CEBLUtils.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.combinatorial;
 
import java.io.File;
import java.util.ArrayList;
import java.util.regex.Pattern;
 
import org.apache.commons.io.FileUtils;
 
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
 
import denoptim.constants.DENOPTIMConstants;
import denoptim.exception.DENOPTIMException;
import denoptim.files.SingletonFileAccess;
import denoptim.graph.DGraph;
import denoptim.io.DenoptimIO;
import denoptim.programs.combinatorial.CEBLParameters;
 
 
public class CEBLUtils
{
 
//------------------------------------------------------------------------------
 
    public static String getNameOfStorageDir(CEBLParameters settings, int level)
    {
        String dirName = settings.getDBRoot()
                          + DENOPTIMConstants.FSEP
                          + DENOPTIMConstants.FSEIDXNAMEROOT
                          + level;
        return dirName;
    }
 
//------------------------------------------------------------------------------
 
    public static int getGraphIdFromStorageFile(String fileName) 
                                                        throws DENOPTIMException
    {
        String msg ="";
        if (fileName.contains(Pattern.quote(DENOPTIMConstants.SERGFILENAMEROOT)) 
                && fileName.contains(Pattern.quote(".")))
        {
             msg = "Failed attempt to extract a graphId from String '" 
                         + fileName + "'";
            throw new DENOPTIMException(msg);
        }
        String[] p1 = fileName.split(Pattern.quote(
                DENOPTIMConstants.SERGFILENAMEROOT));
        String[] p2 = p1[1].split(Pattern.quote("."));
        int graphId = -1;
        try
        {
            graphId = Integer.parseInt(p2[0]);
        }
        catch (Throwable t)
        {
            throw new DENOPTIMException(msg);
        }
        return graphId;
    }
 
//------------------------------------------------------------------------------
 
    public static String getBaseNameOfStorageFile(int graphId)
    {
        String baseName = DENOPTIMConstants.SERGFILENAMEROOT
                          + graphId + "."
                          + DENOPTIMConstants.SERGFILENAMEEXT;
        return baseName;
    }
 
//------------------------------------------------------------------------------
 
    public static String getNameOfStorageFile(CEBLParameters settings, int level,
            int graphId)
    {
        String fileName = settings.getDBRoot()
                          + DENOPTIMConstants.FSEP
                          + DENOPTIMConstants.FSEIDXNAMEROOT
                          + level
                          + DENOPTIMConstants.FSEP
                          + getBaseNameOfStorageFile(graphId);
        return fileName;
    }
 
//------------------------------------------------------------------------------
 
    public static String getNameOfStorageIndexFile(CEBLParameters settings, 
            int level)
    {
        String fileName = settings.getDBRoot()
                          + DENOPTIMConstants.FSEP
                          + DENOPTIMConstants.FSEIDXNAMEROOT
                          + level
                          + DENOPTIMConstants.FSEP
                          + DENOPTIMConstants.FSEIDXNAMEROOT
                          + level + ".txt";
        return fileName;
    }
 
//------------------------------------------------------------------------------
 
    protected static void storeAllGraphsOfLevel(CEBLParameters settings, 
            ArrayList<DGraph> lstGraphs, int level) throws DENOPTIMException
    {
        for (DGraph g : lstGraphs)
        {
            //NOTE: the arraylist is supposed to hold the indeces used to 
            //      create the next combination of fragments, but this method
            //      is used only for graphs built with the base scaffolds or 
            //      the naked root graphs. Therefore there is no set of indeces
            //      to store and we fed the method with an empty array.
            // NOTE2: the root Id is set to zero for the same reason.
            
            DGraph c = g.clone();
            
            storeGraphOfLevel(settings, c,level,0,new ArrayList<Integer>());
        }
    }
 
//------------------------------------------------------------------------------
 
    protected static void storeGraphOfLevel(CEBLParameters settings, 
            DGraph graph, int level, int rootId, 
            ArrayList<Integer> nextIds) throws DENOPTIMException
    {
        String outDir = getNameOfStorageDir(settings, level);
        if (!denoptim.files.FileUtils.checkExists(outDir))
        {
            try
            {
                FileUtils.forceMkdir(new File(outDir));
            }
            catch (Throwable t)
            {
                String msg = "Cannot create folder " + outDir;
                throw new DENOPTIMException(msg,t);
            }
        }
 
        String fileSer = getNameOfStorageFile(settings, level, 
                graph.getGraphId());
        String indexFile = getNameOfStorageIndexFile(settings, level);
        String indexLine = graph.toString() + " => " + graph.getGraphId() + " " 
                           + rootId + " " + nextIds;
        
        SingletonFileAccess.getInstance().writeData(fileSer, graph.toJson(),
                false);
        SingletonFileAccess.getInstance().writeData(indexFile, indexLine, true);
    }
 
//------------------------------------------------------------------------------
 
    protected static void serializeCheckPoint(CEBLParameters settings) 
            throws DENOPTIMException
    {
        Gson writer = new GsonBuilder().setPrettyPrinting().create();
        DenoptimIO.writeData(settings.getCheckPointName(), writer.toJson(
                settings.getCheckPoint()), false);
    }
 
//------------------------------------------------------------------------------
 
    public static CheckPoint deserializeCheckpoint(String file)
            throws DENOPTIMException
    {
        String s = DenoptimIO.readText(file);
        Gson writer = new GsonBuilder().create();
        CheckPoint chkpt = writer.fromJson(s, CheckPoint.class);
        return chkpt;
    }
 
//------------------------------------------------------------------------------
 
}