--- /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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