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CTXReader.java
/* $RCSfile: $
 * $Author$
 * $Date$
 * $Revision$
 *
 * Copyright (C) 2006-2007  Egon Willighagen <egonw@users.sf.net>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This library 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.
 *
 *  This library 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 library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package org.openscience.cdk.io;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.Symbols;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.io.formats.CTXFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.BondManipulator;

import java.io.*;

/**
 * Reader that extracts information from the IDENT, NAME, ATOMS and BONDS
 * blocks in CTX files.
 * 
 * @cdk.module io
 * @cdk.githash
 */
@TestClass("org.openscience.cdk.io.CTXReaderTest")
00047 public class CTXReader extends DefaultChemObjectReader {

    private BufferedReader input;
    private LoggingTool logger;
    
    private IChemFile file;

    public CTXReader() {
        logger = new LoggingTool(this);
        file = null;
    }

    public CTXReader(Reader input) {
        this();
        if (input instanceof BufferedReader) {
            this.input = (BufferedReader)input;
        } else {
            this.input = new BufferedReader(input);
        }
    }

    public CTXReader(InputStream input) {
        this(new InputStreamReader(input));
    }
    
    @TestMethod("testGetFormat")
00073     public IResourceFormat getFormat() {
        return CTXFormat.getInstance();
    }

    @TestMethod("testSetReader_Reader")
00078     public void setReader(Reader reader) throws CDKException {
        if (reader instanceof BufferedReader) {
            this.input = (BufferedReader)reader;
        } else {
            this.input = new BufferedReader(reader);
        }
    }

    @TestMethod("testSetReader_InputStream")
00087     public void setReader(InputStream input) throws CDKException {
        setReader(new InputStreamReader(input));
    }

      @TestMethod("testAccepts")
    public boolean accepts(Class classObject) {
            Class[] interfaces = classObject.getInterfaces();
            for (int i=0; i<interfaces.length; i++) {
                  if (IChemFile.class.equals(interfaces[i])) return true;
            }
    Class superClass = classObject.getSuperclass();
    if (superClass != null) return this.accepts(superClass);
            return false;
      }

00102     public IChemObject read(IChemObject object) throws CDKException {
        if (object instanceof IChemFile) {
            file = (IChemFile)object;
            return readChemFile();
        } else {
            throw new CDKException("Only supported is reading of ChemFile.");
        }
    }

    private IChemFile readChemFile() throws CDKException {
        IChemSequence seq = file.getBuilder().newChemSequence();
        IChemModel model = file.getBuilder().newChemModel();
        IMoleculeSet containerSet = file.getBuilder().newMoleculeSet();
        IMolecule container = file.getBuilder().newMolecule();
        
        int lineNumber = 0;
        
        try {
            String line = input.readLine();
            while (input.ready() && line != null) {
                logger.debug((lineNumber++) + ": ", line);
                String command = null;
                if (isCommand(line)) { 
                  command = getCommand(line);
                  int lineCount = getContentLinesCount(line);
                        if ("ATOMS".equals(command)) {
                              processAtomsBlock(lineCount, container);
                        } else if ("BONDS".equals(command)) {
                              processBondsBlock(lineCount, container);
                        } else if ("IDENT".equals(command)) {
                              processIdentBlock(lineCount, container);
                        } else if ("NAME".equals(command)) {
                              processNameBlock(lineCount, container);
                        } else {
                              // skip lines
                              logger.warn("Dropping block: ", command);
                              for (int i=0; i<lineCount; i++) input.readLine();
                        }
                } else {
                  logger.warn("Unexpected content at line: ", lineNumber);
                }
                line = input.readLine();
            }
            containerSet.addAtomContainer(container);
            model.setMoleculeSet(containerSet);
            seq.addChemModel(model);
            file.addChemSequence(seq);
        } catch (Exception exception) {
            String message = "Error while parsing CTX file: " + exception.getMessage();
            logger.error(message);
            logger.debug(exception);
            throw new CDKException(message, exception);
        }
        return file;
    }
    
    private void processIdentBlock(int lineCount, IAtomContainer container) throws IOException {
      String identifier = "";
      for (int i=0; i<lineCount; i++) {
                  identifier = identifier + input.readLine().trim();
      }
      container.setID(identifier);
    }
    
    private void processNameBlock(int lineCount, IAtomContainer container) throws IOException {
      String name = "";
      for (int i=0; i<lineCount; i++) {
            name = name + input.readLine().trim();
      }
      container.setProperty(CDKConstants.TITLE, name);
    }
    
      private void processAtomsBlock(int lineCount, IAtomContainer container) throws IOException {
            for (int i=0; i<lineCount; i++) {
                  String line = input.readLine();
                  int atomicNumber = Integer.parseInt(line.substring(7,10).trim());
                  IAtom atom = container.getBuilder().newAtom();
                  atom.setAtomicNumber(atomicNumber);
                  atom.setSymbol(Symbols.byAtomicNumber[atomicNumber]);
                  container.addAtom(atom);
            }
      }

      private void processBondsBlock(int lineCount, IAtomContainer container) throws IOException {
            for (int i=0; i<lineCount; i++) {
                  String line = input.readLine();
                  int atom1 = Integer.parseInt(line.substring(10,13).trim())-1;
                  int atom2 = Integer.parseInt(line.substring(16,19).trim())-1;
                  if (container.getBond(container.getAtom(atom1), container.getAtom(atom2)) == null) {
                        IBond bond = container.getBuilder().newBond(
                              container.getAtom(atom1), 
                              container.getAtom(atom2)
                        );
                        int order = Integer.parseInt(line.substring(23).trim());
                        bond.setOrder(BondManipulator.createBondOrder((double)order));
                        container.addBond(bond);
                  } // else: bond already present; CTX store the bonds twice
            }
      }

      private int getContentLinesCount(String line) {
            return Integer.parseInt(line.substring(18,21).trim());
      }

      private String getCommand(String line) {
            return line.substring(2,10).trim();
      }

      private boolean isCommand(String line) {
            return (line.length() > 1 && line.charAt(0) == ' ' && line.charAt(1) == '/');
      }

      @TestMethod("testClose")
00215   public void close() throws IOException {
        input.close();
    }
}

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