ParallelConformerExtractionAlgorithm.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 Marco Foscato <marco.foscato@uib.no>
 * 
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU Affero General Public License as published
 *   by the Free Software Foundation, either version 3 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 Affero General Public License for more details.
 *
 *   You should have received a copy of the GNU Affero General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
package denoptim.fragmenter;
 
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
 
import denoptim.graph.Vertex;
import denoptim.graph.Vertex.BBType;
import denoptim.io.DenoptimIO;
import denoptim.programs.fragmenter.FragmenterParameters;
import denoptim.task.ParallelAsynchronousTaskExecutor;
 
 
public class ParallelConformerExtractionAlgorithm extends ParallelAsynchronousTaskExecutor
{
    
    private FragmenterParameters settings = null;
    
    
//-----------------------------------------------------------------------------
 
    public ParallelConformerExtractionAlgorithm(FragmenterParameters settings)
    {
        super(settings.getNumTasks(), settings.getLogger());
        this.settings = settings;
    }
 
//------------------------------------------------------------------------------
 
    protected boolean doPreFlightOperations()
    {
        return true;
    }
        
//------------------------------------------------------------------------------
 
    protected void createAndSubmitTasks()
    {
        // Looping over the current champions. These are just the first fragment 
        // found for each isomorphic family's sample.
        for (File mwSlotFile : ParallelFragmentationAlgorithm
                .getFilesCollectingIsomorphicFamilyChampions(new File(
                        settings.getWorkDirectory())))
        {
            List<Vertex> oldChampions;
            try
            {
                oldChampions = DenoptimIO.readVertexes(mwSlotFile,
                        BBType.UNDEFINED);
            } catch (Throwable e)
            {
                throw new Error("Unable to extract representative "
                        + "conformations. Problems opening file '"
                        + mwSlotFile + "'.", e);
            }
            for (Vertex oldChampion : oldChampions)
            {
                ConformerExtractorTask task;
                try
                {
                    task = new ConformerExtractorTask(oldChampion, settings);
                } catch (SecurityException | IOException e)
                {
                    throw new Error("Unable to start fragmentation thread.",e);
                }
                submitTask(task, task.getLogFilePathname());
            }
        }
    }
 
//------------------------------------------------------------------------------
 
    protected boolean doPostFlightOperations()
    {
        return true;
    }
 
//------------------------------------------------------------------------------
    
 
    public List<String> getResults()
    {
        List<String> pathnames = new ArrayList<String>();
        results.stream().forEach(o -> pathnames.add((String) o));
        return pathnames;
    }
    
//------------------------------------------------------------------------------    
 
}