IteratingAtomContainerReader.java

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package denoptim.io;
 
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
 
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.io.FormatFactory;
import org.openscience.cdk.io.formats.IChemFormat;
import org.openscience.cdk.io.formats.MDLV2000Format;
import org.openscience.cdk.io.formats.MDLV3000Format;
import org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader;
import org.openscience.cdk.io.iterator.IteratingSDFReader;
import org.openscience.cdk.io.iterator.IteratingSMILESReader;
 
import denoptim.exception.DENOPTIMException;
 
public class IteratingAtomContainerReader implements Iterator<IAtomContainer>
{
 
    private List<IAtomContainer> results;
    
    private Iterator<IAtomContainer> listIterator;
    
    private DefaultIteratingChemObjectReader<IAtomContainer> fileIterator;
    
    private boolean usingIteratingReader = false;
    
//------------------------------------------------------------------------------
    
    public IteratingAtomContainerReader(File input) 
            throws FileNotFoundException, IOException, CDKException,
            DENOPTIMException
    {
        FormatFactory factory = new FormatFactory();
        factory.registerFormat(new SMILESListFormat());
        
        BufferedReader headReader = new BufferedReader(new FileReader(input));
        IChemFormat chemFormat = factory.guessFormat(headReader);
        headReader.close();
        
        if (chemFormat instanceof MDLV2000Format
                || chemFormat instanceof MDLV3000Format)
        {
            FileInputStream fis = new FileInputStream(input);
            fileIterator = new IteratingSDFReader(fis, 
                    DefaultChemObjectBuilder.getInstance());
            usingIteratingReader = true;
        } else if (chemFormat instanceof SMILESListFormat) {
 
            FileInputStream fis = new FileInputStream(input);
            fileIterator = new IteratingSMILESReader(fis,
                    DefaultChemObjectBuilder.getInstance());
            usingIteratingReader = true;
        } else { 
            results = DenoptimIO.readAllAtomContainers(input);
            listIterator = results.iterator();
        }
    }
 
//------------------------------------------------------------------------------
      
    @Override
    public boolean hasNext()
    {
        if (usingIteratingReader)
            return fileIterator.hasNext();
        else
            return listIterator.hasNext();
    }
 
//------------------------------------------------------------------------------
      
    @Override
    public IAtomContainer next()
    {
        if (usingIteratingReader)
            return fileIterator.next();
        else
            return listIterator.next();
    }
    
//------------------------------------------------------------------------------
    
    public void close() throws IOException
    {
        if (fileIterator!=null)
            fileIterator.close();
    }
  
//------------------------------------------------------------------------------
    
    public Class<?> getIteratorType()
    {
        if (usingIteratingReader)
            return fileIterator.getClass();
        else
            return listIterator.getClass();
    }
 
//------------------------------------------------------------------------------
}