GraphUtils.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2019 Vishwesh Venkatraman <vishwesh.venkatraman@ntnu.no> and
 *   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.utils;
 
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
 
import org.openscience.cdk.interfaces.IAtomContainer;
 
import denoptim.constants.DENOPTIMConstants;
import denoptim.exception.DENOPTIMException;
import denoptim.graph.DGraph;
import denoptim.graph.Vertex;
 
 
public class GraphUtils
{
    public static AtomicLong vertexCounter = new AtomicLong(1);
    private static AtomicInteger graphCounter = new AtomicInteger(1);
    private static AtomicInteger molCounter = new AtomicInteger(1);
 
//------------------------------------------------------------------------------
    
    public static synchronized void ensureVertexIDConsistency(long l) 
            throws DENOPTIMException
    {   
        if (GraphUtils.getUniqueVertexIndex() <= l)
        {
            GraphUtils.resetUniqueVertexCounter(l+1);
        }
    }
 
//------------------------------------------------------------------------------
 
    public static synchronized void resetUniqueVertexCounter(long l)
            throws DENOPTIMException
    {
        if (vertexCounter.get() >= l)
        {
            String msg = "Attempt to reset the unique vertex ID using "
                         + l + " while the current value is "
                         + vertexCounter.get();
            throw new DENOPTIMException(msg);
        }
        vertexCounter = new AtomicLong(l);
    }
 
//-----------------------------------------------------------------------------
 
    public static synchronized long getUniqueVertexIndex()
    {
        if (vertexCounter.get() >= Long.MAX_VALUE-10)
            throw new Error("Reached maximum value for "
                    + "Vertex identifier. It is highly likely that you should "
                    + "not be in this situation as it means you have generated "
                    + "too many vertices. Contact the authors is you really "
                    + "think you need vertex identifiers bigger than 2^64.");
        return vertexCounter.getAndIncrement();
    }
 
//------------------------------------------------------------------------------
 
    public static synchronized void resetUniqueGraphCounter(int val) 
            throws DENOPTIMException
    {
        if (graphCounter.get() >= val)
        {
            String msg = "Attempt to reset the unique graph ID using "
                         + val + " while the current value is "
                         + graphCounter.get();
            throw new DENOPTIMException(msg);
        }
        graphCounter = new AtomicInteger(val);
    }
 
//------------------------------------------------------------------------------
    
    public static synchronized int getUniqueGraphIndex()
    {
        if (graphCounter.get() >= Integer.MAX_VALUE-10)
            throw new Error("Reached maximum value for "
                    + "Graph identifier. Please contact the authors to "
                    + "request use of 'long' IDs.");
        return graphCounter.getAndIncrement();
    }
 
//------------------------------------------------------------------------------
 
    public static synchronized void resetUniqueMoleculeCounter(int val) 
                                                        throws DENOPTIMException
    {
        if (molCounter.get() >= val)
        {
            String msg = "Attempt to reser the unique mol ID using "
                         + val + " while the current value is "
                         + molCounter.get();
            throw new DENOPTIMException(msg);
        }
        molCounter = new AtomicInteger(val);
    }
 
//------------------------------------------------------------------------------
    
    public static synchronized int getUniqueMoleculeIndex()
    {
        if (molCounter.get() >= Integer.MAX_VALUE-10)
            throw new Error("Reached maximum value for "
                    + "Molecule identifier. Please contact the authors to "
                    + "request use of 'long' IDs.");
        return molCounter.getAndIncrement();
    }
  
//------------------------------------------------------------------------------
 
    public static void writeSDFFields(IAtomContainer iac, DGraph g)
            throws DENOPTIMException
    {
        iac.setProperty(DENOPTIMConstants.GCODETAG, g.getGraphId());
        iac.setProperty(DENOPTIMConstants.GRAPHTAG, g.toString());
        iac.setProperty(DENOPTIMConstants.GRAPHJSONTAG, g.toJson());
        if (g.getLocalMsg() != null
                && !g.getLocalMsg().toString().equals(""))
        {
            iac.setProperty(DENOPTIMConstants.PROVENANCE,g.getLocalMsg());
        }
    }
    
//------------------------------------------------------------------------------
 
    public static String getLabel(Vertex v)
    {
        if (!v.hasProperty("Label"))
            return "";
        return v.getGraphOwner().getGraphId()+"@"+v.getProperty(
                "Label").toString();
    }
    
//------------------------------------------------------------------------------
    
    public static String getLabel(DGraph g, int vIdx)
    {
        if (!g.getVertexAtPosition(vIdx).hasProperty("Label"))
            return "";
        return g.getGraphId() + "@" + g.getVertexAtPosition(vIdx).getProperty(
                "Label").toString();
    }
    
//------------------------------------------------------------------------------
 
}