program_extension.cpp

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/***************************************************************************
 * Authors:     J.M. de la Rosa Trevin (jmdelarosam@cnb.csic.es)
 *
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * 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.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/

#include "program_extension.h"

//Needed includes for instantiate programs
#include <data/filters.h>
#include "angular_project_library.h"
#include "angular_projection_matching.h"
#include "angular_discrete_assign.h"
#include "volume_from_pdb.h"
#include "pdb_nma_deform.h"
#include "pdb_sph_deform.h"
#include "angular_continuous_assign.h"
#include "micrograph_automatic_picking2.h"
#include "program_filter.h"
#include <data/mask.h>
#include <classification/analyze_cluster.h>

void runSystem(const String &program, const String &arguments, bool useSystem) {
    if (useSystem) {
        String cmd = formatString("%s %s", program.c_str(), arguments.c_str());
        if (system(cmd.c_str())==-1)
            REPORT_ERROR(ERR_UNCLASSIFIED,"Cannot open shell");
    } else {
        runProgram(program, arguments);
    }
}

int runProgram(XmippProgram * program, const String &arguments, bool destroy)
{
    if (program == nullptr)
        REPORT_ERROR(ERR_PARAM_INCORRECT, "Received a NULL as program pointer");
    program->read(arguments);
    int retCode = program->tryRun();
    if (destroy)
        delete program;
    return retCode;
}

int runProgram(const String &programName, const String &arguments)
{
    XmippProgram * program = getProgramByName(programName);
    return runProgram(program, arguments);
}

XmippProgram * getProgramByName(const String &programName)
{
    //  if (programName == "xmipp_tranform_filter")
    //    return new ProgFilter();

    if (programName == "xmipp_volume_from_pdb")
        return new ProgPdbConverter();

    if (programName == "xmipp_angular_project_library")
        return new ProgAngularProjectLibrary();

    if (programName == "xmipp_angular_projection_matching")
        return new ProgAngularProjectionMatching();

    if (programName == "xmipp_mask")
        return new ProgMask();

    if (programName == "xmipp_angular_discrete_assign")
        return new ProgAngularDiscreteAssign();

    if (programName == "xmipp_angular_continuous_assign")
        return new ProgAngularContinuousAssign();

    if (programName == "xmipp_pdb_nma_deform")
        return new ProgPdbNmaDeform();
    
    if (programName == "xmipp_pdb_sph_deform")
        return new ProgPdbSphDeform();

    if (programName == "xmipp_micrograph_automatic_picking")
        return new ProgMicrographAutomaticPicking2();

    if (programName == "xmipp_classify_analyze_cluster")
        return new ProgAnalyzeCluster();

    if (programName == "xmipp_transform_filter")
        return new ProgFilter();

    return nullptr;
}