DescriptorForFitness.java

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/*
 *   DENOPTIM
 *   Copyright (C) 2022 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.fitness;
 
import java.lang.reflect.Constructor;
import java.util.ArrayList;
import java.util.List;
 
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.IImplementationSpecification;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.qsar.IDescriptor;
 
import denoptim.exception.DENOPTIMException;
 
public class DescriptorForFitness 
{
    protected String className;
    
    protected IDescriptor implementation;
 
    protected String shortName;
 
    protected List<Variable> variables = new ArrayList<Variable>();
    
    protected int resultId = 0;
    
    protected String[] dictClasses;
    
    protected String dictDefinition;
    
    protected String dictTitle;
    
    private static IChemObjectBuilder cdkBuilder = 
            DefaultChemObjectBuilder.getInstance();
    
//------------------------------------------------------------------------------
 
    public DescriptorForFitness(String shortName, String className, 
            IDescriptor implementation, int resultId)
    {
        this.shortName = shortName;
        this.className = className;
        this.implementation = implementation;
        this.resultId = resultId;
    }
 
//------------------------------------------------------------------------------
 
    public DescriptorForFitness(String shortName, String className, 
            IDescriptor implementation, int resultId,
            String[] dictClasses, String dictDefinition, String dictTitle)
    {
        this(shortName, className, implementation, resultId);
        this.dictClasses = dictClasses;
        this.dictDefinition = dictDefinition;
        this.dictTitle = dictTitle;
    }
    
//------------------------------------------------------------------------------
    
    public String getShortName()
    {
        return shortName;
    }
    
//------------------------------------------------------------------------------
    
    public void setVariables(List<Variable> variables)
    {
        this.variables = variables;
    }
    
//------------------------------------------------------------------------------
 
    public List<Variable> getVariables()
    {
        return variables;
    }
    
//------------------------------------------------------------------------------
 
    public String getClassName()
    {
        return className;
    }
    
//------------------------------------------------------------------------------
 
    public IDescriptor getImplementation()
    {
        return implementation;
    }
    
//------------------------------------------------------------------------------
 
    public String getDictTitle()
    {
        return dictTitle;
    }
    
//------------------------------------------------------------------------------
 
    public String getDictDefinition()
    {
        return dictDefinition;
    }
 
//------------------------------------------------------------------------------
 
    public String[] getDictClasses()
    {
        return dictClasses;
    }
    
//------------------------------------------------------------------------------
    
    @Override
    public String toString()
    {
        StringBuilder sb = new StringBuilder();
        sb.append("DescriptorForFitness [shortName:").append(shortName);
        sb.append(", variables:[");
        for (Variable v : variables)
        {
            sb.append(v.getName() + ", ");
        }
        sb.append("]");
        sb.append(", className:").append(className);
        sb.append(", resultId:").append(resultId);
        IImplementationSpecification specs = implementation.getSpecification();
        sb.append(", specReference:").append(
                specs.getSpecificationReference());
        sb.append(", implTitle:").append(
                specs.getImplementationTitle());
        sb.append(", implId:").append(
                specs.getImplementationIdentifier());
        sb.append(", implVendor:").append(
                specs.getImplementationVendor()).append("]");
        return sb.toString();
    }
 
//------------------------------------------------------------------------------
    
    public String getDictString() 
    {
        String NL = System.getProperty("line.separator");
        StringBuilder sb = new StringBuilder();
        sb.append("Titile: ").append(dictTitle).append(NL);
        sb.append("Definition: ").append(dictDefinition).append(NL);
        sb.append("Classes: ");
        if (dictClasses != null)
        {
            for (String c : dictClasses)
            {
                sb.append(c).append(" ");
            }
        }
        sb.append(NL);
        
        return sb.toString();
    }
    
//------------------------------------------------------------------------------
    
    public DescriptorForFitness cloneAllButImpl() 
    {
        DescriptorForFitness dff = new DescriptorForFitness(shortName, 
                className, null, resultId, dictClasses, 
                dictDefinition, dictTitle);
        dff.setVariables(new ArrayList<Variable>(variables));
        return dff;
    }
 
//------------------------------------------------------------------------------
    
    public DescriptorForFitness makeCopy() throws DENOPTIMException
    {
        DescriptorForFitness clone = this.cloneAllButImpl();
        clone.implementation = newDescriptorImplementation(this);
        return clone;
    }
    
//------------------------------------------------------------------------------
    
    private static IDescriptor newDescriptorImplementation(
            DescriptorForFitness oldParent) throws DENOPTIMException
    {
        String className = oldParent.getImplementation().getClass().getName();
        IDescriptor descriptor = null;
        try
        {
            Class<?> cl = Class.forName(className);
            for (Constructor<?> constructor : cl.getConstructors()) 
            {
                Class<?>[] params = constructor.getParameterTypes();
                if (params.length == 0) 
                {
                    descriptor = (IDescriptor) constructor.newInstance();
                } else if (params[0].equals(IChemObjectBuilder.class))
                {
                    //NB potential source of ambiguity on the builder class
                    descriptor = (IDescriptor) constructor.newInstance(cdkBuilder);
                }
            }
        } catch (Throwable t)
        {
            throw new DENOPTIMException("Could not make new instance of '" 
                    + className + "'.", t);
        }
        if (descriptor == null)
        {
            throw new DENOPTIMException("Could not make new instance of '" 
                    + className + "'. No suitable constructor found.");
        }
        descriptor.initialise(cdkBuilder);
        return descriptor;
    }
 
//------------------------------------------------------------------------------
    
    public void addDependentVariable(Variable v)
    {
        variables.add(v);
    }
 
//------------------------------------------------------------------------------
    
}