/***************************************************************************
                          psipred.cpp  -  description
                             -------------------
    begin                : Tue Nov 18 01:45:35 2003
    copyright            : (C) 1999-2008 by Cavalli Andrea
    author               : : cavalli $
    date                 : : 2003/12/09 11:10:33 $
    id                   : : coor.h,v 1.1.2.2 2003/12/09 11:10:33 cavalli Exp $
    email                : cavalli@bioc.unizh.ch amc82@cam.ac.uk
**************************************************************************/
/***************************************************************************
 *                                                                         *
 *   This program 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.                                   *
 *                                                                         *
 ***************************************************************************/

#include <almost.h>
#include <psipred/psipred.h>

extern "C" {
  int psipred_main(int argc, char **argv, FILE * out);
}

namespace Psipred {
  int psipass2_main(int argc, char **argv);
}

namespace Almost {

  int Psipred::run_pass1(string mtx, string out_f){
    //make argc argv
    //$ROOT/psipred  $1".mtx" $DATA/weights.dat $DATA/weights.dat2 $DATA/weights.dat3 $DATA/weights.dat4
    int argc = 6;
    char ** argv = (char **) calloc(argc,sizeof(char*));
    argv[0] = strdup("almost::psipred");
    argv[1] = strdup(mtx.c_str());
    argv[2] = strdup((m_path+"/weights.dat").c_str());
    argv[3] = strdup((m_path+"/weights.dat2").c_str());
    argv[4] = strdup((m_path+"/weights.dat3").c_str());
    argv[5] = strdup((m_path+"/weights.dat4").c_str());

    FILE * out = fopen(out_f.c_str(),"w");

    psipred_main(argc,argv,out);
    
    fclose(out);
    for(int i=0;i<argc;i++) free(argv[i]);
    free(argv);
    return 0;
  }


  int Psipred::run_pass2(string out_f1, string out_f2){
    //Make argc argv
    //$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $rootname.ss
    int argc = 7;
    char ** argv = (char **) calloc(argc,sizeof(char*));
    argv[0] = strdup("almost::psipass2");
    argv[1] = strdup((m_path+"/weights_p2.dat").c_str());
    argv[2] = strdup("1");
    argv[3] = strdup("1.0");
    argv[4] = strdup("1.0");
    argv[5] = strdup(out_f2.c_str());
    argv[6] = strdup(out_f1.c_str());

    ::Psipred::psipass2_main(argc,argv);

    for(int i=0;i<argc;i++) free(argv[i]);
    free(argv);
    return 0;
  }

  int Psipred::run(string mtx,string out_f1, string out_f2){
    int res = run_pass1(mtx,out_f1);
    res = run_pass2(out_f1,out_f2);
    return res;
  }
}
// Local Variables:
// mode:C++
// End: