+++ /dev/null
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-#include <ctype.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "dp_lib_header.h"
-#include "define_header.h"
-
-
-int aln_compare ( int argc, char *argv[])
- {
- int a, b, c,f;
-
- Alignment *A, *B;
- Sequence *SA, *SB, *TOT_SEQ=NULL;
- Sequence *defined_residueA;
- Sequence *defined_residueB;
- char **seq_list;
- int n_seq_file;
-
-
- Sequence *S=NULL;
- Structure *ST=NULL;
- Result *R=NULL;
- char *buf1;
- char *buf2;
-
-/*PARAMETERS*/
- char ***grep_list;
- int n_greps;
- char compare_mode[STRING];
- char sim_aln[STRING];
- char *alignment1_file;
- char *alignment2_file;
-
- char *pep1_file;
- char *pep2_file;
-
- char io_format[STRING];
-
- int n_structure;
- char **struct_file;
- char **struct_format;
- int *n_symbol;
- char ***symbol_list;
- int pep_compare;
- int aln_compare;
- int count;
- int output_aln;
- int output_aln_threshold;
- char output_aln_file[LONG_STRING];
- char output_aln_format[LONG_STRING];
- char output_aln_modif[LONG_STRING];
-/*LIST VARIABLES*/
- Constraint_list *CL_A;
- Constraint_list *CL_B;
- CLIST_TYPE *clist_entry;
- int pos_in_clist;
- Sequence *CLS;
-
-
-/*Column Comparison Variables*/
- int **posA;
- int **posB;
- int **seq_cache;
- int is_same;
- int n;
-/*RESULTS_VARIABLES*/
- int **tot_count;
- int **pos_count;
- int ***pw_tot_count;
- int ***pw_pos_count;
- int *glob;
- int **pw_glob;
- int s1, r1, s2, r2;
-/*IO VARIABLES*/
- int n_categories;
- char ***category;
- char *category_list;
- int *n_sub_categories;
- char sep_l;
- char sep_r;
- char io_file[STRING];
- FILE *fp;
- int **aln_output_count;
- int **aln_output_tot;
-
-/*Sims VARIABLES*/
- float **sim;
- float **sim_param;
- char sim_matrix[STRING];
-
- int sim_n_categories;
- char ***sim_category;
- char *sim_category_list;
- int *sim_n_sub_categories;
-
-
- if ( argc==1|| strm6 ( argv[1], "h", "-h", "help", "-help", "-man", "?"))
- {
- output_informations();
- }
-
- argv=standard_initialisation (argv, &argc);
-/*Declarations and Initializations*/
- alignment1_file=vcalloc ( LONG_STRING, sizeof (char));
- alignment2_file=vcalloc ( LONG_STRING, sizeof (char));
-
- pep1_file=vcalloc ( LONG_STRING, sizeof (char));
- pep2_file=vcalloc ( LONG_STRING, sizeof (char));
-
-
- sprintf (compare_mode, "sp");
- count=0;
- pep_compare=0;
- aln_compare=1;
-
-
- grep_list=vcalloc ( STRING, sizeof (char**));
- for ( a=0; a< STRING; a++)grep_list[a]=declare_char (3, STRING);
- n_greps=0;
-
- n_structure=0;
- struct_file=declare_char ( MAX_N_STRUC, LONG_STRING);
- struct_format=declare_char (MAX_N_STRUC, STRING);
-
- n_symbol=vcalloc ( MAX_N_STRUC, sizeof (int));
- symbol_list=vcalloc (MAX_N_STRUC, sizeof (char**));
- for ( a=0; a< MAX_N_STRUC; a++)symbol_list[a]=declare_char ( 100, 100);
-
-
-
-
- n_categories=1;
- category=vcalloc ( MAX_N_CATEGORIES, sizeof (char**));
- for ( a=0; a< MAX_N_CATEGORIES; a++)category[a]=declare_char(100, STRING);
- n_sub_categories=vcalloc ( 100, sizeof (int));
- category_list=vcalloc ( LONG_STRING, sizeof (char));
- sprintf ( category_list, "[*][*]=[ALL]");
-
-
- sim_n_categories=1;
- sim_category=vcalloc ( MAX_N_CATEGORIES, sizeof (char**));
- for ( a=0; a< MAX_N_CATEGORIES; a++)sim_category[a]=declare_char(100, STRING);
- sim_n_sub_categories=vcalloc ( 100, sizeof (int));
- sim_category_list=vcalloc ( LONG_STRING, sizeof (char));
- sprintf ( sim_category_list, "[*][*]=[ALL]");
- sprintf ( sim_aln, "al1");
- sim_matrix[0]='\0';
- sprintf ( sim_category_list, "[*][*]=[ALL]");
-
- sprintf ( io_format, "ht");
- sprintf ( io_file, "stdout");
- sep_l='[';
- sep_r=']';
-
- output_aln=0;
- output_aln_threshold=100;
- sprintf ( output_aln_file, "stdout");
- sprintf ( output_aln_format, "clustalw");
- sprintf ( output_aln_modif, "lower");
-/*END OF INITIALIZATION*/
-
-
-
-
-/*PARAMETERS INPUT*/
-
- for ( a=1; a< argc; a++)
- {
- if (strcmp ( argv[a], "-f")==0)
- {
- sprintf (io_file,"%s", argv[++a]);
- }
- else if ( strcmp ( argv[a], "-sim_aln")==0)
- {
- sprintf (sim_aln,"%s", argv[++a]);
- }
- else if ( strcmp ( argv[a], "-sim_matrix")==0)
- {
- sprintf (sim_matrix,"%s", argv[++a]);
- }
- else if ( strm ( argv[a], "-compare_mode"))
- {
- sprintf ( compare_mode, "%s", argv[++a]);
- }
- else if ( strcmp ( argv[a], "-sim_cat")==0)
- {
- if ( argv[++a][0]!='[')
- {
- if ( strcmp ( argv[a], "3d_ali")==0)sprintf ( sim_category_list, "[b][b]+[h][h]=[struc]");
- else
- {
- fprintf ( stderr, "\n%s: Unknown category for distance measure", argv[a]);
- }
-
- }
- else
- {
- sprintf ( sim_category_list, "%s", argv[a]);
- }
- }
- else if ( strcmp ( argv[a], "-grep_value")==0)
- {
- sprintf ( grep_list[n_greps][0], "%s", argv[++a]);
- sprintf ( grep_list[n_greps][1], "%s", argv[++a]);
- n_greps++;
-
- }
- else if ( strcmp ( argv[a], "-al1")==0)
- {
-
- sprintf ( alignment1_file, "%s", argv[++a]);
-
- }
- else if ( strcmp ( argv[a], "-al2")==0)
- {
-
- sprintf ( alignment2_file, "%s", argv[++a]);
-
- }
- else if ( strcmp ( argv[a], "-pep1")==0)
- {
- pep_compare=1;
- sprintf ( pep1_file, "%s", argv[++a]);
- }
- else if ( strcmp ( argv[a], "-pep2")==0)
- {
- pep_compare=1;
- sprintf ( pep2_file, "%s", argv[++a]);
- }
- else if ( strcmp ( argv[a], "-pep")==0)
- {
- pep_compare=1;
- }
- else if ( strcmp ( argv[a], "-count")==0)
- {
- count=1;
- }
- else if ( strcmp ( argv[a], "-output_aln")==0)
- {
- output_aln=1;
- }
- else if ( strcmp ( argv[a], "-output_aln_threshold")==0)
- {
- output_aln_threshold=atoi(argv[++a]);
- }
- else if ( strcmp ( argv[a], "-output_aln_file")==0)
- {
- sprintf (output_aln_file,"%s",argv[++a]);
- }
- else if ( strcmp ( argv[a], "-output_aln_format")==0)
- {
- sprintf (output_aln_format,"%s",argv[++a]);
- }
- else if ( strcmp ( argv[a], "-output_aln_modif")==0)
- {
- sprintf (output_aln_modif,"%s",argv[++a]);
- }
- else if ( strcmp ( argv[a], "-st")==0)
- {
- sprintf ( struct_file [n_structure], "%s", argv[++a]);
- if (!NEXT_ARG_IS_FLAG && is_a_struc_format (argv[a+1]))
- sprintf ( struct_format[n_structure], "%s", argv[++a]);
- else
- sprintf ( struct_format[n_structure], "%s", "pep");
-
- if ( !NEXT_ARG_IS_FLAG && strcmp ( argv[a+1], "conv")==0)
- {
- a++;
- while(!NEXT_ARG_IS_FLAG)
- {
- sprintf ( symbol_list[n_structure][n_symbol[n_structure]], "%s", argv[++a]);
- n_symbol[n_structure]++;
- }
- }
- else if (!NEXT_ARG_IS_FLAG)
- {
- symbol_list[n_structure]=make_symbols ( argv[++a], &n_symbol[n_structure]);
- }
-
- else
- {
- symbol_list[n_structure]=make_symbols ( "any", &n_symbol[n_structure]);
- }
-
- n_structure++;
-
- }
- else if ( strcmp (argv[a], "-sep")==0)
- {
- if ( !NEXT_ARG_IS_FLAG)
- get_separating_char ( argv[++a][0], &sep_l, &sep_r);
- else
- sep_l=sep_r=' ';
- }
- else if ( strncmp ( argv[a], "-io_format",5)==0)
- {
- sprintf ( io_format, "%s", argv[++a]);
- }
- else if ( strcmp ( argv[a], "-io_cat")==0)
- {
- if ( argv[++a][0]!='[')
- {
- if ( strcmp ( argv[a], "3d_ali")==0)sprintf ( category_list, "[b][b]+[h][h]=[struc];[*][*]=[tot]");
- }
- else
- {
- sprintf ( category_list, "%s", argv[a]);
- }
- }
- else
- {
- fprintf ( stdout, "\nOPTION %s UNKNOWN[FATAL]\n", argv[a]);
- myexit (EXIT_FAILURE);
- }
- }
-
-/*PARAMETER PROCESSING*/
-
-if ( pep_compare==1 || count==1)aln_compare=0;
-if ( aln_compare==1)pep_compare=0;
-
-/*READ THE TOTAL SEQUENCES*/
- seq_list=declare_char ( 100,STRING);
- n_seq_file=0;
-
- if ( alignment1_file[0] && !check_file_exists ( alignment1_file))
- {
- fprintf (stderr, "\nERROR: %s DOES NOT EXIST[FATAL:%s]\n", alignment1_file, PROGRAM);
- myexit(EXIT_FAILURE);
- }
- if ( alignment2_file[0] && !check_file_exists ( alignment2_file))
- {
- fprintf (stderr, "\nERROR: %s DOES NOT EXIST[FATAL:%s]\n", alignment2_file, PROGRAM);
- myexit(EXIT_FAILURE);
- }
- if ( pep1_file[0] && !check_file_exists ( pep1_file))
- {
- fprintf (stderr, "\nERROR: %s DOES NOT EXIST[FATAL:%s]\n", pep1_file, PROGRAM);
- myexit(EXIT_FAILURE);
- }
- if ( pep2_file[0] && !check_file_exists ( pep2_file))
- {
- fprintf (stderr, "\nERROR: %s DOES NOT EXIST[FATAL:%s]\n", pep2_file, PROGRAM);
- myexit(EXIT_FAILURE);
- }
-
- if ( alignment1_file[0])sprintf ( seq_list[n_seq_file++], "A%s", alignment1_file);
- if ( alignment2_file[0])sprintf ( seq_list[n_seq_file++], "A%s", alignment2_file);
- if ( pep1_file[0])sprintf ( seq_list[n_seq_file++], "S%s", pep1_file);
- if ( pep2_file[0])sprintf ( seq_list[n_seq_file++], "S%s", pep2_file);
-
-
-
- TOT_SEQ=read_seq_in_n_list ( seq_list, n_seq_file, NULL, NULL);
-
- A=declare_aln (TOT_SEQ);
- B=declare_aln (TOT_SEQ);
-
-
-/*1 COMPARISON OF THE SEQUENCES*/
- if ( pep_compare==1 || count==1)
- {
- f=0;
-
- if ( pep1_file[0]!='\0')SA=main_read_seq (pep1_file);
- else if (alignment1_file[0]!='\0')
- {
- main_read_aln ( alignment1_file, A);
- SA=aln2seq ( A);
- }
- else
- {
- main_read_aln ("stdin", A);
- sprintf ( alignment1_file, "stdin");
- SA=aln2seq ( A);
- }
- if ( pep2_file[0]!='\0')SB=main_read_seq (pep2_file);
- else if (alignment2_file[0]!='\0')
- {
- main_read_aln ( alignment2_file, B);
-
- SB=aln2seq (B);
- }
- else
- {
- SB=SA;
- sprintf ( alignment2_file, "%s", alignment1_file );
- }
- buf1=(pep1_file[0]!='\0')?pep1_file: alignment1_file;
- buf2=(pep2_file[0]!='\0')?pep2_file: alignment2_file;
- /*Output of the Results*/
-
- fp=vfopen ( io_file, "w");
-
-
- if ( count==1)
- {
- fprintf (fp, "Number of seq: %d %d\n", SA->nseq,SA->nseq);
- for ( a=0; a< SA->nseq; a++) fprintf (fp, "%-15s %d %d\n", SA->name[a], (int)strlen (SA->seq[a]), (int)strlen (SA->seq[a]));
- }
-
- if (SA->nseq!=SB->nseq)
- {
-
- fprintf ( fp, "DIFFERENCE TYPE 1: Different number of sequences %3d/%3d",SA->nseq,SB->nseq);
- f=1;
- }
-
- trim_seq ( SA, SB);
- for ( a=0; a< SA->nseq; a++)
- {
- lower_string (SA->seq[a]);
- lower_string (SB->seq[a]);
- ungap ( SA->seq[a]);
- ungap ( SB->seq[a]);
-
- if ( strcmp ( SA->seq[a], SB->seq[a])!=0)
- {
- fprintf ( fp, "DIFFERENCE TYPE 2: %s is different in the 2 files\n", SA->name[a]);
- f=1;
- }
- }
- for ( a=0; a< SA->nseq; a++)
- {
- lower_string (SA->seq[a]);
- lower_string (SB->seq[a]);
- ungap ( SA->seq[a]);
- ungap ( SB->seq[a]);
-
- if ( strlen ( SA->seq[a])!= strlen (SB->seq[a]))
- {
- fprintf ( fp, "DIFFERENCE TYPE 3: %s has != length in the 2 files (%d-%d)\n", SA->name[a],(int)strlen ( SA->seq[a]), (int)strlen (SB->seq[a]));
- f=1;
- }
- }
- if ( f==1)
- {
- fprintf ( fp, "\nDIFFERENCES found between:\n\t%s\n\t%s\n**********\n\n",buf1, buf2);
- }
- fclose (fp);
- }
-
-/*2 COMPARISON OF THE ALIGNMENTS*/
- else if ( aln_compare==1)
- {
-
- n_categories=parse_category_list ( category_list, category, n_sub_categories);
- sim_n_categories=parse_category_list ( sim_category_list, sim_category, sim_n_sub_categories);
-
- main_read_aln ( alignment1_file, A);
- main_read_aln ( alignment2_file, B);
- CLS=trim_aln_seq ( A, B);
-
-
- defined_residueA=get_defined_residues (A);
- defined_residueB=get_defined_residues (B);
-
-
- A=thread_defined_residues_on_aln(A, defined_residueA);
- A=thread_defined_residues_on_aln(A, defined_residueB);
- B=thread_defined_residues_on_aln(B, defined_residueA);
- B=thread_defined_residues_on_aln(B, defined_residueB);
-
-
- CL_A=declare_constraint_list ( CLS, NULL, NULL, 0, NULL, NULL);
- CL_B=declare_constraint_list ( CLS, NULL, NULL, 0, NULL, NULL);
-
-
- CL_A=aln2constraint_list (A,CL_A, "sim");
- CL_B=aln2constraint_list (B,CL_B, "sim");
-
- clist_entry=vcalloc ( CL_A->entry_len, CL_A->el_size);
-
- glob=vcalloc ( A->nseq+1, sizeof (int));
- pw_glob=declare_int ( A->nseq+1, A->nseq+1);
-
-
- if ( strm( compare_mode, "sp"))
- {
- for ( b=0,a=0; a<CL_A->ne; a++)
- {
- s1=vread_clist(CL_A, a, SEQ1);
- s2=vread_clist(CL_A, a, SEQ2);
- clist_entry=extract_entry ( clist_entry, a, CL_A);
-
- glob[0]++;
- glob[s1+1]++;
- glob[s2+1]++;
- pw_glob[s1][s2]++;
- pw_glob[s2][s1]++;
-
- clist_entry=extract_entry ( clist_entry, a, CL_A);
-
- if ((main_search_in_list_constraint (clist_entry,&pos_in_clist,4,CL_B))!=NULL)
- {
- vwrite_clist ( CL_A, a, MISC, 1);
- b++;
- }
- else
- {
- vwrite_clist ( CL_A, a, MISC, 0);
- }
- }
- }
- else if ( strm( compare_mode, "column"))
- {
- posA=aln2pos_simple_2(A);
- posB=aln2pos_simple_2(B);
- seq_cache=declare_int ( A->nseq, A->len_aln+1);
- for ( n=0,a=0; a< A->len_aln; a++)
- for ( b=0; b<B->len_aln; b++)
- {
- is_same=compare_pos_column(posA, a, posB, b, A->nseq);
-
- n+=is_same;
- if (is_same)
- {
- for (c=0; c< A->nseq;c++)if ( posA[c][a]>0)seq_cache[c][posA[c][a]]=1;
- }
- }
-
- for ( a=0,b=0; a< CL_A->ne; a++)
- {
- s1=vread_clist(CL_A, a, SEQ1);
- s2=vread_clist(CL_A, a, SEQ2);
- glob[0]++;
- glob[s1+1]++;
- glob[s2+1]++;
- pw_glob[s1][s2]++;
- pw_glob[s2][s1]++;
- r1=vread_clist(CL_A, a, R1);
- if (seq_cache[s1][r1]){b++;vwrite_clist ( CL_A, a, MISC, 1);}
- }
- free_int (posA, -1);
- free_int (posB, -1);
- free_int (seq_cache, -1);
-
- }
-
- for ( a=0; a< n_structure; a++)
- {
- ST=read_structure (struct_file[a],struct_format[a], A,B,ST,n_symbol[a], symbol_list[a]);
- }
-
- /*RESULT ARRAY DECLARATION*/
-
- tot_count=declare_int (n_categories+1, A->nseq+1);
- pos_count=declare_int (n_categories+1, A->nseq+1);
- pw_tot_count=vcalloc ( A->nseq, sizeof (int**));
- for ( a=0; a< A->nseq; a++)pw_tot_count[a]=declare_int ( A->nseq, n_categories);
-
-
- pw_pos_count=vcalloc ( A->nseq, sizeof (int**));
- for ( a=0; a< A->nseq; a++)pw_pos_count[a]=declare_int ( A->nseq, n_categories);
-
- /*COMPARISON MODULE*/
- for ( a=0; a< n_categories; a++)
- {
- for (b=0; b<CL_A->ne; b++)
- {
- s1=vread_clist(CL_A, b, SEQ1);
- s2=vread_clist(CL_A, b, SEQ2);
-
- r1=vread_clist(CL_A, b, R1);
- r2=vread_clist(CL_A, b, R2);
-
- c=vread_clist(CL_A, b, MISC);
-
- if ( is_in_struct_category ( s1, s2, r1, r2, ST, category[a], n_sub_categories[a]))
- {
-
- tot_count[a][0]++;
- tot_count[a][s1+1]++;
- tot_count[a][s2+1]++;
- pw_tot_count[s1][s2][a]++;
- pw_tot_count[s2][s1][a]++;
- if ( c==1)
- {
- pw_pos_count[s1][s2][a]++;
- pw_pos_count[s2][s1][a]++;
- pos_count[a][0]++;
- pos_count[a][s1+1]++;
- pos_count[a][s2+1]++;
- }
- }
-
- }
- }
-
-
-
-
-
- /*Measure of Aligned Sequences Similarity*/
-
- sim=get_aln_compare_sim ((strcmp (sim_aln, "al1")==0)?A:B, ST,sim_category[0], sim_n_sub_categories[0], sim_matrix);
- sim_param=analyse_sim ((strcmp (sim_aln, "al1")==0)?A:B, sim);
-
-
- /*Fill the Result_structure*/
- R=vcalloc ( 1, sizeof (Result));
-
- R->grep_list=grep_list;
- R->n_greps=n_greps;
- R->A=A;
- R->B=B;
-
- R->S=S;
- R->ST=ST;
- R->sim_aln=sim_aln;
- R->alignment1_file=alignment1_file;
- R->alignment2_file=alignment2_file;
- R->io_format=io_format;
- R->n_structure=n_structure;
- R->struct_file=struct_file;
- R->struct_format=struct_format;
- R->n_symbol=n_symbol;
- R->symbol_list=symbol_list;
-
-
- R->tot_count=tot_count;
- R->pos_count=pos_count;
- R->pw_tot_count=pw_tot_count;
- R->pw_pos_count=pw_pos_count;
- R->glob=glob;
- R->pw_glob=pw_glob;
- R->n_categories=n_categories;
- R->category=category;
- R->category_list=category_list;
- R->n_sub_categories=n_sub_categories;
- R->sim=sim;
- R->sim_param=sim_param;
- R->sim_matrix=sim_matrix;
- R->sim_n_categories=sim_n_categories;
- R->sim_category=sim_category;
- R->sim_category_list=sim_category_list;
- R->sim_n_sub_categories=sim_n_sub_categories;
- R->sep_r=sep_r;
- R->sep_l=sep_l;
-
- /*Output of the Results*/
-
- fp=vfopen ( io_file, "w");
- fp=output_format (io_format, fp, R);
- vfclose ( fp);
-
-
- /*Rewriting of Alignment A*/
- if ( output_aln)
- {
- A->residue_case=2;
- aln_output_tot =declare_int ( A->nseq, A->len_aln+1);
- aln_output_count=declare_int ( A->nseq, A->len_aln+1);
-
- for ( a=0; a< CL_A->ne; a++)
- {
- clist_entry=extract_entry ( clist_entry, a, CL_A);
- aln_output_tot[clist_entry[SEQ1]][clist_entry[R1]]++;
- aln_output_tot[clist_entry[SEQ2]][clist_entry[R2]]++;
-
- aln_output_count[clist_entry[SEQ1]][clist_entry[R1]]+=clist_entry[MISC];
- aln_output_count[clist_entry[SEQ2]][clist_entry[R2]]+=clist_entry[MISC];
- }
- for ( a=0; a< A->nseq; a++)
- {
-
- for (c=0, b=0; b< A->len_aln; b++)
- {
- if ( !is_gap(A->seq_al[a][b]))
- {
- c++;
- if ( aln_output_tot[a][c] && ((aln_output_count[a][c]*100)/aln_output_tot[a][c])<output_aln_threshold)
- {
- if ( strm (output_aln_modif, "lower"))
- A->seq_al[a][b]=tolower(A->seq_al[a][b]);
- else
- A->seq_al[a][b]=output_aln_modif[0];
- }
- else A->seq_al[a][b]=toupper(A->seq_al[a][b]);
- }
-
- }
- }
- A->score_aln=(int)(R->tot_count[0][0]==0)?0:((R->pos_count[0][0]*100)/(float)R->tot_count[0][0]);
-
- output_format_aln (output_aln_format,A,NULL,output_aln_file);
-
- free_int ( aln_output_tot, -1);
- free_int ( aln_output_count, -1 );
- }
- }
- return EXIT_SUCCESS;
- }
-/************************************************************************************/
-/* */
-/* OUTPUT */
-/* */
-/* */
-/************************************************************************************/
-FILE *output_format (char *iof,FILE *fp, Result *R)
- {
- int a;
- int l;
-
- /*
- H: files Header
- h: basic header;
- s: sequence results
- t: total results (global);
- p: pairwise_results;
- */
- l=strlen ( iof);
-
- for ( a=0; a< l; a++)
- {
- if ( iof[a]=='H')fp=output_large_header (fp,R);
- else if ( iof[a]=='h')fp=output_header (fp,R);
- else if ( iof[a]=='t')fp=output_total_results (fp, R);
- else if ( iof[a]=='s')fp=output_sequence_results (fp,R);
- else if ( iof[a]=='p')fp=output_pair_wise_sequence_results(fp,R);
- }
- return fp;
- }
-
-FILE *output_pair_wise_sequence_results (FILE *fp, Result *R)
- {
- int a,c,d;
-
-
- for ( c=0; c<(R->A)->nseq-1; c++)
- {
- for ( d=c+1; d< (R->A)->nseq; d++)
- {
- fprintf (fp, "%-10s %-10s%s",(R->A)->name[c],(R->A)->name[d],SSPACE);
- fprintf (fp, "%5.1f%s", R->sim[c][d], SSPACE);
-
- for (a=0; a< R->n_categories; a++)
- {
- fprintf ( fp, "%5.1f ",(R->pw_tot_count[c][d][a]==0)?0:((float)(R->pw_pos_count[c][d][a]*100)/(float)R->pw_tot_count[c][d][a]));
- fprintf ( fp, "%c%5.1f%c%s",(R->sep_l),(R->pw_glob[c][d]==0)?0:((float)(R->pw_tot_count[c][d][a]*100)/(float)R->pw_glob[c][d]),(R->sep_r),SSPACE);
- }
- fprintf ( fp, "%c%5d%c\n",(R->sep_l), R->pw_glob[c][d],(R->sep_r));
- }
- }
-
- return fp;
- }
-FILE *output_sequence_results (FILE *fp, Result *R)
- {
- int a,c;
-
- for ( c=1; c<=R->A->nseq; c++)
- {
- fprintf (fp, "%-10s %-10s%s",(R->A)->name[c-1], "..",SSPACE);
- fprintf (fp, "%5.1f%s", R->sim_param[c-1][0],SSPACE);
- for (a=0; a< R->n_categories; a++)
- {
- fprintf ( fp, "%5.1f ",(R->tot_count[a][c]==0)?0:((float)(R->pos_count[a][c]*100)/(float)R->tot_count[a][c]));
- fprintf ( fp, "%c%5.1f%c%s",(R->sep_l),(R->glob[c]==0)?0:((float)(R->tot_count[a][c]*100)/(float)R->glob[c]),(R->sep_r), SSPACE);
- }
- fprintf ( fp, "%c%5d%c\n",(R->sep_l), R->glob[c],(R->sep_r));
- }
- return fp;
- }
-
-
-FILE *output_total_results (FILE *fp, Result *R)
- {
- int a;
-
-
- fprintf ( fp, "%-13s %-7d%s",extract_suffixe (R->alignment1_file),(R->A)->nseq, SSPACE);
- fprintf (fp, "%5.1f%s", R->sim_param[(R->A)->nseq][0], SSPACE);
- for (a=0; a< R->n_categories; a++)
- {
- fprintf ( fp, "%5.1f ",(R->tot_count[a][0]==0)?0:((float)(R->pos_count[a][0]*100)/(float)R->tot_count[a][0]));
- fprintf ( fp, "%c%5.1f%c%s",(R->sep_l),(R->glob[0]==0)?0:((float)(R->tot_count[a][0]*100)/(float)R->glob[0]),(R->sep_r), SSPACE);
- }
- fprintf ( fp, "%c%5d%c\n",(R->sep_l), R->glob[0],(R->sep_r));
- return fp;
- }
-FILE *output_header (FILE *fp, Result *R)
- {
- int a;
-
-
- fprintf ( fp, "%s\n",generate_string ( R->n_categories*(13+strlen(SSPACE))+31+2*strlen(SSPACE),'*'));
-
- fprintf ( fp, "%-10s %-10s %s%-3s%s", "seq1", "seq2",SSPACE,"Sim",SSPACE);
-
- for ( a=0; a< R->n_categories; a++)
- fprintf ( fp, "%-12s%s ",R->category[a][0], SSPACE);
- fprintf (fp, "%-5s", "Tot");
- fprintf (fp, "\n");
- return fp;
- }
-FILE *output_large_header ( FILE *fp, Result *R)
- {
- int a, b;
-
- fprintf ( fp, "AL1: %s\n", R->alignment1_file);
- fprintf ( fp, "AL2: %s\n", R->alignment2_file);
- for ( a=0; a< R->n_structure; a++)
- {
- fprintf (fp, "ST %d: %s [%s]/[", a, R->struct_file[a], R->struct_format[a]);
- for ( b=0; b< R->n_symbol[a]; b++)fprintf (fp, "%s ", R->symbol_list[a][b]);
- fprintf ( fp, "]\n");
- }
- return (fp);
- }
-
-void get_separating_char ( char s, char *l, char *r)
- {
- if ( s=='{' || s=='}')
- {
- l[0]='{';
- r[0]='}';
- return;
- }
- else if ( s==']' || s=='[')
- {
- l[0]='[';
- r[0]=']';
- return;
- }
- else if ( s==')' || s=='(')
- {
- l[0]='(';
- r[0]=')';
- return;
- }
- else
- {
- l[0]=s;
- r[0]=s;
- return;
- }
- }
-
-/************************************************************************************/
-/* */
-/* SIM MEASURE */
-/* */
-/* */
-/************************************************************************************/
-float **get_aln_compare_sim ( Alignment *A, Structure *ST, char **cat, int n_cat, char *matrix)
- {
- int a, b, c;
-
- float **sim;
- char cr1, cr2;
- int r1, r2;
- int p1, p2;
- float pos,tot;
-
- sim=declare_float ( A->nseq, A->nseq);
-
- for ( a=0; a<A->nseq-1; a++)
- {
- for (b=a+1; b< A->nseq; b++)
- {
- for ( r1=0, r2=0,tot=0, pos=0,c=0; c< A->len_aln; c++)
- {
- p1=is_gap(A->seq_al[a][c]);
- p2=is_gap(A->seq_al[b][c]);
-
- r1+=1-p1;
- r2+=1-p2;
- cr1=A->seq_al[a][c];
- cr2=A->seq_al[b][c];
- if (!p1 && !p2)
- {
- if (is_in_struct_category (a, b, r1, r2, ST, cat, n_cat))
- {
- tot++;
- pos+=is_in_same_group_aa ( cr1, cr2, 0, NULL, matrix);
- }
- }
- }
- sim[a][b]=sim[b][a]=(tot==0)?0:((pos*100)/tot);
- }
- }
- return sim;
- }
-float **analyse_sim ( Alignment *A, float **sim)
- {
- int a,b,c;
-
- float **an, d;
-
-
- an=declare_float ( A->nseq+1,2);
-
- for (d=0, a=0; a< A->nseq;a++)
- {
- for ( b=0; b< A->nseq; b++)
- {
- if ( b!=a)
- {
- an[a][0]+=sim[a][b];
- an[A->nseq][0]+=sim[a][b];
- d++;
- }
- }
- an[a][0]=((float)an[a][0]/(float)(A->nseq-1));
- }
-
-
- an[A->nseq][0]=an[A->nseq][0]/d;
-
- for ( d=0,a=0; a< A->nseq; a++)
- {
- for ( b=0; b< A->nseq; b++)
- {
- if ( b!=a)
- {
- c=an[a][0]-sim[a][b];
- an[a][1]+=(c>0)?c:-c;
- an[A->nseq][1]+=(c>0)?c:-c;
- d++;
- }
- }
- an[a][1]=((float)an[a][1]/(float)(A->nseq-1));
- }
-
- an[A->nseq][1]=an[A->nseq][1]/d;
-
- return an;
- }
-
-
-
-
-
-
-
-
-/************************************************************************************/
-/* */
-/* STRUC ANALYSE */
-/* */
-/* */
-/************************************************************************************/
-int is_in_struct_category ( int s1, int s2, int r1, int r2, Structure *ST, char **cat, int n_cat)
- {
- int a;
- static char *struc_r1;
- static char *struc_r2;
- char first[STRING];
- char second[STRING];
- static int **r;
-
-
-
-
- if ( ST==NULL)return 1;
- if ( struc_r1!=NULL)
- {
- vfree ( struc_r1);
- vfree ( struc_r2);
- }
-
- if ( r==NULL)r=declare_int (2, 2);
- else r[0][0]=r[1][1]=r[1][0]=r[0][1]=0;
-
-
- struc_r1=get_structure_residue ( s1, r1, ST);
- struc_r2=get_structure_residue ( s2, r2, ST);
-
-
- for ( a=1; a< n_cat; a+=2)
- {
- sprintf ( first, "%s", cat[a]);
- sprintf ( second,"%s", cat[a+1]);
- r[0][0]=struc_matches_pattern ( struc_r1, first);
- r[0][1]=struc_matches_pattern ( struc_r2, first);
- r[1][0]=struc_matches_pattern ( struc_r1, second);
- r[1][1]=struc_matches_pattern ( struc_r2, second);
-
- if ( (r[0][0]&&r[1][1])||(r[1][0]&&r[0][1]))return 1;
- }
- return 0;
- }
-
-char * get_structure_residue (int seq, int res, Structure *ST)
- {
- int a;
- char *s;
-
- s=vcalloc ( ST->n_fields+1, sizeof (char));
- for (a=0; a< ST->n_fields; a++)
- s[a]=ST->struc[seq][res][a];
- s[a]='\0';
- return s;
- }
-
-int struc_matches_pattern ( char *struc, char *pattern)
- {
- char p[STRING];
- char *y;
-
- int b,l;
-
-
- sprintf ( p, "%s", pattern);
-
- if ( strcmp (p, "*")==0)return 1;
- else
- {
- l=strlen ( struc);
- y=strtok ( p, ".");
-
- for ( b=0; b<l; b++)
- {
-
- if ( strcmp ( y, "*")==0);
- else if ( strchr(y, struc[b])==NULL)return 0;
- y=strtok ( NULL, ".");
-
- if ( y==NULL && b<(l-1))
- {
- crash ( "\nA Structure is Missing[FATAL]");
- }
- }
- }
-
- return 1;
- }
-
-
-Structure * read_structure (char *fname, char *format, Alignment *A,Alignment *B, Structure *ST, int n_symbols, char **symbol_table)
- {
-
- Alignment *StrucAln;
- Sequence *SEQ=NULL, *SA=NULL;
-
-
-
-
- if (ST==NULL)ST=declare_structure (A->nseq, A->seq_al);
- else
- ST=extend_structure ( ST);
-
- StrucAln=declare_Alignment(NULL);
- if (strm ( format, "pep"))
- {
- SEQ=main_read_seq ( fname);
- StrucAln=seq2aln(SEQ,StrucAln,0);
- }
-
- else if ( strcmp ( format, "aln")==0)
- {
- StrucAln=main_read_aln (fname, StrucAln);
- }
-
- reorder_aln(StrucAln, A->name, A->nseq);
-
- SA=aln2seq(StrucAln);
- string_array_convert (SA->seq, SA->nseq, n_symbols, symbol_table);
- seq2struc (SA, ST);
-
- free_aln(StrucAln);
- if (SEQ)free_sequence (SEQ, SEQ->nseq);
-
- return ST;
- }
-
-int parse_category_list ( char *category_list_in, char ***category, int*n_sub_categories)
- {
- int n,a;
- char *category_list;
- char *y,*z;
- category_list=vcalloc ( strlen(category_list_in)+1, sizeof (char));
- sprintf (category_list, "%s", category_list_in);
-
- n=0;
- z=category_list;
- while ((y=strtok(z, ";"))!=NULL)
- {
- sprintf ( category[n++][2], "%s", y);
- z=NULL;
- }
-
-
- for ( a=0; a< n; a++)
- {
- sprintf (category_list,"%s",strtok(category[a][2], "="));
- sprintf (category[a][0],"%s",strtok (NULL, "="));
- sprintf ( category[a][++n_sub_categories[a]],"%s", strtok(category_list, "[]+"));
- while ( ((y=strtok(NULL, "[]+"))!=NULL))
- {
- if ( strcmp (y, "#")==0)y=category[a][n_sub_categories[a]];
- sprintf ( category[a][++n_sub_categories[a]],"%s",y);
- }
- }
- return n;
- }
-
-
-int is_a_struc_format (char *format)
- {
- if ( strcmp ( format, "pep")==0)return 1;
- if ( strcmp ( format, "aln")==0)return 1;
- return 0;
- }
-/************************************************************************************/
-/* */
-/* Informations */
-/* */
-/* */
-/************************************************************************************/
-void output_informations ()
-{
-fprintf ( stderr, "\nPROGRAM: %s (%s)\n",PROGRAM,VERSION);
-fprintf ( stderr, "******INPUT***************************");
-fprintf ( stderr, "\n-al1 al1_file");
-fprintf ( stderr, "\n-al2 al2_file");
-fprintf ( stderr, "\n-compare_mode [sp] or column");
-fprintf ( stderr, "\n-pep (compare only the sequences");
-fprintf ( stderr, "\n-count");
-fprintf ( stderr, "\n-pep1 pep1_file");
-fprintf ( stderr, "\n-pep1 pep2_file");
-fprintf ( stderr, "\n-st str_file st_format conversion");
-fprintf ( stderr, "\n **st_format: aln, pep");
-fprintf ( stderr, "\n **conversion: 3d_ali, conv abcZ #X");
-fprintf ( stderr, "\nNOTE: Several structures in a row are possible");
-
-fprintf ( stderr, "\n\n****DISTANCE MEASURE*****************");
-fprintf ( stderr, "\n-sim_cat category_format or category_name");
-fprintf ( stderr, "\n **category_format: [*][*]=[tot]");
-fprintf ( stderr, "\n **category_name : 3d_ali (<=>[h][h]+[e][e]=[Struc]");
-fprintf ( stderr, "\n-sim_matrix matrix_name");
-fprintf ( stderr, "\n **matrix_name: idmat,pam250mt..");
-fprintf ( stderr, "\n-sim_aln al1 or al2");
-fprintf ( stderr, "\n\n****COMPARISON***********************");
-fprintf ( stderr, "\n-io_cat category_format or category_name");
-fprintf ( stderr, "\n **category_format: [*][*]=[tot]");
-fprintf ( stderr, "\n **category_name : 3d_ali(<=>[h][h]+[e][e]=[Struc];[*][*]=[Tot]");
-fprintf ( stderr, "\n\nNOTE: if two structures:");
-fprintf ( stderr, "\n[he.123][#]=[he123VShe123];[beh.*][he.2345]=[other]");
-fprintf ( stderr, "\n\n****OUTPUT****************************");
-fprintf ( stderr, "\n-f stdout");
-fprintf ( stderr, "\n stderr");
-fprintf ( stderr, "\n file_name");
-fprintf ( stderr, "\n-io_format hts");
-fprintf ( stderr, "\n H ->large Header");
-fprintf ( stderr, "\n h ->small Header");
-fprintf ( stderr, "\n t->global (average)results");
-fprintf ( stderr, "\n s ->average results for each sequence");
-fprintf ( stderr, "\n p ->results for each pair of sequences");
-fprintf ( stderr, "\n-output_aln Outputs al1 with conserved bits in Upper");
-fprintf ( stderr, "\n-output_aln_threshold [100]");
-fprintf ( stderr, "\n-output_aln_file [stdout]");
-fprintf ( stderr, "\n-output_aln_format [clustalw]");
-fprintf ( stderr, "\n-output_aln_modif [lower]");
-fprintf ( stderr, "\n");
-myexit (EXIT_SUCCESS);
-}
-
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Jul 1 10:00:54 WEST 2008. */
-/*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**********************************/
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*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**********************************/
git://source.jalview.org / jabaws.git / blobdiff