/* $Revision$ $Author$ $Date$
*
* 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.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
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
*/
public class IteratingPCCompoundASNReader extends DefaultIteratingChemObjectReader {
private BufferedReader input;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(IteratingPCCompoundASNReader.class);
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
*/
public IteratingPCCompoundASNReader(Reader in, IChemObjectBuilder builder) {
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
*/
public IteratingPCCompoundASNReader(InputStream in, IChemObjectBuilder builder) {
this(new InputStreamReader(in), builder);
}
@TestMethod("testGetFormat")
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")
public void close() throws IOException {
input.close();
}
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")
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")
public void setReader(InputStream reader) {
setReader(new InputStreamReader(reader));
}
}