/******************************COPYRIGHT NOTICE*******************************/
/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  12 Aug 2014 - 22:07.                                                                    */
/*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*******************************/
struct Job_TC
    {
      int jobid;
      int status;
      
      struct  Job_TC *c;
      struct  Job_TC *p;
      struct  Job_io_TC *io;
      struct  Job_control_TC *control;
      
      struct  Job_param_TC *param;
        
      /*memory mangement*/
      char **pl;
      int np;
};
typedef struct Job_TC Job_TC;

struct Job_control_TC
    {
      
      struct Job_TC* (*submitF) (struct Job_TC*);
      struct Job_TC* (*retrieveF)(struct Job_TC*);
      char *mode;
};
typedef struct Job_control_TC Job_control_TC;

struct Job_io_TC
    {
      char *in;
      char *out;
      struct Constraint_list *CL;
      struct Alignment *A;
};
typedef struct Job_io_TC Job_io_TC;

struct Job_param_TC
{
  char *method;
  struct TC_method *TCM; 
  char *temp_c;
  char *aln_c;
  char *seq_c;
  char *aln_mode;
};
typedef struct Job_param_TC Job_param_TC;

Job_TC* print_lib_job ( Job_TC *job,char *string, ...);
Job_TC *print_lib_job2 ( Job_TC* job, int n, char **name, char **value);


/*Stack Manipulation*/
Job_TC *free_queue  (Job_TC *job);
Job_TC *free_job  (Job_TC *job);
Job_TC * queue2heap (Job_TC*job);
Job_TC * queue2last (Job_TC*job);
int queue2n (Job_TC*job);
Job_TC * descend_queue (Job_TC*job);
Job_TC *queue_cat  (Job_TC *P, Job_TC *C);
Job_TC *delete_job (Job_TC *job);
/*Job Control*/
struct Job_TC* submit_job ( Job_TC *job);
struct Job_TC* retrieve_job ( Job_TC *job);
Job_TC*** split_job_list (Job_TC *job, int ns);
int **n2splits (int nsplits, int nelements);