2=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+ for ( a=0; a< ns1; a++)
+ {
+ rs1= list1[a];
+ s1=A->order[rs1][0];
+ r1=pos1[rs1][col1];
+
+ if (r1<0)n_gap1++;
+ else
+ {
+ is_in_col1[s1][r1]=1;
+ for (b=1; b< CL->residue_index[s1][r1][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][b+SEQ2];
+ t_r=CL->residue_index[s1][r1][b+R2];
+ t_w=CL->residue_index[s1][r1][b+WE];
+ for ( c=1; c< CL->residue_index[t_s][t_r][0]; c+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][c+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][c+R2];
+ q_w=CL->residue_index[t_s][t_r][c+WE];
+ hasch1[q_s][q_r]+=MIN(q_w, t_w);
+ n_hasch1[q_s][q_r]++;
+ }
+ }
+ }
+ }
+
+ for ( a=0; a< ns2; a++)
+ {
+ rs2=list2[a];
+ s2=A->order[rs2][0];
+ r2=pos2[rs2][col2];
+
+ if (r2<0)n_gap2++;
+ else
+ {
+ is_in_col2[s2][r2]=1;
+ for (b=1; b< CL->residue_index[s2][r2][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][b+SEQ2];
+ t_r=CL->residue_index[s2][r2][b+R2];
+ t_w=CL->residue_index[s2][r2][b+WE];
+ for ( c=1; c< CL->residue_index[t_s][t_r][0]; c+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][c+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][c+R2];
+ q_w=CL->residue_index[t_s][t_r][c+WE];
+ hasch2[q_s][q_r]+=MIN(t_w, q_w);
+ n_hasch2[q_s][q_r]++;
+ }
+ }
+ }
+ }
+
+
+ for ( a=0; a< ns2; a++)
+ {
+ rs2=list2[a];
+ s2=A->order[rs2][0];
+ r2=pos1[rs2][col2];
+
+ if (r2<0);
+ else
+ {
+ for (b=1; b< CL->residue_index[s2][r2][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][b+SEQ2];
+ t_r=CL->residue_index[s2][r2][b+R2];
+
+ for ( c=1; c< CL->residue_index[t_s][t_r][0]; c+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][c+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][c+R2];
+ if ( hasch2[q_s][q_r] && hasch1[q_s][q_r]&& !(is_in_col1[q_s][q_r] || is_in_col2[q_s][q_r]))
+ {
+ score+=MIN(hasch2[q_s][q_r]*(n_hasch1[q_s][q_r]),hasch1[q_s][q_r]*(n_hasch2[q_s][q_r]));
+ }
+ else if ( hasch2[q_s][q_r] && is_in_col1[q_s][q_r])
+ {
+ score+=hasch2[q_s][q_r]*(n_hasch1[q_s][q_r]+1);
+ }
+ else if (hasch1[q_s][q_r] && is_in_col2[q_s][q_r])
+ {
+ score+=hasch1[q_s][q_r]*(n_hasch2[q_s][q_r]+1);
+ }
+ hasch2[q_s][q_r]=0;
+ n_hasch2[q_s][q_r]=0;
+ }
+ }
+ hasch2[s2][r2]=0;
+ is_in_col2[s2][r2]=0;
+ }
+ }
+
+
+ for ( a=0; a< ns1; a++)
+ {
+ rs1= list1[a];
+ s1=A->order[rs1][0];
+ r1=pos1[rs1][col1];
+
+ if (r1<0);
+ else
+ {
+ is_in_col1[s1][r1]=0;
+ hasch1[s1][r1]=0;
+ for (b=1; b< CL->residue_index[s1][r1][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][b+SEQ2];
+ t_r=CL->residue_index[s1][r1][b+R2];
+ for ( c=1; c< CL->residue_index[t_s][t_r][0]; c+=ICHUNK)
+ {
+ q_s=CL->residue_index[t_s][t_r][c+SEQ2];
+ q_r=CL->residue_index[t_s][t_r][c+R2];
+ hasch1[q_s][q_r]=0;
+ n_hasch1[q_s][q_r]=0;
+ }
+ }
+ }
+ }
+
+
+ score=(score*SCORE_K)/((ns1-n_gap1)*(ns2-n_gap2));
+ score=(CL->normalise)?((score*CL->normalise)/CL->max_ext_value):score;
+
+ return (int)(score-SCORE_K*CL->nomatch);
+ }
+
+
+int fast_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ /*WARNING: WORKS ONLY WITH List to Extend*/
+
+ double score=0;
+
+ int a,b;
+ int n_gap1=0;
+ int n_gap2=0;
+
+ int s1, rs1, r1, t_r, t_s, s2, rs2, r2;
+ static int **hasch1;
+ static int **hasch2;
+
+ static int **n_hasch1;
+ static int **n_hasch2;
+
+ static int **is_in_col1;
+ static int **is_in_col2;
+
+
+
+
+ if ( !hasch1)
+ {
+
+ hasch1=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ hasch2=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ n_hasch1=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
+ n_hasch2=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ is_in_col1=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ is_in_col2=declare_int( (CL->S)->nseq, (CL->S)->max_len+1);
+ }
+
+ for ( a=0; a< ns1; a++)
+ {
+ rs1= list1[a];
+ s1=A->order[rs1][0];
+ r1=pos1[rs1][col1];
+
+ if (r1<0)n_gap1++;
+ else
+ {
+ is_in_col1[s1][r1]=1;
+ for (b=1; b< CL->residue_index[s1][r1][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][b+SEQ2];
+ t_r=CL->residue_index[s1][r1][b+R2];
+ hasch1[t_s][t_r]+=CL->residue_index[s1][r1][b+WE];
+ n_hasch1[t_s][t_r]++;
+ }
+ }
+ }
+
+
+ for ( a=0; a< ns2; a++)
+ {
+ rs2=list2[a];
+ s2=A->order[rs2][0];
+ r2=pos2[rs2][col2];
+
+ if (r2<0)n_gap2++;
+ else
+ {
+ is_in_col2[s2][r2]=1;
+ for (b=1; b< CL->residue_index[s2][r2][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][b+SEQ2];
+ t_r=CL->residue_index[s2][r2][b+R2];
+
+ hasch2[t_s][t_r]+=CL->residue_index[s2][r2][b+WE];
+ n_hasch2[t_s][t_r]++;
+ }
+ }
+ }
+ /*return 2;*/
+
+ if ( ns2<ns1)
+ {
+ for ( a=0; a< ns2; a++)
+ {
+ rs2=list2[a];
+ s2=A->order[rs2][0];
+ r2=pos1[rs2][col2];
+
+ if (r2<0);
+ else
+ {
+ for (b=1; b< CL->residue_index[s2][r2][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][b+SEQ2];
+ t_r=CL->residue_index[s2][r2][b+R2];
+
+ if ( hasch2[t_s][t_r] && hasch1[t_s][t_r]&& !(is_in_col1[t_s][t_r] || is_in_col2[t_s][t_r]))
+ {
+ score+=MIN(hasch2[t_s][t_r]*(n_hasch1[t_s][t_r]),hasch1[t_s][t_r]*(n_hasch2[t_s][t_r]));
+ }
+ else if ( hasch2[t_s][t_r] && is_in_col1[t_s][t_r])
+ {
+ score+=hasch2[t_s][t_r]*(n_hasch1[t_s][t_r]+1);
+ }
+ else if (hasch1[t_s][t_r] && is_in_col2[t_s][t_r])
+ {
+ score+=hasch1[t_s][t_r]*(n_hasch2[t_s][t_r]+1);
+ }
+ hasch2[t_s][t_r]=0;
+ n_hasch2[t_s][t_r]=0;
+ }
+ hasch2[s2][r2]=0;
+ is_in_col2[s2][r2]=0;
+ }
+ }
+
+
+ for ( a=0; a< ns1; a++)
+ {
+ rs1= list1[a];
+ s1=A->order[rs1][0];
+ r1=pos1[rs1][col1];
+
+ if (r1<0);
+ else
+ {
+ is_in_col1[s1][r1]=0;
+ hasch1[s1][r1]=0;
+ for (b=1; b< CL->residue_index[s1][r1][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][b+SEQ2];
+ t_r=CL->residue_index[s1][r1][b+R2];
+
+ hasch1[t_s][t_r]=0;
+ n_hasch1[t_s][t_r]=0;
+ }
+ }
+ }
+ }
+ else
+ {
+ for ( a=0; a< ns1; a++)
+ {
+ rs1=list1[a];
+ s1=A->order[rs1][0];
+ r1=pos1[rs1][col1];
+
+ if (r1<0);
+ else
+ {
+ for (b=1; b< CL->residue_index[s1][r1][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s1][r1][b+SEQ2];
+ t_r=CL->residue_index[s1][r1][b+R2];
+
+ if ( hasch1[t_s][t_r] && hasch2[t_s][t_r]&& !(is_in_col2[t_s][t_r] || is_in_col1[t_s][t_r]))
+ {
+ score+=MIN(hasch1[t_s][t_r]*(n_hasch2[t_s][t_r]),hasch2[t_s][t_r]*(n_hasch1[t_s][t_r]));
+ }
+ else if ( hasch1[t_s][t_r] && is_in_col2[t_s][t_r])
+ {
+ score+=hasch1[t_s][t_r]*(n_hasch2[t_s][t_r]+1);
+ }
+ else if (hasch2[t_s][t_r] && is_in_col1[t_s][t_r])
+ {
+ score+=hasch2[t_s][t_r]*(n_hasch1[t_s][t_r]+1);
+ }
+ hasch1[t_s][t_r]=0;
+ n_hasch1[t_s][t_r]=0;
+ }
+ hasch1[s1][r1]=0;
+ is_in_col1[s1][r1]=0;
+ }
+ }
+
+
+ for ( a=0; a< ns2; a++)
+ {
+ rs2= list2[a];
+ s2=A->order[rs2][0];
+ r2=pos1[rs2][col2];
+
+ if (r2<0);
+ else
+ {
+ is_in_col2[s2][r2]=0;
+ hasch1[s2][r2]=0;
+ for (b=1; b< CL->residue_index[s2][r2][0]; b+=ICHUNK)
+ {
+ t_s=CL->residue_index[s2][r2][b+SEQ2];
+ t_r=CL->residue_index[s2][r2][b+R2];
+
+ hasch2[t_s][t_r]=0;
+ n_hasch2[t_s][t_r]=0;
+ }
+ }
+ }
+ }
+ score=(score*SCORE_K)/((ns1-n_gap1)*(ns2-n_gap2));
+ score=(CL->normalise)?((score*CL->normalise)/CL->max_ext_value):score;
+
+ return (int)(score-SCORE_K*CL->nomatch);
+ }
+
+int fast_get_dp_cost_2 ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ double score=0;
+
+ int a, b, s1, s2,r1, r2;
+ static int n_pair;
+
+ int s;
+ int res_res=0;
+ int rs1, rs2;
+ static int last_ns1;
+ static int last_ns2;
+ static int last_top1;
+ static int last_top2;
+ static int **check_list;
+
+
+ /*New heuristic get dp_cost on a limited number of pairs*/
+ /*This is the current default*/
+
+
+ if ( last_ns1==ns1 && last_top1==list1[0] && last_ns2==ns2 && last_top2==list2[0]);
+ else
+ {
+
+
+ last_ns1=ns1;
+ last_ns2=ns2;
+ last_top1=list1[0];
+ last_top2=list2[0];
+ if ( check_list) free_int (check_list, -1);
+ check_list=declare_int ( (CL->S)->nseq*(CL->S)->nseq, 3);
+
+ for ( n_pair=0,a=0; a< ns1; a++)
+ {
+ s1 =list1[a];
+ rs1=A->order[s1][0];
+ for ( b=0; b< ns2; b++, n_pair++)
+ {
+ s2 =list2[b];
+ rs2=A->order[s2][0];
+ check_list[n_pair][0]=s1;
+ check_list[n_pair][1]=s2;
+ check_list[n_pair][2]=(!CL->DM)?0:(CL->DM)->similarity_matrix[rs1][rs2];
+ }
+ sort_int ( check_list, 3, 2, 0, n_pair-1);
+ }
+ }
+
+ if ( !CL->evaluate_residue_pair){fprintf ( stderr, "\nWARNING: CL->evaluate_residue_pair Not set\nSet to: extend_residue_pair\n");CL->evaluate_residue_pair= extend_residue_pair;}
+
+
+ for ( a=n_pair-1; a>=0; a--)
+ {
+ s1= check_list[a][0];
+ rs1=A->order[s1][0];
+ r1 =pos1[s1][col1];
+
+ s2= check_list[a][1];
+ rs2=A->order[s2][0];
+ r2 =pos2[s2][col2];
+
+ if ( r1>0 && r2 >0)
+ {res_res++;}
+ if ( rs1>rs2)
+ {
+ SWAP (rs1, rs2);
+ SWAP (r1, r2);
+ }
+
+ if ((s=(CL->evaluate_residue_pair)(CL, rs1, r1, rs2, r2))!=UNDEFINED) score+=s;
+ else
+ {
+
+ return UNDEFINED;
+ }
+ if ( res_res>=CL->max_n_pair && CL->max_n_pair!=0)a=0;
+ }
+
+ score=(res_res==0)?0:( (score)/res_res);
+ score=score-SCORE_K*CL->nomatch;
+
+ return (int)score;
+ }
+
+
+
+
+int slow_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ double score=0;
+
+ int a, b, s1, s2,r1, r2;
+ int s;
+ int gap_gap=0;
+ int gap_res=0;
+ int res_res=0;
+ int rs1, rs2;
+ static int last_tag;
+ static int *dummy;
+
+ if (col1<0 || col2<0) return 0;
+ if ( last_tag !=A->random_tag)
+ {
+ last_tag=A->random_tag;
+ if (!dummy)
+ {
+ dummy=vcalloc (10, sizeof(int));
+ dummy[0]=1;/*Number of Amino acid types on colum*/
+ dummy[1]=5;/*Length of Dummy*/
+ dummy[3]='\0';/*Amino acid*/
+ dummy[4]=1; /*Number of occurences*/
+ dummy[5]=100; /*Frequency in the MSA column*/
+ }
+ }
+
+ if ( !CL->evaluate_residue_pair){fprintf ( stderr, "\nWARNING: CL->evaluate_residue_pair Not set\nSet to: extend_residue_pair\n");CL->evaluate_residue_pair= extend_residue_pair;}
+
+ for ( a=0; a< ns1; a++)
+ {
+ for ( b=0; b<ns2; b++)
+ {
+
+ s1 =list1[a];
+ rs1=A->order[s1][0];
+ r1 =pos1[s1][col1];
+
+ s2 =list2[b];
+ rs2=A->order[s2][0];
+ r2 =pos2[s2][col2];
+
+ if ( rs1>rs2)
+ {
+ SWAP (rs1, rs2);
+ SWAP (r1, r2);
+ }
+
+ if (r1==0 && r2==0)gap_gap++;
+ else if ( r1<0 || r2<0) gap_res++;
+ else
+ {
+ res_res++;
+ if ((s=(CL->evaluate_residue_pair)(CL, rs1, r1, rs2, r2))!=UNDEFINED) score+=s;
+ else
+ {
+
+ return UNDEFINED;
+ }
+ }
+
+ }
+ }
+
+
+ score=(res_res==0)?0:( (score)/res_res);
+
+ return score-SCORE_K*CL->nomatch;
+
+ }
+int slow_get_dp_cost_pc ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ double score=0;
+
+ int a, b, s1, s2,r1, r2;
+ int s;
+ int gap_gap=0;
+ int gap_res=0;
+ int res_res=0;
+ int rs1, rs2;
+ static int last_tag;
+ static int *dummy;
+
+ if (col1<0 || col2<0) return 0;
+ if ( last_tag !=A->random_tag)
+ {
+ last_tag=A->random_tag;
+ if (!dummy)
+ {
+ dummy=vcalloc (10, sizeof(int));
+ dummy[0]=1;/*Number of Amino acid types on colum*/
+ dummy[1]=5;/*Length of Dummy*/
+ dummy[3]='\0';/*Amino acid*/
+ dummy[4]=1; /*Number of occurences*/
+ dummy[5]=100; /*Frequency in the MSA column*/
+ }
+ }
+
+ if ( !CL->evaluate_residue_pair){fprintf ( stderr, "\nWARNING: CL->evaluate_residue_pair Not set\nSet to: extend_residue_pair\n");CL->evaluate_residue_pair= extend_residue_pair;}
+
+ for ( a=0; a< ns1; a++)
+ {
+ for ( b=0; b<ns2; b++)
+ {
+
+ s1 =list1[a];
+ rs1=A->order[s1][0];
+ r1 =pos1[s1][col1];
+
+ s2 =list2[b];
+ rs2=A->order[s2][0];
+ r2 =pos2[s2][col2];
+
+ if ( rs1>rs2)
+ {
+ SWAP (rs1, rs2);
+ SWAP (r1, r2);
+ }
+
+ if (r1==0 && r2==0)gap_gap++;
+ else if ( r1<0 || r2<0) gap_res++;
+ else
+ {
+ res_res++;
+ if ((s=residue_pair_extended_list_pc(CL, rs1, r1, rs2, r2))!=UNDEFINED) score+=s;
+ else
+ {
+
+ return UNDEFINED;
+ }
+ }
+
+ }
+ }
+
+
+ score=(res_res==0)?0:( (score)/res_res);
+
+ return score;
+
+ }
+int slow_get_dp_cost_test ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ double score=0;
+
+ int a, b, s1, s2,r1, r2;
+ int gap_gap=0, gap_res=0, res_res=0, rs1, rs2;
+
+ for ( a=0; a< ns1; a++)
+ {
+ for ( b=0; b<ns2; b++)
+ {
+
+ s1 =list1[a];
+ rs1=A->order[s1][0];
+ r1 =pos1[s1][col1];
+
+ s2 =list2[b];
+ rs2=A->order[s2][0];
+ r2 =pos2[s2][col2];
+
+ if ( rs1>rs2)
+ {
+ SWAP (rs1, rs2);
+ SWAP (r1, r2);
+ }
+
+ if (r1==0 && r2==0)gap_gap++;
+ else if ( r1<0 || r2<0) gap_res++;
+ else
+ {
+ res_res++;
+ score+=residue_pair_extended_list_raw (CL, rs1, r1, rs2, r2);
+ }
+ }
+ }
+
+ return (int)(score*10)/(ns1*ns2);
+ }
+
+int sw_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
+ {
+ int a, b;
+ int s1,r1,rs1;
+ int s2,r2,rs2;
+
+
+
+
+ for ( a=0; a< ns1; a++)
+ {
+ s1 =list1[a];
+ rs1=A->order[s1][0];
+ r1 =pos1[s1][col1];
+ if ( r1<=0)continue;
+ for ( b=0; b< ns2; b++)
+ {
+
+
+ s2 =list2[b];
+ rs2=A->order[s2][0];
+ r2 =pos2[s2][col2];
+
+ if (r2<=0)continue;
+
+
+ if (sw_pair_is_defined (CL, rs1, r1, rs2, r2)==UNDEFINED)return UNDEFINED;
+ }
+ }
+
+ return slow_get_dp_cost ( A, pos1, ns1, list1, col1, pos2, ns2, list2,col2, CL);
+
+ }
+
+
+
+
+
+
+
+
+int get_domain_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2,Constraint_list *CL , int scale , int gop, int gep)
+
+ {
+ int a, b, s1, s2,r1, r2;
+ static int *entry;
+ int *r;
+ int score=0;
+ int gap_gap=0;
+ int gap_res=0;
+ int res_res=0;
+ int rs1, rs2;
+ int flag_list_is_aa_sub_mat=0;
+ int p;
+
+/*Needs to be cleanned After Usage*/
+
+
+
+ if ( entry==NULL) entry=vcalloc (LIST_N_FIELDS , sizeof (int));
+
+ for (a=0; a< ns1; a++)
+ {
+ s1=list1[a];
+ rs1=A->order[s1][0];
+ for ( b=0; b<ns2; b++)
+ {
+ s2 =list2[b];
+ rs2=A->order[s2][0];
+
+ entry[SEQ1]=rs1;
+ entry[SEQ2]=rs2;
+ r1=entry[R1]=pos1[s1][col1];
+ r2=entry[R2]=pos2[s2][col2];
+
+ if ( !flag_list_is_aa_sub_mat)
+ {
+ if ( r1==r2 && rs1==rs2)
+ {
+
+ return UNDEFINED;
+ }
+ else if (r1==0 && r2==0)
+ {
+ gap_gap++;
+ }
+ else if ( r1<=0 || r2<=0)
+ {
+ gap_res++;
+ }
+ else if ((r=main_search_in_list_constraint ( entry,&p,4,CL))!=NULL)
+ {
+ res_res++;
+
+ if (r[WE]!=UNDEFINED)
+ {
+ score+=(r[WE]*SCORE_K)+scale;
+ }
+ else
+ {
+ fprintf ( stderr, "**");
+ return UNDEFINED;
+ }
+ }
+ }
+ }
+ }
+ return score;
+ score=((res_res+gap_res)==0)?0:score/(res_res+gap_res);
+ return score;
+ }
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR ANALYSING AL OR MATRIX */
+/* */
+/*********************************************************************************************/
+
+int aln2n_res ( Alignment *A, int start, int end)
+ {
+ int a, b;
+ int score=0;
+
+ for ( a=start; a<end; a++)for ( b=0; b< A->nseq; b++)score+=!is_gap(A->seq_al[b][a]);
+ return score;
+ }
+
+float get_gop_scaling_factor ( int **matrix,float id, int l1, int l2)
+ {
+ return id* get_avg_matrix_mm(matrix, AA_ALPHABET);
+ }
+
+float get_avg_matrix_mm ( int **matrix, char *alphabet)
+ {
+ int a, b;
+ float naa;
+ float gop;
+ int l;
+
+
+ l=MIN(20,(int)strlen (alphabet));
+ for (naa=0, gop=0,a=0; a<l; a++)
+ for ( b=0; b<l; b++)
+ {
+ if ( a!=b)
+ {
+ gop+=matrix[alphabet[a]-'A'][alphabet[b]-'A'];
+ naa++;
+ }
+ }
+
+ gop=gop/naa;
+ return gop;
+ }
+float get_avg_matrix_match ( int **matrix, char *alphabet)
+ {
+ int a;
+ float gop;
+ int l;
+
+
+
+
+ l=MIN(20,(int)strlen (alphabet));
+ for (gop=0,a=0; a<l; a++)
+ gop+=matrix[alphabet[a]-'A'][alphabet[a]-'A'];
+
+ gop=gop/l;
+ return gop;
+ }
+
+float get_avg_matrix_diff ( int **matrix1,int **matrix2, char *alphabet)
+ {
+ int a, b;
+ float naa;
+ float gop;
+ int l,v1;
+
+
+
+
+ l=MIN(20,(int)strlen (alphabet));
+ for (naa=0, gop=0,a=0; a<l; a++)
+ for (b=0; b<l; b++)
+ {
+ v1=matrix1[alphabet[a]-'A'][alphabet[a]-'A']-matrix2[alphabet[b]-'A'][alphabet[b]-'A'];
+ gop+=v1*v1;
+ naa++;
+ }
+
+ gop=gop/l;
+ return gop;
+ }
+
+float* set_aa_frequencies ()
+ {
+
+ float *frequency;
+ /*frequencies tqken from psw*/
+
+ frequency=vcalloc (100, sizeof (float));
+ frequency ['x'-'A']=0.0013;
+ frequency ['a'-'A']=0.0076;
+ frequency ['c'-'A']=0.0176;
+ frequency ['d'-'A']=0.0529;
+ frequency ['e'-'A']=0.0628;
+ frequency ['f'-'A']=0.0401;
+ frequency ['g'-'A']=0.0695;
+ frequency ['h'-'A']=0.0224;
+ frequency ['i'-'A']=0.0561;
+ frequency ['k'-'A']=0.0584;
+ frequency ['l'-'A']=0.0922;
+ frequency ['m'-'A']=0.0236;
+ frequency ['n'-'A']=0.0448;
+ frequency ['p'-'A']=0.0500;
+ frequency ['q'-'A']=0.0403;
+ frequency ['r'-'A']=0.0523;
+ frequency ['s'-'A']=0.0715;
+ frequency ['t'-'A']=0.0581;
+ frequency ['v'-'A']=0.0652;
+ frequency ['w'-'A']=0.0128;
+ frequency ['y'-'A']=0.0321;
+ frequency ['X'-'A']=0.0013;
+ frequency ['A'-'A']=0.0076;
+ frequency ['C'-'A']=0.0176;
+ frequency ['D'-'A']=0.0529;
+ frequency ['E'-'A']=0.0628;
+ frequency ['F'-'A']=0.0401;
+ frequency ['G'-'A']=0.0695;
+ frequency ['H'-'A']=0.0224;
+ frequency ['I'-'A']=0.0561;
+ frequency ['J'-'A']=0.0584;
+ frequency ['L'-'A']=0.0922;
+ frequency ['M'-'A']=0.0236;
+ frequency ['N'-'A']=0.0448;
+ frequency ['P'-'A']=0.0500;
+ frequency ['Q'-'A']=0.0403;
+ frequency ['R'-'A']=0.0523;
+ frequency ['S'-'A']=0.0715;
+ frequency ['T'-'A']=0.0581;
+ frequency ['V'-'A']=0.0652;
+ frequency ['W'-'A']=0.0128;
+ frequency ['Y'-'A']=0.0321;
+ return frequency;
+ }
+
+float measure_matrix_pos_avg (int **matrix,char *alphabet)
+{
+ float naa=0, tot=0;
+ int a, b;
+
+
+ for ( tot=0,a=0; a< 20; a++)
+ for ( b=0; b<20; b++)
+ {
+ if (matrix[alphabet[a]-'A'][alphabet[b]-'A']>=0){naa++;tot+=matrix[alphabet[a]-'A'][alphabet[b]-'A'];}
+
+ }
+ return tot/naa;
+}
+
+float measure_matrix_enthropy (int **matrix,char *alphabet)
+ {
+
+ int a, b;
+ double s, p, q, h=0, tq=0;
+ float lambda;
+ float *frequency;
+ /*frequencies tqken from psw*/
+
+ frequency=set_aa_frequencies ();
+
+
+ lambda=compute_lambda(matrix,alphabet);
+ fprintf ( stderr, "\nLambda=%f", (float)lambda);
+
+ for ( a=0; a< 20; a++)
+ for ( b=0; b<=a; b++)
+ {
+ s=matrix[alphabet[a]-'A'][alphabet[b]-'A'];
+
+
+ p=frequency[alphabet[a]-'A']*frequency[alphabet[b]-'A'];
+
+ if ( p==0)continue;
+
+ q=exp(lambda*s+log(p));
+
+ tq+=q;
+ h+=q*log(q/p)*log(2);
+
+ }
+
+ fprintf ( stderr,"\ntq=%f\n", (float)tq);
+
+ return (float) h;
+ }
+float compute_lambda (int **matrix,char *alphabet)
+{
+
+ int a, b;
+ double lambda, best_lambda=0, delta, best_delta=0, p, tq,s;
+ static float *frequency;
+
+ if ( !frequency)frequency=set_aa_frequencies ();
+
+ for ( lambda=0.001; lambda<1; lambda+=0.005)
+ {
+ tq=0;
+ for ( a=0; a< 20; a++)
+ for ( b=0; b<20; b++)
+ {
+ p=frequency[alphabet[a]-'A']*frequency[alphabet[b]-'A'];
+ s=matrix[alphabet[a]-'A'][alphabet[b]-'A'];
+ tq+=exp(lambda*s+log(p));
+ }
+ delta=fabs(1-tq);
+ if (lambda==0.001)
+ {
+ best_delta=delta;
+ best_lambda=lambda;
+ }
+ else
+ {
+ if (delta<best_delta)
+ {
+ best_delta=delta;
+ best_lambda=lambda;
+ }
+ }
+
+ fprintf ( stderr, "\n%f %f ", lambda, tq);
+ if ( tq>1)break;
+ }
+ fprintf ( stderr, "\nRESULT: %f %f ", best_lambda, best_delta);
+ return (float) best_lambda;
+}
+
+
+
+float evaluate_random_match (char *mat, int n, int len,char *alp)
+{
+ int **matrix;
+ matrix=read_matrice ( mat);
+ fprintf ( stderr, "Matrix=%15s ", mat);
+ return evaluate_random_match2 (matrix, n,len,alp);
+
+}
+
+float evaluate_random_match2 (int **matrix, int n, int len,char *alp)
+{
+ int a, b, c, d, c1, c2, tot;
+ static int *list;
+ static float *freq;
+ float score_random=0;
+ float score_id=0;
+ float score_good=0;
+ float tot_len=0;
+ float tot_try=0;
+
+
+ if ( !list)
+ {
+ vsrand(0);
+ freq=set_aa_frequencies ();
+ list=vcalloc ( 10000, sizeof (char));
+ }
+
+ for (tot=0,c=0,a=0;a<20; a++)
+ {
+ b=freq[alp[a]-'A']*1000;
+ tot+=b;
+ for (d=0; d<b; d++, c++)
+ {
+ list[c]=alp[a];
+ }
+ }
+
+
+ for (a=0; a< len*n; a++)
+ {
+ c1=rand()%tot;
+ c2=rand()%tot;
+ score_random+=matrix[list[c1]-'A'][list[c2]-'A'];
+ score_id+=matrix[list[c1]-'A'][list[c1]-'A'];
+ }
+ while (tot_len< len*n)
+ {
+ tot_try++;
+ c1=rand()%tot;
+ c2=rand()%tot;
+ if ( matrix[list[c1]-'A'][list[c2]-'A']>=0){score_good+=matrix[list[c1]-'A'][list[c2]-'A']; tot_len++;}
+ }
+
+
+ score_random=score_random/tot_len;
+ score_id=score_id/tot_len;
+ score_good=score_good/tot_len;
+
+ fprintf ( stderr, "Random=%8.3f Id=%8.3f Good=%8.3f [%7.2f]\n",score_random, score_id, score_good, tot_len/tot_try);
+
+ return score_random;
+}
+float compare_two_mat (char *mat1,char*mat2, int n, int len,char *alp)
+{
+ int **matrix1, **matrix2;
+
+ evaluate_random_match (mat1, n, len,alp);
+ evaluate_random_match (mat2, n, len,alp);
+ matrix1=read_matrice ( mat1);
+ matrix2=read_matrice ( mat2);
+ matrix1=rescale_matrix(matrix1, 10, alp);
+ matrix2=rescale_matrix(matrix2, 10, alp);
+ compare_two_mat_array(matrix1,matrix2, n, len,alp);
+ return 0;
+}
+
+
+int ** rescale_two_mat (char *mat1,char*mat2, int n, int len,char *alp)
+{
+ float lambda;
+ int **matrix1, **matrix2;
+
+ lambda=measure_lambda2 (mat1, mat2, n, len, alp)*10;
+
+ fprintf ( stderr, "\nLambda=%.2f", lambda);
+ matrix2=read_matrice(mat2);
+ matrix2=neg_matrix2pos_matrix(matrix2);
+ matrix2=rescale_matrix( matrix2, lambda,"abcdefghiklmnpqrstvwxyz");
+
+ matrix1=read_matrice(mat1);
+ matrix1=neg_matrix2pos_matrix(matrix1);
+ matrix1=rescale_matrix( matrix1,10,"abcdefghiklmnpqrstvwxyz");
+
+ output_matrix_header ( "stdout", matrix2, alp);
+ evaluate_random_match2(matrix1, 1000, 100, alp);
+ evaluate_random_match2(matrix2, 1000, 100, alp);
+ compare_two_mat_array(matrix1,matrix2, n, len,alp);
+
+ return matrix2;
+}
+float measure_lambda2(char *mat1,char*mat2, int n, int len,char *alp)
+{
+ int **m1, **m2;
+ float f1, f2;
+
+ m1=read_matrice (mat1);
+ m2=read_matrice (mat2);
+
+ m1=neg_matrix2pos_matrix(m1);
+ m2=neg_matrix2pos_matrix(m2);
+
+ f1=measure_matrix_pos_avg( m1, alp);
+ f2=measure_matrix_pos_avg( m2, alp);
+
+ return f1/f2;
+}
+
+
+float measure_lambda (char *mat1,char*mat2, int n, int len,char *alp)
+{
+ int c;
+ int **matrix1, **matrix2, **mat;
+ float a;
+ float best_quality=0, quality=0, best_lambda=0;
+
+ matrix1=read_matrice ( mat1);
+ matrix2=read_matrice ( mat2);
+ matrix1=rescale_matrix(matrix1, 10, alp);
+ matrix2=rescale_matrix(matrix2, 10, alp);
+
+ for (c=0, a=0.1; a< 2; a+=0.05)
+ {
+ fprintf ( stderr, "Lambda=%.2f\n", a);
+ mat=duplicate_int (matrix2,-1,-1);
+ mat=rescale_matrix(mat, a, alp);
+ quality=compare_two_mat_array(matrix1,mat, n, len,alp);
+ quality=MAX((-quality),quality);
+
+ if (c==0 || (best_quality>quality))
+ {
+ c=1;
+ fprintf ( stderr, "*");
+ best_quality=quality;
+ best_lambda=a;
+ }
+
+
+ evaluate_random_match2(mat, 1000, 100, alp);
+ evaluate_random_match2(matrix1, 1000, 100, alp);
+ free_int (mat, -1);
+ }
+
+ return best_lambda;
+
+}
+
+float compare_two_mat_array (int **matrix1,int **matrix2, int n, int len,char *alp)
+{
+ int a, b, c, d, c1, c2, tot;
+ static int *list;
+ static float *freq;
+ float delta_random=0;
+ float delta2_random=0;
+
+ float delta_id=0;
+ float delta2_id=0;
+
+ float delta_good=0;
+ float delta2_good=0;
+
+ float delta;
+
+ float tot_len=0;
+ float tot_try=0;
+
+
+
+ if ( !list)
+ {
+ vsrand(0);
+ freq=set_aa_frequencies ();
+ list=vcalloc ( 10000, sizeof (char));
+ }
+
+ for (tot=0,c=0,a=0;a<20; a++)
+ {
+ b=freq[alp[a]-'A']*1000;
+ tot+=b;
+ for (d=0; d<b; d++, c++)
+ {
+ list[c]=alp[a];
+ }
+ }
+
+
+ for (a=0; a< len*n; a++)
+ {
+ c1=rand()%tot;
+ c2=rand()%tot;
+ delta=matrix1[list[c1]-'A'][list[c2]-'A']-matrix2[list[c1]-'A'][list[c2]-'A'];
+ delta_random+=delta;
+ delta2_random+=MAX(delta,(-delta));
+
+ delta=matrix1[list[c1]-'A'][list[c1]-'A']-matrix2[list[c1]-'A'][list[c1]-'A'];
+ delta_id+=delta;
+ delta2_id+=MAX(delta,(-delta));
+ }
+ while (tot_len< len*n)
+ {
+ tot_try++;
+ c1=rand()%tot;
+ c2=rand()%tot;
+ if ( matrix1[list[c1]-'A'][list[c2]-'A']>=0 || matrix2[list[c1]-'A'][list[c2]-'A'] )
+ {
+ delta=matrix1[list[c1]-'A'][list[c2]-'A']-matrix2[list[c1]-'A'][list[c2]-'A'];
+ delta_good+=delta;
+ delta2_good+=MAX(delta,(-delta));
+ tot_len++;
+ }
+ }
+
+
+ delta_random=delta_random/tot_len;
+ delta2_random=delta2_random/tot_len;
+
+
+ delta_id=delta_id/tot_len;
+ delta2_id=delta2_id/tot_len;
+
+ delta_good=delta_good/tot_len;
+ delta2_good=delta2_good/tot_len;
+
+
+ fprintf ( stderr, "\tRand=%8.3f %8.3f\n\tId =%8.3f %8.3f\n\tGood=%8.3f %8.3f\n",delta_random, delta2_random, delta_id,delta2_id, delta_good,delta2_good);
+
+ return delta_good;
+}
+
+
+
+int ** rescale_matrix ( int **matrix, float lambda, char *alp)
+{
+ int a, b;
+
+
+ for ( a=0; a< 20; a++)
+ for ( b=0; b< 20; b++)
+ {
+ matrix[alp[a]-'A'][alp[b]-'A']= matrix[alp[a]-'A'][alp[b]-'A']*lambda;
+ }
+ return matrix;
+}
+int **mat2inverted_mat (int **matrix, char *alp)
+{
+ int a, b, min, max, v,l;
+ int c1,c2, C1, C2;
+
+ l=(int)strlen (alp);
+ min=max=matrix[alp[0]-'A'][alp[0]-'A'];
+ for ( a=0; a<l; a++)
+ for ( b=0; b< l; b++)
+ {
+ v=matrix[alp[a]-'A'][alp[b]-'A'];
+ min=MIN(min,v);
+ max=MAX(max,v);
+ }
+ for ( a=0; a<l; a++)
+ for ( b=0; b< l; b++)
+ {
+ v=matrix[alp[a]-'A'][alp[b]-'A'];
+ v=max-v;
+
+ c1=tolower(alp[a])-'A';
+ c2=tolower(alp[b])-'A';
+
+ C1=toupper(alp[a])-'A';
+ C2=toupper(alp[b])-'A';
+ matrix[C1][C2]=matrix[c1][c2]=matrix[C1][c2]=matrix[c1][C2]=v;
+ }
+ return matrix;
+}
+void output_matrix_header ( char *name, int **matrix, char *alp)
+{
+ int a, b;
+ FILE *fp;
+ char *nalp;
+ int l;
+ nalp=vcalloc ( 1000, sizeof (char));
+
+
+
+ sprintf ( nalp, "ABCDEFGHIKLMNPQRSTVWXYZ");
+ l=(int)strlen (nalp);
+
+ fp=vfopen ( name, "w");
+ fprintf (fp, "\nint []={\n");
+
+ for (a=0; a<l; a++)
+ {
+ for ( b=0; b<=a; b++)
+ fprintf ( fp, "%3d, ",matrix[nalp[a]-'A'][nalp[b]-'A']);
+ fprintf ( fp, "\n");
+ }
+ fprintf (fp, "};\n");
+
+ vfclose (fp);
+}
+
+
+float ** initialise_aa_physico_chemical_property_table (int *n)
+{
+ FILE *fp;
+ int a, b,c;
+ float **p;
+ char c1;
+ float v1, max, min;
+ int in=0;
+
+ n[0]=0;
+ fp=vfopen ("properties.txt", "r");
+ while ((c=fgetc(fp))!=EOF)n[0]+=(c=='#');
+ vfclose (fp);
+
+
+
+ p=declare_float ( n[0], 'z'+1);
+ fp=vfopen ("properties.txt", "r");
+ n[0]=0;
+ while ((c=fgetc(fp))!=EOF)
+ {
+ if (c=='#'){in=0;while (fgetc(fp)!='\n');}
+ else
+ {
+ if ( !in){in=1; ++n[0];}
+ fscanf (fp, "%f %c %*s",&v1, &c1 );
+ p[n[0]-1][tolower(c1)]=v1;
+ while ( (c=fgetc(fp))!='\n');
+ }
+ }
+ vfclose (fp);
+
+ /*rescale so that Delta max=10*/
+ for (a=0; a<n[0]; a++)
+ {
+ min=max=p[a]['a'];
+ for (b='a'; b<='z'; b++)
+ {
+ min=(p[a][b]<min)?p[a][b]:min;
+ max=(p[a][b]>max)?p[a][b]:max;
+ }
+ for (b='a'; b<='z'; b++)
+ {
+ p[a][b]=((p[a][b]-min)/(max-min))*10;
+
+ }
+ }
+
+ return p;
+}
+Constraint_list * choose_extension_mode ( char *extend_mode, Constraint_list *CL)
+{
+ //evaluation_functions: residues start at 1, sequences at 0;
+
+ if ( !CL)
+ {
+ fprintf ( stderr, "\nWarning: CL was not set");
+ return CL;
+ }
+ else if ( strm ( extend_mode, "rna0"))
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "rna1") || strm (extend_mode, "rna"))
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list4rna1;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "rna2"))
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list4rna2;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "rna3"))
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list4rna3;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "rna4"))
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list4rna4;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "pc") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list_pc;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "triplet") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list;
+ CL->get_dp_cost =get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "relative_triplet") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_relative_extended_list;
+ CL->get_dp_cost =fast_get_dp_cost_2;
+ }
+ else if ( strm ( extend_mode, "g_coffee") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list_g_coffee;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "g_coffee_quadruplets") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list_g_coffee_quadruplet;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "fast_triplet") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list;
+ CL->get_dp_cost =fast_get_dp_cost;
+ }
+
+ else if ( strm ( extend_mode, "very_fast_triplet") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list;
+ CL->get_dp_cost =fast_get_dp_cost_2;
+ }
+ else if ( strm ( extend_mode, "slow_triplet") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list;
+ CL->get_dp_cost =slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "mixt") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list_mixt;
+ CL->get_dp_cost=slow_get_dp_cost;
+ }
+ else if ( strm ( extend_mode, "quadruplet") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_extended_list_quadruplet;
+ CL->get_dp_cost =get_dp_cost_quadruplet;
+ }
+ else if ( strm ( extend_mode, "test") && !CL->M)
+ {
+ CL->evaluate_residue_pair=residue_pair_test_function;
+ CL->get_dp_cost =slow_get_dp_cost_test;
+ }
+ else if ( strm ( extend_mode, "ssp"))
+ {
+
+ CL->evaluate_residue_pair=evaluate_ssp_matrix_score;
+ CL->get_dp_cost=slow_get_dp_cost;
+ CL->normalise=1;
+ }
+ else if ( strm ( extend_mode, "tm"))
+ {
+
+ CL->evaluate_residue_pair=evaluate_tm_matrix_score;
+ CL->get_dp_cost=slow_get_dp_cost;
+ CL->normalise=1;
+ }
+ else if ( strm ( extend_mode, "matrix"))
+ {
+
+ CL->evaluate_residue_pair=evaluate_matrix_score;
+ CL->get_dp_cost=cw_profile_get_dp_cost;
+ CL->normalise=1;
+ }
+ else if ( strm ( extend_mode, "curvature"))
+ {
+ CL->evaluate_residue_pair=evaluate_curvature_score;
+ CL->get_dp_cost=slow_get_dp_cost;
+ CL->normalise=1;
+ }
+ else if ( CL->M)
+ {
+ CL->evaluate_residue_pair=evaluate_matrix_score;
+ CL->get_dp_cost=cw_profile_get_dp_cost;
+ CL->normalise=1;
+ }
+ else
+ {
+ fprintf ( stderr, "\nERROR: %s is an unknown extend_mode[FATAL:%s]\n", extend_mode, PROGRAM);
+ myexit (EXIT_FAILURE);
+ }
+
+ return CL;
+}
+int ** combine_two_matrices ( int **mat1, int **mat2)
+{
+ int naa, re1, re2, Re1, Re2, a, b, u, l;
+
+ naa=(int)strlen (BLAST_AA_ALPHABET);
+ for ( a=0; a< naa; a++)
+ for ( b=0; b< naa; b++)
+ {
+ re1=BLAST_AA_ALPHABET[a];
+ re2=BLAST_AA_ALPHABET[b];
+ if (re1=='*' || re2=='*');
+ else
+ {
+
+ Re1=toupper(re1);Re2=toupper(re2);
+ re1-='A';re2-='A';Re1-='A';Re2-='A';
+
+ l=mat1[re1][re2];
+ u=mat2[re1][re2];
+ mat1[re1][re2]=mat2[re1][re2]=l;
+ mat2[Re1][Re2]=mat2[Re1][Re2]=u;
+ }
+ }
+ return mat1;
+}
+
+/* Off the shelves evaluations */
+/*********************************************************************************************/
+/* */
+/* OFF THE SHELVES EVALUATION */
+/* */
+/*********************************************************************************************/
+
+
+int lat_sum_pair (Alignment *A, char *mat)
+{
+ int a,b,c, tot=0, v1, v2, score;
+ int **matrix;
+
+ matrix=read_matrice (mat);
+
+ for (a=0; a<A->nseq; a++)
+ for ( b=0; b<A->nseq; b++)
+ {
+ for (c=1; c<A->len_aln; c++)
+ {
+ char r11, r12;
+
+ r11=A->seq_al[a][c-1];
+ r12=A->seq_al[a][c];
+ if (is_gap(r11) || is_gap(r12))continue;
+ else v1=matrix[r11-'A'][r12-'A'];
+
+ r11=A->seq_al[b][c-1];
+ r12=A->seq_al[b][c];
+ if (is_gap(r11) || is_gap(r12))continue;
+ else v2=matrix[r11-'A'][r12-'A'];
+
+ score+=(v1-v2)*(v1-v2);
+ tot++;
+ }
+ }
+ score=(100*score)/tot;
+ return (float)score;
+}
+
+
+
+/* Off the shelves evaluations */
+/*********************************************************************************************/
+/* */
+/* OFF THE SHELVES EVALUATION */
+/* */
+/*********************************************************************************************/
+
+int comp_pair ( int len,char *sa, char *sb, int seqA, int seqB,int *tgp_a, int *tgp_b,int gap_op,int gap_ex, int start, int end,int **matrix,int MODE);
+int score_gap ( int len, char *sa, char *sb,int seqA, int seqB,int *tgp_a, int *tgp_b, int op, int ex, int start, int end, int MODE);
+void evaluate_tgp_decoded_chromosome ( Alignment *A,int **TGP,int start, int end,int MODE);
+int gap_type ( char a, char b);
+
+
+
+float sum_pair ( Alignment*A,char *mat_name, int gap_op, int gap_ex)
+ {
+ int a,b;
+ float pscore=0;
+
+ int start, end;
+ static int **tgp;
+ double score=0;
+ int MODE=1;
+ int **matrix;
+
+ matrix=read_matrice (mat_name);
+ matrix=mat2inverted_mat (matrix, "acdefghiklmnpqrstvwy");
+
+ start=0;
+ end=A->len_aln-1;
+
+ if ( tgp==NULL)
+ tgp= declare_int (A->nseq,2);
+
+ evaluate_tgp_decoded_chromosome ( A,tgp,start, end,MODE);
+
+ for ( a=0; a< A->nseq-1; a++)
+ for (b=a+1; b<A->nseq; b++)
+ {
+ pscore= comp_pair (A->len_aln,A->seq_al[a], A->seq_al[b],a, b,tgp[a], tgp[b],gap_op,gap_ex, start, end,matrix, MODE);
+ score+=pscore*100;
+ /*score+=(double)pscore*(int)(PARAM->OFP)->weight[A->order[a][0]][A->order[b][0]];*//*NO WEIGHTS*/
+ }
+
+ score=score/(A->nseq*A->nseq);
+
+ return (float)score;
+ }
+
+int comp_pair ( int len,char *sa, char *sb, int seqA, int seqB,int *tgp_a, int *tgp_b,int gap_op,int gap_ex, int start, int end,int **matrix,int MODE)
+ {
+ int score=0, a, ex;
+
+
+
+ if ( end-start>=0)
+ score+= score_gap (len, sa,sb, seqA, seqB,tgp_a, tgp_b, gap_op,gap_ex, start, end,MODE);
+
+ ex=gap_ex;
+
+
+ for (a=start; a<=end; a++)
+ {
+ if ( is_gap(sa[a]) || is_gap(sb[a]))
+ {
+ if (is_gap(sa[a]) && is_gap(sb[a]));
+ else
+ {
+
+ score +=ex;
+ }
+ }
+ else
+ {
+ score += matrix [sa[a]-'A'][sb[a]-'A'];
+
+ }
+ }
+ return score;
+ }
+int score_gap ( int len, char *sa, char *sb,int seqA, int seqB,int *tgp_a, int *tgp_b, int op, int ex, int start, int end, int MODE)
+ {
+ int a,b;
+ int ga=0,gb=0;
+ int score=0;
+
+
+ int right_gap, left_gap;
+
+
+
+
+
+ int type;
+ int flag1=0;
+ int flag2=0;
+ int continue_loop;
+ int sequence_pattern[2][3];
+ int null_gap;
+ int natural_gap=1;
+
+ /*op= gor_gap_op ( 0,seqA, seqB, PARAM);
+ ex= gor_gap_ext ( 0, seqA, seqB, PARAM);*/
+
+
+
+ for (a=start; a<=end; ++a)
+ {
+
+ type= gap_type ( sa[a], sb[a]);
+
+ if ( type==2 && ga<=gb)
+ {++ga;
+ gb=0;
+ score += op;
+ }
+ else if (type==1 && ga >=gb)
+ {
+ ++gb;
+ ga=0;
+ score +=op;
+ }
+ else if (type==0)
+ {
+ ga++;
+ gb++;
+ }
+
+ else if (type== -1)
+ ga=gb=0;
+
+
+ if (natural_gap==0)
+ {
+ if ( type== -1)
+ flag1=flag2=0;
+ else if ( type==0)
+ flag2=1;
+ else if ( (type==flag1) && flag2==1)
+ {
+ score+=op;
+ flag2=0;
+ }
+ else if ( (type!=flag1) && flag2==1)
+ {
+ flag1=type;
+ flag2=0;
+ }
+ else if ( flag2==0)
+ flag1=type;
+ }
+ }
+ /*gap_type -/-:0, X/X:-1 X/-:1, -/X:2*/
+/*evaluate the pattern of gaps*/
+
+ continue_loop=1;
+ sequence_pattern[0][0]=sequence_pattern[1][0]=0;
+ for ( a=start; a<=end && continue_loop==1; a++)
+ {
+ left_gap= gap_type ( sa[a], sb[a]);
+ if ( left_gap!= 0)
+ {
+ if ( left_gap==-1)
+ {
+ sequence_pattern[0][0]=sequence_pattern[1][0]=0;
+ continue_loop=0;
+ }
+ else
+ {
+ null_gap=0;
+ for (b=a; b<=end && continue_loop==1; b++)
+ {type=gap_type( sa[b], sb[b]);
+ if (type==0)
+ null_gap++;
+ if ( type!=left_gap && type !=0)
+ {
+ continue_loop=0;
+ sequence_pattern[2-left_gap][0]= b-a-null_gap;
+ sequence_pattern [1-(2-left_gap)][0]=0;
+ }
+ }
+ if ( continue_loop==1)
+ {
+ continue_loop=0;
+ sequence_pattern[2-left_gap][0]= b-a-null_gap;
+ sequence_pattern [1-(2-left_gap)][0]=0;
+ }
+ }
+ }
+ }
+
+ sequence_pattern[0][2]=sequence_pattern[1][2]=1;
+ for ( a=start; a<=end; a++)
+ {
+ if ( !is_gap(sa[a]))
+ sequence_pattern[0][2]=0;
+ if ( !is_gap(sb[a]))
+ sequence_pattern[1][2]=0;
+
+ }
+ continue_loop=1;
+ sequence_pattern[0][1]=sequence_pattern[1][1]=0;
+ for ( a=end; a>=start && continue_loop==1; a--)
+ {
+ right_gap= gap_type ( sa[a], sb[a]);
+ if ( right_gap!= 0)
+ {
+ if ( right_gap==-1)
+ {
+ sequence_pattern[0][1]=sequence_pattern[1][1]=0;
+ continue_loop=0;
+ }
+ else
+ {
+ null_gap=0;
+ for (b=a; b>=start && continue_loop==1; b--)
+ {type=gap_type( sa[b], sb[b]);
+ if ( type==0)
+ null_gap++;
+ if ( type!=right_gap && type !=0)
+ {
+ continue_loop=0;
+ sequence_pattern[2-right_gap][1]= a-b-null_gap;
+ sequence_pattern [1-(2-right_gap)][1]=0;
+ }
+ }
+ if ( continue_loop==1)
+ {
+ continue_loop=0;
+ sequence_pattern[2-right_gap][1]= a-b-null_gap;
+ sequence_pattern [1-(2-right_gap)][1]=0;
+ }
+ }
+ }
+ }
+
+/*
+printf ( "\n*****************************************************");
+printf ( "\n%c\n%c", sa[start],sb[start]);
+printf ( "\n%d %d %d",sequence_pattern[0][0] ,sequence_pattern[0][1], sequence_pattern[0][2]);
+printf ( "\n%d %d %d",sequence_pattern[1][0] ,sequence_pattern[1][1], sequence_pattern[1][2]);
+printf ( "\n*****************************************************");
+*/
+
+/*correct the scoring*/
+
+
+ if ( MODE==0)
+ {
+ if ( FABS(tgp_a[0])>1 && (FABS(tgp_a[0])>FABS( tgp_b[0])))
+ score-= (sequence_pattern[0][0]>0)?op:0;
+ if ( FABS(tgp_b[0])>1 && (FABS(tgp_b[0])> FABS(tgp_a[0])))
+ score-= (sequence_pattern[1][0]>0)?op:0;
+ }
+ else if ( MODE ==1 || MODE ==2)
+ {
+ if ( FABS(tgp_a[0])>1 && (FABS(tgp_a[0])>FABS( tgp_b[0])) && (tgp_a[1]!=1 || sequence_pattern[0][2]==0))
+ score-= (sequence_pattern[0][0]>0)?op:0;
+ if ( FABS(tgp_b[0])>1 && (FABS(tgp_b[0])> FABS(tgp_a[0])) && (tgp_b[1]!=1 || sequence_pattern[1][2]==0))
+ score-= (sequence_pattern[1][0]>0)?op:0;
+
+
+ if ( tgp_a[0]>=1 && tgp_a[0]==tgp_b[0])
+ score -=(sequence_pattern[0][0]>0)?op:0;
+ if ( tgp_b[0]>=1 && tgp_a[0]==tgp_b[0])
+ score-= (sequence_pattern[1][0]>0)?op:0;
+
+
+ if ( tgp_a[1]==1 && sequence_pattern[0][2]==0)
+ score -= ( sequence_pattern[0][1]>0)?op:0;
+ else if ( tgp_a[1]==1 && sequence_pattern[0][2]==1 && tgp_a[0]<=0)
+ score -= ( sequence_pattern[0][1]>0)?op:0;
+
+
+ if ( tgp_b[1]==1 && sequence_pattern[1][2]==0)
+ score -= ( sequence_pattern[1][1]>0)?op:0;
+ else if ( tgp_b[1]==1 && sequence_pattern[1][2]==1 && tgp_b[0]<=0)
+ score -= ( sequence_pattern[1][1]>0)?op:0;
+
+ if ( MODE==2)
+ {
+ if ( tgp_a[0]>0)
+ score -=sequence_pattern[0][0]*ex;
+ if ( tgp_b[0]>0)
+ score -= sequence_pattern[1][0]*ex;
+ if ( tgp_a[1]>0)
+ score-=sequence_pattern[0][1]*ex;
+ if ( tgp_b[1]>0)
+ score-=sequence_pattern[1][1]*ex;
+ }
+ }
+
+
+ return score;
+
+
+
+ }
+void evaluate_tgp_decoded_chromosome ( Alignment *A,int **TGP,int start, int end,int MODE)
+ {
+ int a,b;
+ int continue_loop;
+
+
+
+ if (MODE==11 || MODE==13|| MODE==14)
+ {
+ if ( start==0)for ( a=0; a<A->nseq; a++)TGP[a][0]=-1;
+ else for ( a=0; a<A->nseq; a++)TGP[a][0]=(is_gap(A->seq_al[a][start-1])==1)?0:1;
+
+ if ( end==A->len_aln-1)for ( a=0; a<A->nseq; a++)TGP[a][1]=-1;
+ else for ( a=0; a<A->nseq; a++)TGP[a][1]=(is_gap(A->seq_al[a][start-1])==1)?0:1;
+ }
+ else
+ {
+ /* 0: in the middle of the alignement
+ 1: natural end
+ 2: q left gap is the continuation of another gap that was open outside the bloc ( don't open it)
+ */
+
+ for ( a=0; a< A->nseq; a++)
+ {
+ TGP[a][0]=1;
+ TGP[a][1]=1;
+ for ( b=0; b< start; b++)
+ if ( !is_gap(A->seq_al[a][b]))
+ TGP[a][0]=0;
+ if ( start>0 )
+ {
+ if (is_gap(A->seq_al[a][start-1]) && TGP[a][0]!=1)
+ {TGP[a][0]=-1;
+ continue_loop=1;
+ for ( b=(start-1); b>=0 && continue_loop==1; b--)
+ {TGP[a][0]-= ( is_gap(A->seq_al[a][b])==1)?1:0;
+ continue_loop= (is_gap(A->seq_al[a][b])==1)?continue_loop:0;
+ }
+ }
+ }
+ else if (is_gap(A->seq_al[a][start-1]) && TGP[a][0]==1)
+ {
+ TGP[a][0]=1;
+ continue_loop=1;
+ for ( b=(start-1); b>=0 && continue_loop==1; b--)
+ {TGP[a][0]+= ( is_gap(A->seq_al[a][b])==1)?1:0;
+ continue_loop= (is_gap(A->seq_al[a][b])==1)?continue_loop:0;
+ }
+ }
+ for ( b=(A->len_aln-1); b>end; b--)
+ if ( !is_gap(A->seq_al[a][b]))
+ TGP[a][1]=0;
+ }
+ }
+ }
+int gap_type ( char a, char b)
+ {
+ /*gap_type -/-:0, X/X:-1 X/-:1, -/STAR:2*/
+
+ if ( is_gap(a) && is_gap(b))
+ return 0;
+ else if ( !is_gap(a) && !is_gap(b))
+ return -1;
+ else if ( !is_gap(a))
+ return 1;
+ else if ( !is_gap(b))
+ return 2;
+ else
+ return -1;
+ }
+
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*All rights reserved.*/
+/*This file is part of T-COFFEE.*/
+/**/
+/* T-COFFEE 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.*/
+/**/
+/* T-COFFEE 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 Foobar; if not, write to the Free Software*/
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
+/*............................................... |*/
+/* If you need some more information*/
+/* cedric.notredame@europe.com*/
+/*............................................... |*/
+/**/
+/**/
+/* */
+/******************************COPYRIGHT NOTICE*******************************/
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