toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxTree/io/batch/BatchProcessingException.java

@@ -0,0 +1,83 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007 
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+*/
+package toxTree.io.batch;
+
+/**
+ * An {@link java.lang.Exception} to be used in {@link toxTree.io.batch.IBatchProcessing}
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-9-4
+ */
+public class BatchProcessingException extends Exception {
+	protected IBatchProcessing batch = null;
+
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = 6837815972092687580L;
+
+	/**
+	 * 
+	 */
+	public BatchProcessingException() {
+		super();
+		// TODO Auto-generated constructor stub
+	}
+
+	/**
+	 * @param message
+	 */
+	public BatchProcessingException(String message) {
+		super(message);
+		// TODO Auto-generated constructor stub
+	}
+	public BatchProcessingException(String message, IBatchProcessing batch) {
+		super(message);
+		this.batch = batch;
+	}
+	public BatchProcessingException(Throwable cause, IBatchProcessing batch) {
+		super(cause);
+		this.batch = batch;
+	}
+	/**
+	 * @param cause
+	 */
+	public BatchProcessingException(Throwable cause) {
+		super(cause);
+		// TODO Auto-generated constructor stub
+	}
+
+	/**
+	 * @param message
+	 * @param cause
+	 */
+	public BatchProcessingException(String message, Throwable cause) {
+		super(message, cause);
+	}
+	public BatchProcessingException(String message, Throwable cause, IBatchProcessing batch) {
+		super(message, cause);
+		this.batch = batch;
+	}
+
+}

data/Toxtree-v2.6.13/src/toxTree/io/batch/ChemObjectBatchProcessing.java

@@ -0,0 +1,281 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007 
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+*/
+package toxTree.io.batch;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.util.logging.Level;
+
+import javax.swing.ProgressMonitorInputStream;
+
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.io.IChemObjectWriter;
+import org.openscience.cdk.io.iterator.IIteratingChemObjectReader;
+import org.openscience.cdk.io.iterator.IteratingSMILESReader;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+
+import ambit2.core.io.DelimitedFileFormat;
+import ambit2.core.io.DelimitedFileWriter;
+import ambit2.core.io.IteratingDelimitedFileReader;
+import ambit2.core.io.MDLWriter;
+import ambit2.core.io.MyIteratingMDLReader;
+
+
+/**
+ * Implements batch processing of chemical files
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-9-4
+ */
+public class ChemObjectBatchProcessing extends BatchProcessing  {
+	protected transient IIteratingChemObjectReader reader;
+	protected transient IChemObjectWriter writer;
+	protected transient IChemObject chemObject;
+
+	public transient static final String[] extensions = {".sdf",".csv",".smi",".txt"};
+	public transient static final String[] extensions_descr = {"SDF files (*.sdf)",
+			"Comma delimited (*.csv)","SMILES (*.smi)","Text files (*.txt)"};
+	protected transient static int SDF_INDEX = 0;
+	protected transient static int CSV_INDEX = 1;
+	protected transient static int SMI_INDEX = 2;
+	protected transient static int TXT_INDEX = 3;
+	
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = -7112745841569991346L;
+
+	/**
+	 * 
+	 */
+	public ChemObjectBatchProcessing() {
+		super();
+	}
+
+	/**
+	 * @param input Input file name
+	 * @param output Output file name
+	 * @throws BatchProcessingException
+	 */
+	public ChemObjectBatchProcessing(String input, String output)
+			throws BatchProcessingException {
+		super(input, output);
+
+	}
+	/**
+	 * 
+	 * @param input Input File
+	 * @param output Output File
+	 * @throws BatchProcessingException
+	 */
+	public ChemObjectBatchProcessing(File input, File output) throws BatchProcessingException {
+		super(input, output);
+	}
+	protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(FileState file,boolean monitor) throws BatchProcessingException {
+		try {
+			String fname = file.filename.toLowerCase(); 
+			if (fname.endsWith(extensions[SDF_INDEX]))
+				if (monitor)
+					return new MyIteratingMDLReader(new ProgressMonitorInputStream(
+                                null,
+                                "Reading " + file.getFile().getName(),
+                                new FileInputStream(file.getFile())),SilentChemObjectBuilder.getInstance());
+				else
+					return new MyIteratingMDLReader(new FileInputStream(file.getFile()),SilentChemObjectBuilder.getInstance());
+			else if (fname.endsWith(extensions[SMI_INDEX])) 
+				return new IteratingSMILESReader(new FileInputStream(file.getFile()));
+			else if (fname.endsWith(extensions[CSV_INDEX]))
+				return new IteratingDelimitedFileReader(new FileInputStream(file.getFile()));
+			else if (fname.endsWith(extensions[TXT_INDEX]))
+				return new IteratingDelimitedFileReader(new FileInputStream(file.getFile()),
+						new DelimitedFileFormat(" \t",'"'));			
+			else throw new BatchProcessingException(MSG_UNSUPPORTEDFORMAT+file.filename,this);
+		} catch (CDKException x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+			throw new BatchProcessingException(x,this);			
+		} catch (UnsupportedEncodingException x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+			throw new BatchProcessingException(x,this);
+		} catch (FileNotFoundException x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+			throw new BatchProcessingException(x,this);
+		}
+	}
+	/**
+	 * Opens the input file as set by constructor and creates {@link IteratingChemObjectReader}
+	 */
+	@Override
+	public void openInputFile() throws BatchProcessingException {
+		super.openInputFile();
+		reader = null;
+		try {
+			logger.fine(MSG_OPEN+inputFile.filename);
+			reader = getReader(inputFile,false);
+			if ((reader != null) && (inputFile.currentRecord>0)) {
+				logger.fine("Have to skip\t"+Long.toString(inputFile.currentRecord)+"\trecords");
+				int count = 0;
+				while (reader.hasNext() && (count < inputFile.currentRecord)) {
+					reader.next();
+					count++;
+				}
+				if (count == inputFile.currentRecord)
+					logger.info(Long.toString(inputFile.currentRecord)+"\trecords skipped.");
+				else { 
+					/*
+					logger.error("Input file is expected to have at least\t",Long.toString(inputFile.currentRecord),
+							"\trecords, but only \t",Long.toString(count),"\t have been found!");
+							*/
+					throw new BatchProcessingException("Input file "+ inputFile.getFilename()+
+							"is expected to have at least\t"+Long.toString(inputFile.currentRecord)+
+							"\trecords, but only \t"+Long.toString(count)+"\t have been found!",this);
+				}
+			}
+		} catch (Exception x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+				throw new BatchProcessingException(x);
+		}
+	}
+	/**
+	 * Creates {@link ChemObjectWriter}
+	 */
+	@Override
+	public void createOutputFile() throws BatchProcessingException {
+		super.createOutputFile();
+		String fname = outputFile.filename.toLowerCase();
+		boolean append = outputFile.currentRecord>0;
+		try {
+			if (fname.endsWith(extensions[SDF_INDEX])) {
+				writer = new MDLWriter(new FileOutputStream(outputFile.getFile(),append));
+				((MDLWriter) writer).dontWriteAromatic();
+			} else if (fname.endsWith(extensions[CSV_INDEX])) 
+				writer = new DelimitedFileWriter(new FileOutputStream(outputFile.getFile(),append));
+			else if ((fname.endsWith(extensions[TXT_INDEX]))) 
+				writer = new DelimitedFileWriter(new FileOutputStream(outputFile.getFile(),append),
+						new DelimitedFileFormat(" \t",'"'));
+			else throw new BatchProcessingException(MSG_UNSUPPORTEDFORMAT+outputFile.filename,this);
+		} catch (Exception x) {
+			logger.log(Level.SEVERE,MSG_ERRORSAVE+outputFile.filename,x);
+			throw new BatchProcessingException(x);
+	}			
+			if ((writer != null) && append) {
+				/*TODO
+				int count = 0;
+				try {
+					IteratingChemObjectReader r = getReader(outputFile,true);
+				
+					while (r.hasNext()) {
+						r.next();
+						count ++;
+					}
+					r.close();
+				} catch (Exception x) {
+					logger.error(MSG_ERRORCOUNTING,outputFile.filename);
+					throw new BatchProcessingException(MSG_ERRORCOUNTING+outputFile.filename,this);
+				}				
+				if (count == outputFile.getCurrentRecord())
+						logger.info("Verifying if the file has indeed \t",Long.toString(outputFile.currentRecord),"\trecords\tYES");
+				else {
+						logger.info("Verifying if the file has indeed \t",Long.toString(outputFile.currentRecord),"\trecords\tNO");
+						throw new BatchProcessingException("Output file "+
+								outputFile.getFilename() +
+								" is expected to have exactly \t"+Long.toString(inputFile.currentRecord)+
+								"\t records, but \t"+Long.toString(count)+"\t records have been found!",this);
+	
+				}
+			*/
+
+			}
+
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.io.BatchProcessing#start()
+	 */
+	@Override
+	public void start() throws BatchProcessingException {
+		super.start();
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.io.IBatchProcessing#closeInputFile()
+	 */
+	public void closeInputFile() throws BatchProcessingException {
+		try {
+			if (reader != null)
+				reader.close(); 
+			reader = null;
+		} catch (IOException x) {
+			throw new BatchProcessingException(x,this);
+		}
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.io.IBatchProcessing#closeOutputFile()
+	 */
+	public void closeOutputFile() throws BatchProcessingException {
+		try {
+			if (writer != null)
+				writer.close(); 
+			writer = null;
+		} catch (IOException x) {
+			throw new BatchProcessingException(x,this);
+		}
+	}
+	/* (non-Javadoc)
+	 * @see toxTree.io.IBatchProcessing#processRecord()
+	 */
+	public void processRecord() throws BatchProcessingException {
+		//do something with chemObject 
+
+	}
+
+	/* (non-Javadoc)
+	 * @see toxTree.io.IBatchProcessing#readRecord()
+	 */
+	public void readRecord() throws BatchProcessingException {
+		chemObject = (IChemObject) reader.next();
+	}	
+
+	/* (non-Javadoc)
+	 * @see toxTree.io.IBatchProcessing#writeRecord()
+	 */
+	public void writeRecord() throws BatchProcessingException {
+		try {
+			writer.write(chemObject);
+		} catch (CDKException x) {
+			throw new BatchProcessingException("Error on writing record\t",x,this);
+		}
+
+	}
+
+	/* (non-Javadoc)
+	 * @see toxTree.io.IBatchProcessing#hasNextRecord()
+	 */
+	public boolean hasNextRecord() {
+		return reader.hasNext();
+	}
+	
+}

data/Toxtree-v2.6.13/src/toxTree/io/batch/FileState.java

@@ -0,0 +1,232 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007 
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+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 General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+*/
+package toxTree.io.batch;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+
+/**
+ * This is to be able to verify if a file has changed since it has been last processed by BatchProcessing
+ * @author Nina Jeliazkova
+ * <b>Modified</b> 2005-9-4
+ */
+public class FileState implements Serializable {
+	/**
+	 * Comment for <code>serialVersionUID</code>
+	 */
+	private static final long serialVersionUID = -9098389880881547516L;
+	protected String filename=null;
+	protected long length=0;
+	protected long lastModified=0;
+	protected int hashCode=0;
+	protected transient File file = null;
+	protected long offset = 0;
+	protected long currentRecord = 0;
+	/**
+	 * 
+	 */
+	public FileState() {
+		super();
+	}
+	public FileState(String filename) {
+		this(new File(filename));
+	}	
+	public FileState(File file) {
+		this();
+		setFile(file);
+		
+	}	
+	/* (non-Javadoc)
+	 * @see java.lang.Object#equals(java.lang.Object)
+	 */
+	@Override
+	public boolean equals(Object obj) {
+		FileState fs = (FileState) obj;
+		return filename.equals(fs.getFilename()) &&
+			   (length == fs.length) &&
+			   (lastModified == fs.lastModified) &&
+			   (hashCode == fs.hashCode) &&
+			   (currentRecord == fs.currentRecord) &&
+			   (offset == fs.offset)
+			   ;
+		
+	}
+
+	/**
+	 * @return Returns the filename.
+	 */
+	public synchronized String getFilename() {
+		return filename;
+	}
+	/**
+	 * @param filename The filename to set.
+	 */
+	public synchronized void setFilename(String filename) {
+		this.filename = filename;
+	}
+	/**
+	 * @return Returns the hashCode.
+	 */
+	public synchronized int getHashCode() {
+		return hashCode;
+	}
+	/**
+	 * @param hashCode The hashCode to set.
+	 */
+	public synchronized void setHashCode(int hashCode) {
+		this.hashCode = hashCode;
+	}
+	/**
+	 * @return Returns the lastModified.
+	 */
+	public synchronized long getLastModified() {
+		return lastModified;
+	}
+	/**
+	 * @param lastModified The lastModified to set.
+	 */
+	public synchronized void setLastModified(long lastModified) {
+		this.lastModified = lastModified;
+	}
+	/**
+	 * @return Returns the length.
+	 */
+	public synchronized long getLength() {
+		return length;
+	}
+	/**
+	 * @param length The length to set.
+	 */
+	public synchronized void setLength(long length) {
+		this.length = length;
+	}
+/*
+	private void writeObject(java.io.ObjectOutputStream out)
+	     throws IOException {
+		
+	}
+	 private void readObject(java.io.ObjectInputStream in)
+	     throws IOException, ClassNotFoundException {
+	 	
+	 }
+	 */
+	 	
+	/**
+	 * @return Returns the file.
+	 */
+	public synchronized File getFile() {
+		return file;
+	}
+	/**
+	 * @param file The file to set.
+	 */
+	public synchronized void setFile(File file) {
+		this.file = file;
+		filename = file.getAbsolutePath();
+		length = file.length();
+		lastModified = file.lastModified();
+		hashCode = file.hashCode();
+		this.file = file;
+		currentRecord = 0;
+		offset = 0;
+	}
+	/**
+	 * @return Returns the currentRecord.
+	 */
+	public synchronized long getCurrentRecord() {
+		return currentRecord;
+	}
+	/**
+	 * @param currentRecord The currentRecord to set.
+	 */
+	public synchronized void setCurrentRecord(long currentRecord) {
+		this.currentRecord = currentRecord;
+	}
+	/**
+	 * @return Returns the offset.
+	 */
+	public synchronized long getOffset() {
+		return offset;
+	}
+	/**
+	 * @param offset The offset to set.
+	 */
+	public synchronized void setOffset(long offset) {
+		this.offset = offset;
+	}
+	public boolean match() throws BatchProcessingException {
+		return match(createFile());
+	}
+	public boolean match(File file) {
+		
+		return filename.equals(file.getAbsolutePath()) &&
+		   (length == file.length()) &&
+		   (lastModified == file.lastModified()) 
+		   //&&   (hashCode == file.hashCode())
+		   ;
+		
+	}
+	public File createFile()  throws BatchProcessingException {
+		try {
+			return new File(filename);
+		} catch (Exception x) {
+			throw new BatchProcessingException(x);
+		}
+	}
+	@Override
+	public String toString() {
+		StringBuffer b = new StringBuffer();
+		b.append(" [");
+		b.append((currentRecord+1));
+		b.append(" ] ");
+		b.append(filename);
+		return b.toString();
+	}
+	private void writeObject(ObjectOutputStream out) throws IOException {
+		out.writeLong(serialVersionUID);
+		out.writeObject(filename);
+		out.writeLong(length);
+		out.writeLong(lastModified);
+		out.writeInt(hashCode);
+		out.writeLong(offset);
+		out.writeLong(currentRecord);
+	}
+
+
+	private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
+		if (in.readLong() != serialVersionUID) throw new ClassNotFoundException();
+		filename =in.readObject().toString();
+		length =in.readLong();
+		lastModified = in.readLong();
+		hashCode = in.readInt();
+		offset = in.readLong();
+		currentRecord = in.readLong();
+		file = new File(filename);
+	}	
+}