GraphEdParameters.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.programs.grapheditor;
 
import java.io.File;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.logging.Level;
 
import org.openscience.cdk.interfaces.IAtomContainer;
 
import denoptim.exception.DENOPTIMException;
import denoptim.files.FileFormat;
import denoptim.files.FileUtils;
import denoptim.graph.DGraph;
import denoptim.io.DenoptimIO;
import denoptim.logging.StaticLogger;
import denoptim.programs.RunTimeParameters;
import denoptim.utils.GraphEdit;
 
 
public class GraphEdParameters extends RunTimeParameters
{   
    private String inGraphsFile = null;
 
    private ArrayList<DGraph> inGraphs = new ArrayList<DGraph>();
 
    private ArrayList<IAtomContainer> inMols;
 
    private String graphEditsFile = null;
 
    private ArrayList<GraphEdit> graphEdits;
 
    private String outGraphsFile = null;
    private FileFormat outGraphsFormat = FileFormat.GRAPHSDF;
 
    private boolean symmetry = false;
 
//-----------------------------------------------------------------------------
    
    public GraphEdParameters()
    {
        super(ParametersType.GE_PARAMS);
    }
 
//-----------------------------------------------------------------------------
 
    public ArrayList<GraphEdit> getGraphEditTasks()
    {
        return graphEdits;
    }
    
//-----------------------------------------------------------------------------
 
    public ArrayList<DGraph> getInputGraphs()
    {
        return inGraphs;
    }
 
//-----------------------------------------------------------------------------
 
    public IAtomContainer getInpMol(int i)
    {
        return inMols.get(i);
    }
 
//-----------------------------------------------------------------------------
 
    public String getOutFile()
    {
        return outGraphsFile;
    }
 
//-----------------------------------------------------------------------------
 
    public boolean symmetryFlag()
    {
        return symmetry;
    }
 
//-----------------------------------------------------------------------------
    
    public FileFormat getOutFormat()
    {
        return outGraphsFormat;
    }
    
//-----------------------------------------------------------------------------
 
    public void interpretKeyword(String key, String value)
                                                      throws DENOPTIMException
    {
        String msg = "";
        switch (key.toUpperCase())
        {
        case "WORKDIR=":
            workDir = value;
            break;
        case "INPUTGRAPHS=":
            inGraphsFile = value;
            break;
        case "ENFORCESYMMETRY=":
            if (value.toUpperCase().equals("YES") 
                || value.toUpperCase().equals("Y"))
            {
                symmetry = true;
            }
            break;
        case "GRAPHSEDITSFILE=":
            graphEditsFile = value;
            break;
        case "OUTPUTGRAPHS=":
            outGraphsFile = value;
            break;
        case "OUTPUTGRAPHSFORMAT=":
            switch (value.toUpperCase())
            {
                case "SDF":
                    outGraphsFormat = FileFormat.GRAPHSDF;
                    break;
                case "JSON":
                    outGraphsFormat = FileFormat.GRAPHJSON;
                    break;
                default:
                    outGraphsFormat = FileFormat.valueOf(value.toUpperCase());
            }
            break;
        case "LOGFILE=":
            logFile = value;
            break;
        case "VERBOSITY=":
            try
            {
                verbosity = Integer.parseInt(value);
            }
            catch (Throwable t)
            {
                msg = "Unable to understand value " + key + "'" + value + "'";
                throw new DENOPTIMException(msg);
            }
            break;
        default:
             msg = "Keyword " + key + " is not a known GraphEditor-"
                                       + "related keyword. Check input files.";
            throw new DENOPTIMException(msg);
        }
    }
    
//------------------------------------------------------------------------------
 
    public String getPrintedList()
    {
        StringBuilder sb = new StringBuilder(1024);
        sb.append(" " + paramTypeName() + " ").append(NL);
        for (Field f : this.getClass().getDeclaredFields()) 
        {
            try
            {
                sb.append(f.getName()).append(" = ").append(
                            f.get(this)).append(NL);
            }
            catch (Throwable t)
            {
                sb.append("ERROR! Unable to print " + paramTypeName() 
                        + " parameters. Cause: " + t);
                break;
            }
        }
        for (RunTimeParameters otherCollector : otherParameters.values())
        {
            sb.append(otherCollector.getPrintedList());
        }
        return sb.toString();
    }
 
//-----------------------------------------------------------------------------
 
    public void checkParameters() throws DENOPTIMException
    {
        String msg = "";
        if (!workDir.equals(".") && !FileUtils.checkExists(workDir))
        {
           msg = "Directory " + workDir + " not found. Please specify an "
                 + "existing directory.";
           throw new DENOPTIMException(msg);
        }
 
        if (inGraphsFile == null)
        {
            msg = "Input file with graphs to edit not defined. Check you input.";
            throw new DENOPTIMException(msg);
        }
        else if (inGraphsFile != null && !FileUtils.checkExists(inGraphsFile))
        {
            msg = "File with input graphs not found. Check " + inGraphsFile;
            throw new DENOPTIMException(msg);
        }
 
        if (graphEditsFile != null && !FileUtils.checkExists(graphEditsFile))
        {
            msg = "File with graph editing tasks not found. Check " + 
                                                                 graphEditsFile;
            throw new DENOPTIMException(msg);
        }
 
        if (outGraphsFile != null && FileUtils.checkExists(outGraphsFile))
        {
            msg = "Ouput file '" + outGraphsFile + "' exists already!";
            throw new DENOPTIMException(msg);
        }
 
        checkOtherParameters();
    }
 
//----------------------------------------------------------------------------
 
    public void processParameters() throws DENOPTIMException 
    {
        processOtherParameters();
        
        if (outGraphsFile == null)
        {
            outGraphsFile = inGraphsFile + ".mod" ;
            if (FileUtils.checkExists(outGraphsFile))
            {
                String msg = "Ouput file '" + outGraphsFile + "' exists already!";
                throw new DENOPTIMException(msg);
            }
        }
 
        if (graphEditsFile != null)
        {
            try
            {
                graphEdits = DenoptimIO.readDENOPTIMGraphEditFromFile( 
                                                               graphEditsFile);
            }
            catch (Throwable t)
            {
                throw new Error("Cannot read in graph editing tasks from " 
            + graphEditsFile);
            }
        }
    }
    
//-----------------------------------------------------------------------------
    
    protected void readInputGraphs() throws DENOPTIMException
    {
        try
        {
            inGraphs = DenoptimIO.readDENOPTIMGraphsFromFile(new File(
                    inGraphsFile));
        }
        catch (Throwable t)
        {
            String msg = "Cannot read in graphs from " + inGraphsFile;
            StaticLogger.appLogger.log(Level.INFO,msg);
            throw new DENOPTIMException(msg,t);
        }
    }
    
//-----------------------------------------------------------------------------
 
}