SDFileReader.java

/*
 * MX Cheminformatics Tools for Java
 * 
 * Copyright (c) 2007, 2008 Metamolecular, LLC
 * 
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package com.chemhack.jsMolEditor.client.io.mdl;

import com.chemhack.jsMolEditor.client.model.Molecule;
import com.chemhack.jsMolEditor.client.model.MoleculeKit;
import com.chemhack.jsMolEditor.client.jre.emulation.java.util.regex.Pattern;
import com.chemhack.jsMolEditor.client.jre.emulation.java.io.IOException;
import com.chemhack.jsMolEditor.client.jre.emulation.java.io.LineNumberReader;
//import java.io.BufferedReader;
//import java.io.FileReader;
//import java.io.IOException;
//import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
//import java.util.regex.Matcher;
//import java.util.regex.Pattern;

/**
 * @author Richard L. Apodaca <rapodaca at metamolecular.com>
 *         Duan Lian
 */
public class SDFileReader
{
  private static String RECORD_END = "$$$$";
  private static String LINEFEED = "\n";
  private LineNumberReader reader;
//  private Reader file;
  private String record;
  private Pattern keyPattern;
  private Pattern molfilePattern;
  private Map<String, Pattern> keyPatterns;

  public SDFileReader(String sdfile) throws IOException
  {
    record = null;
//    file = new FileReader(filename);
    reader = new LineNumberReader(sdfile);
    keyPattern = new Pattern("^> *?<(.*?)>", Pattern.MULTILINE);
//TODO DOTALL mode not supported in js molfilePattern = new Pattern("^(.*M  END)", Pattern.DOTALL);
    molfilePattern = new Pattern("^(.*M  END)");

    keyPatterns = new HashMap<String, Pattern>();
  }

  public void close()
  {
//    try
//    {
//      file.close();
//    }
//    catch (IOException e)
//    {
//      throw new RuntimeException("Error closing file.", e);
//    }
  }

  public boolean hasNextRecord()
  {
      return reader.ready();
  }

  public void nextRecord()
  {
    StringBuffer buff = new StringBuffer();

    try
    {
      String line = reader.readLine();

      while ((!RECORD_END.equals(line)))
      {
        if(line==null){     //sdfile with inproper ending may cause dead loop.
            break;
        }
        buff.append(line + LINEFEED);

        line = reader.readLine();
      }
    }
    catch (IOException e)
    {
      throw new RuntimeException("An unexpected IO error occurred while reading file.", e);
    }

    record = buff.toString();
  }

  public String getData(String key)
  {
    assertRecordLoaded();

    Pattern pattern = keyPatterns.get(key);

    if (pattern == null)
    {
// TODO DOTALL MODE     pattern = new Pattern(".*^> *?<" + key + ">$.(.*?)$.*", Pattern.MULTILINE | Pattern.DOTALL);
      pattern = new Pattern(".*^> *?<" + key + ">$.(.*?)$.*", Pattern.MULTILINE);
      keyPatterns.put(key, pattern);
    }

//    Matcher matcher = pattern.matcher(record);

    String[] matchArray=pattern.match(record);
    return matchArray.length>0? matchArray[1] : "";
  }

  public Molecule getMolecule()
  {
    assertRecordLoaded();

//    Matcher matcher = molfilePattern.matcher(record);
//
//    matcher.find();

    String molfile = molfilePattern.match(record)[1];

    return MoleculeKit.readMolfile(molfile);
  }

  public Molecule getMolecule(boolean virtualizeHydrogens)
  {
    assertRecordLoaded();

//    Matcher matcher = molfilePattern.matcher(record);
//
//    matcher.find();

      String molfile = molfilePattern.match(record)[1];

    return MoleculeKit.readMolfile(molfile, virtualizeHydrogens);
  }

  public List<String> getKeys()
  {
    List<String> result = new ArrayList<String>();
//    Matcher m = keyPattern.matcher(record);
//
//    while (m.find())
//    {
//      result.add(m.group(1));
//    }

//TODO I don't know how to handle this.

    return result;
  }

  private void assertRecordLoaded()
  {
    if (record == null)
    {
      throw new IllegalStateException("No record has been loaded. Make sure you've called nextRecord() first.");
    }
  }
}