+++ /dev/null
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-#include "dp_lib_header.h"
-
-
-
-Job_TC* print_lib_job ( Job_TC *job,char *string, ...)
-{
- va_list ap;
- char **list;
- char **value;
- char **name;
- int a, np, n;
-
- char bname[100];
- char bval[100];
-
- list=string2list2(string, " =");
- n=atoi (list[0]);
-
-
- name =vcalloc ( (n-1)/2, sizeof (char*));
- value=vcalloc ( (n-1)/2, sizeof (char*));
-
-
- va_start (ap, string);
- for (a=1, np=0; a<n; a++)
- {
- if (list[a][0]=='%' && list[a][1]=='s')
- {
- value[np++]=duplicate_string (va_arg (ap,char *));
- }
- else if (list[a][0]=='%')
- {
- if ( list[a][1]=='d')sprintf (bval, "%d", va_arg (ap,int));
- else if ( list[a][1]=='f')sprintf (bval, "%lf",(float) va_arg (ap,double));
- else if ( list[a][1]=='p')sprintf (bval, "%ld", (long)va_arg (ap,void *));
- value[np++]=duplicate_string (bval);
- }
- else
- {
- sprintf (bname, "%s", list[a]);
- name[np]=duplicate_string (bname);
- }
- }
- free_arrayN((void**)list, 2);
-
- va_end (ap);
-
- return print_lib_job2 ( job,np,name,value);
-}
-
-static int njobs;
-Job_TC *print_lib_job2 ( Job_TC* job, int n, char **name, char **value)
-{
- int a;
-
- if ( job==NULL)
- {
- job=vcalloc ( 1, sizeof (Job_TC));
- job->pl=vcalloc (100, sizeof (char*));job->pl[job->np++]=(void*)job->pl;
- job->jobid=njobs++;
- }
-
- for ( a=0; a< n; a++)
- {
- int string=0;
- if ( strstr(name[a], "control") && !job->control){job->control=vcalloc ( 1, sizeof (Job_control_TC));job->pl[job->np++]=(void*)job->control;}
- else if ( strstr(name[a], "io") && !job->io){job->io=vcalloc ( 1, sizeof (Job_io_TC));job->pl[job->np++]=(void*)job->io;}
- else if ( strstr(name[a], "param") && !job->param){job->param=vcalloc ( 1, sizeof (Job_param_TC));job->pl[job->np++]=(void*)job->param;}
-
- if ( strm (name[a], "control")) {job->control=(struct Job_control_TC*)atol(value[a]);string=0;}
- else if ( strm (name[a], "control->submitF")) {(job->control) ->submitF=(struct Job_TC *(*)(struct Job_TC *))atol(value[a]);string=0;}
- else if ( strm (name[a], "control->retrieveF")) {(job->control) ->retrieveF=(struct Job_TC *(*)(struct Job_TC *))atol(value[a]);string=0;}
- else if ( strm (name[a], "control->mode")) {(job->control)->mode=value[a];string=1;}
-
- else if ( strm (name[a], "param")) {job->param=(struct Job_param_TC*)atol(value[a]);string=0;}
- else if ( strm (name[a], "param->method")) {job->pl[job->np++]=((job->param)->method)=value[a];string=1;}
- else if ( strm (name[a], "param->TCM")) {(job->param)->TCM= (TC_method *) atol(value[a]) ;string=0;}
- else if ( strm (name[a], "param->aln_c")) {job->pl[job->np++]=(job->param)->aln_c=value[a] ;string=1;}
- else if ( strm (name[a], "param->seq_c")) {job->pl[job->np++]=(job->param)->seq_c=value[a] ;string=1;}
-
-
- else if ( strm (name[a], "io")) {job->io=(struct Job_io_TC*)atol(value[a]);string=0;}
- else if ( strm (name[a], "io->out")) {job->pl[job->np++]=(job->io)->out=value[a] ;string=1;}
- else if ( strm (name[a], "io->in" )) {job->pl[job->np++]=(job->io)->in =value[a] ;string=1;}
- else if ( strm (name[a], "io->CL")) {(job->io)->CL=(Constraint_list*)atol (value[a]); string=0;}
- else
- {
- fprintf ( stderr, "ERROR: print_lib_job2: %s is unknown [FATAL:%s]", name[a], PROGRAM);
- myexit (EXIT_FAILURE);
- }
- if ( string==0) vfree ( value[a]);
- }
- vfree ( value);
- free_arrayN ((void **)name, 2);
- return job;
-}
-
-
-
-/*Stack Manipulation*/
-Job_TC *queue_cat (Job_TC *P, Job_TC *C)
-{
- if ( !P && !C) return NULL;
- else if (!P || P->jobid==-1)
- {
- vfree (P);
- C->p=NULL;
- return C;
- }
- else
- {
- P->c=C;
- if (C)C->p=P;
- return queue2last(P);
- }
- return NULL;
-}
-Job_TC *free_queue (Job_TC *job)
-{
- return NULL;
- if (!job) return job;
- else
- {
- job=queue2last(job);
- while ( job)
- {
- job=free_job (job);
- }
- return job;
- }
-}
-Job_TC *free_job (Job_TC *job)
- {
- int a;
- Job_TC *p;
-
- if ( !job ) return job;
- else
- {
- for ( a=job->np-1; a>=0; a--)
- vfree ( job->pl[a]);
- p=job->p;
- job->p=job->c=NULL;
- vfree (job);
- return p;
- }
- return NULL;
- }
-Job_TC * queue2heap (Job_TC*job)
-{
-
- while (job && job->p)
- job=job->p;
- return job;
-}
-Job_TC * queue2last (Job_TC*job)
-{
-
- while (job && job->c)
- {
- job=job->c;
- }
- return job;
-}
-
-int queue2n (Job_TC*job)
-{
- int n=0;
-
-
- job=queue2last (job);
- while (job && job->p)
- {
- n++;
- job=job->p;
-
- }
- return n;
-}
-
-Job_TC * descend_queue (Job_TC*job)
-{
-
- if (!job ||!job->c)return job;
- else
- {
- (job->c)->p=job;
- job=job->c;
- }
- return job;
-}
-
-Job_TC* delete_job (Job_TC *job)
-{
- Job_TC *p, *c;
-
- p=job->p;
- c=job->c;
- free_job (job);
-
- return queue_cat (p, c);
-}
-
-Job_TC*** split_job_list (Job_TC *job, int ns)
-{
- int a,u,n,nj,split;
- Job_TC*** jl;
- Job_TC *ljob;
- //retun a pointer to ns splits for joblist
-
-
- if (ns==0)return NULL;
- job=queue2heap(job);
- jl=vcalloc(ns+1, sizeof (Job_TC**));
- jl[0]=vcalloc (2, sizeof (Job_TC*));
-
- nj=queue2n(job);
-
- if (nj==0)return NULL;
- else split=(nj/ns)+1;
-
- n=a=u=0;
- jl[a][0]=job;
- while (job)
- {
- ljob=job;
- if (n==split && a<ns)
- {
- jl[a][1]=job;
- if (a<ns-1)
- {
- jl[a+1]=vcalloc (2, sizeof (Job_TC*));
- jl[a+1][0]=job;
- u++;
- }
- a++;
- n=0;
- }
- n++;
- job=job->c;
- }
-
- /*Display job details when debugging
- a=0;
- while (jl[a])
- {
- Job_TC *start,* end;
- int todo=0;
-
- start=job=jl[a][0];
- end=jl[a][1];
- while (job!=end){todo++;job=job->c;}
- job=start;
- while (job!=end)
- {
- HERE ("--- %d %d %s",a, job, job->param->aln_c);
- job=job->c;
- }
- a++;
- }
-
- a=0;
- while (jl[a]){HERE ("**** %d %d ", jl [a][0], jl[a][1]);a++;}
- myexit (0);
- */
- return jl;
-}
-
-
-
-
-/*Job Control*/
-Job_TC* submit_job ( Job_TC *job)
-{
-
- if (!(job->control)->mode ||!(job->control)->mode[0] || 1==1)
- {
- return (job->control)->submitF (job);
- }
- else
- {
- fprintf ( stderr, "\n%s is an unkown mode for posting jobs [FATAL:%s]",(job->control)->mode, PROGRAM);
- myexit (EXIT_FAILURE);
- return NULL;
- }
-
-}
-
-Job_TC* retrieve_job ( Job_TC *job)
-{
- if (!(job->control)->mode ||!(job->control)->mode[0] || 1==1)
- {
- return (job->control)->retrieveF (job);
- }
- else
- {
- fprintf ( stderr, "\n%s is an unkown mode for posting jobs [FATAL:%s]",(job->control)->mode, PROGRAM);
- myexit (EXIT_FAILURE);
- return NULL;
- }
-}
-int **n2splits (int splits, int tot)
-{
- int **l;
- int a,b,delta;
-
- if (splits==0)return NULL;
- else if ( tot==0)return NULL;
- else
- {
-
- l=declare_int (splits,2);
- delta=tot/splits;
-
- for (a=0,b=0; a<splits && b<tot; a++,b+=delta)
- {
- l[a][0]=b;
- l[a][1]=MIN((b+delta),tot);
- }
- l[splits-1][1]=MAX((l[splits-1][1]),tot);
- return l;
- }
-}
-
-/******************************COPYRIGHT NOTICE*******************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE is free software; you can redistribute it and/or modify*/
-/* it under the terms of the GNU General Public License as published by*/
-/* the Free Software Foundation; either version 2 of the License, or*/
-/* (at your option) any later version.*/
-/**/
-/* T-COFFEE is distributed in the hope that it will be useful,*/
-/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
-/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
-/* GNU General Public License for more details.*/
-/**/
-/* You should have received a copy of the GNU General Public License*/
-/* along with Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/******************************COPYRIGHT NOTICE*******************************/
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