+++ /dev/null
-#include <stdlib.h>
-
-#include <stdio.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-#include <ctype.h>
-#include <sched.h>
-
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-#include "dp_lib_header.h"
-static int entry_len;
-int compare_constraint_list_entry ( const void*vx, const void*vy);
-int compare_constraint_list_entry4bsearch ( const void*vx, const void*vy);
-/*********************************************************************/
-/* */
-/* PRODUCE IN LIST */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list * make_test_lib(Constraint_list *CL);
-Constraint_list *fork_line_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode,Job_TC *job, FILE *loca_stderr);
-Constraint_list *fork_cell_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode,Job_TC *job, FILE *local_stderr);
-Constraint_list *nfork_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode,Job_TC *job, FILE *local_stderr);
-Constraint_list *fork_subset_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode, Job_TC *job, FILE *local_stderr);
-int job2first_seq(Job_TC *job);
-Constraint_list *produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode)
-{
- Job_TC *job=NULL;
- FILE *local_stderr;
- int njob;
-
- store_seq_type (S->type);
- if ( CL==NULL)CL=declare_constraint_list ( S,NULL, NULL, 0,(strm(mem_mode, "disk"))?vtmpfile():NULL, NULL);
- local_stderr=(CL->local_stderr!=NULL)?CL->local_stderr:stderr;
-
- CL->local_stderr=vfopen("/dev/null", "w");
- job=queue2heap(method2job_list ( method,S,weight, CL->lib_list,CL->DM, CL));
- njob=queue2n(job)+1;
-
- if ( get_nproc()==1 || njob==1)return nfork_produce_list (CL, S, method, weight, mem_mode,job, local_stderr);
- else if (strstr ( CL->multi_thread, "jobcells"))return fork_cell_produce_list (CL, S, method, weight, mem_mode,job,local_stderr);
- else if (strstr ( CL->multi_thread, "joblines"))return fork_line_produce_list (CL, S, method, weight, mem_mode,job, local_stderr);
- else if (strstr ( CL->multi_thread, "jobs"))return fork_subset_produce_list (CL, S, method, weight, mem_mode,job, local_stderr); //Recommended default
- else return nfork_produce_list (CL, S, method, weight, mem_mode,job, local_stderr);
-}
-int job2first_seq(Job_TC *job)
-{
- int *seqlist;
- int r;
-
- if (!job) return -1;
- else if ( !job->param)return -1;
- else if ( !(job->param)->seq_c) return -1;
- seqlist=string2num_list ((job->param)->seq_c);
- if (seqlist[0]<2)r=-1;
- else r=seqlist[2];
- vfree (seqlist);
- return r;
-}
-
-Constraint_list *fork_subset_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode, Job_TC *job, FILE *local_stderr)
-{
- //forks lines of the matrix
- int a,b;
- Job_TC *heap,*end,*start, ***jl;
- TC_method *M;
- int n_elements_in, n_new_elements;
- char **pid_tmpfile;
- int *pid_list;
- int pid,npid, njob;
- int nproc, max_nproc, submited;
- int cseq, seq, nlines;
- int n_aln;
-
- max_nproc=nproc=get_nproc();
- max_nproc*=2;
- /*OUT_MODE:
- A-> alignment provided in a file
- L-> list provided in a file
- aln-> alignment computed and provided in a file
- list->list computed and provided in a file
- */
-
-
-
-
- if ( job->jobid==-1)
- {
- M=(job->param)->TCM;
- fprintf (local_stderr, "\n\tMethod %s: No Suitable Sequences [Type: %s]\n", method,M->seq_type);
- return CL;
- }
-
- job=queue2heap (job_list2multi_thread_job_list (job, CL->multi_thread, CL));
- heap=job;
- njob=queue2n (job);
- n_elements_in=CL->ne;
- M=(job->param)->TCM;
- if (M)M->PW_CL=method2pw_cl ( M, CL);
- pid_tmpfile=vcalloc (MAX(njob,get_nproc())+1, sizeof (char*));
- pid_list =vcalloc (MAX_N_PID, sizeof (int *));
-
- fprintf ( local_stderr, "\n\tMulti Core Mode: %d processors [subset]\n", get_nproc());
-
- jl=split_job_list(job,get_nproc());
- a=npid=0;
-
- a=npid=0;
- while (jl[a])
- {
-
- start=job=jl[a][0];
- end=jl[a][1];
- pid_tmpfile[a]=vtmpnam(NULL);
- pid=vfork();
-
- if (pid==0)//child process
- {
- FILE *fp;
- int done, todo, t;
-
- initiate_vtmpnam(NULL);
- fp=vfopen (pid_tmpfile[a],"a");
- todo=0;
- while (job!=end){todo++;job=job->c;}
- job=start;
-
- done=0;
- while (job!=end)
- {
- if (a==0)output_completion ( local_stderr,done,todo,1, "Submit Job");
- job=print_lib_job (job, "io->CL=%p control->submitF=%p control->retrieveF=%p control->mode=%s",duplicate_constraint_list4lib_computation (CL),submit_lib_job, retrieve_lib_job, CL->multi_thread );
- job=submit_job (job);
- retrieve_job (job);
- t=((job->io)->CL)->ne*((job->io)->CL)->entry_len;
- for (b=0; b<t; b++)fprintf ( fp, "%d ", ((job->io)->CL)->L[b]);
- job=job->c;
- done++;
- }
- vfclose (fp);
- exit (EXIT_SUCCESS);
- }
- else
- {
- pid_list[pid]=npid;
- set_pid(pid);
- npid++;
- a++;
- }
- }
-
- //wait for all processes to finish
- for (a=0; a<npid; a++)
- {
- pid=vwait(NULL);
- CL=read_constraint_list_raw_file (CL,pid_tmpfile[pid_list[pid]]);
- remove(pid_tmpfile[pid_list[pid]]);
- }
-
- vfree (pid_list);
- vfree (pid_tmpfile);
-
- job=heap;
- while (job) job=delete_job (job);
- n_new_elements=CL->ne - n_elements_in;
- compact_list (CL, n_elements_in,n_new_elements, "best");
- compact_list (CL, 0, CL->ne, "default");
- CL->local_stderr=local_stderr;
- free_queue (heap);
- return CL;
-}
-
-
-Constraint_list *fork_line_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode, Job_TC *job, FILE *local_stderr)
-{
- //forks lines of the matrix
- int a,b;
- Job_TC *heap;
- TC_method *M;
- int n_elements_in, n_new_elements;
- char **pid_tmpfile;
- int *pid_list;
- int pid,npid, njob;
- int nproc, max_nproc, submited;
- int cseq, seq, nlines;
-
- max_nproc=nproc=get_nproc();
- max_nproc*=2;
- /*OUT_MODE:
- A-> alignment provided in a file
- L-> list provided in a file
- aln-> alignment computed and provided in a file
- list->list computed and provided in a file
- */
-
-
-
-
- if ( job->jobid==-1)
- {
- M=(job->param)->TCM;
- fprintf (local_stderr, "\n\tMethod %s: No Suitable Sequences [Type: %s]\n", method,M->seq_type);
- return CL;
- }
-
-
- job=queue2heap (job_list2multi_thread_job_list (job, CL->multi_thread, CL));
-
- heap=job;
- M=(job->param)->TCM;
- if (M)M->PW_CL=method2pw_cl ( M, CL);
- n_elements_in=CL->ne;
-
- /* Cf. parse method for possible out_mode flags*/
-
- njob=queue2n(job)+1;
- pid_tmpfile=vcalloc (njob, sizeof (char*));
-
- pid_list =vcalloc (MAX_N_PID, sizeof (int *));
- fprintf ( local_stderr, "\n\tMulti Core Mode: %d processors [jobline]\n", get_nproc());
-
-
- //count the number of lines
- cseq=-1;
- nlines=0;
- while (job)
- {
- nlines++;
- seq=job2first_seq(job);
- if ( seq!=cseq)
- {
- cseq=seq;
- while (job && cseq==job2first_seq(job))job=job->c;
- }
- }
- job=heap;
-
- npid=submited=0;
- cseq=-1;
- while (job)
- {
- seq=job2first_seq(job);
- if ( seq!=cseq)
- {
- cseq=seq;
- pid_tmpfile[npid]=vtmpnam(NULL);
-
- pid=vfork();
-
- if (pid==0)//Child Process
- {
- initiate_vtmpnam(NULL);
- while (job && cseq==job2first_seq(job))
- {
- job=print_lib_job (job, "io->CL=%p control->submitF=%p control->retrieveF=%p control->mode=%s",duplicate_constraint_list4lib_computation (CL),submit_lib_job, retrieve_lib_job, CL->multi_thread );
- job=submit_job (job);
- retrieve_job (job);
- constraint_list2raw_file ((job->io)->CL,pid_tmpfile[npid], "a");
- job=job->c;
- }
- exit (EXIT_SUCCESS);
- }
- else //parent process
- {
-
- pid_list[pid]=npid;
- set_pid (pid);
- npid++;
- submited++;
- if (submited>max_nproc)
- {
- //wait for nproc
- for (a=0; a<nproc; a++)
- {
- int index;
- local_stderr=output_completion ( local_stderr,npid,nlines,1, "Processed Job");
- pid=vwait(NULL);
- index=pid_list[pid];
- CL=read_constraint_list_raw_file (CL,pid_tmpfile[index]);
- remove (pid_tmpfile[index]);
- submited--;
- }
- }
- }
- }
- else
- {
- job=job->c;
- }
- }
-
- for (a=0; a<submited; a++)
- {
- int index;
- local_stderr=output_completion ( local_stderr,npid-(submited-a),nlines,1, "Processed Job");
- pid=vwait(NULL);
- index=pid_list[pid];
- CL=read_constraint_list_raw_file (CL,pid_tmpfile[index]);
- remove (pid_tmpfile[index]);
- }
-
- vfree (pid_list);
- vfree (pid_tmpfile);
-
- n_new_elements=CL->ne - n_elements_in;
- compact_list (CL, n_elements_in,n_new_elements, "best");
- compact_list (CL, 0, CL->ne, "default");
- CL->local_stderr=local_stderr;
-
- free_queue (heap);
-
- return CL;
-}
-
-Constraint_list *fork_cell_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode, Job_TC *job, FILE *local_stderr)
- {
- //forks cells of the matrix
- int a,b, n;
- Job_TC *heap;
- TC_method *M;
- int n_elements_in, n_new_elements;
- int *pid_list;
- char **pid_tmpfile;
- int pid,npid, njob;
- int nproc, max_nproc;
- int submited;
-
- max_nproc=nproc=get_nproc();
-
- /*OUT_MODE:
- A-> alignment provided in a file
- L-> list provided in a file
- aln-> alignment computed and provided in a file
- list->list computed and provided in a file
- */
-
-
- if ( job->jobid==-1)
- {
- M=(job->param)->TCM;
- fprintf (local_stderr, "\n\tMethod %s: No Suitable Sequences [Type: %s]\n", method,M->seq_type);
- return CL;
- }
-
-
- job=queue2heap (job_list2multi_thread_job_list (job, CL->multi_thread, CL));
-
- heap=job;
- M=(job->param)->TCM;
- if (M)M->PW_CL=method2pw_cl ( M, CL);
- n_elements_in=CL->ne;
-
- /* Cf. parse method for possible out_mode flags*/
-
- njob=queue2n(job)+1;
- pid_tmpfile=vcalloc (njob, sizeof (char*));
- pid_list =vcalloc (MAX_N_PID, sizeof (int *));
-
- fprintf ( local_stderr, "\n\tMulti Core Mode: %d processors:\n", get_nproc());
- npid=0;
- submited=0;
- while (job)
- {
- job=print_lib_job (job, "io->CL=%p control->submitF=%p control->retrieveF=%p control->mode=%s",duplicate_constraint_list4lib_computation (CL),submit_lib_job, retrieve_lib_job, CL->multi_thread );
- pid_tmpfile[npid]=vtmpnam(NULL);
- pid=vfork ();
- if ( pid==0)
- {
- initiate_vtmpnam (NULL);
- job=submit_job (job);
- retrieve_job (job);
- constraint_list2raw_file ((job->io)->CL,pid_tmpfile[npid], "w");
- exit (EXIT_SUCCESS);
- }
- else
- {
- job=job->c;
- pid_list[pid]=npid;
- set_pid(pid);
- npid++;
- submited++;
-
- if (submited>max_nproc)
- {
- for (a=0; a<nproc; a++)
- {
- int index;
- local_stderr=output_completion ( local_stderr,npid,njob,1, "Processed Job");
- pid=vwait(NULL);
- index=pid_list[pid];
- CL=read_constraint_list_raw_file (CL,pid_tmpfile[index]);
- remove (pid_tmpfile[index]);
- submited--;
- }
- }
- }
- }
-
- for (a=0; a<submited; a++)
- {
- int index;
- local_stderr=output_completion ( local_stderr,npid-a, npid,1, "Processed Job");
- pid=vwait(NULL);
- index=pid_list[pid];
- CL=read_constraint_list_raw_file (CL,pid_tmpfile[index]);
- remove (pid_tmpfile[index]);
- }
- vfree (pid_list);
- vfree (pid_tmpfile);
-
- n_new_elements=CL->ne - n_elements_in;
- compact_list (CL, n_elements_in,n_new_elements, "best");
- compact_list (CL, 0, CL->ne, "default");
- CL->local_stderr=local_stderr;
-
- free_queue (heap);
-
- return CL;
- }
-Constraint_list *nfork_produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode, Job_TC *job, FILE *local_stderr)
- {
- int b;
- int n_aln;
- Job_TC *heap;
- TC_method *M;
- int n_elements_in, n_new_elements;
-
-
- /*OUT_MODE:
- A-> alignment provided in a file
- L-> list provided in a file
- aln-> alignment computed and provided in a file
- list->list computed and provided in a file
- */
-
-
- if ( job->jobid==-1)
- {
- M=(job->param)->TCM;
- fprintf (local_stderr, "\n\tMethod %s: No Suitable Sequences [Type: %s]\n", method,M->seq_type);
- return CL;
- }
-
-
- job=queue2heap (job_list2multi_thread_job_list (job, CL->multi_thread, CL));
-
- heap=job;
- n_aln=queue2n (job);
- M=(job->param)->TCM;
-
- if (M)M->PW_CL=method2pw_cl ( M, CL);
-
-
- n_elements_in=CL->ne;
-
-
- /* Cf. parse method for possible out_mode flags*/
-
-
-
- b=0;
-
- while (job)
- {
- local_stderr=output_completion ( local_stderr, b, n_aln+1,1, "Submit Job");
- job=print_lib_job (job, "io->CL=%p control->submitF=%p control->retrieveF=%p control->mode=%s",duplicate_constraint_list4lib_computation (CL),submit_lib_job, retrieve_lib_job, CL->multi_thread );
- job=submit_job (job);
- if (retrieve_job (job))
- {
- CL=merge_constraint_list ((job->io)->CL, CL, "default");
- free_constraint_list4lib_computation ( (job->io)->CL);
- }
- job=job->c;
- b++;
- }
- job=heap;
- fprintf ( local_stderr, "\n");
-
- while (job) job=delete_job (job);
-
- n_new_elements=CL->ne - n_elements_in;
- compact_list (CL, n_elements_in,n_new_elements, "best");
- compact_list (CL, 0, CL->ne, "default");
- CL->local_stderr=local_stderr;
-
- free_queue (heap);
-
- return CL;
- }
-
-
-Job_TC *job_list2multi_thread_job_list (Job_TC* ojob, char *mt, Constraint_list *CL)
-{
- FILE *fp=NULL;
- int mtv, n, nj;
- char *met_file, *seq_file, *lib_file, *lib_list;
- char common[1000], command[1000], T_file[100];
- Job_TC *njob, *heap;
- TC_method *TCM;
-
-
- mtv=(mt==NULL)?0:atoi (mt);
- if ( !mtv || mtv==1)return ojob;
-
- HERE ("***"); exit (0);
- heap=ojob;
- nj=(queue2n(ojob)/mtv)+1;
- nj=(nj==0)?1:nj;
-
- met_file=vtmpnam (NULL);
- TC_method2method_file ((ojob->param)->TCM,met_file=vtmpnam (NULL));
-
- TCM=method_file2TC_method (method_name2method_file ("tc2"));
- sprintf (T_file,"%s",(CL->S)->template_file);
-
- HERE ("2");
-
- seq_file=vtmpnam (NULL);
- sprintf ( common, "%s -in M%s S%s -lib_only ", TCM->executable, met_file, seq_file);
- if ( T_file[0] && check_file_exists (T_file))
- {
- strcat (common, " -template_file ");strcat (common, T_file); strcat ( common , " ");
- }
-
- njob=vcalloc ( 1, sizeof (Job_TC));
- njob->jobid=-1;
- n=0;
-
- HERE ("3");
-
- while ( ojob && n<nj)
- {
- if (n==0)
- {
- lib_file=vtmpnam ( NULL);
- lib_list=vtmpnam ( NULL);
- fp=vfopen (lib_list, "w");
- sprintf ( command, "%s -out_lib=%s -lib_list=%s -quiet", common, lib_file, lib_list);
- njob->c=print_lib_job (NULL, "param->TCM=%p param->method=%s param->aln_c=%s io->in=%s io->out=%s",TCM, "tc2", command,seq_file, lib_file);
-
- njob=queue_cat (njob, njob->c);
- }
-
- fprintf ( fp, "%s\n", (ojob->param)->seq_c);
- ojob=ojob->c;
- if ( (++n)==nj){vfclose (fp);n=0;}
- }
- HERE ("4");
- if (fp && n)vfclose (fp);
- free_queue (heap);
- return njob;
-}
-
-
-
-
-
-
-
-Job_TC *retrieve_lib_job ( Job_TC *job)
-{
- Job_param_TC *p;
- Job_io_TC *io;
- TC_method *M;
-
- p=job->param;
- io=job->io;
- M=(job->param)->TCM;
-
-
- if ( job->status==EXIT_SUCCESS)
- {
- static char *log_output;
- static int log;
-
- if ( !M) return job;
- else if (strm2(M->out_mode, "aln", "A"))
- {
- io->CL=read_constraint_list (io->CL,io->out,"aln","disk",M->weight);
- }
- else if (strm2(M->out_mode, "lib","L"))
- {
- io->CL=read_constraint_list (io->CL,io->out,"lib","disk",M->weight);
- }
- return job;
- }
- else
- return NULL;
-}
-
-int add_method_output2method_log (char *l,char *command,Alignment *A, Constraint_list *CL, char *io_file)
-{
- static int header;
- static int log;
- static char *file, *log_file;
- static int set;
-
- if ( set && log_file==NULL && l==NULL) return 0;
- if (!set ){log_file=get_string_variable ("method_log");if (log_file && strm (log_file, "no"))log_file=NULL; set=1;}
- if (!file)file=vtmpnam (NULL);
-
- if ( l);
- else if (!l && log_file) l=log_file;
- else return 0;
-
-
- if (!header){printf_file ( l, "w", "# CONC_MSF_FORMAT_01\n");header=1;}
- if (command)printf_file (l, "a", "%s\n#----------------------------------------------\n#%s\n", TC_REC_SEPARATOR,command);
-
-
- if ( A)
- {
-
- io_file=file;
- output_fasta_aln (io_file, A);
- }
- else if (CL)
- {
- io_file=file;
- vfclose (save_constraint_list ( CL, 0, CL->ne,io_file, NULL, "ascii",CL->S));
- }
- else
- file_cat (io_file,l);
-
-
- return 1;
-}
-
-
-
-Job_TC *submit_lib_job ( Job_TC *job)
-{
- Job_param_TC *p;
- Job_io_TC *io;
- TC_method *M;
- static char *l;
- static int log;
-
- p=job->param;
- io=job->io;
- M=(job->param)->TCM;
- add_method_output2method_log (NULL, p->aln_c, NULL, NULL, NULL);
- if ( getenv4debug ("DEBUG_LIBRARY"))fprintf ( stderr, "\n[DEBUG_LIBRARY:produce_list] Instruction: %s\n", p->aln_c);
-
- if ( !M)
- {
- return job;
- }
- else if (strm4 (M->out_mode,"A", "L", "aln", "lib"))
- {
-
- seq_list2in_file ( M, (io->CL)->S, p->seq_c, io->in);
-
- my_system (p->aln_c);/*Multi Threaded jobs must be sent here*/
-
- add_method_output2method_log (NULL,NULL, NULL, NULL, io->out);
-
- if (!evaluate_sys_call_io (io->out,p->aln_c, "") || (strm (M->out_mode, "aln") && !(is_aln (io->out) || is_seq(io->out))) )
- {
- add_warning (stderr, "\nFAILED TO EXECUTE:%s [SERIOUS:%s]", p->aln_c, PROGRAM);
- job->status=EXIT_FAILURE;
- //myexit (EXIT_FAILURE);
- return job;
- }
- }
- else if ( strm2 (M->out_mode, "fA", "fL"))
- {
- io->CL= seq2list(job);
- if (!io->CL)
- {
- add_warning (stderr, "\nFAILED TO EXECUTE:%s [SERIOUS:%s]", p->aln_c, PROGRAM);
- job->status=EXIT_FAILURE;
- }
- }
- else
- {
- fprintf ( stderr, "\nERROR: Unknown out_mode=%s for method[FATAL:%s]\n", M->out_mode, M->executable);
- myexit (EXIT_FAILURE);
- }
-
-return job;
-}
-
-
-
-Job_TC* method2job_list ( char *method_name,Sequence *S, char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL)
- {
- int preset_method;
- static char *fname, *bufS, *bufA;
- char *in,*out;
- TC_method *method;
- char aln_mode[100];
- char out_mode[100];
- Job_TC *job;
- int hijack_P_jobs=1;
-
- /*A method can be:
- 1- a pre computed alignment out_mode=A
- 2- a precomputed Library out_mode=L
- 3- a method producing an alignment out_mode=aln
- 4- a method producing an alignment out_mode=list
- 5- a function producing an alignment out_mode=faln
- 6- a function producing a library out_mode=flist
- */
-
- if ( !fname)
- {
- fname=vcalloc ( 1000, sizeof (char));
- bufS=vcalloc ( S->nseq*10, sizeof (char));
- }
-
- /*Make sure that fname is a method*/
-
-
- sprintf(fname, "%s", method_name);
-
- if ( fname[0]=='A' || fname[0]=='L')
- {
- method=method_file2TC_method("no_method");
- sprintf ( method->out_mode, "%c", fname[0]);
-
- if (!strm (weight, "default"))sprintf ( method->weight, "%s", weight);
-
- return print_lib_job(NULL,"param->out=%s param->TCM=%p",fname+1, method);
- }
- else if ( fname[0]=='M' && is_in_pre_set_method_list (fname+1))
- {
- preset_method=1;
- fname++;
- }
- else if ( is_in_pre_set_method_list (fname))
- {
- preset_method=1;
- }
- else
- {
- char buf[1000];
- if ( check_file_exists ( fname));
- else if (fname[0]=='M' && check_file_exists(fname+1));
- else
- {
- sprintf ( buf, "%s/%s", get_methods_4_tcoffee(), fname);
- if( check_file_exists(buf)){sprintf ( fname, "%s", buf);}
- else
- {
- fprintf ( stderr, "\n%s (%s) is not a valid method [FATAL:%s]\n", buf,fname, PROGRAM);
- myexit (EXIT_FAILURE);
- }
- }
- }
-
-
- method=method_file2TC_method(fname);
- job=print_lib_job (NULL, "param->TCM=%p", method);
- job->jobid=-1;
-
- if (!strm (weight, "default"))sprintf ( method->weight, "%s", weight);
-
- sprintf ( aln_mode, "%s", method->aln_mode);
- sprintf ( out_mode, "%s", method->out_mode);
-
-
- if (lib_list && lib_list[0])
- {
- static char **lines, **list=NULL;
- int a,i, x, n, nl;
-
-
-
- if ( lines) free_char (lines, -1);
-
-
- if ( strstr (lib_list, "prune"))
- {
- lines=file2lines (list2prune_list (S,DM->similarity_matrix));
- }
- else
- {
- lines=file2lines (lib_list);
- }
-
- nl=atoi (lines[0]);
- for (a=1; a<nl; a++)
- {
-
- if (list) free_char (list, -1);
- if (isblanc (lines[a]))continue;
-
- list=string2list (lines[a]);n=atoi(list[1]);
- if ( n> 2 && strm (aln_mode, "pairwise"))continue;
- if ( n==2 && strm (aln_mode, "multiple"))continue;
-
- for (i=2; i<n+2; i++)
- {
- if ( is_number (list[i]));
- else if ((x=name_is_in_list (list[i], S->name, S->nseq, 100))!=-1)sprintf(list[i], "%d", x);
- else
- {
- add_warning ( stderr, "\nWARNING: %s is not part of the sequence dataset \n", list[i]);
- continue;
- }
- }
- sprintf ( bufS, "%s", list[1]);
- for ( i=2; i<n+2; i++) {strcat (bufS, " ");strcat ( bufS, list[i]);}
-
-
- bufA=make_aln_command (method, in=vtmpnam(NULL),out=vtmpnam(NULL));
-
- if (strrchr(bufA, '>')==NULL)strcat (bufA,TO_NULL_DEVICE);
- if ( check_seq_type ( method, bufS, S))
- {
- job->c=print_lib_job (NULL, "param->TCM=%p param->method=%s param->aln_c=%s param->seq_c=%s io->in=%s io->out=%s ", method, fname, bufA, bufS, in, out);
- job=queue_cat (job, job->c);
- }
- vfree (bufA);
-
- }
- }
- else if ( strcmp (aln_mode, "multiple")==0)
- {
- int d;
- char buf[1000];
-
- sprintf (bufS, "%d",S->nseq);
- for (d=0; d< S->nseq; d++)
- {
- sprintf ( buf," %d",d);
- strcat ( bufS, buf);
- }
-
- bufA=make_aln_command (method, in=vtmpnam(NULL),out=vtmpnam(NULL));
-
- if (strrchr(bufA, '>')==NULL)strcat (bufA,TO_NULL_DEVICE);
-
- if ( check_seq_type ( method, bufS, S))
- {
-
- job->c=print_lib_job (NULL, "param->TCM=%p param->method=%s param->aln_c=%s param->seq_c=%s io->in=%s io->out=%s ", method, fname, bufA, bufS, in, out, S->template_file);
-
- job=queue_cat (job, job->c);
-
- }
- vfree (bufA);
-
- }
- else if ( strstr(aln_mode, "pairwise"))
- {
-
- int do_mirror, do_self, x, y, id;
- do_mirror=(strstr(aln_mode, "m_"))?1:0;
- do_self=(strstr(aln_mode, "s_"))?1:0;
-
-
- for (x=0; x< S->nseq; x++)
- for ( y=(do_mirror)?0:x; y< S->nseq; y++)
- {
-
- id=DM->similarity_matrix[x][y];
-
- if ( x==y && !do_self);
- else if ( !is_in_range(id,method->minid, method->maxid));
- else
- {
- sprintf (bufS, "2 %d %d",x,y);
- bufA=make_aln_command (method,in=vtmpnam(NULL),out=vtmpnam (NULL));
-
- if (strrchr(bufA, '>')==NULL)strcat (bufA, TO_NULL_DEVICE);
- if (check_seq_type (method, bufS, S))
- {
- job->c=print_lib_job (job->c, "param->TCM=%p param->method=%s param->aln_c=%s param->seq_c=%s io->in=%s io->out=%s ",method,fname,bufA, bufS, in, out);
- job=queue_cat (job, job->c);
- }
- else if ( method->seq_type[0]=='P' && hijack_P_jobs)
- {
- //Hijack _P_ jobs without enough templates
- static TC_method *proba_pairM;
-
- fprintf (stderr, "\n\t Information: Method %s cannot be applied to [%s vs %s]. Use proba_pair instead", method, (CL->S)->name[x], (CL->S)->name [y]);
- if (!proba_pairM)
- {
- proba_pairM=method_file2TC_method(method_name2method_file ("proba_pair"));
- proba_pairM->PW_CL=method2pw_cl(proba_pairM, CL);
- }
- job->c=print_lib_job (job->c, "param->TCM=%p param->method=%s param->aln_c=%s param->seq_c=%s io->in=%s io->out=%s ",proba_pairM,fname,bufA, bufS, in, out);
- job=queue_cat (job, job->c);
- }
-
- vfree (bufA);
- }
- }
- }
-
- return job;
- }
-
-int check_seq_type (TC_method *M, char *list,Sequence *S)
-{
- char t1, t2;
- int s1, s2, n1, nseq, ntype, i;
- int *slist;
- Template *T1, *T2;
-
-
- slist=string2num_list (list);
-
- nseq=slist[1];
- ntype=strlen (M->seq_type);
- t1=M->seq_type[0];
- t2=M->seq_type[1];
- n1=0;
-
- /*Profiles and Sequences MUST NOT be distinguished so that sequences and profiles can easily be aligned*/
- if ( tolower(t1)=='r')t1='S';
- if ( tolower(t2)=='r')t2='S';
-
-
- if ( strm ( M->aln_mode, "pairwise") && nseq>2)n1=0;
- else if (strm ( M->aln_mode, "multiple" ) && ntype>1)n1=0;
- else if (ntype==1)
- {
-
- for (n1=0, i=0; i<nseq; i++)
- {
- s1=slist[i+2];
- T1=S->T[s1];
-
- n1+=(strchr (T1->seq_type,t1) || check_profile_seq_type (S, s1, t1))?1:0;
- }
- n1=(n1==nseq)?1:0;
- }
- else if (ntype==2)
- {
- int s1_has_t1;
- int s1_has_t2;
- int s2_has_t1;
- int s2_has_t2;
-
- s1=slist[2];
- s2=slist[3];
- T1=(S->T[s1]);
- T2=(S->T[s2]);
-
- s1_has_t1=(strchr ( T1->seq_type, t1) || check_profile_seq_type (S, s1, t1))?1:0;
- s1_has_t2=(strchr ( T1->seq_type, t2) || check_profile_seq_type (S, s1, t2))?1:0;
- s2_has_t1=(strchr ( T2->seq_type, t1) || check_profile_seq_type (S, s2, t1))?1:0;
- s2_has_t2=(strchr ( T2->seq_type, t2) || check_profile_seq_type (S, s2, t2))?1:0;
- n1=((s1_has_t1 && s2_has_t2) || (s1_has_t2 && s2_has_t1))?1:0;
- }
-
- vfree (slist);
- return n1;
-}
-
-int check_profile_seq_type (Sequence *S, int i, char t)
-{
- Alignment *A;
- Template *T;
- int a;
-
- /*returns 1 if the sequence S is associated with a profile containing the right sequence*/
- A=seq2R_template_profile (S, i);
- if (A==NULL || A->S==NULL) return 0;
- for ( a=0; a< A->nseq; a++)
- {
-
- T=(A->S)->T[a];
- if ( T && strchr( T->seq_type,t))return 1;
-
- }
- return 0;
-}
-
-
-char **method_list2method4dna_list ( char **list, int n)
-{
- int a;
- static char *buf;
-
- if ( !buf)buf=vcalloc ( 1000, sizeof (char));
-
- if ( !list || n==0)return list;
- buf=vcalloc ( 1000, sizeof (char));
-
- for ( a=0; a< n; a++)
- {
-
- sprintf ( buf,"%s",list[a]);
-
- if ( strm ( list[a], "4dna"));
- else
- {
-
- char **para ;
- int b;
-
- para=string2list2 (list[a], "@");
- sprintf ( buf, "%s4dna", para[1]);
- if (method_name2method_file (buf) || method_name2method_file(buf+1))
- {
- sprintf ( list[a],"%s", buf);
- for (b=2; b< atoi (para[0]); b++)
- {
- strcat (list[a], "@");
- strcat (list[a], para[b]);
- }
- }
-
- free_char (para, -1);
- }
- }
- return list;
-}
-
-int is_in_pre_set_method_list ( char *method)
-{
- char *new_name;
-
-
-
-
- new_name=method_name2method_file (method);
-
- if ( !new_name) return 0;
- else
- {
-
- sprintf ( method, "%s", new_name);
- return 1;
- }
-}
-char *** display_method_names (char *mode, FILE *fp)
-{
- char ***list, ***l2;
- int n=0, a, ml1=0, ml2=0, ml3=0;
- int status;
-
-
-
-
-
-
- list=produce_method_file (NULL);
- l2=declare_arrayN(3,sizeof (char), 1000, 10, 100);
-
- fprintf ( fp, "\n####### Compiling the list of available methods ... (will take a few seconds)\n");
- a=0;
- while (list[a])
- {
-
-
- sprintf (l2[a][0], "%s", method_file_tag2value (list[a][1],"ADDRESS"));
- sprintf (l2[a][1], "%s", method_file_tag2value (list[a][1],"PROGRAM"));
- sprintf (l2[a][2], "%s", method_file_tag2value (list[a][1],"ALN_MODE"));
- sprintf (l2[a][3], "%s", method_file_tag2value (list[a][1],"SEQ_TYPE"));
- ml1=MAX((strlen (list[a][0])),ml1);
- ml2=MAX((strlen (l2 [a][0])),ml2);
- ml3=MAX((strlen (l2 [a][1])),ml3);
- l2[a][4][0]= check_program_is_installed (l2[a][1],NULL,NULL,l2[a][0],NO_REPORT);
- if (l2[a][4][0])l2[a][5]=pg2path (l2[a][1]);
- a++;
- }
-
- fprintf ( fp, "\n####### Methods For which an Interface is available in T-Coffee\n");
- fprintf ( fp, "You must install the packages yourself when required (use the provided address)\n");
- fprintf ( fp, "Contact us if you need an extra method to be added [%s]\n", EMAIL);
-
-
- fprintf ( fp, "\n****** Pairwise Sequence Alignment Methods:\n");
- fprintf ( fp, "--------------------------------------------\n");
- a=0;
- while (list[a])
- {
- if ( strm (l2[a][2], "pairwise") && !strstr (l2[a][3], "P"))
- fprintf ( fp, "%-*s %-*s [pg: %*s is %s Installed][%s]\n", ml1,list[a][0],ml2, l2[a][0], ml3,l2[a][1], (l2[a][4][0]==0)?"NOT":"",(l2[a][5])?l2[a][5]:"");
- a++;
- }
-
- fprintf ( fp, "\n****** Pairwise Structural Alignment Methods:\n");
- fprintf ( fp, "--------------------------------------------\n");
- a=0;
- while (list[a])
- {
- if ( strm (l2[a][2], "pairwise") && strstr (l2[a][3], "P"))
- fprintf ( fp, "%-*s %-*s [pg: %*s is %s Installed][%s]\n", ml1,list[a][0],ml2, l2[a][0], ml3,l2[a][1], (l2[a][4][0]==0)?"NOT":"",(l2[a][5])?l2[a][5]:"");
- a++;
- }
- fprintf ( fp, "\n****** Multiple Sequence Alignment Methods:\n");
- fprintf ( fp, "--------------------------------------------\n");
- a=0;
- while (list[a])
- {
- if ( strm (l2[a][2], "multiple"))
- fprintf ( fp, "%-*s %-*s [pg: %*s is %s Installed][%s]\n", ml1,list[a][0],ml2, l2[a][0], ml3,l2[a][1], (l2[a][4][0]==0)?"NOT":"",(l2[a][5])?l2[a][5]:"");
- a++;
- }
- fprintf ( fp, "\n####### Prediction Methods available to generate Templates\n");
- fprintf ( fp, "-------------------------------------------------------------\n");
- a=0;
- while (list[a])
- {
- if ( strm (l2[a][2], "predict"))
- fprintf ( fp, "%-*s %-*s [pg: %*s is %s Installed][%s]\n", ml1,list[a][0],ml2, l2[a][0], ml3,l2[a][1], (l2[a][4][0]==0)?"NOT":"",(l2[a][5])?l2[a][5]:"");
- a++;
- }
- fprintf ( fp, "\n\n\nAll these Methods are supported by T-Coffee, but you HAVE to install them yourself [use the provided address]\n\n");
- fprintf ( fp, "\nThese methods were selected because they are freeware opensource, easy to install and well supported");
- fprintf ( fp, "\nContact us if you need an extra method to be added [%s]\n", EMAIL);
-
- return l2;
-}
-
-char* method_name2method_file (char *method)
- {
- char *fname=NULL;
- char ***mlist, *p;
- char address[100];
- char program[100];
- int a;
-
- if ( check_file_exists (method) || (toupper(method[0])==method[0] && check_file_exists (method+1)))return NULL;
-
- if ( (p=strstr (method, "@"))!=NULL && !strstr (method, "em@"))p[0]='\0';
- mlist=produce_method_file (method);
-
-
-
- a=0;
- while (mlist[a])
- {
- if ( lstrstr (method,mlist[a][0])){fname=mlist[a][1];break;}
- else {a++;}
- }
- if (p)p[0]='@';
- if ( fname==NULL) return NULL;
- else
- {
- sprintf (address, "%s", method_file_tag2value (fname,"ADDRESS"));
- sprintf (program, "%s", method_file_tag2value (fname,"PROGRAM"));
- check_program_is_installed (program,NULL,NULL,address,INSTALL_OR_DIE);
- if ( (method=strstr (method, "EP@"))!=NULL)
- {
- int a;
- char **list;
- FILE *fp;
- list=string2list2 ( method, "@");
- fp=vfopen (fname, "a");
- for ( a=2; a<atoi (list[0]); a+=2)
- {
- fprintf (fp, "%s %s\n", list[a], list[a+1]);
-
- }
-
- vfclose (fp);
- free_char (list, -1);
- }
- return fname;
- }
- }
-char *method_file_tag2value (char *method, char *tag)
-{
- FILE *fp;
- char c, *p;
- static char *buf, *line;
- if (!buf) buf=vcalloc ( 1000, sizeof (char));
- else buf[0]='\0';
-
- if (!line)
- {
- line=vcalloc (LONG_STRING+1, sizeof ( char));
- }
-
- fp=vfopen (method, "r");
- while ( (c=fgetc (fp))!=EOF)
- {
- ungetc ( c, fp);
- fgets ( line,LONG_STRING, fp);
-
- if ( (line && (line[0]=='*' || line[0]=='#' || line[0] == '$'|| line[0]==' ' || line[0]=='\0' )));
- else if ( (p=strstr (line, tag )))
-
- {
- sscanf (p+strlen (tag), " %s" , buf);
- vfclose (fp);
- return buf;
- }
- }
- vfclose ( fp);
- return buf;
-}
-struct TC_method * method_file2TC_method( char *method)
-{
- TC_method *m;
- static char *subcommand;
- static char *line;
- char *p;
- FILE *fp;
- int c;
- //<EXECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM2><OUT_FLAG><outname><PARAM>
- if (!line)
- {
- line=vcalloc (LONG_STRING+1, sizeof ( char));
- subcommand=vcalloc ( LONG_STRING, sizeof (char));
- }
-
- m=vcalloc ( 1, sizeof (TC_method));
-
- /*set default parameter values*/
- m->gop=m->gep=UNDEFINED;
- sprintf (m->seq_type, "S");
- sprintf (m->weight, "sim");
- m->minid=0;
- m->maxid=100;
-
- fp=vfopen (method, "r");
- while ( (c=fgetc (fp))!=EOF)
- {
- ungetc ( c, fp);
- fgets ( line,LONG_STRING, fp);
-
-
- line=substitute (line, "\n", " ");
- line=substitute (line, "%s", " ");
- line=substitute (line, "%e", "=");
- line=substitute (line, "%m", "-");
-
- if ( (line && (line[0]=='*' || line[0]=='#' || line[0] == '$'|| line[0]==' ' || line[0]=='\0' )))subcommand[0]='\0';
- //Parse PARAM, PARM1 and PARAM2 first because they may contain keywords
- else if ( (p=strstr (line, "PARAM1" )))
- {
- sprintf (subcommand, " %s ", p+6);
- strcat ( m->param1, subcommand);
- }
- else if ( (p=strstr (line, "PARAM2" )))
- {
- sprintf (subcommand, " %s ", p+6);
- strcat ( m->param2, subcommand);
- }
- else if ( (p=strstr (line, "PARAM" )))
- {
- sprintf (subcommand, " %s ", p+5);
- strcat ( m->param, subcommand);
- }else if ( (p=strstr (line, "EXECUTABLE2" )))
- {
- sscanf (p, "EXECUTABLE2 %s", m->executable2);
- }
- else if ( (p=strstr (line, "EXECUTABLE" )))
- {
- sscanf (p, "EXECUTABLE %s", m->executable);
- }
- else if ( (p=strstr (line, "IN_FLAG2" ))) sscanf (p, "IN_FLAG2 %s" , m->in_flag2);
- else if ( (p=strstr (line, "IN_FLAG" ))) sscanf (p, "IN_FLAG %s" , m->in_flag);
- else if ( (p=strstr (line, "OUT_FLAG" ))) sscanf (p, "OUT_FLAG %s" , m->out_flag);
- else if ( (p=strstr (line, "OUT_MODE" ))) sscanf (p, "OUT_MODE %s" , m->out_mode);
- else if ( (p=strstr (line, "ALN_MODE" ))) sscanf (p, "ALN_MODE %s" , m->aln_mode);
- else if ( (p=strstr (line, "SEQ_TYPE" ))) sscanf (p, "SEQ_TYPE %s" , m->seq_type);
- else if ( (p=strstr (line, "WEIGHT" ))) sscanf (p, "WEIGHT %s" , m->weight);
- else if ( (p=strstr (line, "MATRIX" ))){ sscanf (p, "MATRIX %s" , m->matrix);}
- else if ( (p=strstr (line, "GOP" ))) sscanf (p, "GOP %d" , &m->gop);
- else if ( (p=strstr (line, "GEP" ))) sscanf (p, "GEP %d" , &m->gep);
- else if ( (p=strstr (line, "MAXID" ))) sscanf (p, "MAXID %d" , &m->maxid);
- else if ( (p=strstr (line, "MINID" ))) sscanf (p, "MINID %d" , &m->minid);
-
- }
- vfclose ( fp);
-
-
-
- return m;
-}
-
-int TC_method2method_file( struct TC_method*m,char *fname )
-{
- FILE *fp;
- if ( !m) return 0;
- fp=vfopen ( fname, "w");
- if ( m->executable[0])fprintf (fp, "EXECUTABLE %s\n", m->executable);
- if (m->in_flag[0])fprintf (fp, "IN_FLAG %s\n", m->in_flag);
- if (m->out_flag[0])fprintf (fp, "OUT_FLAG %s\n", m->out_flag);
- if (m->out_mode[0])fprintf (fp, "OUT_MODE %s\n", m->out_mode);
- if (m->aln_mode[0])fprintf (fp, "ALN_MODE %s\n", m->aln_mode);
- if (m->seq_type)fprintf (fp, "SEQ_TYPE %s\n", m->seq_type);
- if (m->weight[0])fprintf (fp, "WEIGHT %s\n", m->weight);
- if (m->matrix[0])fprintf (fp, "MATRIX %s\n", m->matrix);
- if (m->gop!=UNDEFINED)fprintf (fp, "GOP %d\n", m->gop);
- if (m->gep!=UNDEFINED)fprintf (fp, "GEP %d\n", m->gep);
- if (m->minid!=0 )fprintf (fp, "MINID %d\n", m->minid);
- if (m->maxid!=100)fprintf (fp, "MAXID %d\n", m->maxid);
- if (m->param[0])fprintf (fp, "PARAM %s\n", m->param);
- if (m->param1[0])fprintf (fp, "PARAM1 %s\n", m->param1);
- if (m->param2[0])fprintf (fp, "PARAM1 %s\n", m->param2);
- if (m->in_flag2[0])fprintf (fp, "IN_FLAG2 %s\n", m->in_flag2);
-
- vfclose ( fp);
- return 1;
-}
-
-char *make_aln_command(TC_method *m, char *seq, char *aln)
- {
- char *command;
- char buf[1000];
-
- // sprintf ( buf, "%s %s %s%s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param);
- sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param);
- command=vcalloc ( strlen (buf)+100, sizeof (char));
- sprintf ( command, "%s", buf);
-
-
- command=substitute (command, "&bnsp", " ");
- command=substitute (command, "no_name", "");
-
- return command;
- }
-
-
-
-
-
-/*********************************************************************/
-/* */
-/* WRITE IN LIST */
-/* */
-/* */
-/*********************************************************************/
-
-
-int dump_constraint_list (Constraint_list *CL)
-{
- int *L;
- int a, b;
- if (!CL->L) return 0;
- L=CL->L;
- CL->L=NULL;
- CL->fp=tmpfile ();
-
- for ( a=0; a<CL->ne; a++)
- for (b=0; b<CL->entry_len; b++)
- vwrite_clist (CL, a, b, L[a*CL->entry_len+b]);
-
- vfree (CL->L); CL->L=NULL;
- return 1;
-}
-
-int vread_clist ( Constraint_list *CL, int a, int b )
- {
- int x;
-
- if ( a>= CL->ne)
- {
- return UNDEFINED_2;
-
- }
- else if (CL->fp)
- {
-
- fseek (CL->fp, a*CL->el_size*CL->entry_len+b*CL->el_size, SEEK_SET);
- fread (&x, CL->el_size, 1, CL->fp);
-
- return x;
- }
- else if ( CL->L)
- {
- return CL->L[a*CL->entry_len+b];
- }
- else if (CL->M)
- {
- return (CL->M)[a][b];
- }
- else
- {
- return UNDEFINED_2;
-
- }
- return UNDEFINED_2;
- }
-int vwrite_clist ( Constraint_list *CL, int a, int b, CLIST_TYPE x)
- {
-
- CL->seq_indexed=0;
- CL->residue_indexed=0;
-
-
- if (CL->fp)
- {
- fseek (CL->fp, a*CL->el_size*CL->entry_len+b*CL->el_size, SEEK_SET);
- fwrite(&x, CL->el_size, 1, CL->fp);
- }
- else if (!CL->M)
- {
- int i,l;
-
-
- i=a*CL->entry_len+b;
- if (CL->L)
- {
- Memcontrol *p;
- p=(Memcontrol *)CL->L;
- p-=2;
- l=(int)p[0].size/p[0].size_element;
- //read_size_int (CL->L,sizeof (int));
- }
- else
- {
- l=CL->chunk;
- (CL->L)=vcalloc (l,sizeof (int));
- }
-
- if (l<=i)
- {
- l+=CL->chunk;
- (CL->L)=vrealloc ( (CL->L),l*sizeof (int));
- }
- (CL->L)[i]=x;
-#ifdef gagaga
- if (((a*CL->entry_len)+b)>=(CL->entry_len*CL->max_L_len))
- {
-
- if (!(CL->L))
- {
- (CL->L)=vcalloc ((CL->chunk+a)*CL->entry_len+b, sizeof (int));
- }
- else
- {
- CL->max_L_len+=CL->chunk;
- (CL->L)=vrealloc ( (CL->L),CL->entry_len*sizeof (int)*CL->max_L_len+b);
- }
- }
-
- (CL->L)[i]=x;
-#endif
- }
- return x;
- }
-
-
-/*********************************************************************/
-/* */
-/* INDEXING FUNCTIONS */
-/* */
-/* */
-/*********************************************************************/
-
-Constraint_list *index_res_constraint_list ( Constraint_list *CL, int field)
- {
- /*
- function documentation: start
- Constraint_list *index_res_constraint_list ( Constraint_list *CL, int field)
- This function reorganises the content of the CL->L matrix, so that a single look up gives
- the constraints associated with any residue
-
- 1-if CL->residue_indexed=1 return
- 2-CL->residue_index[Seq X][Res Y of Seq X][0]=Z
- Z=Number of residues matching X(Y)*3+1
- CL->residue_index[Seq X][Res Y of Seq X][0]=Z
- CL->residue_index[Seq X][Res Y of Seq X][c+0]=seq W
- CL->residue_index[Seq X][Res Y of Seq X][c+1]=res V
- CL->residue_index[Seq X][Res Y of Seq X][c+2]=weight W(V) Vs X(Y)
-
- NOTE: Works All right with a sequence against itself
- NOTE: Any modification of CL->L should result in residue_indexed to be reset
- function documentation: end
- */
- int a, b, s1, s2, r1, r2, w;
-
-
-
-
-
-
-
- if ( CL->residue_indexed && CL->residue_field==field);
- else
- {
-
- if ( CL->residue_index)
- {
- for ( a=0; a< (CL->S)->nseq; a++)
- for ( b=0; b<= (CL->S)->len[a]; b++)
- {
- vfree(CL->residue_index[a][b]);
- CL->residue_index[a][b]=vcalloc_nomemset (1, sizeof (int));
- CL->residue_index[a][b][0]=1;
- }
- }
- else if ( !CL->residue_index)
- {
-
-
- CL->residue_index=vcalloc_nomemset ( (CL->S)->nseq, sizeof (int**));
- for ( a=0; a< (CL->S)->nseq; a++)
- {
-
- CL->residue_index[a]=vcalloc_nomemset ( ((CL->S)->len[a]+1), sizeof (int*));
- for ( b=0; b<= (CL->S)->len[a]; b++)
- {
- CL->residue_index[a][b]=vcalloc_nomemset (1,sizeof (int));
- CL->residue_index[a][b][0]=1;
- }
- }
- }
- for (a=0;a<CL->ne; a++)
- {
-
- s1=vread_clist (CL, a, SEQ1);
- s2=vread_clist (CL, a, SEQ2);
- r1=vread_clist (CL, a, R1);
- r2=vread_clist (CL, a, R2);
- w=vread_clist (CL, a, field);
-
-
- CL->residue_index[s1][r1][0]+=3;
- CL->residue_index[s1][r1]=vrealloc ( CL->residue_index[s1][r1], CL->residue_index[s1][r1][0]*sizeof (int));
- CL->residue_index[s1][r1][CL->residue_index[s1][r1][0]-3]=s2;
- CL->residue_index[s1][r1][CL->residue_index[s1][r1][0]-2]=r2;
- CL->residue_index[s1][r1][CL->residue_index[s1][r1][0]-1]=w;
-
- CL->residue_index[s2][r2][0]+=3;
- CL->residue_index[s2][r2]=vrealloc ( CL->residue_index[s2][r2], CL->residue_index[s2][r2][0]*sizeof (int));
- CL->residue_index[s2][r2][CL->residue_index[s2][r2][0]-3]=s1;
- CL->residue_index[s2][r2][CL->residue_index[s2][r2][0]-2]=r1;
- CL->residue_index[s2][r2][CL->residue_index[s2][r2][0]-1]=w;
-
- }
- CL->residue_indexed=1;
- CL->residue_field=field;
- }
- return CL;
- }
-
-Constraint_list *index_constraint_list ( Constraint_list *CL)
- {
- /*
- Function Documentation: start
- Constraint_list *index_constraint_list ( Constraint_list *CL);
- Indexes a constraint list
- 1-Checks the flag seq_indexed
- 2-if flag set to 0
- CL->start_index[seq1][seq2] indicatse the first position for seq1 Vs seq2
- CL->end_index[seq1][seq3] indicatse the last position for seq1 Vs seq2
- Any modif to CL->L should cause the flag 1 to be set to 0;
- Function Documentation: end
- */
- int a, csA, csB, sA, sB;
-
-
- if ( CL->seq_indexed);
- else
- {
- if ( CL->start_index!=NULL)free_int ( CL->start_index,-1);
- CL->start_index=declare_int ( (CL->S)->nseq, (CL->S)->nseq);
-
- if ( CL->end_index!=NULL)free_int ( CL->end_index,-1);
- CL->end_index=declare_int ( (CL->S)->nseq, (CL->S)->nseq);
-
- csA=vread_clist (CL, 0, SEQ1);
- csB=vread_clist (CL, 0, SEQ2);
-
- CL->start_index[csA][csB]=0;
- CL->start_index[csB][csA]=0;
- for ( a=1; a<CL->ne; a++)
- {
- sA=vread_clist (CL, a, SEQ1);
- sB=vread_clist (CL, a, SEQ2);
- if (sA!=csA || sB!=csB)
- {
- CL->end_index[csA][csB]=a;
- CL->end_index[csB][csA]=a;
- csA=sA;
- csB=sB;
- CL->start_index[csA][csB]=a;
- CL->start_index[csB][csA]=a;
- }
- }
- CL->end_index[csB][csA]=CL->ne;
- CL->end_index[csA][csB]=CL->ne;
- CL->seq_indexed=1;
- }
- return CL;
- }
-
-
-char ** reindex_constraint_list (char **profile, int np,char **list, int *inL, Sequence *S)
-{
- int a, nl=0, l;
- int ***cache, **index, *entry;
- char **nlist, **cons, *nlib_name;
- Sequence *NS;
- Alignment **P, *A;
- Constraint_list *CL, *NCL;
-
-
- l=inL[0];
- /*1: Pre-Process the profiles*/
- cache=vcalloc (np, sizeof (int**));
- cons=vcalloc (np, sizeof (char*));
- P=vcalloc (np, sizeof (Alignment *));
-
- for ( a=0; a< np; a++)
- {
- int e,b,c, **ca;
- A=P[a]=main_read_aln (profile[a], NULL);
-
- ca=cache[a]=declare_int (A->nseq, A->len_aln+1);
- cons[a]=aln2cons_seq_mat ( A, "blosum62mt");
- for (b=0;b<A->nseq; b++)
- {
- for (e=0,c=0; c<A->len_aln; c++)
- {
- if (is_gap(A->seq_al[b][c]));
- else ca[b][++e]=c+1;
- }
- }
- }
-
- /*2: Index The Sequences*/
- index=declare_int (S->nseq,2);
- for (a=0; a<S->nseq; a++)index[a][0]=index[a][1]=-1;
- for (a=0; a< S->nseq; a++)
- {
- char *name;
- int p, b;
- name=S->name[a];
- for (b=0; b< np; b++)
- {
- if ((p=name_is_in_list(name, (P[b])->name, (P[b])->nseq, MAXNAMES))!=-1)
- {
- index[a][0]=b;
- index[a][1]=p;
- }
- }
- }
-
- /*3: Read the primary Library*/
-
- nlist=declare_char (read_array_size_new ((void *)list), read_array_size_new ((void *)list[0]));
- for (nl=0,a=0; a< l; a++)
- if ( list[a][0]=='L' || list[a][0]=='A')
- nlist[nl++]=list[a];
-
- CL=declare_constraint_list ( S,NULL, NULL, 0,NULL, NULL);
- CL=read_n_constraint_list (nlist,nl,NULL,NULL,"sim",S->type,stdout, CL, "S");
- vfree (nlist);
-
- NS=fill_sequence_struc (np, cons, profile);
- NCL=declare_constraint_list ( NS,NULL, NULL, 0,NULL, NULL);
- entry=vcalloc ( CL->entry_len, CL->el_size);
- for (a=0; a<CL->ne; a++)
- {
- int s1, s2, r1, r2, ps1, ps2, pps1, pps2;
-
- entry=extract_entry (entry, a, CL);
- s1=entry[SEQ1]; s2=entry[SEQ2];
- r1=entry[R1]; r2=entry[R2];
- ps1=index[s1][0];ps2=index[s2][0];
- pps1=index[s1][1];pps2=index[s2][1];
-
- if (ps1==ps2 || ps1==-1 || ps2==-1)continue;
- entry[SEQ1]=ps1;
- entry[SEQ2]=ps2;
-
- entry[R1]=cache[ps1][pps1][r1];
- entry[R2]=cache[ps2][pps2][r2];
-
- add_entry2list (entry, NCL);
-
- }
-
- compact_list (NCL, 0, NCL->ne, "default");
- nlib_name=vtmpnam(NULL);
- vfclose(save_constraint_list ( NCL, 0, NCL->ne,nlib_name, NULL, "lib",NCL->S));
-
-
- nlist=declare_char (read_array_size_new ((void *)list), read_array_size_new ((void *)list[0]));
- for (nl=0,a=0; a< l; a++)
- if ( list[a][0]!='L' && list[a][0]!='A')
- sprintf (nlist[nl++], "%s",list[a]);
- sprintf (nlist[nl++], "L%s", nlib_name);
-
- free_arrayN ((void *)cache, 3);
- free_arrayN ((void *)cons, 2);
- free_arrayN ((void *)index, 2);
- vfree (entry);
- for (a=0;a<np; a++)free_aln (P[a]);
- vfree (P);
- free_constraint_list_full (CL);
- free_constraint_list_full (NCL);
-
- inL[0]=nl;
- return nlist;
-}
-
-
-Constraint_list * progressive_index_res_constraint_list ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
-{
- int **index_seq;
- int **index_res;
- static Constraint_list *NCL;
-
- int a, b, c, d,s,l, max_len;
- int s1, s2, r1, r2;
- int *L, *NL;
- char *seq;
- Sequence *S, *NS;
-
-
-
- if ( NCL==NULL)
- {
- NCL=duplicate_constraint_list (CL);
- }
-
- S=CL->S;
- NS=NCL->S;
-
- L=CL->L;
- NL=NCL->L;
-
-
-
- if (NCL->residue_index)
- {
- free_arrayN((void*)NCL->residue_index, 3);
- NCL->residue_index=NULL;
- }
-
- for ( a=0; a< S->nseq; a++)
- {
- sprintf ( NS->seq[a], "%s", S->seq[a]);
- NS->len[a]=strlen (S->seq[a]);
- }
-
-
- for ( a=0; a<2; a++)
- {
- s=A->order[ls[a][0]][0];
- vfree (NS->seq[s]);
- NS->seq[s]=sub_aln2cons_seq_mat (A, ns[a], ls[a], "blosum62mt");
- NS->len[s]=strlen (NS->seq[s]);
- }
- for ( max_len=0, a=0; a<S->nseq; a++)max_len=MAX(max_len, S->len[a]);
- index_seq=declare_int ( NS->nseq, max_len+1);
- index_res=declare_int ( NS->nseq, max_len+1);
-
-
- for ( a=0; a< 2; a++)
- {
- for (b=0; b< ns[a]; b++)
- {
- s=A->order[ls[a][b]][0];
- seq=A->seq_al[ls[a][b]];
- l=strlen (seq);
-
- for ( d=0, c=0; c<l; c++)
- {
- if ( !is_gap(seq[c]))
- {
- d++;
-
- index_res[s][d]=c+1;
- index_seq[s][d]=A->order[ls[a][0]][0];
- }
- }
- }
- }
-
- for ( a=0; a< CL->ne; a++)
- {
- s1=L[a*CL->entry_len+SEQ1];
- s2=L[a*CL->entry_len+SEQ2];
- r1=L[a*CL->entry_len+R1];
- r2=L[a*CL->entry_len+R2];
-
- if ( index_res[s1][r1])
- {
- NL[a*CL->entry_len+SEQ1]=index_seq[s1][r1];
- NL[a*CL->entry_len+R1]=index_res[s1][r1];
- }
- else
- {
- NL[a*CL->entry_len+SEQ1]=s1;
- NL[a*CL->entry_len+R1]=r1;
- }
-
- if ( index_res[s2][r2])
- {
- NL[a*CL->entry_len+SEQ2]=index_seq[s2][r2];
- NL[a*CL->entry_len+R2]=index_res[s2][r2];
- }
- else
- {
- NL[a*CL->entry_len+SEQ2]=s2;
- NL[a*CL->entry_len+R2]=r2;
- }
- }
-
- NCL->ne=CL->ne;
- NCL->residue_indexed=0;
-
- NCL=compact_list (NCL, 0, NCL->ne, "best");
-
- NCL=index_res_constraint_list (NCL, WE);
-
- free_int ( index_res, -1); free_int (index_seq, -1);
-
- return NCL;
-}
-/*********************************************************************/
-/* */
-/* LIST EXTENTION */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list *extend_list_pair (Constraint_list *CL,char *store_mode, int s1, int s2)
- {
- static Sequence *S;
- Constraint_list *CLout;
- /*
- function documentation: start
- Constraint_list *extend_list_pair (Constraint_list *CL,char *store_mode, int s1, int s2)
- This function takes a pair of sequences s1, s2 and perrforms the extention
- It returns the incoming list CL, with CL->L[s1][s2] now extended
- See main documentation for store_mode
- function documentation: end
- */
-
- if ( S==NULL)S=declare_sequence ((CL->S)->min_len, (CL->S)->max_len,(CL->S)->nseq);
- sprintf ( S->name[0], "%s",(CL->S)->name[s1]);
- sprintf ( S->name[1],"%s",(CL->S)->name[s2]);
- S->nseq=2;
-
- CLout=extend_list (CL, store_mode, CL->extend_clean_mode, CL->extend_compact_mode,CL->do_self, S);
- return CLout;
- }
-Constraint_list *extend_list (Constraint_list *CLin, char *store_mode,char *clean_mode, char *compact_mode,int do_self, Sequence *DO_LIST)
- {
- int a, b, c, d, e, f;
- int wA, wC,w, rA, rC, miscA, miscC, misc;
- static int **posA;
- static int **posC;
- int start_ba, end_ba, start_bc, end_bc, start_ac, end_ac;
- int len;
- int lenA=0;
- int lenC=0;
- int *translation;
- Constraint_list *CLout=NULL;
-
-
- /*Do not extend if the List is a Matrix*/
- if ( !CLin->L && CLin->M)
- {
- CLin->extend_jit=0;
- return CLin;
- }
-
- translation=vcalloc ( (CLin->S)->nseq, sizeof (int));
- for ( a=0; a<(CLin->S)->nseq; a++)
- {
- translation[a]=name_is_in_list ((CLin->S)->name[a],DO_LIST->name, DO_LIST->nseq, 100);
- translation[a]++;/* set translation to -1+1=0 if seq not in list*/
- }
-
- CLout=declare_constraint_list (CLin->S, NULL,NULL,0, strm("disk", store_mode)?tmpfile():NULL, NULL);
-
- for ( a=0; a<(CLin->S)->nseq-(1-do_self); a++)
- {
- fprintf (CLin->local_stderr, "\nSeq %3d: %5d", a+1,CLout->ne);
- for ( c=a+(1-do_self); c<(CLin->S)->nseq; c++)
- {
- if ( translation[a] && translation[c])
- {
- get_bounds (CLin,a, c, &start_ac, &end_ac);
- for ( d=start_ac; d<end_ac; d++)
- {
- for ( e=0; e< CLin->entry_len; e++)
- vwrite_clist(CLout,CLout->ne, e, vread_clist(CLin,d, e));
- CLout->ne++;
- }
-
- for ( b=0; b<(CLin->S)->nseq; b++)
- {
- len=strlen ( (CLin->S)->seq[b]);
-
- get_bounds (CLin,b, a, &start_ba, &end_ba);
- posA=fill_pos_matrix (CLin,start_ba, end_ba, len, posA, &lenA,(b>a));
-
- if ((c!=b && a!=b) ||(do_self==1))
- {
-
- get_bounds (CLin, b, c, &start_bc, &end_bc);
- posC=fill_pos_matrix (CLin, start_bc, end_bc, len, posC, &lenC, (b>c));
-
- for (d=1; d<=len; d++)
- {
- if ( posA[d][1]==0 || posC[d][1]==0);
- else
- {
- for (e=2; e<=posA[d][1]+1; e+=(CLin->entry_len-4))
- for ( f=2; f<=posC[d][1]+1; f+=(CLin->entry_len-4))
- {
- wA =posA[d][e+1];
- miscA=posA[d][e+2];
-
- wC =posC[d][f+1];
- miscC=posC[d][f+2];
-
- rA=posA[d][e];
- rC=posC[d][f];
-
- w =MIN(wA,wC);
-
- misc=MAX(miscA, miscC);
-
- vwrite_clist( CLout, CLout->ne, SEQ1, a);
- vwrite_clist( CLout, CLout->ne, SEQ2, c);
- vwrite_clist( CLout, CLout->ne, R1 ,rA);
- vwrite_clist( CLout, CLout->ne, R2 ,rC);
- vwrite_clist( CLout, CLout->ne, WE , w);
- vwrite_clist( CLout, CLout->ne, CONS, 1);
- vwrite_clist( CLout, CLout->ne, MISC,misc);
- CLout->ne++;
- }
- }
- }
- }
- }
-
- CLout=compact_list (CLout,0,CLout->ne,"mirror_sum");
- CLout=clean ( clean_mode,CLout, 0, CLout->ne);
- }
- }
- }
-
-
- vfree (translation);
- return CLout;
- }
-void get_bounds (Constraint_list *CL, int s1, int s2, int *start, int *end)
- {
-
- CL=index_constraint_list (CL);
-
- if ( s1>s2)SWAP(s1, s2);
-
- start[0]=CL->start_index[s1][s2];
- end [0]=CL->end_index [s1][s2];
- }
-
-
-int ** fill_pos_matrix (Constraint_list *CL, int beg, int end, int slen, int **pos, int *len, int mirrored)
- {
- int small_chunck;
- int a, r1,r2;
-
-
- small_chunck=2*CL->entry_len;
-
- if ( pos==NULL)
- {
- pos=declare_int (slen+1, small_chunck);
- for ( a=0; a<=slen; a++)pos[a][0]=small_chunck;
- len[0]=slen+1;
- }
- else if ( len[0]<=slen)
- {
- free_int ( pos, len[0]);
- pos=declare_int (slen+1, small_chunck);
- for ( a=0; a<=slen; a++)pos[a][0]=small_chunck;
- len[0]=slen+1;
- }
- else
- {
- for ( a=0; a<=slen; a++)pos[a][1]=0;
- }
-
-
-
-
- for ( a=beg; a<end; a++)
- {
-
- if (!mirrored) {r1=vread_clist (CL, a, R1);r2=vread_clist (CL, a, R2);}
- else if ( mirrored){r1=vread_clist (CL, a, R2);r2=vread_clist (CL, a, R1);}
-
- if ( ((pos[r1][1])+(CL->entry_len))>pos[r1][0])
- {
- pos[r1]=vrealloc (pos[r1], (pos[r1][0]+small_chunck)*sizeof (int));
- pos[r1][0]+=small_chunck;
- }
- pos[r1][pos[r1][1]+2]=r2;
- pos[r1][pos[r1][1]+3]=vread_clist(CL,a,WE);
- pos[r1][pos[r1][1]+4]=vread_clist(CL,a,MISC);
- pos[r1][1]+=(CL->entry_len-4);
- }
- return pos;
- }
-Constraint_list * evaluate_constraint_list_reference ( Constraint_list *CL)
- {
- static CLIST_TYPE *entry;
- int a, b, c, s1, s2, r1, r2, w;
- int ***max_res;
-
-
-
- if ( CL->M)
- {
- CL->max_value=CL->max_ext_value=20;
-
- }
- else
- {
-
- CL->max_value=CL->max_ext_value=0;
- max_res=vcalloc ( (CL->S)->nseq, sizeof (int**));
-
- for ( a=0; a< (CL->S)->nseq; a++)
- {
- max_res[a]=vcalloc ( strlen ((CL->S)->seq[a])+1, sizeof (int*));
- for ( b=0; b<=(CL->S)->len[a]; b++)
- {
- max_res[a][b]=vcalloc ( (CL->S)->nseq+1, sizeof (int));
- }
- }
-
- for ( a=0; a< CL->ne; a++)
- {
- entry=extract_entry ( entry, a, CL);
- s1=entry[SEQ1];
- s2=entry[SEQ2];
- r1=entry[R1];
- r2=entry[R2];
- w= entry[WE];
- if ( w==UNDEFINED || ( (CL->moca) && (CL->moca)->forbiden_residues && ((CL->moca)->forbiden_residues[s1][r1]==UNDEFINED || (CL->moca)->forbiden_residues[s2][r2]==UNDEFINED)));
- else
- {
-
- max_res[s1][r1][s2]+=w;
- max_res[s2][r2][s1]+=w;
- CL->max_value=MAX(w, CL->max_value);
- }
- }
-
- for ( a=0; a< (CL->S)->nseq; a++)
- for ( b=1; b<=(CL->S)->len[a]; b++)
- {
- for ( c=0; c< (CL->S)->nseq; c++)
- {
- max_res[a][b][(CL->S)->nseq]+= max_res[a][b][c];
- }
- CL->max_ext_value=MAX(max_res[a][b][c],CL->max_ext_value);
- }
-
- for ( a=0; a< (CL->S)->nseq; a++)
- {
- for ( b=0; b<=(CL->S)->len[a]; b++)
- vfree ( max_res[a][b]);
- vfree (max_res[a]);
- }
- CL->max_ext_value=MAX(1,CL->max_ext_value);
- vfree ( max_res);
- }
-
- if (CL->normalise)
- {
-
- CL->nomatch=(CL->nomatch*CL->normalise)/CL->max_ext_value;
- }
-
- return CL;
- }
-
-/*********************************************************************/
-/* */
-/* ENTRY MANIPULATION */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list * add_list_entry2list (Constraint_list *CL, int n_para, ...)
- {
- int a;
- int *entry;
- int field, val;
- va_list ap;
-
- if (n_para>LIST_N_FIELDS)
- {
- crash ("Too Many Fields in List [FATAL/add_list_entry2list]");
- }
-
- va_start (ap,n_para);
- entry=vcalloc (CL->entry_len, sizeof (int));
-
- for ( a=0; a<n_para; a++)
- {
- field=va_arg(ap, int);
- val =va_arg(ap, CLIST_TYPE);
- entry[field]=val;
- }
- va_end (ap);
- add_entry2list(entry, CL);
- vfree(entry);
- return CL;
- }
-
-Constraint_list *add_entry2list ( CLIST_TYPE *entry, Constraint_list *CL)
- {
- return insert_entry2list (entry, CL->ne++, CL);
- }
-Constraint_list* insert_entry2list(CLIST_TYPE * entry, int pos, Constraint_list *CL)
- {
- int a;
- for ( a=0; a< CL->entry_len; a++)
- vwrite_clist ( CL,pos, a,entry[a]);
- return CL;
- }
-CLIST_TYPE* extract_entry(CLIST_TYPE * entry, int pos, Constraint_list *CL)
- {
- int a;
-
- if ( entry==NULL)entry=vcalloc ( CL->entry_len, CL->el_size);
-
- for (a=0; a< CL->entry_len; a++)entry[a]=vread_clist(CL, pos, a);
- return entry;
- }
-
-
-/*********************************************************************/
-/* */
-/* SEARCH IN LIST (ARRAY AND FILE) */
-/* */
-/* */
-/*********************************************************************/
-FILE * compare_list (FILE *OUT, Constraint_list *CL1,Constraint_list *CL2)
- {
- int a;
- float nw_score=0;
- float w_score=0;
- int *l;
-
- CLIST_TYPE *entry=NULL;
- int p;
-
- entry_len=CL1->entry_len;
- qsort ( (void *)CL1->L, CL1->ne, CL1->entry_len*sizeof (int), compare_constraint_list_entry);
- qsort ( (void *)CL2->L, CL2->ne, CL2->entry_len*sizeof (int), compare_constraint_list_entry);
-
- entry=vcalloc ( CL1->entry_len, CL1->el_size);
- for ( a=0; a<CL1->ne; a++)
- {
- entry=extract_entry (entry,a,CL1);
- if ((l=main_search_in_list_constraint (entry,&p,4,CL2))!=NULL)
- {
- vwrite_clist ( CL2, p,MISC, 1);
- vwrite_clist ( CL1, a,MISC, 1);
- nw_score++;
- w_score+=l[WE];
- }
- }
- fprintf ( OUT, "%-15s:%d pairs (Evaluated matrix), %d pairs in the other (%s)\n", CL2->list_name, CL2->ne, CL1->ne, CL1->list_name);
- fprintf ( OUT, "%-15s:%d pairs\n", CL1->list_name, CL1->ne);
- fprintf ( OUT, "Acurracy=%.2f%%\n", (nw_score/CL1->ne)*MAXID);
- fprintf ( OUT, "Sensitiv=%.2f%%\n\n", (nw_score/CL2->ne)*MAXID);
- return OUT;
- }
-
-
-CLIST_TYPE *main_search_in_list_constraint ( int *key,int *p,int k_len,Constraint_list *CL)
- {
-
-
- CLIST_TYPE *l=NULL;
- int start, end;
-
- CL=index_constraint_list (CL);
-
- start=CL->start_index[key[SEQ1]][key[SEQ2]];
- end =CL->end_index [key[SEQ1]][key[SEQ2]];
-
-
-
- entry_len=CL->entry_len;
- l=bsearch (key, (CL->L)+(start*CL->entry_len), (end-start), sizeof (int)*CL->entry_len, compare_constraint_list_entry4bsearch);
- p[0]=CL->L-l;
- return l;
- }
-CLIST_TYPE return_max_constraint_list ( Constraint_list *CL, int field)
- {
- CLIST_TYPE max=0;
- int a;
- for ( a=0; a< CL->ne; a++)max=MAX( vread_clist(CL,a,field), max);
- return max;
- }
-
- /*********************************************************************/
-/* */
-/* */
-/* LIST SORTING */
-/* */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list *sort_constraint_list_inv (Constraint_list *CL, int start, int len)
- {
- CL=sort_constraint_list (CL, start,len);
-
-
- CL=invert_constraint_list (CL, start,len);
- if ( start+len==CL->ne)
- {
- while (vread_clist(CL,CL->ne-1, SEQ1)==-1)CL->ne--;
- }
-
-
- return CL;
- }
-
-Constraint_list *invert_constraint_list (Constraint_list *CL, int start,int len)
- {
- int a, b, c;
- CLIST_TYPE tp;
-
-
- for ( a=start, b=start+len-1; a<=b; a++, b--)
- {
- for (c=0; c< CL->entry_len; c++)
- {
- tp=vread_clist(CL, a, c);
- vwrite_clist(CL,a, c, vread_clist(CL, b, c));
- vwrite_clist(CL,b, c, tp);
- }
- }
- return CL;
- }
-
-Constraint_list * sort_constraint_list(Constraint_list *CL, int start, int len)
- {
-
- CL=sort_constraint_list_on_n_fields (CL, start, len, 0, CL->entry_len);
-
- return CL;
- }
-
-Constraint_list * sort_constraint_list_on_n_fields (Constraint_list *CL, int start, int len, int first_field, int n_fields)
- {
- entry_len=CL->entry_len;
-
- if (CL->fp)
- {
- rewind( CL->fp);
- fseek ( CL->fp, start*CL->el_size*CL->entry_len , SEEK_SET);
- hsort_list_file ( CL->fp, len, CL->el_size, CL->entry_len,first_field,n_fields);
- }
- else if ( CL->L)
- {
- qsort ( (void *)CL->L, CL->ne, CL->entry_len*sizeof (int), compare_constraint_list_entry);
- //hsort_list_array ((void**)(CL->L)+start, len, CL->el_size, CL->entry_len,first_field,n_fields);
- }
- return CL;
- }
-int compare_constraint_list_entry4bsearch ( const void*vx, const void*vy)
-{
- int a;
- const int *x=vx, *y=vy;
- for (a=SEQ1; a<=R2; a++)
- {
- if (x[a]<y[a])return -1;
- else if (x[a]>y[a]) return 1;
- }
- return 0;
-}
-int compare_constraint_list_entry ( const void*vx, const void*vy)
-{
- int a;
- const int *x=vx, *y=vy;
-
- for (a=SEQ1; a<=WE; a++)
- {
- if (x[a]<y[a])return -1;
- else if (x[a]>y[a]) return 1;
- }
- return 0;
-}
-/*********************************************************************/
-/* */
-/* LIST PARSING */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode, char *type,FILE *local_stderr, Constraint_list *CL, char *seq_source);
-Constraint_list* nfork_read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode, char *type,FILE *local_stderr, Constraint_list *CL, char *seq_source);
-
-Constraint_list* read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode, char *type,FILE *local_stderr, Constraint_list *CL, char *seq_source)
-{
-
- if ( get_nproc()==1 || n_list<=2)return nfork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode,type,local_stderr, CL, seq_source);
- else if ( strstr (CL->multi_thread, "methods"))
- return fork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode,type,local_stderr, CL, seq_source);
- else
- return nfork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode,type,local_stderr, CL, seq_source);
-}
-Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode, char *type,FILE *local_stderr, Constraint_list *CL, char *seq_source)
- {
- int a, b;
- Sequence *S;
- char **tmp_list;
- int*proclist;
- int nproc, ns;
-
- nproc=get_nproc();
-
- proclist=vcalloc (65536, sizeof (int));
- tmp_list=vcalloc (n_list+1, sizeof (char*));
- for (a=0; a<n_list; a++)tmp_list[a]=vtmpnam(NULL);
-
- if (!(CL->S) && (S=read_seq_in_n_list (fname, n_list,type,seq_source))==NULL)
- {
- fprintf ( stderr, "\nNO SEQUENCE WAS SPECIFIED[FATAL]\n");
- myexit(EXIT_FAILURE);
- }
- else if (CL->S==NULL)
- {
- CL->S=S;
- }
-
- /*CHECK IF THERE IS A MATRIX AND GET RID OF OTHER METHODS*/
- for (b=0, a=0; a< n_list; a++)if (is_matrix(fname[a]) ||is_matrix(fname[a]+1) )b=a+1;
-
- if ( b)
- {
- if ( b==1);
- else sprintf ( fname[0], "%s", fname[b-1]);
- n_list=1;
- return nfork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode, type,local_stderr, CL, seq_source);
- }
-
- if (!CL)CL=declare_constraint_list ( S,NULL, NULL, 0,(strm(mem_mode, "disk"))?tmpfile():NULL, NULL);
-
- if (CL->ne)
- {
- constraint_list2raw_file(CL,tmp_list[n_list], "w");
- CL->ne=0;
- }
-
- CL->local_stderr=local_stderr;
- fprintf ( local_stderr, "\n\tMulti Core Mode: %d processors:\n", nproc);
- for (ns=0,a=0; a< n_list; a++)
- {
- int pid;
- ns++;
- pid=vfork ();
- if ( pid==0)
- {
- int in;
- initiate_vtmpnam (NULL);
- CL->local_stderr=vfopen("/dev/null", "w");
- in=CL->ne;
- CL=read_constraint_list (CL, fname[a], in_mode, mem_mode,weight_mode);
- if (CL->ne>in)constraint_list2raw_file (CL,tmp_list[a], "w");
- exit (EXIT_SUCCESS);
- }
- else
- {
-
- set_pid (pid);
- fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns);
- proclist[pid]=a;
- if (ns>=nproc)
- {
- b=proclist[vwait(NULL)];
- fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);
- if (tmp_list[b] && check_file_exists (tmp_list[b]))
- {
- CL=read_constraint_list_raw_file (CL,tmp_list[b]);
- compact_list (CL, 0, CL->ne, (strm (weight_mode, "cons")?"cons":"default"));
- }
- ns--;
- }
- }
- }
-
- while (ns)
- {
- int pid2;
- pid2=vwait(NULL);
- a=proclist[pid2];
- fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);
- if (tmp_list[a] && check_file_exists (tmp_list[a]))
- {
- CL=read_constraint_list_raw_file (CL,tmp_list[a]);
- compact_list (CL, 0, CL->ne, (strm (weight_mode, "cons")?"cons":"default"));
- }
- ns--;
- }
- fprintf ( local_stderr, "\n\n\tAll Methods Retrieved\n");
-
- if (tmp_list[n_list] && check_file_exists (tmp_list[n_list]))
- {
- CL=read_constraint_list_raw_file (CL,tmp_list[n_list]);
- compact_list (CL, 0, CL->ne, (strm (weight_mode, "cons")?"cons":"default"));
- }
-
- CL->local_stderr=local_stderr;
- CL=evaluate_constraint_list_reference (CL);
- vfree (proclist);
- vfree (tmp_list);
- return CL;
- }
-Constraint_list* nfork_read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode, char *type,FILE *local_stderr, Constraint_list *CL, char *seq_source)
- {
- int a, b;
- Sequence *S;
-
-
- if (!(CL->S) && (S=read_seq_in_n_list (fname, n_list,type,seq_source))==NULL)
- {
- fprintf ( stderr, "\nNO SEQUENCE WAS SPECIFIED[FATAL]\n");
- myexit(EXIT_FAILURE);
- }
- else if (CL->S==NULL)
- {
- CL->S=S;
- }
-
- /*CHECK IF THERE IS A MATRIX AND GET RID OF OTHER METHODS*/
- for (b=0, a=0; a< n_list; a++)if (is_matrix(fname[a]) ||is_matrix(fname[a]+1) )b=a+1;
-
- if ( b)
- {
- if ( b==1);
- else sprintf ( fname[0], "%s", fname[b-1]);
- n_list=1;
-
- }
-
- if (!CL)CL=declare_constraint_list ( S,NULL, NULL, 0,(strm(mem_mode, "disk"))?tmpfile():NULL, NULL);
- CL->local_stderr=local_stderr;
- fprintf ( CL->local_stderr,"\nREAD/MAKE LIBRARIES:[%d]\n",n_list );
-
- CL=read_constraint_list (CL, fname[0], in_mode, mem_mode,weight_mode);
- compact_list (CL, 0, CL->ne, "default");
- for ( a=1; a< n_list; a++)
- {
- CL=read_constraint_list (CL, fname[a], in_mode, mem_mode,weight_mode);
- if (strm (weight_mode, "cons"))compact_list (CL, 0, CL->ne, "cons");
- else
- compact_list (CL, 0, CL->ne, "default");
- }
- CL->local_stderr=local_stderr;
-
- CL=evaluate_constraint_list_reference (CL);
-
- return CL;
- }
-Constraint_list* read_constraint_list(Constraint_list *CL,char *in_fname,char *in_mode, char *mem_mode,char *weight_mode)
- {
- Sequence *SL=NULL, *TS=NULL;
- int a;
- Constraint_list *SUBCL=NULL;
- static char *read_mode;
- char *fname;
-
- fname=in_fname;
- if ( !read_mode)read_mode=vcalloc ( STRING, sizeof (char));
-
- if ( is_lib_list (in_fname))sprintf ( read_mode, "lib_list");
- else if ( in_mode)sprintf (read_mode, "%s", in_mode);
- else if ( fname[0]=='A'){sprintf ( read_mode, "aln");fname++;}
- else if ( fname[0]=='L'){sprintf ( read_mode, "lib");fname++;}
- else if ( fname[0]=='M'){sprintf ( read_mode, "method");fname++;}
- else if ( fname[0]=='S'){sprintf ( read_mode, "sequence");return CL;}
- else if ( fname[0]=='P'){sprintf ( read_mode, "pdb") ;return CL;}
- else if ( fname[0]=='R'){sprintf ( read_mode, "profile") ;return CL;}
- else if ( fname[0]=='X'){sprintf ( read_mode, "matrix");++fname;}
- else if ( fname[0]=='W'){sprintf ( read_mode, "structure");fname++;}
-
- else
- {
- fprintf ( stderr, "\nERROR: The descriptor %s could not be identified as a file or a method.[FATAL]\nIf it is a method file please indicate it with M%s\n", fname, fname);
- myexit (EXIT_SUCCESS);
- }
-
- fprintf (CL->local_stderr, "\n\t%s [%s]\n", fname, read_mode);
-
-
- if ( strm (read_mode, "lib_list"))
- {
- int n, a;
- char **l;
- l=read_lib_list (fname, &n);
- for ( a=0; a<n; a++)
- CL=read_constraint_list (CL,l[a],in_mode, mem_mode,weight_mode);
- free_char (l,-1);
- }
- else if (strm(read_mode, "binary"))
- {
- fprintf ( stderr, "\nERROR: Library %s: binary mode is not any more supported [FATAL:%s]\n", fname,PROGRAM);
- myexit (EXIT_FAILURE);
- }
- else if ( strm (fname, "make_test_lib"))
- {
- CL=make_test_lib (CL);
- }
- else if ( strm2 (read_mode,"ascii","lib"))
- {
- SUBCL=read_constraint_list_file(NULL, fname);
- }
- else if (strm(read_mode, "method"))
- {
- CL=produce_list ( CL, CL->S, fname,weight_mode,mem_mode);
- }
- else if (strm(read_mode, "matrix"))
- {
- CL->L=NULL;
- CL->extend_jit=0;
- CL->M=read_matrice ( fname);
- }
- else if ( strm ( read_mode, "structure"))
- {
- if ( CL->ne>0)
- {
- fprintf ( stderr, "\nERROR: Wstructure must come before Mmethod or Aaln [FATAL:%s]",PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
- if ( !(CL->STRUC_LIST))
- {
- CL->STRUC_LIST=declare_sequence (1,1,10000);
- (CL->STRUC_LIST)->nseq=0;
- }
- SL=CL->STRUC_LIST;
-
- if ( check_file_exists(fname))
- {
- TS=main_read_seq ( fname);
- for (a=0; a<TS->nseq; a++)sprintf (SL->name[SL->nseq++], "%s", TS->name[a]);
- free_sequence (TS, TS->nseq);
- }
- else
- {
- sprintf (SL->name[SL->nseq++], "%s", fname);
- }
- }
- else if (strm (read_mode, "aln"))
- {
- SUBCL=aln_file2constraint_list ( fname,SUBCL,weight_mode);
- }
- else
- {
- SUBCL=read_constraint_list_file(SUBCL, fname);
- }
-
- if (SUBCL)
- {
- CL=merge_constraint_list (SUBCL, CL, "default");
- free_constraint_list_full (SUBCL);
- }
-
- return CL;
- }
-
-#define is_seq_source(Symbol,Mode,SeqMode) (Symbol==Mode && (SeqMode==NULL || strm (SeqMode, "ANY") || (SeqMode[0]!='_' && strchr (SeqMode,Symbol)) || (SeqMode[0]=='_' && !strchr (SeqMode,Symbol))))
-Sequence * read_seq_in_n_list(char **fname, int n, char *type, char *SeqMode)
- {
- int nseq=0;
- int a, b;
- Alignment *A;
- char **sequences=NULL;
- char **seq_name=NULL;
- Sequence *S=NULL;
- Sequence *S1;
- char mode;
-
-
-
- /*THE TYPE OF EACH FILE MUST BE INDICATED*/
- /*SeqMode indicates the type of file that can be used as sequence sources*/
- /*
- ANY: any mode
- SL: only sequences from Libraries and Sequences
- _A: anything BUT sequences from A(lignments)
- */
-
- if ( n==0)
- {
- fprintf ( stderr, "\nERROR: NO IN FILE [FATAL:%s]\n", PROGRAM);
- myexit (EXIT_FAILURE);
- }
- else
- {
- for ( a=0; a< n ; a++)
- {
- static char *buf;
- char *lname;
- if (buf)vfree (buf);
-
- buf=name2type_name(fname[a]);mode=buf[0];lname=buf+1;
-
- if (is_seq_source ('A', mode, SeqMode))
- {
-
-
- A=main_read_aln (lname,NULL);
- S1=aln2seq(A);
- S1=seq2unique_name_seq (S1);
- if ((S=merge_seq ( S1, S))==NULL){fprintf ( stderr, "\nERROR: Sequence Error in %s [FATAL:%s]\n",lname, PROGRAM); myexit(EXIT_FAILURE);}
- free_aln (A);
- free_sequence (S1, S1->nseq);
- }
- else if ( is_seq_source ('R', mode, SeqMode))
- {
- S=add_prf2seq (lname, S);
-
- }
- else if (is_seq_source ('P', mode, SeqMode))
- {
- int i;
-
- S1=get_pdb_sequence (lname);
- if (S1==NULL)
- {
- add_warning ( stderr, "\nWarning: Could not use PDB: %s", lname);
- }
- else
- {
- if ((S=merge_seq ( S1, S))==NULL){fprintf ( stderr, "\nERROR: Sequence Error in %s [FATAL:%s]\n",lname, PROGRAM); myexit(EXIT_FAILURE);}
- i=name_is_in_list (S1->name[0], S->name, S->nseq, 100);
- (S->T[i])->P=fill_P_template (S->name[i], lname, S);
- }
- free_sequence (S1, S1->nseq);
- }
- else if ( mode=='M');
- else if ( mode=='X');
- else if ( mode=='W');
-
- else if (is_seq_source ('S', mode, SeqMode))
- {
- /*1 Try with my routines (read t_coffee and MSF)*/
- if ( (A=main_read_aln ( lname, NULL))!=NULL)
- {
-
- S1=aln2seq(A);
- free_aln(A);
- }
- else
- {
- S1=main_read_seq (lname);
- }
-
- for ( b=0; b< S1->nseq; b++)ungap(S1->seq[b]);
- S1=seq2unique_name_seq (S1);
-
-
- if ((S=merge_seq ( S1, S))==NULL){fprintf ( stderr, "\nSequence Error in %s [FATAL:%s]\n",lname,PROGRAM); myexit(EXIT_FAILURE);}
-
- free_sequence (S1,S1->nseq);
-
- }
- else if (is_seq_source ('L', mode, SeqMode))
- {
-
- read_seq_in_list (lname,&nseq,&sequences,&seq_name);
-
- S1=fill_sequence_struc ( nseq, sequences, seq_name);
-
- for ( b=0; b< S1->nseq; b++)sprintf ( S1->file[b], "%s", lname);
- nseq=0;free_char (sequences, -1); free_char ( seq_name, -1);
- sequences=NULL;
- seq_name=NULL;
- S1=seq2unique_name_seq (S1);
-
- if ((S=merge_seq( S1, S))==NULL){fprintf ( stderr, "\nSequence Error in %s [FATAL:%s]\n",lname,PROGRAM); myexit(EXIT_FAILURE);}
- free_sequence(S1, S1->nseq);
- }
-
- else if ( !strchr ( "ALSMXPRWG", mode))
- {
- fprintf ( stderr, "\nERROR: %s is neither a file nor a method [FATAL:%s]\n", lname, PROGRAM);
- crash ("");
-
- }
- }
-
- S=remove_empty_sequence (S);
-
-
- if ( type && type[0] )sprintf ( S->type, "%s", type);
- else S=get_sequence_type (S);
-
- if ( strm (S->type, "PROTEIN_DNA"))
- {
- for ( a=0; a< S->nseq; a++)
- {
- if (strm ( get_string_type ( S->seq[a]), "DNA") ||strm ( get_string_type ( S->seq[a]), "RNA") );
- else if ( strm ( get_string_type ( S->seq[a]), "PROTEIN"))
- {
- S->seq[a]=thread_aa_seq_on_dna_seq (S->seq[a]);
- S->len[a]=strlen (S->seq[a]);
- S->max_len=MAX(S->max_len, S->len[a]);
- }
- }
- }
-
-
-
- return S;
- }
-
-
-
- return NULL;
- }
-
-int read_cpu_in_list ( char *fname)
- {
- FILE *fp;
- int c;
- int cpu=0;
-
- fp=vfopen ( fname, "r");
- while ( (c=fgetc(fp))!='#');
- while ( (c=fgetc(fp))!='C' && c!=EOF);
- if ( c=='C')fscanf( fp, "PU %d\n", &cpu);
- vfclose ( fp);
- return cpu;
- }
-char * expand_constraint_list_file ( char *file)
-{
- char *new_file;
- FILE *IN, *OUT;
- int a, b, c, n;
- char **list;
- static char *buf;
-
- if ( !grep_function ( "'+BLOCK+'", file))return file;
-
- new_file=vtmpnam (NULL);
- IN=vfopen ( file,"r");
- OUT=vfopen (new_file, "w");
-
- while ( (c=fgetc (IN))!=EOF)
- {
- ungetc (c, IN);
- buf=vfgets (buf, IN);
- if ( !strstr (buf, "+BLOCK+"))
- fprintf (OUT, "%s", buf);
- else
- {
- list=string2list (buf);
- n=atoi (list[2]);
-
- for (a=0; a< n; a++)
- {
- fprintf ( OUT, "%5d %5d ",atoi(list[3])+a, atoi(list[4])+a);
- for (b=5; b<atoi(list[0]); b++) fprintf ( OUT, "%s ", list[b]);
- fprintf (OUT, "\n");
- }
- free_char (list, -1);
- }
- }
- vfclose (IN); vfclose (OUT);
- return new_file;
-}
-
-
-Constraint_list * make_test_lib(Constraint_list *CL)
-{
- int a, b, c, l1;
- Sequence *S;
- HERE ("cncn: making artificial lib");//Keep this warning alive
- S=CL->S;
-
- fprintf ( stderr, "\n");
- for (a=0; a< S->nseq-1; a++)
- {
- fprintf ( stderr, "[%d-%d]", a, CL->ne);
- for ( b=a+1; b< S->nseq; b++)
- {
- l1=MIN(S->len[a], S->len[b]);
- l1=MIN(10, l1);
- for (c=0; c<l1; c++)
- {
- vwrite_clist( CL,CL->ne,0,a);
- vwrite_clist( CL,CL->ne,1,b);
- vwrite_clist( CL,CL->ne,2,c+1);
- vwrite_clist( CL,CL->ne,3,c+1);
- vwrite_clist( CL,CL->ne,4,100);
- CL->ne++;
- }
- }
- }
- return CL;
-}
-Constraint_list * read_constraint_list_file(Constraint_list *CL, char *fname)
- {
- int a, c,e,n,z;
- int seq_len, sn;
- int s1, s2;
- FILE *fp;
- static char *name;
- char *sequence;
- static char *mat;
- static char *dp_mode;
- int max_nseq=0;
- static int *sn_list;
- static int line=2;
- int list_nseq;
- static CLIST_TYPE *entry;
- Sequence *S;
- Sequence *small_S;
- int seq_1_to_n=0;
- Alignment *B=NULL;
- char *buf;
- int lline;
- char *stripped_file1;
- char *stripped_file;
-
-
-
-
-
- stripped_file1=strip_file_from_comments ("!", fname);
- stripped_file=expand_constraint_list_file (stripped_file1);
- small_S=read_seq_in_n_list (&fname, 1,NULL, NULL);
-
- if ( !CL)
- {
- CL=declare_constraint_list ( small_S,NULL, NULL, 0,NULL, NULL);
- CL->S=small_S;
- }
-
- small_S=read_seq_in_n_list (&fname, 1, (CL->S)->type, NULL);
-
- B=seq2aln (small_S, NULL, 1);
- B=fix_aln_seq ( B, (CL->S));
-
- if ( CL->S!=small_S)free_sequence (small_S, B->nseq);
-
- lline=measure_longest_line_in_file (fname)+1;
-
- if ( !mat) mat=vcalloc (STRING, sizeof (char));
- if ( !dp_mode) dp_mode=vcalloc (STRING, sizeof (char));
- fp=vfopen (fname, "r");
- while((c=fgetc(fp))!='#')if ( c=='\n')max_nseq++;
- vfclose (fp);
-
- buf=vcalloc (lline, sizeof (char));
- sequence=vcalloc (lline, sizeof (char));
- if ( !name)name=vcalloc ( 100, sizeof (char));
- if ( !entry)entry=vcalloc ( CL->entry_len, CL->el_size);
- if ( !sn_list)sn_list=vcalloc (max_nseq, sizeof (int));
- else
- {
- sn_list=vrealloc (sn_list, max_nseq*sizeof (int));
- }
- S=CL->S;
-
- seq_1_to_n=((fp=find_token_in_file (fname, NULL, "SEQ_1_TO_N"))!=NULL);
- vfclose (fp);
- if ( sn_list==NULL)sn_list=vcalloc (max_nseq, sizeof (int));
-
- /*Read Constraint list*/
- fp=vfopen(stripped_file,"r");
- fscanf ( fp, "%d\n", &list_nseq);
- for ( a=0; a<list_nseq; a++)
- {
- fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence);
- line++;
- lower_string (sequence);
-
- if ((sn=name_is_in_list (name,S->name, S->nseq, 100))==-1){continue;}
- else
- {
- sn_list[a]=sn;
- }
- }
-
- while ((c=fgetc(fp))!=EOF)
- {
- ungetc(c, fp);
- if ( c=='#')
- {
- fscanf ( fp, "#%d %d\n", &s1, &s2);line++;
- /*Check If the sequence numbering is legal*/
- if ( seq_1_to_n){s1--; s2--;}
-
- if (s1<0 || s2 <0)
- {
- fprintf (stderr, "ERROR: Wrong Sequence Numbering in %s [FATAL:%s]\n",fname, PROGRAM);
- myexit (EXIT_FAILURE);
- }
-
-
-
- s1=sn_list[s1];
- s2=sn_list[s2];
-
- while (isdigit((c=fgetc(fp))))
- {
-
- for ( z=0; z< CL->entry_len; z++)entry[z]=0;
- ungetc(c, fp);
- n=0;
- entry[n++]=s1;
- entry[n++]=s2;
- while ( (c=fgetc(fp))!='\n')
- {
-
- if ( isspace (c));
- else
- {
- ungetc(c, fp);
- fscanf ( fp, "%d", &entry[n]);
- n++;
- }
-
- if ( n>CL->entry_len)
- {
- add_warning ( stderr, "\nWARNING:PARSING ERROR #1 (Too many Fields) IN %s AT LINE %d: C=%c n=%d\n", fname,line, c,n);
- for ( e=2; e<LIST_N_FIELDS; e++)
- fprintf ( stderr, "%d ", entry[e]);
-
- myexit (EXIT_FAILURE);
- }
- }
- if (c=='\n')line++;
-
- if ( n<=CONS)entry[CONS]=1;
-
-
- /*Check The legality of the entry*/
- if ( n>0 && n<3)
- {
- add_warning ( stderr, "\nWARNING:PARSING ERROR #2 IN %s (Not enough Fields) AT LINE %d: C=%c\n", fname,line-1, c);
- for ( e=2; e<LIST_N_FIELDS; e++)
- fprintf ( stderr, "%d ",entry[e]);
-
- myexit (EXIT_FAILURE);
- }
-
- entry[R1]=(B->seq_cache)?B->seq_cache[entry[SEQ1]][entry[R1]]:entry[R1];
- entry[R2]=(B->seq_cache)?B->seq_cache[entry[SEQ2]][entry[R2]]:entry[R2];
-
- if ( entry[R1] && entry[R2])
- {
- if ( entry[R1]<=0 || entry[R1]>(CL->S)->len[s1])
- {
- fprintf ( stderr, "\nERROR: Seq1=%d (len=%d, name=%s), Seq2=%d (len=%d, name=%s), Res1 %d, Res2 %d\n", entry[SEQ1]+1,(CL->S)->len[s1],(CL->S)->name[s1], entry[SEQ2]+1,(CL->S)->len[s2],(CL->S)->name[s2],entry[R1], entry[R2]);
- fprintf ( stderr, "\nERROR: Library %s, line %d, Field 1: Bad residue numbering (%d)[FATAL:%s]\n", fname, line-1,entry[R1], PROGRAM);
- myexit (EXIT_FAILURE);
- }
- else if (entry[R2]<=0 || entry[R2]>(CL->S)->len[s2])
- {
- fprintf ( stderr, "\nERROR: Seq1=%d (len=%d, name=%s), Seq2=%d (len=%d, name=%s), Res1 %d, Res2 %d\n", entry[SEQ1]+1,(CL->S)->len[s1],(CL->S)->name[s1], entry[SEQ2]+1,(CL->S)->len[s2],(CL->S)->name[s2],entry[R1], entry[R2]);
-
- fprintf ( stderr, "\nERROR: Seq1: %d, Seq2 %d, Res1 %d, Res2 %d\n", entry[SEQ1], entry[SEQ2], entry[R1], entry[R2]);
- fprintf ( stderr, "\nERROR: Library %s, line %d, Field 2: Bad residue numbering (%d)[FATAL:%s]\n", fname, line-1, entry[R2],PROGRAM);
- myexit (EXIT_FAILURE);
- }
- fscanf ( fp, "\n");
- if ( (entry[SEQ1]>entry[SEQ2])|| (entry[SEQ1]==entry[SEQ2] && entry[R1]>entry[R2]))
- {
- SWAP(entry[SEQ1],entry[SEQ2]);
- SWAP(entry[R1], entry[R2]);
- }
-
- for ( z=0; z< CL->entry_len; z++)vwrite_clist( CL,CL->ne, z, entry[z]);
-
- CL->ne++;
- }
- }
- ungetc ( c, fp);
-
- }
- else if ( c=='!' || c=='C' || c=='\n' || c=='\r'){while ((c=fgetc(fp))!='\n' && c!=EOF && c!='\r');}
- else
- {
- fprintf ( stderr, "\n\n PARSING ERROR 3 IN %s AT LINE %d: [%c] \n[read_constraint_list_file]", fname,line,c);
- while ((c=fgetc(fp))!='\n' && c!=EOF)fprintf ( stderr, "%c", c);
- fprintf ( stderr, "\n");
- printf_system ( "cp %s faulty_library.tc_lib", fname);
- myexit (EXIT_FAILURE);
- }
- if ( c==EOF)ungetc(c, fp);
- }
-
- free_aln (B);
- vfree(buf);
- vfree(sequence);
- vfclose (fp);
- remove(stripped_file);
- return CL;
- }
-
-Constraint_list * read_constraint_list_raw_file(Constraint_list *CL, char *fname)
-{
- FILE *fp;
- int n=0, v;
- static int *entry;
-
- if ( !entry)entry=vcalloc (CL->entry_len, sizeof (int));
- fp=vfopen (fname, "r");
-
- while (fscanf (fp, "%d ", &v)==1)
- {
- if (n==CL->entry_len)
- {
- add_entry2list (entry, CL);
- n=0;
- }
- entry[n++]=v;
- }
- if (n==CL->entry_len)
- {
- add_entry2list (entry, CL);
- n=0;
- }
- vfclose (fp);
- return CL;
-}
-
-Constraint_list * fast_read_constraint_list_file(Constraint_list *CL, char *in_fname)
- {
- Sequence *NS;
- int **index;
- int *list=NULL;
- int c;
- FILE *fp;
- CLIST_TYPE *entry=NULL;
- char *buf=NULL, *buf2;
- char *fname;
- int i;
-
-
-
- fname=expand_constraint_list_file (in_fname);
-
- if (!CL)
- {
- return read_constraint_list_file (CL,fname);
- }
-
- entry=vcalloc (sizeof (int), CL->entry_len);
- NS=read_seq_in_n_list (&fname, 1,NULL, NULL);
- index=index_seq_name(NS,CL->S);
-
-
- /*Read Constraint list*/
- fp=vfopen(fname,"r");
- i=0;
- while (i<=NS->nseq)
- {
- buf=vfgets ( buf, fp);
- if (buf[0]!='!')i++;
- }
-
- while ( (c=fgetc (fp))!='#' && c!=EOF);
- if (c==EOF)
- {
- vfclose (fp);
- vfree (list);
- free_sequence (NS,-1);
- vfree (entry);
- vfree (buf);
- add_warning (stderr, "Warning: incomplete library [%s]",PROGRAM);
- return CL;
- }
- ungetc (c, fp);
-
-
-
- while ((buf2=vfgets ( buf, fp))!=NULL)
- {
- if (buf2[0]=='!')continue;
- buf=buf2;
-
- list=string2num_list2 (buf, " #\n");
-
- if (buf[0]=='#')
- {
- sscanf ( buf, "#%d %d", &entry[SEQ1], &entry[SEQ2]);
- entry[SEQ1]=index[entry[SEQ1]-1][0];
- entry[SEQ2]=index[entry[SEQ2]-1][0];
-
- }
- else
- {
- sscanf (buf, "%d %d %d %d %d", &entry[R1], &entry[R2], &entry[WE], &entry[CONS], &entry[MISC]);
-
-
-
-
-
-
- if ( (entry[SEQ1]>entry[SEQ2])|| (entry[SEQ1]==entry[SEQ2] && entry[R1]>entry[R2]))
- {
- SWAP(entry[SEQ1],entry[SEQ2]);SWAP(entry[R1], entry[R2]);
- }
- add_entry2list (entry, CL);
- }
- }
- vfclose (fp);
-
-
-
- vfree (list);
- free_sequence (NS,-1);
- vfree (entry);
- vfree (buf);
-
- return CL;
- }
-
-int read_seq_in_list ( char *fname, int *nseq, char ***sequences, char ***seq_name)
- {
- int a;
- int seq_len, sn;
-
- FILE *fp;
- char name[1000];
- char *sequence;
- static int max_nseq;
- static int *sn_list;
- int list_nseq;
- int lline;
-
-
-
- fp=vfopen (fname, "r");
- fp=skip_commentary_line_in_file ('!', fp);
- fscanf (fp, "%d\n", &max_nseq);
- for ( lline=0,a=0; a<max_nseq; a++)
- {
- int l;
- fscanf (fp, "%*s %d %*s\n", &l);
- lline=MAX(lline, l);
- }
- vfclose (fp);
- sequence=vcalloc (lline, sizeof (char)+1);
-
-
-
- if ( seq_name[0]==NULL)
- {
- seq_name[0]= declare_char (max_nseq,0);
- sequences[0]=declare_char (max_nseq,0);
- }
- if ( sn_list==NULL)sn_list=vcalloc ( max_nseq, sizeof (int));
- else sn_list=vrealloc (sn_list, max_nseq*sizeof (int));
-
- fp=vfopen (fname,"r");
- fp=skip_commentary_line_in_file ('!', fp);
- if (fscanf ( fp, "%d\n", &list_nseq)!=1)return 0;
- for ( a=0; a<max_nseq; a++)
- {
- fp=skip_commentary_line_in_file ('!', fp);
-
- fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence);
- lower_string (sequence);
-
- if ((sn=name_is_in_list (name, seq_name[0], nseq[0], 100))==-1)
- {
- seq_name[0][nseq[0]]=vcalloc (strlen (name)+1, sizeof (char));
- sprintf (seq_name[0][nseq[0]], "%s", name);
- sequences[0][nseq[0]]=vcalloc (strlen (sequence)+1, sizeof (char));
- sprintf (sequences[0][nseq[0]], "%s", sequence);
- sn_list[a]=nseq[0];
- nseq[0]++;
- }
- else
- {
- sn_list[a]=sn;
- }
- }
- vfclose (fp);
- vfree (sequence);
- return 1;
- }
-
-
-/*********************************************************************/
-/* */
-/* EXTENDED LIST OUTPUT */
-/* */
-/* */
-/*********************************************************************/
-
-FILE * save_extended_constraint_list ( Constraint_list *CL, char *mode, FILE *fp)
-{
- int a, b;
-
- if ( !fp)fp=stdout;
-
-
- fp=save_list_header (fp,CL);
-
-
- for ( a=0; a< (CL->S)->nseq; a++)
- {
- for ( b=a; b<(CL->S)->nseq; b++)
- {
-
- if ( a==b && !CL->do_self)continue;
- fp=save_extended_constraint_list_pair(CL, mode, (CL->S)->name[a], (CL->S)->name[b], fp);
- }
- }
- fprintf (fp, "! SEQ_1_TO_N\n");
- return fp;
-}
-
-
-FILE * save_extended_constraint_list_pair ( Constraint_list *CL, char *mode, char* seq1, char * seq2,FILE *fp)
- {
- int a, b, t;
- int s1, s2, score;
- char *p;
-
-
- if ((p=strstr (mode, "THR"))!=NULL)t=atoi(p+3);
- else t=0;
-
- s1=name_is_in_list (seq1,(CL->S)->name, (CL->S)->nseq, 100);
- s2=name_is_in_list (seq2,(CL->S)->name, (CL->S)->nseq, 100);
-
- if ( s1==-1)
- {
- fprintf ( stderr, "Output Error: %s is not a sequence [FATAL:%s]\n", seq1, PROGRAM);
- crash ("");
- }
- if ( s2==-1)
- {
- fprintf ( stderr, "Output Error: %s is not a sequence [FATAL:%s]\n", seq2, PROGRAM);
- crash ("");
- }
-
- if ( strstr (mode, "pair"))fprintf (fp, "# 1 2\n");
- else if ( strstr (mode, "lib"))fprintf (fp, "# %d %d\n", s1+1, s2+1);
-
- for ( a=0; a<(CL->S)->len[s1]; a++)
- {
- for ( b=0; b<(CL->S)->len[s2]; b++)
- {
- if ( a>=b && s1==s2)continue;
- if ( strstr (mode, "pc"))score=residue_pair_extended_list_pc (CL, s1,a+1, s2, b+1);
- else if ( strstr (mode, "raw"))score=residue_pair_extended_list_raw (CL, s1,a+1, s2, b+1);
- else
- score=CL->evaluate_residue_pair (CL, s1,a+1, s2, b+1);
-
- if (score<=t) continue;
- fprintf (fp, "%5d %5d %5d \n", a+1, b+1, score);
-
- }
- }
- return fp;
- }
-
-
-/*********************************************************************/
-/* */
-/* LIST OUTPUT */
-/* */
-/* */
-/*********************************************************************/
-#ifdef MMMMMMMM
-FILE *save_extended_constraint_list ( Constraint_list *CL,Sequence *S, char *fname)
-{
- int a, b, c, d;
- int *tr, *ns;
- int **pos0, **l_s;
- int epsilon=0;
- Alignment *A;
- FILE *fp;
-
- fp=vfopen (fname, "w");
- fp=save_sub_list_header(fp, S->nseq, S->name, CL);
-
- tr=vcalloc (S->nseq+1, sizeof (int));
- for ( b=0,a=0; a< S->nseq; a++)
- {
- int i;
- if ( (i=name_is_in_list(S->name[a],(CL->S)->name,(CL->S)->nseq, 100))==-1)
- {
- printf_exit (EXIT_FAILURE, stderr, "\nERROR: Sequence %s is not part of the sequence dataset [FATAL:%s]", S->name[a], PROGRAM);
-
- }
- else
- {
- tr[a]=i;
- }
- }
-
- A=declare_aln (S);
- pos0=vcalloc ( S->nseq, sizeof (int*));
- for (a=0; a<S->nseq; a++)
- {
- int l;
- l=strlen (S->seq[a]);
- A->seq_al[a]=S->seq[a];
- pos0[a]=vcalloc (l+1, sizeof (int));
- for (b=0; b<l; b++)pos[a][b]=b+1;
- }
- l_s=declare_int (2,2);
- ns=vcalloc ( 2, sizeof (int));
-
-
- for ( a=0; a< S->nseq-1; a++)
- for ( b=a+1; b<S->nseq; b++)
- {
- int pos_i, pos_j, s;
- l_s[0]=tr[a];l_s[1]=tr[b];
- for ( pos_i=0; pos_i< S->len[a]; pos_i++)
- for (pos_j=0; pos_j<S->len[b]; pos_j++)
- {
- s=(CL->get_dp_cost) ( A, pos0, ns[0], l_s[0], i-1, pos0, ns[1], l_s[1],pos_j-1, CL);
- if (s>epsilon)fprintf (fp, "%d %d %d", i, j, s);
- }
- }
- return fp;
-}
-#endif
-
-FILE * save_constraint_list ( Constraint_list *CL,int start, int len, char *fname, FILE *fp,char *mode, Sequence *S)
- {
- int a, b;
- static int* translation;
-
-
-
-
- if ( fp==NULL)
- {
- if ( translation!=NULL)vfree(translation);
- translation=vcalloc ( (CL->S)->nseq+1, sizeof (int));
- for ( b=0,a=0; a< (CL->S)->nseq; a++)
- {
- if ( name_is_in_list((CL->S)->name[a],S->name,S->nseq, 100)==-1)
- {
- (CL->S)->len[a]=-1;
- translation [a]=-1;
- }
- else
- {
- translation[a]=b++;
- }
- }
-
- }
- if (strm2(mode, "lib","ascii"))
- {
- if ( fp==NULL)fp=vfopen ( fname, "w");
- fp=save_list_header (fp,CL);
- fp=save_constraint_list_ascii(fp, CL, 0, CL->ne, translation);
- }
- else if (strm(mode, "binary"))
- {
- if ( fp==NULL)fp=vfopen ( fname, "wb");
- fp=save_constraint_list_bin (fp, CL, 0, CL->ne, translation);
- }
- else
- {
- fprintf (stderr,"\nUNKOWN MODE FOR OUTPUT: %s [FATAL]\n",mode);
- crash ("");
- }
- return fp;
- }
-
-FILE * save_sub_list_header ( FILE *OUT, int n, char **name, Constraint_list *CL)
- {
- int a,b;
- int nseq=0;
-
-
-
- for ( a=0; a<(CL->S)->nseq; a++)
- for ( b=0; b<n; b++)
- if (strm (name[b] , (CL->S)->name[a]))
- nseq+=((CL->S)->len[a]!=-1);
-
- fprintf ( OUT, "! TC_LIB_FORMAT_01\n%d\n",nseq);
- for ( a=0; a<n; a++)
- for ( b=0; b<(CL->S)->nseq; b++)
- if (strm (name[a] , (CL->S)->name[b]))
- if ((CL->S)->len[b]!=-1) fprintf ( OUT, "%s %d %s\n", (CL->S)->name[b], (CL->S)->len[b],(CL->S)->seq[b]);
-
- return OUT;
- }
-FILE * save_list_header ( FILE *OUT,Constraint_list *CL)
- {
- int a;
- int nseq=0;
-
- for ( a=0; a<(CL->S)->nseq; a++)nseq+=((CL->S)->len[a]!=-1);
-
-
- fprintf ( OUT, "! TC_LIB_FORMAT_01\n%d\n",nseq);
- for ( a=0; a<(CL->S)->nseq; a++)
- if ((CL->S)->len[a]!=-1)
- {
- fprintf ( OUT, "%s %d %s\n", (CL->S)->name[a], (CL->S)->len[a],(CL->S)->seq[a]);
-
- }
- return OUT;
- }
-
-FILE *save_list_footer (FILE *OUT,Constraint_list *CL)
- {
- if ( CL->cpu)fprintf (OUT, "! CPU %d\n",get_time());
- fprintf (OUT, "! SEQ_1_TO_N\n");
- return OUT;
- }
-int constraint_list2raw_file ( Constraint_list *CL, char *fname, char *mode)
-{
- FILE *fp;
- if ( !CL || !CL->ne || !fname){return 0;}
-
- fp=vfopen (fname,mode);
- fp=save_raw_constraint_list (fp, CL, 0, CL->ne, NULL);
- vfclose (fp);
- return CL->ne;
- }
-FILE * save_raw_constraint_list ( FILE *fp,Constraint_list *CL, int start,int len, int *translation)
-{
- int a, b;
- for ( b=0; b<CL->entry_len*CL->ne; b++)
- {
- fprintf ( fp, "%d ", CL->L[b]);
- }
-
- fprintf (fp, "\n");
- return fp;
-}
-FILE * save_constraint_list_ascii ( FILE *OUT,Constraint_list *CL, int start,int len, int *translation)
- {
- int a, b, s1, s2;
- CLIST_TYPE x1, x2;
-
- if (len==start && CL->cpu!=-1)
- {
- fprintf (OUT, "! CPU %d\n",get_time());
- return OUT;
- }
- else
- {
-
- s1=translation[vread_clist(CL,start,SEQ1)];
- s2=translation[vread_clist(CL,start,SEQ2)];
-
-
- if ( s1!=-1 && s2!=-1)fprintf ( OUT, "#%d %d\n", s1+1, s2+1);
- for ( a=start; a<(len+start); a++)
- {
- x1=translation[vread_clist(CL,a,SEQ1)];
- x2=translation[vread_clist(CL,a,SEQ2)];
- if ( x1==-1 || x2==-1);
- else
- {
- if ( x1!=s1 || x2!=s2)
- {
- s1=x1;
- s2=x2;
- fprintf ( OUT, "#%d %d\n", s1+1, s2+1);
- }
- for ( b=2; b<CL->entry_len; b++) fprintf ( OUT, "%5d ", vread_clist(CL, a, b));
- fprintf (OUT, "\n");
- }
- }
- }
- return save_list_footer (OUT, CL);
-
- }
-FILE * save_constraint_list_bin ( FILE *OUT,Constraint_list *CL, int start,int len, int *translation)
- {
- int a, b;
-
- CLIST_TYPE x1, x2;
-
-
- if (len==start && CL->cpu!=-1)
- {
-
- return OUT;
- }
- else
- {
- for ( a=start; a<(len+start); a++)
- {
- x1=translation[vread_clist(CL,a,SEQ1)];
- x2=translation[vread_clist(CL,a,SEQ2)];
- if ( x1==-1 || x2==-1);
- else
- {
- for ( b=2; b<CL->entry_len; b++)
- {
- x1=vread_clist(CL,a,b);
- fwrite (&x1, CL->el_size, 1, OUT);
- }
- }
- }
- }
- return OUT;
- }
-
-/*********************************************************************/
-/* */
-/* LIST CONVERTION */
-/* */
-/* */
-/*********************************************************************/
-Constraint_list * filter_constraint_list (Constraint_list *CL, int field, int T)
-{
- int a,b,c;
- if (!CL || !CL->L)return CL;
- for (a=0, b=0; a<CL->ne; a++)
- {
- if (CL->L[a*CL->entry_len+field]<T);
- else
- {
- for (c=0; c<CL->entry_len; c++)CL->L[b*CL->entry_len+c]=CL->L[a*CL->entry_len+c];
- b++;
- }
- }
- CL->ne=b;
- CL->residue_indexed=0;
- return CL;
-}
-int constraint_list_is_connected ( Constraint_list *CL)
-{
- int a, b, c, s1, s2;
- int *connexions;
- int rv =1;
- Sequence*S;
-
- if (!CL->ne) return 1;
-
- S=CL->S;
-
- connexions=vcalloc ((CL->S)->nseq+1, sizeof (int));
- for ( a=0; a< CL->ne; a++)
- {
- s1=CL->L[a*CL->entry_len+SEQ1];
- s2=CL->L[a*CL->entry_len+SEQ2];
- connexions[s1]++;
- connexions[s2]++;
- }
- for (a=0; a<S->nseq; a++)
- {
- if (!connexions[a])
- {
- add_warning ( stderr, "ERROR: Sequence %s is not connected\n", (CL->S)->name[a]);
- rv=0;
- }
- }
- return rv;
-}
-Constraint_list * nfork_relax_constraint_list (Constraint_list *CL);
-Constraint_list * fork_relax_constraint_list (Constraint_list *CL);
-Constraint_list * relax_constraint_list (Constraint_list *CL)
-{
- if ( get_nproc()==1)return nfork_relax_constraint_list (CL);
- else if (strstr ( CL->multi_thread, "relax"))return fork_relax_constraint_list (CL);
- else return nfork_relax_constraint_list (CL);
-}
-
-Constraint_list * fork_relax_constraint_list (Constraint_list *CL)
-{
- int a, s1, s2, r1, r2,n;
- int score;
- int thr;
- int chunk, npid, job,pid;
- FILE *fp;
- char **pid_tmpfile;
- int * pid_list;
- int in;
-
- in=CL->ne;
- if (!CL || !CL->L)return CL;
-
- fprintf ( CL->local_stderr, "\nLibrary Relaxation: Multi_proc [%d] ", get_nproc());
-
- if ((chunk=CL->ne/get_nproc())==0)chunk=get_nproc();
-
-
- pid_tmpfile=vcalloc ((CL->ne/chunk)+1, sizeof (char*));
- pid_list =vcalloc (MAX_N_PID, sizeof (int *));
-
- for (npid=0,job=0; job<CL->ne; job+=chunk)
- {
- pid_tmpfile[npid]=vtmpnam(NULL);
- pid=vfork ();
- if (pid==0)
- {
- int s,e;
-
- initiate_vtmpnam (NULL);
- s=job;
- e=MIN((s+chunk),CL->ne);
- fp=vfopen (pid_tmpfile[npid], "w");
- for (a=s; a<e; a++)
- {
- if (job==0)output_completion (CL->local_stderr,a,chunk,1, "Submit Job");
- s1=CL->L[a*CL->entry_len+SEQ1];
- s2=CL->L[a*CL->entry_len+SEQ2];
-
- r1=CL->L[a*CL->entry_len+R1];
- r2=CL->L[a*CL->entry_len+R2];
- score=residue_pair_extended_list_pc (CL,s1, r1,s2, r2);
- CL->L[a*CL->entry_len+WE]=score;
- fprintf (fp, "%d %d ", a, score);
- }
- vfclose (fp);
- exit (EXIT_SUCCESS);
- }
- else
- {
- pid_list[pid]=npid;
- set_pid (pid);
- npid++;
- }
- }
-
- for (a=0; a<npid; a++)
- {
- int i;
- int j=0;
-
- pid=vwait (NULL);
- fp=vfopen (pid_tmpfile[pid_list[pid]], "r");
- while (fscanf (fp, "%d %d ",&i, &score)==2){CL->L[i*CL->entry_len+WE]=score;j++;}
- vfclose (fp);
- remove(pid_tmpfile[pid_list[pid]]);
- }
-
- vfree (pid_list);
- vfree (pid_tmpfile);
-
- thr=10;
-
- for (n=0,a=0; a< CL->ne; a++)
- {
- score=CL->L[a*CL->entry_len+WE];
-
- if (score<=thr);
- else
- {
- CL->L[n*CL->entry_len+SEQ1]=CL->L[a*CL->entry_len+SEQ1];
- CL->L[n*CL->entry_len+SEQ2]=CL->L[a*CL->entry_len+SEQ2];
- CL->L[n*CL->entry_len+R1]=CL->L[a*CL->entry_len+R1];
- CL->L[n*CL->entry_len+R2]=CL->L[a*CL->entry_len+R2];
- CL->L[n*CL->entry_len+WE]=score;
- n++;
- }
-
- }
-
- CL->L=vrealloc (CL->L, n*CL->entry_len*sizeof (int));
- CL->ne=n;
-
- fprintf ( CL->local_stderr, "\nTotal Relaxation: [%d]--->[%d] Entries\n",in, CL->ne);
- CL->residue_indexed=0;
- return CL;
-
-}
-
-Constraint_list * nfork_relax_constraint_list (Constraint_list *CL)
-{
- int a, s1, s2, r1, r2;
- int max, score, n;
- int thr;
-
- if (!CL || !CL->L)return CL;
-
- fprintf ( CL->local_stderr, "\nLibrary Relaxation:[%d] ", CL->ne);
- for (max=0,a=0; a<CL->ne; a++)
- {
-
- s1=CL->L[a*CL->entry_len+SEQ1];
- s2=CL->L[a*CL->entry_len+SEQ2];
-
- r1=CL->L[a*CL->entry_len+R1];
- r2=CL->L[a*CL->entry_len+R2];
-
- score=residue_pair_extended_list_pc (CL,s1, r1,s2, r2);
- //HERE ("%d %d", CL->L[a*CL->entry_len+WE],score);
- CL->L[a*CL->entry_len+WE]=score;
-
- }
-
- thr=10;
-
- for (n=0,a=0; a< CL->ne; a++)
- {
- score=CL->L[a*CL->entry_len+WE];
-
- if (score<=thr);
- else
- {
- CL->L[n*CL->entry_len+SEQ1]=CL->L[a*CL->entry_len+SEQ1];
- CL->L[n*CL->entry_len+SEQ2]=CL->L[a*CL->entry_len+SEQ2];
- CL->L[n*CL->entry_len+R1]=CL->L[a*CL->entry_len+R1];
- CL->L[n*CL->entry_len+R2]=CL->L[a*CL->entry_len+R2];
- CL->L[n*CL->entry_len+WE]=score;
- n++;
- }
-
- }
- CL->L=vrealloc (CL->L, n*CL->entry_len*sizeof (int));
- CL->ne=n;
-
- fprintf ( CL->local_stderr, "--->[%d]\n", CL->ne);
- CL->residue_indexed=0;
- return CL;
-
-}
-
-Constraint_list * shrink_constraint_list (Constraint_list *CL)
-{
- int a, b, n, tot;
- Constraint_list *CL2;
- Alignment *A, *B;
- int *ns, **ls;
-
- ns=vcalloc (2, sizeof (int));
- ls=declare_int ((CL->S)->nseq, 2);
-
- A=seq2aln (CL->S,NULL, RM_GAP);
- B=seq2aln (CL->S,NULL, RM_GAP);
- CL2=declare_constraint_list (CL->S,NULL, NULL, 0,NULL, NULL);
- n=(CL->S)->nseq;
- tot=((n*n)-n)/2;
- fprintf ( CL->local_stderr, "\n\n\tSHRINK Constraint List [%d element(s)]", CL->ne);
- for (n=0,a=0; a<(CL->S)->nseq-1; a++)
- for (b=a+1; b<(CL->S)->nseq; b++, n++)
- {
- output_completion (CL->local_stderr,n, tot, 100, "slow_pair");
- ns[0]=ns[1]=1;
- ls[0][0]=a;
- ls[1][0]=b;
- ungap (A->seq_al[a]);
- ungap (A->seq_al[b]);
- linked_pair_wise (A, ns, ls, CL);
- B->seq_al[0]=A->seq_al[a];
- B->seq_al[1]=A->seq_al[b];
- sprintf (B->name[0], "%s", A->name[a]);
- sprintf (B->name[1], "%s", A->name[b]);
- B->nseq=2;
- B->len_aln=strlen (B->seq_al[0]);
- CL2=aln2constraint_list (B, CL2, "sim");
- }
- vfree(CL->L);
- CL->L=CL2->L;
- CL->ne=CL2->ne;
- return CL;
-}
-
-
-Constraint_list *aln_file2constraint_list (char *alname, Constraint_list *CL,char *weight_mode)
- {
- Alignment *A;
- A=main_read_aln ( alname, NULL);
-
- CL=aln2constraint_list (A, CL, weight_mode);
- free_aln (A);
- return CL;
- }
-
-int *seqpair2weight (int s1, int s2, Alignment *A,Constraint_list *CL, char *weight_mode, int *weight)
-{
- int *col;
- int a,c, ref_weight;
-
-
- if ( !weight)weight=vcalloc (MAX(2,A->len_aln), sizeof (int));
-
- weight[0]=FORBIDEN;
- if ( weight_mode==NULL || strcmp (weight_mode, "no")==0 || is_number (weight_mode))
- {
-
- if (is_number (weight_mode))ref_weight=atoi(weight_mode);
- else ref_weight=1;
- weight[1]=ref_weight;
-
- }
- else if ( strstr ( weight_mode, "cons"))
- {
- ref_weight=weight[1]=1000;
- }
- else if ( strstr ( weight_mode, "OW"))
- {
- int ow;
- sscanf ( weight_mode, "OW%d", &ow);
- weight[1]=ow*get_seq_sim ( A->seq_al[s1], A->seq_al[s2], "-", NULL);
-
- }
- else if ( strncmp ( weight_mode, "len",3)==0)
- {
- weight[1]=A->len_aln;
- }
- else if ( strnm ( weight_mode, "sim", 3) || strm (weight_mode, "default"))
- {
-
- ref_weight=get_seq_sim ( A->seq_al[s1], A->seq_al[s2], "-", (strm (weight_mode, "default"))?NULL:(weight_mode+3));
- weight[1]=ref_weight;
-
- }
- else if ( strnm ( weight_mode, "subset", 6))
- {
- ref_weight=get_seq_sim ( A->seq_al[s1], A->seq_al[s2], "-",NULL);
- weight[1]=ref_weight;
- }
-
- else if ( strncmp (weight_mode, "winsim", 6)==0)
- {
- weight=get_seq_winsim ( A->seq_al[s1], A->seq_al[s2], "-", weight_mode+6, weight);
- }
- else if ( strncmp ( weight_mode, "cdna", 4)==0)
- {
- ref_weight=get_seq_sim ( A->seq_al[s1], A->seq_al[s2], "-", weight_mode+4);
- col=vcalloc ( A->len_aln+1, sizeof (int));
- if (A->cdna_cache)
- for ( a=0; a<=A->len_aln; a++)col[a]=A->cdna_cache[0][a];
- else
- for ( a=0; a<=A->len_aln; a++)col[a]=1;
- for ( c=0; c< A->len_aln; c++)weight[c]=ref_weight*col[c];
- vfree (col);
- }
- else if ( strm ( weight_mode, "pdb"))
- {
- if ( !(A->CL) || !(A->CL)->T)
- {
- fprintf ( stderr, "\nCould not find the PDB structure: [FATAL:%s]\n", PROGRAM);
- crash ("");
- }
- }
- else if ( strm (weight_mode, "overaln"))
- {
- ref_weight=get_seq_sim ( A->seq_al[s1], A->seq_al[s2], "-","idmat");
- //weight=pw_aln2clean_aln_weight (A->seq_al[s1], A->seq_al[s2], ref_weight,0, 0, 0, 0, NULL);
- printf_exit (EXIT_FAILURE, stderr,"ERROR: mode overaln not currently supported [FATAL:%s]", PROGRAM);
- }
- else
- {
- fprintf ( stderr, "\nERROR: Weight Mode %s is unknown [FATAL:%s]", weight_mode, PROGRAM);
- crash ("");
- }
- return weight;
-}
-Constraint_list *aln2constraint_list (Alignment *A, Constraint_list *CL,char *in_weight_mode)
- {
- Constraint_list *CLB=NULL;
- int a, b, c,nres1, nres2;
- int *weight=NULL;
- int s1, s2;
- int fixed_nres1, fixed_nres2;
- int do_pdb=0;
- int pdb_weight=0;
- int set_misc;
- char*alp=NULL;
- char *p, *s;
- char weight_mode [100];
-
-
- sprintf ( weight_mode , "%s", (!in_weight_mode || strm (in_weight_mode, "default"))?"sim":in_weight_mode);
-
- if ( !A) return CL;
-
- if ( !CL)
- {
- Sequence *S;
- S=aln2seq (A);
- CL=declare_constraint_list (S,NULL, NULL, 0,NULL, NULL);
- CL->S=S;
- }
- CLB=(Constraint_list *)A->CL;
-
-
- do_pdb=(strstr ( weight_mode, "pdb"))?1:0;
- if ( (p=strstr (weight_mode, "_subset_")))
- {
- alp=strchr (weight_mode, '_')+1;
- p[0]='\0';
- }
-
-
- for ( a=0; a<A->nseq-1; a++)
-
- {
- for (set_misc=0,b=a+1; b< A->nseq; b++)
- {
- s1=name_is_in_list (A->name[a], (CL->S)->name, (CL->S)->nseq, 100);
- s2=name_is_in_list (A->name[b], (CL->S)->name, (CL->S)->nseq, 100);
-
- if ( s1==-1 || s2==-1)
- {
- if ( getenv4debug ("DEBUG_LIBRARY"))fprintf ( stderr, "\n[DEBUG_LIBRARY:aln2constraint_list]Could use a pair of constraints");
- }
- else if ( s1!=-1 && s2!=-1)
- {
- int use_pair;
-
- weight=seqpair2weight (a, b, A, CL, weight_mode, weight);
-
- for (nres1=A->order[a][1], nres2=A->order[b][1], c=0; c< A->len_aln; c++)
- {
- int isgop1, isgop2;
-
- isgop1=is_gop(c, A->seq_al[a]);
- isgop2=is_gop(c, A->seq_al[b]);
- nres1+=!is_gap(A->seq_al[a][c]);
- nres2+=!is_gap(A->seq_al[b][c]);
-
- if ( strm ( weight_mode, "pdb") && CLB)
- {
-
- pdb_weight=MAX(0,(CLB->evaluate_residue_pair)(CLB,0, nres1,1,nres2));
- }
-
- use_pair=1;
- use_pair=use_pair && !is_gap(A->seq_al[a][c]);
- use_pair=use_pair && !is_gap(A->seq_al[b][c]);
- use_pair=use_pair && A->seq_al[b][c]!=UNDEFINED_RESIDUE;
- use_pair=use_pair && A->seq_al[a][c]!=UNDEFINED_RESIDUE;
- use_pair=use_pair && !(do_pdb && pdb_weight==0);
- use_pair=use_pair && ((weight[0]==FORBIDEN)?weight[1]:weight[c]);
-
- if (alp)use_pair=use_pair && is_in_set (A->seq_al[b][c], alp) && is_in_set (A->seq_al[a][c], alp);
-
- /*if ( !is_gap(A->seq_al[a][c]) && !is_gap(A->seq_al[b][c]) && A->seq_al[b][c]!=UNDEFINED_RESIDUE && A->seq_al[a][c]!=UNDEFINED_RESIDUE && !(do_pdb && pdb_weight==0))*/
- if (use_pair)
- {
-
- fixed_nres1=(!A->seq_cache)?nres1:A->seq_cache[s1][nres1];
- fixed_nres2=(!A->seq_cache)?nres2:A->seq_cache[s2][nres2];
-
-
- if ( fixed_nres1==-1 || fixed_nres2==-1)
- {
- fprintf ( stderr, "\nPB: Sequence %s, Residue %d : Cache=%d",A->name[a], nres1,fixed_nres1 );
- fprintf ( stderr, "\nPB: Sequence %s, Residue %d : Cache=%d",A->name[b], nres2,fixed_nres2 );
-
- myexit(EXIT_FAILURE);
- }
-
- if ( fixed_nres1 && fixed_nres2)
- {
-
-
-
- /*
- This code was uncommented to make profile2seq simpler
- Must check how this affects other functions
-
- vwrite_clist (CL,CL->ne, SEQ1, (s1<s2)?s1:s2);
- vwrite_clist (CL,CL->ne, SEQ2, (s1<s2)?s2:s1);
- vwrite_clist (CL,CL->ne, R1, (s1<s2)?fixed_nres1:fixed_nres2);
- vwrite_clist (CL,CL->ne, R2, (s1<s2)?fixed_nres2:fixed_nres1);
- */
-
- vwrite_clist (CL,CL->ne, SEQ1, s1);
- vwrite_clist (CL,CL->ne, SEQ2, s2);
- vwrite_clist (CL,CL->ne, R1,fixed_nres1);
- vwrite_clist (CL,CL->ne, R2,fixed_nres2);
-
- if (do_pdb)
- {
-
- vwrite_clist (CL,CL->ne, WE,(NORM_F/MAXID)*pdb_weight );
- }
- else
- {
-
- vwrite_clist (CL,CL->ne, WE,(NORM_F/MAXID)*((weight[0]==FORBIDEN)?weight[1]:weight[c]) );
-
- }
- vwrite_clist (CL,CL->ne, CONS,1);
- if (!set_misc)
- {
- vwrite_clist (CL,CL->ne, MISC,A->len_aln);
- set_misc=1;
- }
- else
- {
- vwrite_clist (CL,CL->ne, MISC,0);
- }
- CL->ne++;
- /*
- if (isgop1)
- {
-
- vwrite_clist (CL,CL->ne, SEQ1, s1);
- vwrite_clist (CL,CL->ne, SEQ2, s1);
- vwrite_clist (CL,CL->ne, R1,fixed_nres1);
- vwrite_clist (CL,CL->ne, R2,fixed_nres1);
- vwrite_clist (CL,CL->ne, WE, (weight[0]==FORBIDEN)?weight[1]:weight[c] );
- vwrite_clist (CL,CL->ne, CONS,1);
- CL->ne++;
- }
- if (isgop2)
- {
-
- vwrite_clist (CL,CL->ne, SEQ1, s2);
- vwrite_clist (CL,CL->ne, SEQ2, s2);
- vwrite_clist (CL,CL->ne, R1,fixed_nres2);
- vwrite_clist (CL,CL->ne, R2,fixed_nres2);
- vwrite_clist (CL,CL->ne, WE, (weight[0]==FORBIDEN)?weight[1]:weight[c] );
- vwrite_clist (CL,CL->ne, CONS,1);
- CL->ne++;
- }
- */
- }
-
- }
- }
- }
- }
- }
-
- vfree (weight);
- if (A->A)
- {
- return aln2constraint_list (A->A, CL, weight_mode);
- }
- else
- return CL;
- }
-double **list2mat (Constraint_list *CLin,int s1,int s2, double *min, double *max)
- {
- double ** mat;
- int a, r1, r2;
- int min_def=0;
- Constraint_list *CL;
- static Sequence *S;
-
-
- int row, column;
- if ( S==NULL)S=declare_sequence ((CLin->S)->min_len, (CLin->S)->max_len,(CLin->S)->nseq);
- sprintf ( S->name[0], "%s",(CLin->S)->name[s1]);
- sprintf ( S->name[1],"%s",(CLin->S)->name[s2]);
- S->nseq=2;
-
- row =(CLin->S)->len[s1];
- column=(CLin->S)->len[s2];
-
- if ( CLin->extend_jit)
- CL=extend_list(CLin,"mem",CLin->extend_clean_mode, CLin->extend_compact_mode, CLin->do_self, S);
- else
- CL=CLin;
-
-
- min[0]=max[0];
- mat=declare_double ( row, column);
-
- for ( a=0; a<CL->ne; a++)
- {
- r1=vread_clist(CL,a,R1)-1;
- r2=vread_clist(CL,a,R2)-1;
- if ( vread_clist(CL,a,SEQ1)==s1 &&vread_clist(CL,a,SEQ2)==s2)
- {
- mat[r1][r2]=(double)vread_clist(CL,a,WE);
- if (min_def==0)
- {
- min_def=1;
- min[0]=mat[r1][r2];
- max[0]=mat[r1][r2];
- }
- else
- {
- min[0]=(min[0]<mat[r1][r2])?min[0]:mat[r1][r2];
- max[0]=(max[0]>mat[r1][r2])?max[0]:mat[r1][r2];
- }
- }
- else if (vread_clist(CL,a,SEQ2)==s1 &&vread_clist(CL,a,SEQ1)==s2)
- {
- mat[r2][r1]=(double)vread_clist(CL,a,WE);
- if (min_def==0)
- {
- min_def=1;
- min[0]=mat[r2][r1];
- max[0]=mat[r2][r1];
- }
- else
- {
- min[0]=(min[0]<mat[r2][r1])?min[0]:mat[r2][r1];
- max[0]=(max[0]>mat[r2][r1])?max[0]:mat[r2][r1];
- }
- }
- }
- return mat;
- }
-
-Constraint_list * constraint_list2bin_file(Constraint_list *clist)
- {
- int a,b;
-
- clist->fp=tmpfile();
- for ( a=0; a< clist->ne; a++)
- for ( b=0; b<clist->entry_len; b++)
- {
- fwrite (&clist->L[a*clist->entry_len+b],clist->el_size, 1,clist->fp);
- }
- return clist;
- }
-
-FILE * bin_file2constraint_list ( Constraint_list *CL, FILE *fp, char *name)
- {
- int a, b, s1, s2;
- CLIST_TYPE *entry;
-
- if ( fp==NULL)fp=vfopen ( name, "w");
- entry=vcalloc ( CL->entry_len, CL->el_size);
- fprintf ( fp, "%d\n", (CL->S)->nseq);
- for ( a=0; a< (CL->S)->nseq; a++)fprintf (fp, "%s %d %s\n", (CL->S)->name[a], (CL->S)->len[a], (CL->S)->seq[a]);
-
-
- rewind ( CL->fp);
- fread(entry, CL->el_size, CL->entry_len, CL->fp);
- s1=entry[SEQ1];
- s2=entry[SEQ2];
- fprintf (fp, "#%d %d\n", s1, s2);
- for ( b=2; b< CL->entry_len; b++)fprintf (fp, "%5d ",entry[b]);
- fprintf (fp, "\n");
- for ( a=1; a< (CL->ne); a++)
- {
- fread(entry, CL->el_size, CL->entry_len, CL->fp);
- if ( entry[SEQ1]!=s1 || entry[SEQ2]!=s2)
- {
- s1=entry[SEQ1];
- s2=entry[SEQ2];
- fprintf (fp, "#%d %d\n", s1, s2);
- }
- for ( b=2; b< CL->entry_len; b++)fprintf (fp, "%5d ",entry[b]);
- fprintf (fp, "\n");
- }
- fprintf (fp, "! CPU %d\n",get_time());
-
- return fp;
- }
-int **list2residue_total_weight ( Constraint_list *CL)
- {
- /*Returns
- tot_weight[nseq][maxlen]
- where each residue is associated with the total of its weights in CL
- ####IMPORTANT
-
- -the numbering of the residues goes from 1 to L:
- -the numbering of the sequences goes from 0 to N-1:
- */
-
- int **tot_weight;
- int s1, s2, r1, r2, w, a;
-
-
- tot_weight=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
- for ( a=0; a<CL->ne; a++)
- {
- r1=vread_clist(CL,a,R1)-1;
- r2=vread_clist(CL,a,R2)-1;
- s1=vread_clist(CL,a,SEQ1);
- s2=vread_clist(CL,a,SEQ2);
- w=vread_clist(CL,a,WE);
-
- tot_weight[s1][r1]+=w;
- tot_weight[s2][r2]+=w;
- }
- return tot_weight;
- }
-
-int **list2residue_total_extended_weight ( Constraint_list *CL)
- {
- /*Returns
- tot_extended_weight[nseq][maxlen]
- where each residue is associated with the total of its weights in CL
- ####IMPORTANT
-
- -the numbering of the residues goes from 1 to L:
- -the numbering of the sequences goes from 0 to N-1:
- */
-
- static int **tot_extended_weight;
- int s1, s2, r1, r2, w;
-
- if (CL->residue_indexed && tot_extended_weight);
- else
- {
- if (tot_extended_weight) free_int (tot_extended_weight, -1);
- if (CL->residue_indexed==0)index_res_constraint_list (CL,WE);
-
-
- tot_extended_weight=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
-
- for ( s1=0; s1< (CL->S)->nseq-1; s1++)
- for ( s2=s1+1; s2< (CL->S)->nseq; s2++)
- for (r1=1; r1<=(CL->S)->len[s1]; r1++)
- for (r2=1; r2<=(CL->S)->len[s2]; r2++)
- {
- w=(CL->evaluate_residue_pair)( CL, s1, r1, s2, r2);
- tot_extended_weight[s1][r1]+=w;
- tot_extended_weight[s2][r2]+=w;
- }
- }
- return tot_extended_weight;
- }
-int **list2residue_partial_extended_weight ( Constraint_list *CL)
- {
- /*Returns
- tot_extended_weight[nseq][maxlen]
- where each residue is associated with the total of its weights in CL
- ####IMPORTANT
-
- -the numbering of the residues goes from 1 to L:
- -the numbering of the sequences goes from 0 to N-1:
- */
-
- int **tot_extended_weight;
- int s1, s2, r1, r2, w1, w2, a;
-
-
- tot_extended_weight=declare_int ( (CL->S)->nseq, (CL->S)->max_len+1);
- for ( a=0; a<CL->ne; a++)
- {
- r1=vread_clist(CL,a,R1);
- r2=vread_clist(CL,a,R2);
- s1=vread_clist(CL,a,SEQ1);
- s2=vread_clist(CL,a,SEQ2);
- w1=(CL->evaluate_residue_pair)( CL, s1, r1, s2, r2);
- w2=(CL->evaluate_residue_pair)( CL, s2, r2, s1, r1);
- if ( w1!=w2)fprintf ( stderr, "*");
-
- tot_extended_weight[s1][r1]+=w1;
- tot_extended_weight[s2][r2]+=w2;
- }
- return tot_extended_weight;
- }
-
-
-/*******************************************************************************************/
-/* */
-/* */
-/* clean functions */
-/* */
-/* */
-/* */
-/*******************************************************************************************/
-Constraint_list *clean ( char *clean_mode,Constraint_list *CL,int start, int len)
- {
-
- if ( strm ( clean_mode, "shadow")) CL=clean_shadow (CL,start,len);
- else if ( strm5( clean_mode, "","NO","no","No","default"));
- else add_warning ( CL->local_stderr, "\nWARNING: The %s CLEANING MODE DOES NOT EXIST\n", clean_mode);
-
- return CL;
- }
-
-
-Constraint_list * clean_shadow ( Constraint_list *CL, int start, int len)
- {
- int s1, s2, r1, a, b, end;
- int max, min;
-
- s1=vread_clist (CL, start, SEQ1);
- s2=vread_clist (CL, start, SEQ2);
- r1=vread_clist (CL, start, R1);
-
-
- for ( a=start; a<(start+len);)
- {
-
- max=min=vread_clist (CL, a, WE);
- while ( a<CL->ne && vread_clist (CL, a, SEQ1)==s1 && vread_clist (CL, a, SEQ2)==s2 && vread_clist (CL, a, R1)==r1)
- {
- max=(vread_clist (CL, a, WE)>max)?vread_clist (CL, a, WE):max;
- min=(vread_clist (CL, a, WE)<min)?vread_clist (CL, a, WE):min;
- a++;
- }
- end=a;
-
- if ((end-start)>1)
- {
- for ( b=start; b<end; b++)
- if ( vread_clist (CL, b, WE)<max)vwrite_clist (CL, b, SEQ1,-1);
- }
- start=end;
- if ( start<CL->ne)
- {
- s1=vread_clist (CL, start, SEQ1);
- s2=vread_clist (CL, start, SEQ2);
- r1=vread_clist (CL, start, R1);
- }
- }
- CL=sort_constraint_list_inv (CL, start, (CL->ne-start));
- CL=sort_constraint_list (CL,start,(CL->ne-start) );
-
- return CL;
- }
-/*********************************************************************/
-/* */
-/* LIST FUNCTIONS */
-/* */
-/* */
-/*********************************************************************/
-
-static Constraint_list *fast_merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode);
-static Constraint_list *slow_merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode);
-
-Constraint_list *merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode)
-{
-
-
- if ( !ML)
- {
- return SL;
- }
- else if ( SL->S == ML->S)
- {
- return fast_merge_constraint_list (SL, ML, mode);
- }
- else
- {
- return slow_merge_constraint_list (SL, ML, mode);
- }
-}
-
-Constraint_list *fast_merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode)
-{
- int l;
-
- l=ML->ne+SL->ne;
-
- ML->max_L_len=l;
- ML->seq_indexed=0;
- ML->residue_indexed=0;
- if (ML->ne==0 || !ML->L)ML->L=vcalloc (l*ML->entry_len, sizeof (int));
- else ML->L=vrealloc (ML->L, sizeof (int)*l*ML->entry_len);
-
- memcpy (ML->L+(ML->ne*ML->entry_len), SL->L, SL->ne*sizeof (int)*SL->entry_len);
-
- ML->ne+=SL->ne;
- return ML;
-
-}
-
-Constraint_list *slow_merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode)
-{
- int a, s1, s2;
- Sequence *S1, *S2;
- int **name_index;
- int **seq_index;
- CLIST_TYPE *entry=NULL;
-
- if ( !ML)return SL;
-
- S1=SL->S;S2=ML->S;
-
- name_index=index_seq_name(S1,S2);
- seq_index=index_seq_res (S1,S2, name_index);
-
- for ( a=0; a< SL->ne; a++)
- {
-
- entry=extract_entry ( entry, a, SL);
- //HERE ("BEF: %d %d %d %d", entry[SEQ1], entry[SEQ2], entry[R1], entry[R2]);
- s1=entry[SEQ1]; s2=entry[SEQ2];
-
- if ( S1==S2)
- {
- add_entry2list(entry, ML);
- }
- else if (name_index[s1][0]==-1 || name_index[s2][0]==-1 || !seq_index[s1] || !seq_index[s2]);
- else
- {
- int r1, r2;
- r1=seq_index[s1][entry[R1]-1];
- r2=seq_index[s2][entry[R2]-1];
-
- entry[SEQ1]=name_index[s1][0];
- entry[SEQ2]=name_index[s2][0];
- if ( r1!=-1 && r2!=-1 && entry[SEQ1]!=entry[SEQ2])
- {
- entry[R1]=r1+1; entry[R2]=r2+1;
- add_entry2list(entry, ML);
- }
- //HERE ("AFT: %d %d %d %d", entry[SEQ1], entry[SEQ2], entry[R1], entry[R2]);
- }
- }
- free_int (name_index, -1);
- free_int ( seq_index, -1);
- vfree ( entry);
- return ML;
-}
-
-Constraint_list *modify_weight( Constraint_list *CL,int start, int end, char *modify_mode)
- {
- int a;
- CLIST_TYPE x;
-
- if ( strm(modify_mode, "default"))return CL;
- for ( a=start; a<end; a++)
- {
- x=vread_clist(CL, a, WE);
-
- if (strm2 (modify_mode,"sc_eq_cons", "we_eq_cons"))
- if(x!=UNDEFINED)
- vwrite_clist(CL, a, WE, vread_clist(CL, a, CONS));
-
- if (strm2(modify_mode,"sc_eq_wePcons","sc_eq_consPwe"))
- if(x!=UNDEFINED)
- vwrite_clist(CL, a, WE, vread_clist(CL, a, CONS)*x);
- }
- return CL;
- }
-
-Constraint_list *compact_list (Constraint_list *CL, int start, int len, char *compact_mode)
- {
- int a;
- int r1, r2, rr1, rr2, s1, rs1, s2, rs2, ra;
- CLIST_TYPE x;
- int debug_compact=0;
-
- if (debug_compact)fprintf ( stderr, "\n[In: %d %s start=%d len=%d", CL->ne, compact_mode, start, len);
-
- if ( len==0 || strm3(compact_mode, "no", "No", "NO"))return CL;
- else if ( strm2(compact_mode,"mirror","mirror_sum"));
- else if ( strm4(compact_mode, "default","shrink","shrink_best","shrink_worst"))
- {
-
- for ( a=start; a<(start+len) ; a++)
- {
-
- if ( vread_clist(CL, a, SEQ1)> vread_clist(CL, a, SEQ2) ||\
- ( vread_clist(CL, a, SEQ1)==vread_clist(CL, a, SEQ2) &&\
- vread_clist(CL, a, R1) > vread_clist(CL, a, R2) ))
-
-
- {
- s1=vread_clist(CL, a, SEQ1);
- s2=vread_clist(CL, a, SEQ2);
- r1=vread_clist(CL, a, R1);
- r2=vread_clist(CL, a, R2);
- vwrite_clist(CL, a, SEQ1,s2);
- vwrite_clist(CL, a, SEQ2,s1);
- vwrite_clist(CL, a, R1,r2);
- vwrite_clist(CL, a, R2,r1);
- }
- }
- }
-
- if (debug_compact)fprintf ( stderr, "\n[2: %d %s start=%d len=%d", CL->ne, compact_mode, start, len);
-
- sort_constraint_list ( CL, start, len);
-
- rs1=vread_clist(CL, start, SEQ1);
- rs2=vread_clist(CL, start, SEQ2);
- rr1=vread_clist(CL, start, R1);
- rr2=vread_clist(CL, start, R2);
- ra=start;
-
- if (debug_compact)fprintf ( stderr, "\n[3: %d %s start=%d len=%d", CL->ne, compact_mode, start, len);
-
-
- if ( (rs1==rs2) && (rr1==rr2))vwrite_clist(CL, start, SEQ1,-1);
- for ( a=start+1; a<(start+len); a++)
- {
- s1=vread_clist(CL, a, SEQ1);
- s2=vread_clist(CL, a, SEQ2);
- r1=vread_clist(CL, a, R1);
- r2=vread_clist(CL, a, R2);
-
- //if ( (s1==s2) && (r1==r2))vwrite_clist(CL, a, SEQ1, -1);
- if ( s1==rs1 && s2==rs2 && r1==rr1 && r2==rr2)
- {
- x=vread_clist(CL, ra, WE);
- if (strm ( compact_mode, "shrink"));
- else if (strm( compact_mode,"default"))//default is set to best
- vwrite_clist(CL, ra, WE,MAX(vread_clist(CL, a, WE),x));
- else if ( strm ( compact_mode,"mirror_sum"))
- vwrite_clist(CL, ra, WE, vread_clist(CL, a, WE)+x);
- else if (strm2 ( compact_mode,"best", "shrink_best"))
- vwrite_clist(CL, ra, WE,MAX(vread_clist(CL, a, WE),x));
- else if (strm2 ( compact_mode, "worst","shrink_worst"))
- vwrite_clist(CL, ra, WE,MIN(vread_clist(CL, a, WE), vread_clist(CL, a, WE)));
-
- if ( strm(compact_mode, "shrink"));
- else
- {
- vwrite_clist(CL, ra, CONS, vread_clist(CL, ra, CONS)+ vread_clist(CL, a, CONS));
- vwrite_clist(CL, ra, MISC, vread_clist(CL, ra, MISC)+ vread_clist(CL, a, MISC));
- }
- vwrite_clist(CL,a, SEQ1, -1);
-
- }
- else
- {
- rs1=s1;
- rs2=s2;
- rr1=r1;
- rr2=r2;
- ra=a;
- }
- }
-
-
- sort_constraint_list_inv(CL,0,CL->ne);
-
- sort_constraint_list (CL,0,CL->ne);
-
-
- if ( strm3 (compact_mode, "consPwe", "wePcons","cons"))
- {
- for ( a=start; a<(start+len); a++)
- {
- if ( strm2(compact_mode,"consPwe", "wePcons"))
- vwrite_clist(CL, a, WE, vread_clist(CL,a,WE)* vread_clist(CL,a,CONS));
- else if (strm (compact_mode, "cons"))
- vwrite_clist(CL, a, WE, vread_clist(CL,a,CONS)*100);
- }
- }
- if (debug_compact)fprintf ( stderr, "....OUT: %d]\n", CL->ne);
- return CL;
- }
-
-
-Constraint_list *rescale_list_simple (Constraint_list *CL,int start, int len,int new_min, int new_max)
- {
- int a, min, max;
- double x;
- /*Rescales between 0 and max2
- Any value above max1 is set to max1 first and then to max2
- */
-
-
-
- min=max=vread_clist ( CL,start, WE);
-
- for ( a=start; a<(start+len); a++)
- {
- x=(double)vread_clist ( CL,a, WE);
- if ( x>max)max=(int)x;
- if ( x< min)min=(int)x;
- }
-
- fprintf ( CL->local_stderr, "\n[%d-%d]=>[%d-%d]", min, max, new_min, new_max);
-
- for ( a=start; a<(start+len); a++)
- {
-
- x=vread_clist(CL,a, WE);
-
- if ((max-min)==0)x=100;
- else x=(((x-min)/(max-min))*new_max)+new_min;
-
- vwrite_clist(CL, a, WE,(CLIST_TYPE) x);
- }
- return CL;
- }
-Constraint_list *rescale_list (Constraint_list *CL,int start, int len,int max1, int max2)
- {
- int a, min_val, max_val;
- CLIST_TYPE x;
-
- /*Rescales between 0 and max2
- Any value above max1 is set to max1 first and then to max2
- */
-
-
- min_val=0;
- max_val=max1;
-
-
-
- for ( a=start; a<len; a++)
- {
- if (vread_clist ( CL,a, WE)>max1)vwrite_clist(CL, a, WE, max1);
- }
-
- for ( a=start; a<len; a++)
- {
- x=vread_clist(CL,a, WE);
- vwrite_clist(CL, a, WE, (((x-min_val)*max2)/(max_val-min_val)));
- }
- return CL;
- }
-
-
-Constraint_list* filter_list (Constraint_list *CL, int start, int len,int T)
- {
- int a;
- int field;
-
- if (T==0)return CL;
-
- field=WE;
- if (T>0)field=WE;
- else if ( T<0)
- {
- field=CONS;
- T=-T;
- }
-
-
- for ( a=start; a<len; a++)
- if (vread_clist(CL, a, field)<=T)vwrite_clist(CL,a,SEQ1,-1);
-
- CL=sort_constraint_list_inv (CL, 0, CL->ne);
- CL=sort_constraint_list (CL, 0, CL->ne);
- return CL;
- }
-
-
-
-
-
-Constraint_list *undefine_list (Constraint_list *CL)
- {
- int a, b;
- int undefined_flag;
-
- for ( a=0;a<CL->ne; a++)
- {
- for ( b=0, undefined_flag=0; b< LIST_N_FIELDS; b++)
- {
-
- if ( vread_clist (CL, a, b)==UNDEFINED)undefined_flag=1;
- if ( undefined_flag)
- {
- for ( b=0; b< LIST_N_FIELDS; b++)
- if ( b!=SEQ1 && b!=SEQ2 && b!=R1 && b!=R2)
- {
- vwrite_clist(CL, a, b, UNDEFINED);
- }
- }
- }
- }
- return CL;
- }
-
-int ** seq2defined_residues ( Sequence *S, Constraint_list *CL)
-{
- int **seq_count;
- int *entry=NULL;
- int a;
-
- seq_count=declare_int (S->nseq, S->max_len+1);
- for (a=0; a< CL->ne; a++)
- {
- entry=extract_entry(entry, a, CL);
- seq_count[entry[SEQ1]][entry[R1]]++;
- seq_count[entry[SEQ2]][entry[R2]]++;
- }
- vfree (entry);
- return seq_count;
-}
-
-int ** aln2defined_residues ( Alignment *A, Constraint_list *CL)
-{
-
- int **seq_count;
- int **aln_count;
- int **pos;
- int a,ra, b;
-
- pos=aln2pos_simple(A, A->nseq);
- seq_count=seq2defined_residues(CL->S, CL);
- aln_count=declare_int (A->nseq, A->len_aln);
- for (a=0; a< A->nseq; a++)
- {
- ra=name_is_in_list(A->name[a], (CL->S)->name, (CL->S)->nseq, 100);
- if ( ra==-1) continue;
- for ( b=0; b<A->len_aln; b++)
- if (pos[a][b]>0 && seq_count[ra][pos[a][b]]>0)aln_count[a][b]=1;
- }
-
- free_int (seq_count, -1);
- free_int (pos,-1);
- return aln_count;
-}
-
-/*********************************************************************/
-/* */
-/* DEBUG CONSTRAINT_LIST */
-/* */
-/* */
-/*********************************************************************/
-void check_seq_pair_in_list(Constraint_list *CLin,int seq1, int seq2)
- {
- int a, s1, s2, r1, r2;
-
- for ( a=0; a< CLin->ne; a++)
- {
- s1=vread_clist(CLin,a,SEQ1);
- s2=vread_clist(CLin,a,SEQ2);
- if ( s1==seq1 && s2==seq2)
- {
- r1=vread_clist(CLin,a,R1);
- r2=vread_clist(CLin,a,R2);
- fprintf ( stderr, "\n[%d][%d %d] [%d %d]",a,s1, r1, s2, r2);
- }
- }
- }
-
-void print_CL_mem(Constraint_list *CL, char *function)
- {
- fprintf ( stderr,"%s\n", function);
- if ( CL->fp==NULL && CL->L==NULL) fprintf ( stderr, "\n\tNOTHING");
- if ( CL->fp)fprintf ( stderr, "\n\tFILE SET");
- if ( CL->L)fprintf ( stderr, "\n\tMEM SET\n");
- }
-
-int constraint_list_is_sorted ( Constraint_list *CL)
- {
- int a,b, x1, x2;
- for ( a=0; a< CL->ne-1; a++)
- {
- for ( b=0; b< CL->entry_len; b++)
- {
- x1=vread_clist( CL, a, b);
- x2=vread_clist( CL, a+1,b);
- if ( x1<x2)break;
- else if ( x1>x2)
- {
- fprintf ( stderr, "\n[%d][%d]=>%d\n[%d][%d]=>%d\n\n",a, b, x1, a+1, b, x2);
- return 0;
- }
-
- }
- }
- return 1;
- }
-/*********************************************************************/
-/* */
-/* PRUNE CONSTRAINT_LIST */
-/* */
-/* */
-/*********************************************************************/
-char * list2prune_list_old ( Sequence *S, int **sm)
-{
- int a, b, i;
- char *aln, *seq, *file;
- FILE *fp;
- Sequence *subS;
- Alignment *A;
-
- aln=vtmpnam (NULL);
- seq=vtmpnam (NULL);
- file=vtmpnam (NULL);
-
- output_fasta_seq (seq, A=seq2aln (S,NULL,RM_GAP));
- free_aln (A);
-
- printf_system ( "t_coffee %s -in Xblosum62mt -outfile=%s -msa_mode iterative_tree_aln", seq, aln);
- printf_system ( "t_coffee -other_pg seq_reformat -in %s -action +trim _aln_n5 -output fasta_seq > %s",aln, seq );
- subS=main_read_seq ( seq);
-
- fp=vfopen (file, "w");
- for ( a=0; a< subS->nseq; a++)
- {
- i=name_is_in_list (subS->name[a], S->name, S->nseq, 100);
- if ( i==-1) continue;
- for ( b=0; b<S->nseq; b++)
- if (i!=b)fprintf ( fp, "\n2 %d %d",i, b);
- }
- vfclose (fp);
- return file;
-}
-
-char * list2prune_list ( Sequence *S, int **sm)
-{
- int a, b, c;
- int **mat, *used, *keep;
- int nk=0, n=0;
- int ns=4;
- char *file;
- FILE *fp;
-
- n=S->nseq;
-
- if (get_string_variable("prune_lib_mode"))
- ns=atoi(get_string_variable("prune_lib_mode"));
-
- HERE ("NS=%d", ns);
- if (ns==0)ns=n;
- else if (ns<0)ns=-(n*ns)/100;
- else if (ns>=n)ns=n;
-
-
- HERE ("NS=%d", ns);
-
-
- keep=vcalloc (n, sizeof (int));
- used=vcalloc (n, sizeof (int));
- mat=declare_int (n, n);
- file=vtmpnam (NULL);
-
- //1-Identify the seed sequence: the one on average the further away from the rest
- for (a=0; a<n;a++)
- {
- mat[a][0]=a;
- for (b=0; b<n; b++)
- {
- mat[a][1]+=sm[a][b];
- }
- sort_int_inv (mat, 2, 1, 0, n-1);
- }
-
- keep[nk++]=mat[0][0];
- used[mat[0][0]]=1;
-
- for (a=1; a<ns; a++)
- {
- for (c=0; c<n; c++)
- {
- mat[c][0]=c;
- if (used[c]){mat[c][1]=n*1000;continue;}
- for (b=0; b<nk; b++)
- {
- mat[c][1]+=sm[c][keep[b]];
- }
- }
- sort_int (mat, 2, 1, 0,n-1);
- keep[nk++]=mat[0][0];
- used[mat[0][0]]=1;
- }
-
- fp=vfopen (file, "w");
- for ( a=0; a<nk; a++)
- {
- for (b=0; b<S->nseq; b++)
- if (keep[a]!=b)
- {
- fprintf ( fp, "\n2 %d %d", keep[a], b);
- }
- }
- vfclose (fp);
- vfree (keep); vfree (used);free_int (mat, -1);
-
- return file;
-}
-
-
-char * list2prune_list_old3 ( Sequence *S, int **sm)
-{
- int **keep;
- int a,b,c,n,s1,s2, tot, nseq;
-
- char *file;
- FILE *fp;
- nseq=S->nseq;
-
- keep=declare_int (nseq, nseq);
-
- for (a=0; a< nseq; a++)
- for (b=a+1; b< nseq; b++)
- {
- int bc=0,bsim=0;
- s1=sm[a][b];
- for (c=0; c< nseq; c++)
- {
- if ( c==a || c==b) continue;
- s2=MIN(sm[a][c], sm[c][b]);
-
- if (s2>s1 && s2>bsim)
- {
- bsim=s2;
- bc=c;
- }
- }
- if ( bsim)
- {
- keep[a][bc]=1;
- keep[bc][a]=1;
- keep[b][bc]=1;
- keep[bc][b]=1;
- }
- }
-
- file=vtmpnam (NULL);
- fp=vfopen (file, "w");
-
- for (n=0,tot=0,a=0; a< nseq; a++)
- for ( b=a+1; b< nseq; b++)
- {
- if (keep[a][b])
- fprintf (fp, "\n 2 %d %d", a, b);
- }
- vfclose (fp);
- return file;
-}
-
-/*********************************************************************/
-/* */
-/* WEIGHT CONSTRAINT_LIST */
-/* */
-/* */
-/*********************************************************************/
-
-Constraint_list *weight_constraint_list(Constraint_list * CL, char *seq_weight)
-
- {
- Weights *W;
-
- if ( CL->ne==0)return CL;
- else if ( strm(seq_weight, "t_coffee")) W=compute_t_coffee_weight(CL);
- else if (check_file_exists (seq_weight))
- {
- W=read_seq_weight ((CL->S)->name, (CL->S)->nseq, seq_weight);
- }
- else
- {
- int a;
- W=declare_weights((CL->S)->nseq);
- sprintf ( W->mode, "no_seq_weight");
- for ( a=0; a<(CL->S)->nseq; a++)
- {
- sprintf ( W->seq_name[a], "%s", (CL->S)->name[a]);
- W->SEQ_W[a]=1;
- }
- CL->W=W;
- return CL;
- }
-
- CL=re_weight_constraint_list (CL,W);
-
- CL->W=W;
-
-
- return CL;
-
-
- }
-
-
-
-Weights* compute_t_coffee_weight(Constraint_list * CL)
- {
- int a, b;
- float p, d;
- Weights *W;
- int nseq;
-
-
-
-
-
- if (!CL->L)return NULL;
-
- nseq=(CL->S)->nseq;
- W=declare_weights(nseq);
- sprintf ( W->mode, "t_coffee");
- for ( a=0; a< nseq; a++)
- {
- sprintf ( W->seq_name[a], "%s", (CL->S)->name[a]);
- W->SEQ_W[a]=1;
- }
-
-
- for (a=0; a< (CL->S)->nseq-1; a++)
- for ( b=a+1; b< (CL->S)->nseq; b++)
- {
- if ( b==a){d=1;}
- else if ( !(CL->S)->len[b] || !(CL->S)->len[a])d=1;
- else
- {
- d=((float)(CL->DM)->similarity_matrix[a][b]/MAXID)*10;
- }
- p=pow(d,3);
-
- W->SEQ_W[a]+=p;
- W->SEQ_W[b]+=p;
-
- }
-
- for ( p=0,b=0; b< (CL->S)->nseq; b++)
- {
- if ((CL->S)->len[b]==0)W->SEQ_W[b]=0;
- else W->SEQ_W[b]=2/W->SEQ_W[b];
- p+=W->SEQ_W[b];
- }
- for ( b=0; b< (CL->S)->nseq; b++)
- {
- W->SEQ_W[b]=W->SEQ_W[b]*((float)W->nseq/p);
- }
-
-
- return W;
- }
-
-Constraint_list *re_weight_constraint_list(Constraint_list * CL,Weights *W)
- {
- int a;
- float w;
- float *weight;
- int sA, sB;
-
-
-
- weight=W->SEQ_W;
-
- if (!CL->L)return CL;
-
-
-
- for ( a=0; a< CL->ne; a++)
- {
- sA=CL->L[a*CL->entry_len+SEQ1];
- sB=CL->L[a*CL->entry_len+SEQ2];
-
- w=MIN(weight[sA], weight[sB]);
-
- CL->L[a*CL->entry_len+WE]*=w;
- }
- CL=evaluate_constraint_list_reference (CL);
- return CL;
- }
-
-Distance_matrix* cl2distance_matrix (Constraint_list *CL, Alignment *A, char *in_mode, char *in_sim_mode, int print)
-{
-
- char mode[100];
- char sim_mode [100];
-
-
-
- if ( !CL)return NULL;
- sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode);
- sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode);
-
- if ( !CL->DM ||!strm ((CL->DM)->mode, mode) || !strm ((CL->DM)->sim_mode, sim_mode) || A )
- {
- return seq2distance_matrix (CL, A, mode, sim_mode, print);
- }
- else
- {
-
- return CL->DM;
- }
-}
-
-
-Distance_matrix *seq2distance_matrix (Constraint_list *CL, Alignment *A,char *mode, char *sim_mode, int print)
-{
- /*Compute the distance matrix associated with the Constraint List and the sequences*/
- /*Computation only occurs if the similiraty matrix is undefined : CL->similarity_matrix*/
- /*Undefine CL->similarity_matrix to force computation*/
-
- int a, b;
- Alignment *B;
- Constraint_list *NCL;
- float score=0;
- int *ns;
- int **l_s;
- float id;
- int max_name=0;
- int id_score;
- static float **g_matrix;
- float ref=0;
- int n_coor=0;
- Distance_matrix *DM;
- int **sim_table=NULL;
-
- //mode: computation mode
- //sim_mode: mode for computing the similarity
-
- //Composite modes
-
- if (strm (mode, "ktup2"))
- {
- B=seq2aln ( CL->S, NULL, 1);
- B=very_fast_aln (B, B->nseq,NULL);
- sprintf ( CL->distance_matrix_mode, "aln");
- DM=cl2distance_matrix (CL, B, NULL, NULL, 1);
- sprintf ( CL->distance_matrix_mode, "ktup2");
- sprintf ( DM->mode, "%s", mode);
- sprintf ( DM->sim_mode, "%s", sim_mode);
- free_aln (B);
- return DM;
- }
-
- if ( !CL) return NULL;
- else
- {
- for ( max_name=0,a=0; a< (CL->S)->nseq; a++)max_name=MAX(strlen ((CL->S)->name[a]), max_name);
-
-
- if ( CL->DM)DM=CL->DM;
- else
- {
- DM=vcalloc ( 1, sizeof (Distance_matrix));
- DM->nseq=(CL->S)->nseq;
- DM->similarity_matrix=declare_int ( (CL->S)->nseq, (CL->S)->nseq);
- DM->distance_matrix =declare_int ( (CL->S)->nseq, (CL->S)->nseq);
- DM->score_similarity_matrix=declare_int ( (CL->S)->nseq, (CL->S)->nseq);
- }
-
- sprintf ( DM->mode, "%s", mode);
- sprintf ( DM->sim_mode, "%s", sim_mode);
-
- NCL=duplicate_constraint_list_soft (CL);
- NCL->pw_parameters_set=1;
-
- if (!A)
- {
- if ( CL->tree_aln)B=CL->tree_aln;
- else B=seq2aln ( NCL->S, NULL, 1);
- }
- else
- {
- B=copy_aln (A, NULL);
- B=reorder_aln (B, (CL->S)->name, (CL->S)->nseq);
- }
-
- if ( strm (mode, "very_fast"))
- {
- sprintf ( NCL->dp_mode, "very_fast_pair_wise");
- NCL->evaluate_residue_pair=evaluate_matrix_score;
- if ( strm ((CL->S)->type, "DNA") ||strm ((CL->S)->type, "RNA") )
- {
- NCL->M=read_matrice ("idmat");
- NCL->gop=-10;
- NCL->gep=-1;
- CL->ktup=6;
- }
- else
- {
- NCL->M=read_matrice ("blosum62mt");
- NCL->gop=get_avg_matrix_mm (NCL->M, AA_ALPHABET)*10;
- NCL->gep=-1;
- CL->ktup=2;
- }
- NCL->use_fragments=1;
- CL->diagonal_threshold=6;
- }
-
- else if ( strm (mode, "ktup"))
- {
-
- NCL->ktup=6;
- sim_table=ktup_dist_mat((CL->S)->seq,(CL->S)->nseq,NCL->ktup, (CL->S)->type);
- }
-
-
- else if (strm (mode, "aln"))
- {
-
- sim_table=aln2sim_mat (A, sim_mode);
- }
- else if ( strm (mode, "fast") || strm ("idscore", mode))
- {
- sprintf ( NCL->dp_mode, "myers_miller_pair_wise");
- NCL->evaluate_residue_pair=evaluate_matrix_score;
- if ( strm ((CL->S)->type, "DNA") || strm ((CL->S)->type, "RNA"))
- {
- NCL->M=read_matrice ("idmat");
- NCL->gop=-10;
- NCL->gep=-1;
- }
- else
- {
- NCL->M=read_matrice ("blosum62mt");
- NCL->gop=get_avg_matrix_mm (NCL->M, AA_ALPHABET)*10;
- NCL->gep=-1;
- }
- }
- else if ( strm (mode, "cscore"))
- {
- if (!CL || !CL->L || CL->ne==0)
- return seq2distance_matrix (CL, A,"idscore",sim_mode, print);
- }
- else if ( strm (mode, "geometric") );
- else if (strm (mode, "slow"));
- else if (strm (mode, "clustalw"));
- else if (strm (mode, "no"))
- print=1;
- else if (strm (mode, "random"))
- print=1;
- else
- {
- fprintf ( stderr, "\nError: %s is an unknown distance_matrix_mode [FATAL:%s]", mode,PROGRAM);
- crash ("");
- }
-
- //Special Geometric Mode
- if ( strm (NCL->distance_matrix_mode, "geometric"))
- {
- free_arrayN(g_matrix, 2);
- g_matrix=declare_float ((CL->S)->nseq, 3);
- n_coor=MIN(3,((CL->S)->nseq));
-
- for ( a=0; a<(CL->S)->nseq; a++)
- {
- for (b=0; b<n_coor; b++)
- {
- B=align_two_sequences ((CL->S)->seq[a], (CL->S)->seq[b], "pam250mt", -10, -1, "fasta_pair_wise");
- g_matrix[a][b]=get_seq_sim ( B->seq_al[0], B->seq_al[1], "-", NULL);
- free_aln(B);B=NULL;
- }
- }
- ref=(float)sqrt((double)(10000*n_coor));
- }
-
-
- ns=vcalloc ( 2, sizeof(int));
- l_s=declare_int ( 2, 1);
- ns[0]=ns[1]=1;
- l_s[0][0]=0;
- l_s[1][0]=1;
-
- if (CL->local_stderr && print>0)fprintf ( (CL->local_stderr), "\nCOMPUTE PAIRWISE SIMILARITY [dp_mode: %s] [distance_matrix_mode: %s][Similarity Measure: %s] \n", NCL->dp_mode,mode, sim_mode);
-
- for (a=0; a< (CL->S)->nseq; a++)
- {
- if (CL->local_stderr && print>0)fprintf ( (CL->local_stderr), "\n\tSeq: %s", (CL->S)->name[a]);
- for ( b=a; b< (CL->S)->nseq; b++)
- {
- if ( b==a){DM->similarity_matrix[a][b]=MAXID;}
- else
- {
- l_s[0][0]=a;
- l_s[1][0]=b;
- if ( !strm(mode, "ktup2") && ! strm (mode, "geometric"))
- {
- ungap ( B->seq_al[a]);
- ungap ( B->seq_al[b]);
- }
-
- if ( strm (mode, "slow"))
- {
-
- B->score_aln=pair_wise (B, ns, l_s,NCL);
-
- id=get_seq_sim ( B->seq_al[a], B->seq_al[b], "-", sim_mode);
- if ( CL->L)
- {
- score=(int)(((float)B->score_aln)/(B->len_aln*SCORE_K));
- score=(int)(CL->L && CL->normalise)?((score*MAXID)/(CL->normalise)):(score);
- }
- else if ( CL->M)score=id;
-
-
- if ( score>MAXID)score=(int)(CL->L)?sub_aln2sub_aln_score (B, CL, CL->evaluate_mode, ns, l_s):id;
-
- }
- else if ( strm2 (mode,"fast", "very_fast"))
- {
- B->score_aln=pair_wise (B, ns, l_s,NCL);
- id=get_seq_sim ( B->seq_al[a], B->seq_al[b], "-", sim_mode);
- score=(int)(id)*SCORE_K;
- }
- else if ( strm (mode, "cscore"))
- {
- ungap ( B->seq_al[a]);
- ungap ( B->seq_al[b]);
- score=(int)linked_pair_wise (B, ns, l_s, NCL);
-
-
- score/=(B->len_aln*SCORE_K);
- id=score/SCORE_K;
- }
- else if ( strm (mode, "idscore"))
- {
- score=id=idscore_pairseq (B->seq_al[a], B->seq_al[b], NCL->gop, NCL->gep, NCL->M, sim_mode);
- //HERE ("%s %d %d ->%d", sim_mode, a, b, (int)id);
- }
- else if (strm (mode, "ktup"))
- {
- id=sim_table[a][b];
- score=id*SCORE_K;
-
- }
- else if (strm (mode, "aln"))
- {
- score=id=sim_table[a][b];
- score*=SCORE_K;
- }
-
- else if ( strm (mode, "geometric"))
- {
- id=get_geometric_distance (g_matrix,n_coor, a, b, "euclidian");
- id=MAXID*(1-((id/ref)));
- score=(int)(id)*SCORE_K;
- }
- else if ( strm (mode, "no"))
- {
- id=100;
- score=id*SCORE_K;
- }
- else if ( strm (mode, "random"))
- {
- id=rand()%100;
- score=id*SCORE_K;
- }
- else
- {
- id=B->score_aln=pair_wise (B, ns, l_s,NCL);
- score=id*SCORE_K;
- }
- /*Sim mat*/
- DM->similarity_matrix[a][b]=DM->similarity_matrix[b][a]=(int)(id);
- /*Dist mat*/
- DM->distance_matrix[a][b]=DM->distance_matrix[b][a]=MAXID-(int)(id);
- /*Score mat*/
-
-
- DM->score_similarity_matrix[a][b]=DM->score_similarity_matrix[b][a]=(int)score;
- id_score=id;
- if (CL->local_stderr && print>1) fprintf (CL->local_stderr, "\n\t%-*s %-*s identity=%3d%% score=%3d", max_name,(CL->S)->name[a], max_name,(CL->S)->name[b], id_score, (int)score);
- }
- }
- }
- vfree (ns);
- free_int(l_s, -1);
-
- }
-
-
- if (CL->local_stderr) fprintf (CL->local_stderr, "\n");
- free_constraint_list (NCL);
-
-
-
- if (!CL->tree_aln)
- {
- free_aln (B);
- }
-
- free_int (sim_table, -1);
-
-
-
- return DM;
-}
-/*********************************************************************/
-/* */
-/* RNA FUNCTIONS */
-/* */
-/* */
-/*********************************************************************/
-char * seq2rna_lib ( Sequence *S, char *name)
-{
- int a;
- FILE *fp;
-
-
- if (!name)name=vtmpnam (NULL);
- fp=vfopen (name, "w");
- for ( a=0; a<S->nseq; a++)
- {
-
- fprintf (fp, "%s\n", rna_struc2rna_lib(S->name[a], S->seq[a], NULL));
- }
- vfclose (fp);
-
- return name;
-}
-
-Constraint_list *read_rna_lib ( Sequence *S, char *fname)
-{
- Constraint_list *R;
- char **list;
- int n=0,a;
-
-
- if (check_file_exists (fname))
- {
-
- list=read_lib_list ( fname, &n);
- }
- else
- {
- X_template *F;
-
- list=vcalloc (S->nseq, sizeof (char*));
- for ( a=0; a<S->nseq; a++)
- {
- if ((F=seq_has_template (S, a, "_F_")))
- {
- list[n++]=F->template_file;
- }
- }
- }
-
- R=declare_constraint_list ( S,NULL, NULL, 0,NULL, NULL);
-
- for (a=0; a< n; a++)
- {
-
- if (list[a])R=fast_read_constraint_list_file (R, list[a]);
- }
-
- R=index_res_constraint_list (R,WE);
-
- return R;
-}
-
-Constraint_list * rna_lib_extension ( Constraint_list *CL, Constraint_list *R)
-{
- CLIST_TYPE *entry=NULL;
- int a,b,c,n1,n2, ne,s1, s2, r1, r2,w;
- int list1[100], list2[100];
-
-
- entry=vcalloc ( CL->entry_len, CL->el_size);
- ne=CL->ne;
-
-
- for ( a=0; a<ne; a++)
- {
-
-
- extract_entry (entry, a, CL);
- s1=entry[SEQ1];
- s2=entry[SEQ2];
- r1=entry[R1];
- r2=entry[R2];
- w=entry[WE];
-
- n1=n2=0;
- list1[n1++]=r1;
- for (b=1; b<R->residue_index[s1][r1][0]; b+=3)
- {
- list1[n1++]=R->residue_index[s1][r1][b+1];
- }
- list2[n2++]=r2;
- for (b=1; b<R->residue_index[s2][r2][0]; b+=3)
- {
- list2[n2++]=R->residue_index[s2][r2][b+1];
- }
-
- for (b=1; b<n1; b++)
- for (c=1; c<n2; c++)
- {
-
-
- entry[R1]=list1[b];
- entry[R2]=list2[c];
- add_entry2list ( entry,CL);
- }
- }
-
- return CL;
-}
-
-char *** produce_method_file ( char *method)
-{
- static char ***list;
- int n=0;
- FILE *fp;
-
- if (!list)list=declare_arrayN(3, sizeof (char),200,2, 100);
-
-
- /*
- sprintf (list[n][0], "t_coffee");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE t_coffee\n");
- fprintf ( fp, "ADDRESS built_in");
- fprintf ( fp, "ALN_MODE any\n");
- fprintf ( fp, "OUT_MODE L\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
-
- vfclose (fp);}
- */
- /*Space holder method to analyze very large dATASETS*/
- sprintf (list[n][0], "test_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE test_pair\n");
- fprintf ( fp, "DOC Fast alignmnents on the best diagonals\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "fast_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE fast_pair\n");
- fprintf ( fp, "DOC Fast alignmnents on the best diagonals\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- if (strm (retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- fprintf ( fp, "MATRIX dna_idmat\n");
- fprintf ( fp, "GOP -50\n");
- fprintf ( fp, "GEP -1\n");
- }
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "exon3_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE exon3_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE G\n");
- fprintf ( fp, "MATRIX exon2mt\n");
- fprintf ( fp, "GOP 0\n");
- fprintf ( fp, "GEP -1\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "exon2_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE exon2_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE G\n");
- fprintf ( fp, "MATRIX exon2mt\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -1\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "exon_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE exon_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE G\n");
- fprintf ( fp, "MATRIX exon2mt\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -1\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
-
- sprintf (list[n][0], "clean_slow_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC regular dynamic Programming\n");
- fprintf ( fp, "EXECUTABLE slow_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "WEIGHT clean\n");
- if ( strm ( retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- fprintf ( fp, "MATRIX dna_idmat\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -1\n");
- }
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "slow_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC regular dynamic Programming\n");
- fprintf ( fp, "EXECUTABLE slow_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- if ( strm ( retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- fprintf ( fp, "MATRIX dna_idmat\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -1\n");
- }
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "biphasic_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC bi-phasic dynamic Programming\n");
- fprintf ( fp, "EXECUTABLE biphasic_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- if ( strm ( retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- fprintf ( fp, "MATRIX dna_idmat\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -1\n");
- }
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "proba_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Probabilistic pairwise alignment\n");
- fprintf ( fp, "EXECUTABLE proba_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- if ( strm ( retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- fprintf ( fp, "GOP %d\n",CODE4DNA);//code for DNA
- }
- else
- {
- fprintf ( fp, "GOP %d\n",CODE4PROTEINS);//Code for Proteins
- }
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
-
- sprintf (list[n][0], "best_pair4prot");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Combination of the best template methods\n");
- fprintf ( fp, "EXECUTABLE best_pair4prot\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- if (strm (retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- printf_exit (EXIT_FAILURE, stderr, "\nERROR: The mode best_pair4prot is only suited for Proteins [FATAL:%s]\n", PROGRAM);
- }
- vfclose (fp);}
-
-
- sprintf (list[n][0], "best_pair4rna");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Combination of the best template methods\n");
- fprintf ( fp, "EXECUTABLE best_pair4rna\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
-// if (strm(retrieve_seq_type(), "RNA"))
-// {
-// printf_exit (EXIT_FAILURE, stderr, "\nERROR: The mode best_pair4rna is only suited for RNA [FATAL:%s]\n", PROGRAM);
-// }
- vfclose (fp);}
-
-
- //Llaign ID PAIR
- sprintf (list[n][0], "lalign_id_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC local alignment reporting the N best pairwise local alignments\n");
- fprintf ( fp, "EXECUTABLE lalign_id_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- if ( strm (retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))
- {
- fprintf ( fp, "MATRIX dna_idmat\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -1\n");
- }
- else
- {
- fprintf ( fp, "MATRIX blosum50mt\n");
- fprintf ( fp, "GOP -10\n");
- fprintf ( fp, "GEP -4\n");
- }
- fprintf ( fp, "MAXID 100\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "align_pdbpair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE align_pdb_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "lalign_pdbpair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE lalign_pdb_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "ktup_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE ktup_msa\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE s\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "seq_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE seq_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE s\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "extern_pdbpair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE tc_P_generic_method.pl\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE A\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "externprofile_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE tc_R_generic_method\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE A\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE R\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "thread_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- /*This runs thread_pair@EP@EXECUTABLE2@threpg*/
- fprintf ( fp, "EXECUTABLE thread_pair\n");
- fprintf ( fp, "EXECUTABLE2 t_coffee\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile1=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE Ps\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "fugue_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- /*This runs thread_pair@EP@EXECUTABLE2@threpg*/
- fprintf ( fp, "EXECUTABLE thread_pair\n");
- fprintf ( fp, "EXECUTABLE2 fugueali\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile1=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE Ps\n");
- fprintf ( fp, "ADDRESS %s\n", FUGUE_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", FUGUE_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "pdb_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE pdb_pair\n");
- fprintf ( fp, "EXECUTABLE2 t_coffee\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -pdbfile1=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "hh_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE profile_pair\n");
- fprintf ( fp, "EXECUTABLE2 hhalign\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -profile1=\n");
- fprintf ( fp, "IN_FLAG2 -profile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE R\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- fprintf ( fp, "SUPPORTED NO");
- vfclose (fp);}
-
- sprintf (list[n][0], "profile_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE profile_pair\n");
- fprintf ( fp, "EXECUTABLE2 clustalw\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -profile1=\n");
- fprintf ( fp, "IN_FLAG2 -profile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE R\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- fprintf ( fp, "SUPPORTED NO");
- vfclose (fp);}
-
-
- //Switch to TM_align if SAP is not installed
- //Intercept sap
- if (method && strm (method, "sap_pair") && !check_program_is_installed (SAP_4_TCOFFEE,NULL,NULL,SAP_ADDRESS,INSTALL))
- {
- static int issued;
- if (!issued)
- {
- add_warning (stderr, "\n******************** WARNING: ****************************************\nSAP is not installed\nTMalign will be used instead\ntmalign is FASTER than SAP and *almost* as accurate\n**********************************************************************\n");
- issued=1;
- }
-
- sprintf (list[n][0], "sap_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;
-
- fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: TM-Align: pairwise structural aligner [%s]\n", TMALIGN_ADDRESS);
- fprintf ( fp, "EXECUTABLE pdb_pair\n");
- fprintf ( fp, "EXECUTABLE2 TMalign\n" );
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -pdbfile1=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "ADDRESS %s\n", TMALIGN_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", TMALIGN_4_TCOFFEE);
- fprintf ( fp, "SEQ_TYPE P\n");
- vfclose (fp);
- }
- else
- {
-
- sprintf (list[n][0], "sap_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;
- if (method==NULL || strm (method, list[n-1][0]))
- {
- fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: sap: pairwise structural aligner [%s]\n", SAP_ADDRESS);
- fprintf ( fp, "EXECUTABLE sap_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "WEIGHT 100\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", SAP_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", SAP_4_TCOFFEE);
- vfclose (fp);
- }
- }
- sprintf (list[n][0], "sara_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;
- if (method==NULL || strm (method, list[n-1][0])){
- fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: SARA: pairwise structural RNA aligner [%s]\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "EXECUTABLE rna_pair\n");
- fprintf ( fp, "EXECUTABLE2 runsara.py\n" );
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -pdbfile1=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);
- }
-
- sprintf (list[n][0], "dali_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;
- if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: Dalilite: pairwise structural aligner [%s]\n", DALILITEc_ADDRESS);
- fprintf ( fp, "EXECUTABLE pdbid_pair\n");
- fprintf ( fp, "EXECUTABLE2 dalilite\n" );
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -pdbfile1=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", DALILITEc_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", DALILITEc_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mustang_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: Mustang: pairwise structural aligner [%s]\n", MUSTANG_ADDRESS);
- fprintf ( fp, "EXECUTABLE pdb_pair\n");
- fprintf ( fp, "EXECUTABLE2 mustang\n" );
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -pdbfile1=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE P\n");
- fprintf ( fp, "ADDRESS %s\n", MUSTANG_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MUSTANG_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "TMalign_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: TM-Align: pairwise structural aligner [%s]\n", TMALIGN_ADDRESS);
- fprintf ( fp, "EXECUTABLE pdb_pair\n");
- fprintf ( fp, "EXECUTABLE2 TMalign\n" );
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -pdbfile1=\n");
- fprintf ( fp, "IN_FLAG2 -pdbfile2=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "ADDRESS %s\n", TMALIGN_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", TMALIGN_4_TCOFFEE);
- fprintf ( fp, "SEQ_TYPE P\n");
- vfclose (fp);}
-
- sprintf (list[n][0], "cdna_fast_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE cdna_fast_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "cdna_cfast_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE cdna_cfast_pair\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG no_name\n");
- fprintf ( fp, "OUT_FLAG no_name\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);}
-
- sprintf (list[n][0], "blast_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: BLAST multiple Aligner [%s]\n", NCBIBLAST_ADDRESS);
- fprintf ( fp, "EXECUTABLE seq_msa\n");
- fprintf ( fp, "EXECUTABLE2 blastpgp\n" );
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE fL\n");
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", NCBIBLAST_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", NCBIBLAST_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "clustalw2_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW2_ADDRESS);
- fprintf ( fp, "EXECUTABLE clustalw\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG %sINFILE=\n",CWF);
- fprintf ( fp, "OUT_FLAG %sOUTFILE=\n",CWF);
- fprintf ( fp, "PARAM %sOUTORDER=INPUT %sNEWTREE=cw.tmp.dnd %salign\n",CWF,CWF,CWF);
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", CLUSTALW2_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", CLUSTALW2_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "clustalw2_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW2_ADDRESS);
- fprintf ( fp, "EXECUTABLE clustalw2\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG %sINFILE=\n",CWF);
- fprintf ( fp, "OUT_FLAG %sOUTFILE=\n", CWF);
- fprintf ( fp, "PARAM %sOUTORDER=INPUT %sNEWTREE=cw.tmp.dnd %salign\n",CWF,CWF,CWF);
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", CLUSTALW2_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", CLUSTALW2_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "clustalw_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW_ADDRESS);
- fprintf ( fp, "EXECUTABLE clustalw\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG %sINFILE=\n", CWF);
- fprintf ( fp, "OUT_FLAG %sOUTFILE=\n",CWF);
- fprintf ( fp, "PARAM %sOUTORDER=INPUT %sNEWTREE=cw.tmp.dnd %salign\n",CWF,CWF,CWF);
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", CLUSTALW_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", CLUSTALW_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "clustalw_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW_ADDRESS);
- fprintf ( fp, "EXECUTABLE clustalw\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG %sINFILE=\n", CWF);
- fprintf ( fp, "OUT_FLAG %sOUTFILE=\n", CWF);
- fprintf ( fp, "PARAM %sOUTORDER=INPUT %sNEWTREE=cw.tmp.dnd %salign\n",CWF,CWF,CWF);
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", CLUSTALW_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", CLUSTALW_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafftdef_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE mafft\n");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 \n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
-
- sprintf (list[n][0], "mafftdef_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE mafft\n");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 --localpair --maxiterate 1000 \n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafft_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE mafft\n");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 --localpair --maxiterate 1000 \n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafft_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE mafft\n");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 --localpair --maxiterate 1000 \n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafftjtt_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "EXECUTABLE mafft \n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM1 --jtt 250 --localpair --maxiterate 1000 \n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafftjtt_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "EXECUTABLE mafft \n");
-
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM1 --jtt 250 --localpair --maxiterate 1000 \n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafftgins_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE mafft\n");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 --globalpair --maxiterate 1000 \n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "mafftgins_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE mafft\n");
- fprintf ( fp, "DOC Mafft [%s]\n", MAFFT_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 --globalpair --maxiterate 1000 \n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MAFFT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MAFFT_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "dialigntx_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC dialign-tx [%s]\n", DIALIGNTX_ADDRESS);
- fprintf ( fp, "EXECUTABLE dialign-tx\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- if ( isdir (DIALIGNTX_DIR))
- fprintf ( fp, "PARAM1 %s \n", DIALIGNTX_DIR);
- else
- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG &bnsp\n");
- fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", DIALIGNTX_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", DIALIGNTX_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "dialigntx_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC dialign-tx [%s]\n", DIALIGNTX_ADDRESS);
- fprintf ( fp, "EXECUTABLE dialign-tx\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- if ( isdir (DIALIGNTX_DIR))
- fprintf ( fp, "PARAM1 %s \n", DIALIGNTX_DIR);
- else
- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG &bnsp\n");
- fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", DIALIGNTX_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", DIALIGNTX_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "dialignt_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC dialign-tx [%s]\n", DIALIGNT_ADDRESS);
- fprintf ( fp, "EXECUTABLE dialign-tx\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- if ( isdir (DIALIGNT_DIR))
- fprintf ( fp, "PARAM1 %s \n", DIALIGNT_DIR);
- else
- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG &bnsp\n");
- fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", DIALIGNT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", DIALIGNT_4_TCOFFEE);
-
- vfclose (fp);}
-
- sprintf (list[n][0], "dialignt_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC dialign-tx [%s]\n", DIALIGNT_ADDRESS);
- fprintf ( fp, "EXECUTABLE dialign-tx\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- if ( isdir (DIALIGNT_DIR))
- fprintf ( fp, "PARAM1 %s \n", DIALIGNT_DIR);
- else
- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG &bnsp\n");
- fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", DIALIGNT_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", DIALIGNT_4_TCOFFEE);
-
- vfclose (fp);}
-
- sprintf (list[n][0], "poa_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Partial Order Graph Alignment [%s]\n", POA_ADDRESS);
- fprintf ( fp, "EXECUTABLE poa\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 -toupper \n");
- fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
- fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
- if (file_exists (POA_DIR, POA_FILE1))
- fprintf ( fp, "PARAM %s/%s&bnsp2>/dev/null\n",POA_DIR,POA_FILE1);
- else
- fprintf ( fp, "PARAM %s/%s&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee(), POA_FILE1);
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", POA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n",POA_4_TCOFFEE);
-
- vfclose (fp);}
-
- sprintf (list[n][0], "poa_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Partial Order Graph Alignment [%s]\n", POA_ADDRESS);
- fprintf ( fp, "EXECUTABLE poa\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 -toupper \n");
- fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
- fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
- if (file_exists (POA_DIR, POA_FILE1))
- fprintf ( fp, "PARAM %s/%s&bnsp2>/dev/null\n",POA_DIR,POA_FILE1);
- else
- fprintf ( fp, "PARAM %s/%s&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee(), POA_FILE1);
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", POA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n",POA_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "probcons_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC probcons [%s]\n", PROBCONS_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- if ( strm (retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))fprintf ( fp, "EXECUTABLE probconsRNA\n");
- else fprintf ( fp, "EXECUTABLE probcons\n");
- fprintf ( fp, "ADDRESS %s\n", PROBCONS_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n",PROBCONS_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "probcons_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC probcons [%s]\n", PROBCONS_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- if ( strm (retrieve_seq_type(), "DNA") || strm (retrieve_seq_type(), "RNA"))fprintf ( fp, "EXECUTABLE probconsRNA\n");
- else fprintf ( fp, "EXECUTABLE probcons\n");
- fprintf ( fp, "ADDRESS %s\n", PROBCONS_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n",PROBCONS_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "probconsRNA_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC probcons [%s]\n", PROBCONSRNA_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "EXECUTABLE probconsRNA\n");
- fprintf ( fp, "ADDRESS %s\n", PROBCONSRNA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n",PROBCONSRNA_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "probconsRNA_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC probcons [%s]\n", PROBCONSRNA_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "EXECUTABLE probconsRNA\n");
- fprintf ( fp, "ADDRESS %s\n", PROBCONSRNA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n",PROBCONSRNA_4_TCOFFEE);
- vfclose (fp);}
-
-
-
- sprintf (list[n][0], "muscle_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Muscle [%s]\n", MUSCLE_ADDRESS);
- fprintf ( fp, "EXECUTABLE muscle\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -in&bnsp\n");
- fprintf ( fp, "OUT_FLAG -out&bnsp\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MUSCLE_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MUSCLE_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "muscle_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC Muscle [%s]\n", MUSCLE_ADDRESS);
- fprintf ( fp, "EXECUTABLE muscle\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -in&bnsp\n");
- fprintf ( fp, "OUT_FLAG -out&bnsp\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", MUSCLE_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", MUSCLE_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "t_coffee_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE t_coffee\n");
- fprintf ( fp, "DOC T-Coffee [%s]\n", TCOFFEE_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -infile&bnsp\n");
- fprintf ( fp, "OUT_FLAG -outfile&bnsp\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", TCOFFEE_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", TCOFFEE_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "t_coffee_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE t_coffee\n");
- fprintf ( fp, "DOC T-Coffee [%s]\n", TCOFFEE_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -infile&bnsp\n");
- fprintf ( fp, "OUT_FLAG -outfile&bnsp\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", TCOFFEE_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", TCOFFEE_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "pcma_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC PCMA [%s]\n", PCMA_ADDRESS);
- fprintf ( fp, "EXECUTABLE pcma\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", PCMA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", PCMA_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "pcma_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC PCMA [%s]\n", PCMA_ADDRESS);
- fprintf ( fp, "EXECUTABLE pcma\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", PCMA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", PCMA_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "kalign_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE kalign\n");
- fprintf ( fp, "DOC kalign [%s]\n", KALIGN_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -i&bnsp\n");
- fprintf ( fp, "OUT_FLAG -o&bnsp\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", KALIGN_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", KALIGN_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "kalign_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE kalign\n");
- fprintf ( fp, "DOC kalign [%s]\n", KALIGN_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -i&bnsp\n");
- fprintf ( fp, "OUT_FLAG -o&bnsp\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", KALIGN_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", KALIGN_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "amap_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE amap\n");
- fprintf ( fp, "DOC amap [%s]\n", AMAP_ADDRESS);
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", AMAP_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", AMAP_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "amap_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE amap\n");
- fprintf ( fp, "DOC amap [%s]\n", AMAP_ADDRESS);
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", AMAP_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", AMAP_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "proda_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC proda [%s]\n", PRODA_ADDRESS);
- fprintf ( fp, "EXECUTABLE proda\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", PRODA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", PRODA_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "proda_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC proda [%s]\n", PRODA_ADDRESS);
- fprintf ( fp, "EXECUTABLE proda\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG >\n");
- fprintf ( fp, "PARAM &bnsp2>/dev/null\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", PRODA_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", PRODA_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "prank_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC prank [%s]\n", PRANK_ADDRESS);
- fprintf ( fp, "EXECUTABLE tc_generic_method.pl\n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM -method=%s -mode=seq_msa -tmpdir=%s\n",(getenv("PRANK_4_TCOFFEE"))?getenv("PRANK_4_TCOFFEE"):PRANK_4_TCOFFEE, get_tmp_4_tcoffee());
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", PRANK_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", PRANK_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "prank_msa");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC prank [%s]\n", PRANK_ADDRESS);
- fprintf ( fp, "EXECUTABLE tc_generic_method.pl\n");
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM -method=%s -mode=seq_msa -tmpdir=%s\n",(getenv("PRANK_4_TCOFFEE"))?getenv("PRANK_4_TCOFFEE"):PRANK_4_TCOFFEE, get_tmp_4_tcoffee());
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", PRANK_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", PRANK_4_TCOFFEE);
- vfclose (fp);}
-
-
- sprintf (list[n][0], "em");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;
- if (method==NULL || lstrstr (method,"em@"))
- {
-
- fp=vfopen (list[n-1][1], "w");
- if (method)
- {
- char **l2;
- l2=string2list2 ( method, "@");
- fprintf ( fp, "PARAM -method=%s -mode=seq_msa -tmpdir=%s\n",l2[2], get_tmp_4_tcoffee());
- fprintf ( fp, "ALN_MODE %s\n", l2[3]);
- free_char (l2, -1);
- }
- fprintf ( fp, "EXECUTABLE tc_generic_method.pl\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -infile=\n");
- fprintf ( fp, "OUT_FLAG -outfile=\n");
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", ADDRESS_BUILT_IN);
- fprintf ( fp, "PROGRAM %s\n", PROGRAM_BUILT_IN);
- vfclose (fp);
- }
-
- sprintf (list[n][0], "consan_pair");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "DOC consan (sfold) RNA pairwise sequence aligner [%s]\n", CONSAN_ADDRESS);
- fprintf ( fp, "EXECUTABLE fasta_seq2consan_aln.pl \n");
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "IN_FLAG -i&bnsp\n");
- fprintf ( fp, "OUT_FLAG -o&bnsp\n");
- fprintf ( fp, "PARAM -d&bnsp%s&bnsp2>/dev/null\n",get_mcoffee_4_tcoffee());
- fprintf ( fp, "SEQ_TYPE S\n");
- fprintf ( fp, "ADDRESS %s\n", CONSAN_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", CONSAN_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "RNAplfold");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE RNAplfold \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE RNA\n");
- fprintf ( fp, "ADDRESS %s\n", RNAPLFOLD_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", RNAPLFOLD_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "HMMtop");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE HMMtop \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE PROTEIN\n");
- fprintf ( fp, "ADDRESS %s\n", HMMTOP_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", HMMTOP_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "GOR4");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE GORIV \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE PROTEIN\n");
- fprintf ( fp, "ADDRESS %s\n", GOR4_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", GOR4_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "wublast_client");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE wublast.pl \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE PROTEIN\n");
- fprintf ( fp, "ADDRESS %s\n", EBIWUBLASTc_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", EBIWUBLASTc_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "blastpgp_client");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE blastpgp.pl \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE PROTEIN\n");
-
- fprintf ( fp, "ADDRESS %s\n", EBIBLASTPGPc_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", EBIBLASTPGPc_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "ncbi_netblast");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE blastcl3 \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE PROTEIN\n");
-
- fprintf ( fp, "ADDRESS %s\n", NCBIWEBBLAST_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", NCBIWEBBLAST_4_TCOFFEE);
- vfclose (fp);}
-
- sprintf (list[n][0], "local_ncbiblast");
- sprintf (list[n][1], "%s", vtmpnam(NULL));
- n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w");
- fprintf ( fp, "EXECUTABLE blastall \n");
- fprintf ( fp, "ALN_MODE predict\n");
- fprintf ( fp, "SEQ_TYPE PROTEIN\n");
-
- fprintf ( fp, "ADDRESS %s\n", NCBIBLAST_ADDRESS);
- fprintf ( fp, "PROGRAM %s\n", NCBIBLAST_4_TCOFFEE);
- vfclose (fp);}
-
- list[n]=NULL;
- return list;
-}
-
-
-
-/*********************************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