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IteratingPCCompoundASNReader.java

/* $Revision$ $Author$ $Date$
 * 
 * Copyright (C) 2008  Egon Willighagen <egonw@users.sf.net>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * 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 Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.io.iterator;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.NoSuchElementException;

import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.PCCompoundASNReader;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemSubstancesASNFormat;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Iterating PubChem PCCompound ASN reader.
 *
 * @cdk.module io
 * @cdk.githash
 *
 * @see org.openscience.cdk.io.PCCompoundASNReader
 * 
 * @author       Egon Willighagen <egonw@users.sf.net>
 * @cdk.created  2008-05-05
 *
 * @cdk.keyword  file format, ASN
 * @cdk.keyword  PubChem
 */
00061 public class IteratingPCCompoundASNReader extends DefaultIteratingChemObjectReader {

    private BufferedReader input;
    private LoggingTool logger;
    private IChemObjectBuilder builder;
    
    private boolean nextAvailableIsKnown;
    private boolean hasNext;
    private IMolecule nextMolecule;
    
    private String currentLine;
    private int depth;
    
    /**
     * Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given Reader.
     *
     * @param  in  The Reader to read from
     */
00079     public IteratingPCCompoundASNReader(Reader in, IChemObjectBuilder builder) {
        logger = new LoggingTool(this);
        this.builder = builder;
        setReader(in);
    }

    /**
     * Constructs a new IteratingPCCompoundASNReader that can read Molecule from a given InputStream and IChemObjectBuilder.
     *
     * @param in      The input stream
     * @param builder The builder
     */
00091     public IteratingPCCompoundASNReader(InputStream in, IChemObjectBuilder builder) {
        this(new InputStreamReader(in), builder);
    }


    @TestMethod("testGetFormat")
00097     public IResourceFormat getFormat() {
        return PubChemSubstancesASNFormat.getInstance();
    }

    public boolean hasNext() {
        if (!nextAvailableIsKnown) {
            hasNext = false;
            
            // now try to read the next molecule
            try {
                currentLine = input.readLine();
                  boolean endMoleculeFound = false;
                  boolean startMoleculeFound = false;
                  
                  StringBuffer buffer = new StringBuffer();
                  while (!startMoleculeFound && currentLine != null) {
                        int depthDiff = countBrackets(currentLine);
                        depth += depthDiff;
                        if (depthDiff > 0 && depth == 3) {
                              String command = getCommand(currentLine);
                              if (command.equals("compound")) {
                                    startMoleculeFound = true;
                                    buffer.append("PC-Compound ::= {\n");
                              }
                        }
                        currentLine = input.readLine();
                  }
                  while (!endMoleculeFound && currentLine != null) {
                        int depthDiff = countBrackets(currentLine);
                        depth += depthDiff;
                        if (depthDiff < 0 && depth == 2) {
                              endMoleculeFound = true;
                              buffer.append("}\n");
                              break;
                        } else {
                              buffer.append(currentLine).append("\n");
                        }
                        currentLine = input.readLine();
                  }
                  if (startMoleculeFound && endMoleculeFound) {
                        hasNext = true;
                        PCCompoundASNReader asnReader = new PCCompoundASNReader(
                              new StringReader(buffer.toString())
                        );
                        IChemFile cFile = (IChemFile)asnReader.read(builder.newChemFile());
                        IAtomContainer container = ChemFileManipulator.getAllAtomContainers(cFile).get(0);
                        if (container instanceof IMolecule) {
                              nextMolecule = (IMolecule)container;
                        } else {
                              nextMolecule = builder.newMolecule(container);
                        }
                  }
            } catch (Exception exception) {
                logger.error("Error while reading next molecule: ", exception.getMessage());
                logger.debug(exception);
                exception.printStackTrace();
                hasNext = false;
            }
            if (!hasNext) nextMolecule = null;
            nextAvailableIsKnown = true;
        }
        return hasNext;
    }
    
    private int countChars(String copy, char character) {
      int occurences = 0;
      for (int i=0; i<copy.length(); i++) {
            if (character == copy.charAt(i)) occurences++;
      }
      return occurences;
    }
    
    private int countBrackets(String currentLine) {
            int bracketsOpen = countChars(currentLine, '{');
            int bracketsClose = countChars(currentLine, '}');
            return bracketsOpen - bracketsClose;
      }

      public IChemObject next() {
        if (!nextAvailableIsKnown) {
            hasNext();
        }
        nextAvailableIsKnown = false;
        if (!hasNext) {
            throw new NoSuchElementException();
        }
        return nextMolecule;
    }
    
    @TestMethod("testClose")
00187         public void close() throws IOException {
        input.close();
    }
    
00191     public void remove() {
        throw new UnsupportedOperationException();
    }
    
    private String getCommand(String line) {
      StringBuffer buffer = new StringBuffer();
      int i = 0;
      boolean foundBracket = false;
      while (i<line.length() && !foundBracket) {
            char currentChar = line.charAt(i);
            if (currentChar == '{') {
                  foundBracket = true;
            } else {
                  buffer.append(currentChar);
            }
            i++;
      }
      return foundBracket ? buffer.toString().trim() : null;
    }

      @TestMethod("testSetReader_Reader")
00212     public void setReader(Reader reader) {
            if (reader instanceof BufferedReader) {
                  input = (BufferedReader)reader;
            } else {
                  input = new BufferedReader(reader);
            }
        nextMolecule = null;
        nextAvailableIsKnown = false;
        hasNext = false;
    }

      @TestMethod("testSetReader_InputStream")
00224     public void setReader(InputStream reader) {
          setReader(new InputStreamReader(reader));
    }

}


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