From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Fri, 12 Aug 2011 13:35:18 +0000 (+0000)
Subject: Javadoc fixes
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ba2d4e920e433bd080f448248e7dacade69a27a0;p=jabaws.git

Javadoc fixes

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4508 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
index 2656046..fc44c44 100644
--- a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
+++ b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java
@@ -200,7 +200,7 @@ public final class ClustalAlignmentUtil {
 	 * consensus. Potential bug - records 60 chars length alignment where
 	 * Clustal would have recorded 50 chars.
 	 * 
-	 * @param outStream
+	 * @param out
 	 * 
 	 * @param alignment
 	 * @throws IOException
diff --git a/datamodel/compbio/data/sequence/FastaReader.java b/datamodel/compbio/data/sequence/FastaReader.java
index 38f1ccb..1641d34 100644
--- a/datamodel/compbio/data/sequence/FastaReader.java
+++ b/datamodel/compbio/data/sequence/FastaReader.java
@@ -71,7 +71,7 @@ public class FastaReader implements Iterator<FastaSequence> {
 	/**
 	 * Header data can contain non-ASCII symbols and read in UTF8
 	 * 
-	 * @param input
+	 * @param inputFile
 	 *            the file containing the list of FASTA formatted sequences to
 	 *            read from
 	 * @throws FileNotFoundException
diff --git a/datamodel/compbio/data/sequence/Score.java b/datamodel/compbio/data/sequence/Score.java
index c8cbfb4..ec4cadc 100644
--- a/datamodel/compbio/data/sequence/Score.java
+++ b/datamodel/compbio/data/sequence/Score.java
@@ -128,7 +128,7 @@ public class Score implements Comparable<Score> {
 	/**
 	 * Return Ranges if any Collections.EMPTY_SET otherwise
 	 * 
-	 * @return
+	 * @return ordered set of Range
 	 */
 	public TreeSet<Range> getRanges() {
 		return ranges;
@@ -200,8 +200,7 @@ public class Score implements Comparable<Score> {
 	 * 
 	 * @param scores
 	 *            the list of scores to output
-	 * @param output
-	 *            the stream to output the data to
+	 * @param writer
 	 * @throws IOException
 	 *             if the OutputStream cannot be written into
 	 * @throws NullPointerException
diff --git a/datamodel/compbio/data/sequence/SequenceUtil.java b/datamodel/compbio/data/sequence/SequenceUtil.java
index 16b65f2..6e20988 100644
--- a/datamodel/compbio/data/sequence/SequenceUtil.java
+++ b/datamodel/compbio/data/sequence/SequenceUtil.java
@@ -290,7 +290,7 @@ public final class SequenceUtil {
 	 * Read IUPred output
 	 * 
 	 * @param result
-	 * @return
+	 * @return Map key->sequence name, value->Score
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
@@ -427,7 +427,7 @@ public final class SequenceUtil {
 	 * 
 	 * @param inStream
 	 *            the InputStream connected to the JRonn output file
-	 * @return List of {@link AnnotatedSequence} objects
+	 * @return Map key=sequence name value=Score
 	 * @throws IOException
 	 *             is thrown if the inStream has problems accessing the data
 	 * @throws UnknownFileFormatException
@@ -533,7 +533,8 @@ public final class SequenceUtil {
 	 * 
 	 * 
 	 * @param input
-	 * @return
+	 *            the InputStream
+	 * @return Map key=sequence name, value=set of score
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
@@ -655,7 +656,7 @@ public final class SequenceUtil {
 	 * 
 	 * 
 	 * @param input
-	 * @return
+	 * @return Map key=sequence name, value=set of score
 	 * @throws IOException
 	 * @throws UnknownFileFormatException
 	 */
diff --git a/engine/compbio/engine/Cleaner.java b/engine/compbio/engine/Cleaner.java
index e4e2923..4813388 100644
--- a/engine/compbio/engine/Cleaner.java
+++ b/engine/compbio/engine/Cleaner.java
@@ -26,6 +26,7 @@ import compbio.engine.client.ConfiguredExecutable;
 import compbio.engine.client.PathValidator;
 import compbio.engine.local.ExecutableWrapper;
 
+@Deprecated
 public class Cleaner {
 
 	private static final Logger log = Logger.getLogger(Cleaner.class);
@@ -37,7 +38,8 @@ public class Cleaner {
 	 * 
 	 * @param workDirectory
 	 * @param files
-	 * @return
+	 * @return This method returns true if all files specified by List files
+	 *         were successfully removed, false otherwise
 	 */
 	public static boolean deleteFiles(ConfiguredExecutable<?> exec) {
 
@@ -71,12 +73,11 @@ public class Cleaner {
 			if (success) {
 				log.trace(type + filename + " was successfully removed");
 			} else {
-				log
-						.debug("Could not remove "
-								+ type
-								+ ": "
-								+ filename
-								+ " reportedly created by executable. Insufficient access right?");
+				log.debug("Could not remove "
+						+ type
+						+ ": "
+						+ filename
+						+ " reportedly created by executable. Insufficient access right?");
 			}
 		} else {
 			log.debug("File: " + filename
diff --git a/engine/compbio/engine/FilePuller.java b/engine/compbio/engine/FilePuller.java
index d040838..98a44bc 100644
--- a/engine/compbio/engine/FilePuller.java
+++ b/engine/compbio/engine/FilePuller.java
@@ -32,284 +32,285 @@ import compbio.util.FileWatcher;
 
 public class FilePuller implements Delayed {
 
-    private static final Logger log = Logger.getLogger(FilePuller.class);
-
-    // 5 minutes in nanosec
-    private static long defaultDelay = 1000 * 1000 * 1000L * 5 * 60;
-    private final File file;
-    private long lastAccessTime;
-    private FileWatcher watcher;
-    final int chunkSize;
-
-    // used for testing only
-    long delay = 0;
-
-    private FilePuller(String file, int size) {
-	FileWatcher.validateInput(file, size);
-	if (compbio.util.Util.isEmpty(file)) {
-	    throw new NullPointerException("File name must be provided!");
+	private static final Logger log = Logger.getLogger(FilePuller.class);
+
+	// 5 minutes in nanosec
+	private static long defaultDelay = 1000 * 1000 * 1000L * 5 * 60;
+	private final File file;
+	private long lastAccessTime;
+	private FileWatcher watcher;
+	final int chunkSize;
+
+	// used for testing only
+	long delay = 0;
+
+	private FilePuller(String file, int size) {
+		FileWatcher.validateInput(file, size);
+		if (compbio.util.Util.isEmpty(file)) {
+			throw new NullPointerException("File name must be provided!");
+		}
+		// The fact that the file may not exist at a time does not matter here
+		if (!PathValidator.isAbsolutePath(file)) {
+			throw new IllegalArgumentException("Absolute path to the File "
+					+ file + " is expected but not provided!");
+		}
+		this.file = new File(file);
+		this.chunkSize = size;
+		this.lastAccessTime = System.nanoTime();
 	}
-	// The fact that the file may not exist at a time does not matter here
-	if (!PathValidator.isAbsolutePath(file)) {
-	    throw new IllegalArgumentException("Absolute path to the File "
-		    + file + " is expected but not provided!");
+
+	private FilePuller(String file) {
+		if (compbio.util.Util.isEmpty(file)) {
+			throw new NullPointerException("File name must be provided!");
+		}
+		// The fact that the file may not exist at a time does not matter here
+		if (!PathValidator.isAbsolutePath(file)) {
+			throw new IllegalArgumentException("Absolute path to the File "
+					+ file + " is expected but not provided!");
+		}
+		this.file = new File(file);
+		this.chunkSize = 3;
+		this.lastAccessTime = System.nanoTime();
 	}
-	this.file = new File(file);
-	this.chunkSize = size;
-	this.lastAccessTime = System.nanoTime();
-    }
-
-    private FilePuller(String file) {
-	if (compbio.util.Util.isEmpty(file)) {
-	    throw new NullPointerException("File name must be provided!");
+
+	public static FilePuller newFilePuller(String file, int chunkSize) {
+		return new FilePuller(file, chunkSize);
 	}
-	// The fact that the file may not exist at a time does not matter here
-	if (!PathValidator.isAbsolutePath(file)) {
-	    throw new IllegalArgumentException("Absolute path to the File "
-		    + file + " is expected but not provided!");
+
+	/**
+	 * Progress Puller is designed to read 3 characters from the beginning of
+	 * the file, nothing more. Intended to be used in conjunction with a tool
+	 * which output progress as a percent value from 0 to 100. In any cases
+	 * progress could not be more than the largest byte value 255.
+	 * 
+	 * @param file
+	 * @return instance
+	 */
+	public static FilePuller newProgressPuller(String file) {
+		return new FilePuller(file);
 	}
-	this.file = new File(file);
-	this.chunkSize = 3;
-	this.lastAccessTime = System.nanoTime();
-    }
-
-    public static FilePuller newFilePuller(String file, int chunkSize) {
-	return new FilePuller(file, chunkSize);
-    }
-
-    /**
-     * Progress Puller is designed to read 3 characters from the beginning of
-     * the file, nothing more. Intended to be used in conjunction with a tool
-     * which output progress as a percent value from 0 to 100. In any cases
-     * progress could not be more than the largest byte value 255.
-     * 
-     * @param file
-     * @return
-     */
-    public static FilePuller newProgressPuller(String file) {
-	return new FilePuller(file);
-    }
-
-    public ChunkHolder pull(long position) throws IOException {
-	initPull();
-	String valueUTF16 = watcher.pull(position);
-	String value = null;
-	if (valueUTF16 != null) {
-	    value = removeInvalidXMLCharacters(valueUTF16);
+
+	public ChunkHolder pull(long position) throws IOException {
+		initPull();
+		String valueUTF16 = watcher.pull(position);
+		String value = null;
+		if (valueUTF16 != null) {
+			value = removeInvalidXMLCharacters(valueUTF16);
+		}
+		return new ChunkHolder(value, watcher.getCursorPosition());
 	}
-	return new ChunkHolder(value, watcher.getCursorPosition());
-    }
-
-    /**
-     * This method ensures that the output String has only valid XML unicode
-     * characters as specified by the XML 1.0 standard. For reference, please
-     * see the standard.
-     * 
-     * @param The
-     *            String whose non-valid characters we want to remove.
-     * 
-     * @return The in String, stripped of non-valid characters.
-     */
-    static String removeInvalidXMLCharacters(String str) {
-	assert str != null;
-
-	StringBuilder out = new StringBuilder(); // Used to hold the output.
-	int codePoint; // Used to reference the current character.
-
-	// For test
-	// String ss = "\ud801\udc00"; // This is actualy one unicode character,
-	// represented by two code units!!!.
-	// System.out.println(ss.codePointCount(0, ss.length()));// See: 1
-	int i = 0;
-	String value = null;
-	try {
-	    // make sure the string contain only UTF-8 characters
-	    value = new String(str.getBytes("UTF-8"), "UTF-8");
-	} catch (UnsupportedEncodingException e) {
-	    // will not happen
-	    throw new AssertionError("UTF-8 charset is not supported!!!");
+
+	/**
+	 * This method ensures that the output String has only valid XML unicode
+	 * characters as specified by the XML 1.0 standard. For reference, please
+	 * see the standard.
+	 * 
+	 * @param The
+	 *            String whose non-valid characters we want to remove.
+	 * 
+	 * @return The in String, stripped of non-valid characters.
+	 */
+	static String removeInvalidXMLCharacters(String str) {
+		assert str != null;
+
+		StringBuilder out = new StringBuilder(); // Used to hold the output.
+		int codePoint; // Used to reference the current character.
+
+		// For test
+		// String ss = "\ud801\udc00"; // This is actualy one unicode character,
+		// represented by two code units!!!.
+		// System.out.println(ss.codePointCount(0, ss.length()));// See: 1
+		int i = 0;
+		String value = null;
+		try {
+			// make sure the string contain only UTF-8 characters
+			value = new String(str.getBytes("UTF-8"), "UTF-8");
+		} catch (UnsupportedEncodingException e) {
+			// will not happen
+			throw new AssertionError("UTF-8 charset is not supported!!!");
+		}
+		while (i < value.length()) {
+			codePoint = value.codePointAt(i); // This is the unicode code of the
+			// character.
+			if ((codePoint == 0x9)
+					|| // Consider testing larger ranges first to
+						// improve speed.
+					(codePoint == 0xA) || (codePoint == 0xD)
+					|| ((codePoint >= 0x20) && (codePoint <= 0xD7FF))
+					|| ((codePoint >= 0xE000) && (codePoint <= 0xFFFD))
+					|| ((codePoint >= 0x10000) && (codePoint <= 0x10FFFF))) {
+
+				out.append(Character.toChars(codePoint));
+			}
+
+			i += Character.charCount(codePoint);
+			/*
+			 * Increment with the number of code units(java chars) needed to
+			 * represent a Unicode char.
+			 */
+		}
+		return out.toString();
 	}
-	while (i < value.length()) {
-	    codePoint = value.codePointAt(i); // This is the unicode code of the
-	    // character.
-	    if ((codePoint == 0x9)
-		    || // Consider testing larger ranges first to
-		    // improve speed.
-		    (codePoint == 0xA) || (codePoint == 0xD)
-		    || ((codePoint >= 0x20) && (codePoint <= 0xD7FF))
-		    || ((codePoint >= 0xE000) && (codePoint <= 0xFFFD))
-		    || ((codePoint >= 0x10000) && (codePoint <= 0x10FFFF))) {
-
-		out.append(Character.toChars(codePoint));
-	    }
-
-	    i += Character.charCount(codePoint);
-	    /*
-	     * Increment with the number of code units(java chars) needed to
-	     * represent a Unicode char.
-	     */
+
+	public void initPull() {
+		this.lastAccessTime = System.nanoTime();
+		if (!isFileCreated()) {
+			throw new IllegalStateException("File " + file.getAbsolutePath()
+					+ " has not been created yet! Cannot pull.");
+		}
+		if (watcher == null) {
+			init();
+		}
 	}
-	return out.toString();
-    }
-
-    public void initPull() {
-	this.lastAccessTime = System.nanoTime();
-	if (!isFileCreated()) {
-	    throw new IllegalStateException("File " + file.getAbsolutePath()
-		    + " has not been created yet! Cannot pull.");
+
+	public String getFile() {
+		return file.getAbsolutePath();
 	}
-	if (watcher == null) {
-	    init();
+
+	public boolean isFileCreated() {
+		this.lastAccessTime = System.nanoTime();
+		return file.exists();
 	}
-    }
-
-    public String getFile() {
-	return file.getAbsolutePath();
-    }
-
-    public boolean isFileCreated() {
-	this.lastAccessTime = System.nanoTime();
-	return file.exists();
-    }
-
-    public void waitForFile(long maxWaitSeconds) {
-	long waited = 0;
-	int step = 500;
-	while (true) {
-	    if (isFileCreated()) {
-		break;
-	    }
-	    try {
-		Thread.sleep(step);
-		// TODO is this needed? this.lastAccessTime = System.nanoTime();
-	    } catch (InterruptedException e) {
-		// Propagate interruption up the stack trace for anyone
-		// interested
-		Thread.currentThread().interrupt();
-		log.debug("Thread interruped during waiting for file "
-			+ file.getAbsolutePath() + " to be created. Message: "
-			+ e.getMessage());
-		break;
-	    }
-	    waited += step;
-	    if (waited / 1000 >= maxWaitSeconds) {
-		break;
-	    }
+
+	public void waitForFile(long maxWaitSeconds) {
+		long waited = 0;
+		int step = 500;
+		while (true) {
+			if (isFileCreated()) {
+				break;
+			}
+			try {
+				Thread.sleep(step);
+				// TODO is this needed? this.lastAccessTime = System.nanoTime();
+			} catch (InterruptedException e) {
+				// Propagate interruption up the stack trace for anyone
+				// interested
+				Thread.currentThread().interrupt();
+				log.debug("Thread interruped during waiting for file "
+						+ file.getAbsolutePath() + " to be created. Message: "
+						+ e.getMessage());
+				break;
+			}
+			waited += step;
+			if (waited / 1000 >= maxWaitSeconds) {
+				break;
+			}
+		}
 	}
-    }
 
-    public boolean hasMoreData() throws IOException {
-	this.lastAccessTime = System.nanoTime();
-	if (!isFileCreated()) {
-	    throw new IllegalStateException("File " + file.getAbsolutePath()
-		    + " has not been created yet! Cannot pull.");
+	public boolean hasMoreData() throws IOException {
+		this.lastAccessTime = System.nanoTime();
+		if (!isFileCreated()) {
+			throw new IllegalStateException("File " + file.getAbsolutePath()
+					+ " has not been created yet! Cannot pull.");
+		}
+		if (watcher == null) {
+			init();
+		}
+		return watcher.hasMore();
 	}
-	if (watcher == null) {
-	    init();
+
+	private synchronized void init() {
+		// Check watcher==null is duplicated to avoid adding synchronization to
+		// access methods
+		if (watcher == null) {
+			if (chunkSize < FileWatcher.MIN_CHUNK_SIZE_BYTES) {
+				watcher = FileWatcher
+						.newProgressWatcher(file.getAbsolutePath());
+				log.debug("Init Progress watcher with file: "
+						+ file.getAbsolutePath());
+			} else {
+				watcher = FileWatcher.newFileWatcher(file.getAbsolutePath(),
+						chunkSize);
+				log.debug("Init File watcher with file: "
+						+ file.getAbsolutePath());
+			}
+
+		}
 	}
-	return watcher.hasMore();
-    }
-
-    private synchronized void init() {
-	// Check watcher==null is duplicated to avoid adding synchronization to
-	// access methods
-	if (watcher == null) {
-	    if (chunkSize < FileWatcher.MIN_CHUNK_SIZE_BYTES) {
-		watcher = FileWatcher
-			.newProgressWatcher(file.getAbsolutePath());
-		log.debug("Init Progress watcher with file: "
-			+ file.getAbsolutePath());
-	    } else {
-		watcher = FileWatcher.newFileWatcher(file.getAbsolutePath(),
-			chunkSize);
-		log.debug("Init File watcher with file: "
-			+ file.getAbsolutePath());
-	    }
 
+	@Override
+	public int compareTo(Delayed o) {
+		return new Long(this.getDelay(TimeUnit.NANOSECONDS)).compareTo(o
+				.getDelay(TimeUnit.NANOSECONDS));
 	}
-    }
-
-    @Override
-    public int compareTo(Delayed o) {
-	return new Long(this.getDelay(TimeUnit.NANOSECONDS)).compareTo(o
-		.getDelay(TimeUnit.NANOSECONDS));
-    }
-
-    /*
-     * This must return remaining delay associated with the object!
-     * (non-Javadoc)
-     * 
-     * @see java.util.concurrent.Delayed#getDelay(java.util.concurrent.TimeUnit)
-     */
-    @Override
-    public long getDelay(final TimeUnit unit) {
-	long idleTime = System.nanoTime() - lastAccessTime;
-	long delayVal = (delay == 0 ? defaultDelay : delay);
-	return unit.convert(delayVal - idleTime, TimeUnit.NANOSECONDS);
-    }
-
-    void setDelay(long delay, TimeUnit unit) {
-	assert delay > 0;
-	this.delay = TimeUnit.NANOSECONDS.convert(delay, unit);
-	assert delay < defaultDelay;
-    }
-
-    long getDelayValue(TimeUnit unit) {
-	return (delay == 0 ? unit.convert(defaultDelay, TimeUnit.NANOSECONDS)
-		: unit.convert(delay, TimeUnit.NANOSECONDS));
-    }
-
-    public void disconnect() {
-	synchronized (this) {
-	    if (watcher != null) {
-		watcher.disconnect();
-		watcher = null;
-	    }
+
+	/*
+	 * This must return remaining delay associated with the object!
+	 * (non-Javadoc)
+	 * 
+	 * @see java.util.concurrent.Delayed#getDelay(java.util.concurrent.TimeUnit)
+	 */
+	@Override
+	public long getDelay(final TimeUnit unit) {
+		long idleTime = System.nanoTime() - lastAccessTime;
+		long delayVal = (delay == 0 ? defaultDelay : delay);
+		return unit.convert(delayVal - idleTime, TimeUnit.NANOSECONDS);
 	}
-    }
-
-    boolean disconnected() {
-	return watcher == null;
-    }
-
-    @Override
-    public String toString() {
-	String value = "File: " + this.file.getAbsolutePath() + "\n";
-	value += "Delay (s): " + getDelayValue(TimeUnit.SECONDS) + "\n";
-	long exp = getDelay(TimeUnit.MILLISECONDS);
-	if (exp > 0) {
-	    value += "Expire in (ms): " + exp + "\n";
-	} else {
-	    value += "This object has expired" + "\n";
+
+	void setDelay(long delay, TimeUnit unit) {
+		assert delay > 0;
+		this.delay = TimeUnit.NANOSECONDS.convert(delay, unit);
+		assert delay < defaultDelay;
 	}
-	value += "ChunkSize  " + this.chunkSize + "\n";
-	return value;
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-	if (obj == null) {
-	    return false;
+
+	long getDelayValue(TimeUnit unit) {
+		return (delay == 0
+				? unit.convert(defaultDelay, TimeUnit.NANOSECONDS)
+				: unit.convert(delay, TimeUnit.NANOSECONDS));
+	}
+
+	public void disconnect() {
+		synchronized (this) {
+			if (watcher != null) {
+				watcher.disconnect();
+				watcher = null;
+			}
+		}
 	}
-	if (!(obj instanceof FilePuller)) {
-	    return false;
+
+	boolean disconnected() {
+		return watcher == null;
+	}
+
+	@Override
+	public String toString() {
+		String value = "File: " + this.file.getAbsolutePath() + "\n";
+		value += "Delay (s): " + getDelayValue(TimeUnit.SECONDS) + "\n";
+		long exp = getDelay(TimeUnit.MILLISECONDS);
+		if (exp > 0) {
+			value += "Expire in (ms): " + exp + "\n";
+		} else {
+			value += "This object has expired" + "\n";
+		}
+		value += "ChunkSize  " + this.chunkSize + "\n";
+		return value;
 	}
-	FilePuller fp = (FilePuller) obj;
-	if (!this.file.equals(fp.file)) {
-	    return false;
+
+	@Override
+	public boolean equals(Object obj) {
+		if (obj == null) {
+			return false;
+		}
+		if (!(obj instanceof FilePuller)) {
+			return false;
+		}
+		FilePuller fp = (FilePuller) obj;
+		if (!this.file.equals(fp.file)) {
+			return false;
+		}
+		// Other fields does not matter
+		return true;
+	}
+
+	@Override
+	public int hashCode() {
+		return this.file.hashCode();
+	}
+
+	public byte getProgress() throws IOException {
+		initPull();
+		return watcher.getProgress();
 	}
-	// Other fields does not matter
-	return true;
-    }
-
-    @Override
-    public int hashCode() {
-	return this.file.hashCode();
-    }
-
-    public byte getProgress() throws IOException {
-	initPull();
-	return watcher.getProgress();
-    }
 
 }
diff --git a/engine/compbio/engine/PulledFileCache.java b/engine/compbio/engine/PulledFileCache.java
index 50a75c2..8e464c6 100644
--- a/engine/compbio/engine/PulledFileCache.java
+++ b/engine/compbio/engine/PulledFileCache.java
@@ -49,7 +49,7 @@ public final class PulledFileCache {
 	 * the called to ensure this will not happen!
 	 * 
 	 * @param fpuller
-	 * @return
+	 * @return true if the same filepooler is already in cache
 	 */
 	public static boolean put(final FilePuller fpuller) {
 		sweep();
diff --git a/engine/compbio/engine/client/CommandBuilder.java b/engine/compbio/engine/client/CommandBuilder.java
index dae6696..db5992b 100644
--- a/engine/compbio/engine/client/CommandBuilder.java
+++ b/engine/compbio/engine/client/CommandBuilder.java
@@ -116,9 +116,10 @@ public class CommandBuilder<T> {
 	}
 
 	boolean setParam(Parameter param) {
-		boolean overriden= paramList.put(param.name, param) != null;
-		if(overriden) {
-			log.warn("Key " + param.name + " in the command list has been overriden! ");
+		boolean overriden = paramList.put(param.name, param) != null;
+		if (overriden) {
+			log.warn("Key " + param.name
+					+ " in the command list has been overriden! ");
 		}
 		return overriden;
 	}
@@ -137,10 +138,9 @@ public class CommandBuilder<T> {
 		// paramValue!
 		// e.g. paramName could be a path to the file with spaces
 		if (paramValue != null && paramName.contains(nameValueSeparator)) {
-			log
-					.warn("WARN: paramName "
-							+ paramName
-							+ " contains nameValue separator. Removing the separator...");
+			log.warn("WARN: paramName "
+					+ paramName
+					+ " contains nameValue separator. Removing the separator...");
 			paramName = paramName.trim().substring(0, paramName.length() - 1);
 		}
 		if (paramValue != null && paramName.contains(nameValueSeparator)) {
@@ -163,7 +163,7 @@ public class CommandBuilder<T> {
 	}
 
 	public boolean setParam(String paramName, String paramValue) {
-		return setParam( new Parameter(paramName, paramValue));
+		return setParam(new Parameter(paramName, paramValue));
 	}
 
 	public List<String> getCommands() {
@@ -198,7 +198,7 @@ public class CommandBuilder<T> {
 	 * is that it accepts a List of Options as an input
 	 * 
 	 * @param arguments
-	 * @return
+	 * @return the instance of the CommandBuilder
 	 */
 	public static <T> CommandBuilder<T> newCommandBuilder(
 			List<? extends Option<T>> arguments, String nameValueSeparator) {
@@ -216,7 +216,7 @@ public class CommandBuilder<T> {
 	}
 
 	boolean isWhiteSpaceSeparator() {
-		return nameValueSeparator.trim().length()==0;
+		return nameValueSeparator.trim().length() == 0;
 	}
 
 	List<Parameter> getCommandList() {
diff --git a/engine/compbio/engine/client/ConfExecutable.java b/engine/compbio/engine/client/ConfExecutable.java
index 23d0793..14c023f 100644
--- a/engine/compbio/engine/client/ConfExecutable.java
+++ b/engine/compbio/engine/client/ConfExecutable.java
@@ -249,7 +249,7 @@ public class ConfExecutable<T> implements ConfiguredExecutable<T> {
 	 * 
 	 * @param <V>
 	 * @param clazz
-	 * @return
+	 * @return LimitsManager instance
 	 * @throws IOException
 	 */
 	public static <V> LimitsManager<V> getRunnerLimits(Class<V> clazz)
diff --git a/engine/compbio/engine/client/PathValidator.java b/engine/compbio/engine/client/PathValidator.java
index 92c5999..a10d82e 100644
--- a/engine/compbio/engine/client/PathValidator.java
+++ b/engine/compbio/engine/client/PathValidator.java
@@ -82,7 +82,7 @@ public final class PathValidator {
 	 * Whether a certain path is absolute or not is operation system dependent!
 	 * 
 	 * @param path
-	 * @return
+	 * @return true is the path is absolute, false otherwise
 	 */
 	public static boolean isAbsolutePath(String path) {
 		assert path != null : "Path is NULL! Not NULL path expected";
diff --git a/engine/compbio/engine/client/PipedExecutable.java b/engine/compbio/engine/client/PipedExecutable.java
index a460062..058cc9c 100644
--- a/engine/compbio/engine/client/PipedExecutable.java
+++ b/engine/compbio/engine/client/PipedExecutable.java
@@ -25,7 +25,7 @@ package compbio.engine.client;
  * handling
  * 
  * @author pvtroshin
- * @date October 2009
+ * @version 1.0 October 2009
  * @param <T>
  */
 public interface PipedExecutable<T> extends Executable<T> {
diff --git a/engine/compbio/engine/client/Util.java b/engine/compbio/engine/client/Util.java
index 634112f..aff3ca5 100644
--- a/engine/compbio/engine/client/Util.java
+++ b/engine/compbio/engine/client/Util.java
@@ -272,7 +272,7 @@ public final class Util {
 	/**
 	 * Returns the absolute path to the Java executable from JAVA_HOME
 	 * 
-	 * @return
+	 * @return returns the absolute path to the Java executable from JAVA_HOME
 	 */
 	public static String getJava() {
 		String javahome = System.getProperty("java.home");
diff --git a/engine/compbio/engine/cluster/drmaa/AsyncJobRunner.java b/engine/compbio/engine/cluster/drmaa/AsyncJobRunner.java
index 46debcc..940c4ad 100644
--- a/engine/compbio/engine/cluster/drmaa/AsyncJobRunner.java
+++ b/engine/compbio/engine/cluster/drmaa/AsyncJobRunner.java
@@ -33,11 +33,11 @@ import compbio.metadata.ResultNotAvailableException;
  * Single cluster job runner class
  * 
  * @author pvtroshin
- * @date August 2009
+ * @version 1.0 August 2009
  * 
- *       TODO after call to submitJob() no setters really work as the job
- *       template gets deleted, this needs to be taken into account in this
- *       class design!
+ *          TODO after call to submitJob() no setters really work as the job
+ *          template gets deleted, this needs to be taken into account in this
+ *          class design!
  */
 public class AsyncJobRunner implements AsyncExecutor {
 
diff --git a/engine/compbio/engine/cluster/drmaa/ClusterSession.java b/engine/compbio/engine/cluster/drmaa/ClusterSession.java
index e8b17b9..ca2f531 100644
--- a/engine/compbio/engine/cluster/drmaa/ClusterSession.java
+++ b/engine/compbio/engine/cluster/drmaa/ClusterSession.java
@@ -207,8 +207,9 @@ public final class ClusterSession {
 		// Once the job has been waited for it will be finished
 		// Next time it will not be found in the session, so removed from the
 		// job list
-		compbio.engine.client.Util.writeStatFile(compbio.engine.Configurator
-				.getWorkDirectory(jobId), JobStatus.FINISHED.toString());
+		compbio.engine.client.Util.writeStatFile(
+				compbio.engine.Configurator.getWorkDirectory(jobId),
+				JobStatus.FINISHED.toString());
 
 		return status;
 	}
@@ -285,46 +286,46 @@ public final class ClusterSession {
 	 * in therms of a Sessions, not a JobStatus Should only be used for testing!
 	 * 
 	 * @param status
-	 * @return
+	 * @return job status
 	 * @throws DrmaaException
 	 */
 	@Deprecated
 	public static String getJobStatus(final int status) throws DrmaaException {
 		String statusString = null;
 		switch (status) {
-		case Session.UNDETERMINED:
-			statusString = "Job status cannot be determined\n";
-			break;
-		case Session.QUEUED_ACTIVE:
-			statusString = "Job is queued and active\n";
-			break;
-		case Session.SYSTEM_ON_HOLD:
-			statusString = "Job is queued and in system hold\n";
-			break;
-		case Session.USER_ON_HOLD:
-			statusString = "Job is queued and in user hold\n";
-			break;
-		case Session.USER_SYSTEM_ON_HOLD:
-			statusString = "Job is queued and in user and system hold\n";
-			break;
-		case Session.RUNNING:
-			statusString = "Job is running\n";
-			break;
-		case Session.SYSTEM_SUSPENDED:
-			statusString = "Job is system suspended\n";
-			break;
-		case Session.USER_SUSPENDED:
-			statusString = "Job is user suspended\n";
-			break;
-		case Session.USER_SYSTEM_SUSPENDED:
-			statusString = "Job is user and system suspended\n";
-			break;
-		case Session.DONE:
-			statusString = "Job finished normally\n";
-			break;
-		case Session.FAILED:
-			statusString = "Job finished, but failed\n";
-			break;
+			case Session.UNDETERMINED :
+				statusString = "Job status cannot be determined\n";
+				break;
+			case Session.QUEUED_ACTIVE :
+				statusString = "Job is queued and active\n";
+				break;
+			case Session.SYSTEM_ON_HOLD :
+				statusString = "Job is queued and in system hold\n";
+				break;
+			case Session.USER_ON_HOLD :
+				statusString = "Job is queued and in user hold\n";
+				break;
+			case Session.USER_SYSTEM_ON_HOLD :
+				statusString = "Job is queued and in user and system hold\n";
+				break;
+			case Session.RUNNING :
+				statusString = "Job is running\n";
+				break;
+			case Session.SYSTEM_SUSPENDED :
+				statusString = "Job is system suspended\n";
+				break;
+			case Session.USER_SUSPENDED :
+				statusString = "Job is user suspended\n";
+				break;
+			case Session.USER_SYSTEM_SUSPENDED :
+				statusString = "Job is user and system suspended\n";
+				break;
+			case Session.DONE :
+				statusString = "Job finished normally\n";
+				break;
+			case Session.FAILED :
+				statusString = "Job finished, but failed\n";
+				break;
 		}
 		return statusString;
 	}
diff --git a/engine/compbio/engine/cluster/drmaa/_DrmaaExample.java b/engine/compbio/engine/cluster/drmaa/_DrmaaExample.java
index 0e8b4ba..dbb312f 100644
--- a/engine/compbio/engine/cluster/drmaa/_DrmaaExample.java
+++ b/engine/compbio/engine/cluster/drmaa/_DrmaaExample.java
@@ -29,7 +29,7 @@ import org.ggf.drmaa.JobTemplate;
 import org.ggf.drmaa.Session;
 import org.ggf.drmaa.SessionFactory;
 
-public class _DrmaaExample {
+class _DrmaaExample {
 
 	private static int NBULKS = 3;
 	private static int JOB_CHUNK = 8;
diff --git a/engine/compbio/engine/cluster/drmaa/_JobStatus.java b/engine/compbio/engine/cluster/drmaa/_JobStatus.java
index 8ddaa5f..38b7410 100644
--- a/engine/compbio/engine/cluster/drmaa/_JobStatus.java
+++ b/engine/compbio/engine/cluster/drmaa/_JobStatus.java
@@ -22,10 +22,8 @@ import org.ggf.drmaa.Session;
 import org.ggf.drmaa.SessionFactory;
 import org.ggf.drmaa.Version;
 
-public class _JobStatus {
+class _JobStatus {
 
-	
-	
 	public static void main(String[] args) {
 
 		SessionFactory factory = SessionFactory.getFactory();
diff --git a/engine/compbio/engine/cluster/dundee/_Queue.java b/engine/compbio/engine/cluster/dundee/_Queue.java
index c0fbb0b..3ee2e0a 100644
--- a/engine/compbio/engine/cluster/dundee/_Queue.java
+++ b/engine/compbio/engine/cluster/dundee/_Queue.java
@@ -16,37 +16,37 @@
  * must include this copyright and license notice.
  */
 package compbio.engine.cluster.dundee;
-import static compbio.engine.cluster.dundee._QueueConstraints.*;
+import static compbio.engine.cluster.dundee._QueueConstraints.FIRST_MEMORY_LIMIT;
+import static compbio.engine.cluster.dundee._QueueConstraints.LONG_TIME_LIMIT;
+import static compbio.engine.cluster.dundee._QueueConstraints.MAX_MEMORY_LIMIT;
+import static compbio.engine.cluster.dundee._QueueConstraints.SHORT_TIME_LIMIT;
 
+@Deprecated
 public enum _Queue {
 
 	/*
-	 * devel.q 	    4Gb or 16Gb 	 8 hour  I
-	   64bit-pri.q 	4Gb or 16Gb 	24 hours 	B
-       64bit.q   	4Gb or 16Gb 	None 	B
-       bigint.q 	32Gb 	        8 h 	I
-       bigmem.q 	32Gb 	        None 	B 
+	 * devel.q 4Gb or 16Gb 8 hour I 64bit-pri.q 4Gb or 16Gb 24 hours B 64bit.q
+	 * 4Gb or 16Gb None B bigint.q 32Gb 8 h I bigmem.q 32Gb None B
 	 */
 
 	/**
 	 * Order of the constraint reflect the priority of the queue
 	 */
-	DEVEL(FIRST_MEMORY_LIMIT, SHORT_TIME_LIMIT,"devel.q"), 
-	PRIBIT64(FIRST_MEMORY_LIMIT,LONG_TIME_LIMIT,"64bit-pri.q"), 
-	BIT64(FIRST_MEMORY_LIMIT,0,"64bit.q"), 
-	BIGINT(MAX_MEMORY_LIMIT,SHORT_TIME_LIMIT,"bigint.q"), 
-	BIGMEM(MAX_MEMORY_LIMIT,0,"bigmem.q");
-	
-	
+	DEVEL(FIRST_MEMORY_LIMIT, SHORT_TIME_LIMIT, "devel.q"), PRIBIT64(
+			FIRST_MEMORY_LIMIT, LONG_TIME_LIMIT, "64bit-pri.q"), BIT64(
+			FIRST_MEMORY_LIMIT, 0, "64bit.q"), BIGINT(MAX_MEMORY_LIMIT,
+			SHORT_TIME_LIMIT, "bigint.q"), BIGMEM(MAX_MEMORY_LIMIT, 0,
+			"bigmem.q");
+
 	int maxMemory;
 	int maxRuntime;
 	String qname;
 	private _Queue(int maxMemory, int maxRuntime, String qname) {
-		this.maxMemory=maxMemory;
-		this.maxRuntime=maxRuntime;
-		this.qname = qname; 
+		this.maxMemory = maxMemory;
+		this.maxRuntime = maxRuntime;
+		this.qname = qname;
 	}
-	
+
 	// -q 64bit.q -l qname=64bit.q -l h_vmem=8000M -l ram=8000M
 	@Override
 	public String toString() {
@@ -55,92 +55,98 @@ public enum _Queue {
 
 	/**
 	 * 0 - unlimited
+	 * 
 	 * @return max runtime in hours
 	 */
-	public int getTimeLimit() { 
+	public int getTimeLimit() {
 		return this.maxRuntime;
 	}
-	
+
 	/**
 	 * 
-	 * @return true if the queue has time limit, false overwise 
+	 * @return true if the queue has time limit, false overwise
 	 */
-	public boolean hasTimeLimit()  { 
-		return this.maxRuntime != 0; 
+	public boolean hasTimeLimit() {
+		return this.maxRuntime != 0;
 	}
 	/**
 	 * return max memory limit in Mb
+	 * 
 	 * @return
 	 */
-	public int getMemoryLimit() { 
+	public int getMemoryLimit() {
 		return this.maxMemory;
 	}
-	
-	public static _Queue getQueueByMemoryRequirements(int maxMemory) { 
-		if(maxMemory>FIRST_MEMORY_LIMIT) {
+
+	public static _Queue getQueueByMemoryRequirements(int maxMemory) {
+		if (maxMemory > FIRST_MEMORY_LIMIT) {
 			return BIGMEM;
-		} else if(maxMemory<MAX_MEMORY_LIMIT)
-			return BIT64; 
-		else { 
-			throw new UnsupportedOperationException("Cluster does not support tasks requiring more than 30000M of memory");
+		} else if (maxMemory < MAX_MEMORY_LIMIT)
+			return BIT64;
+		else {
+			throw new UnsupportedOperationException(
+					"Cluster does not support tasks requiring more than 30000M of memory");
 		}
 	}
 
-	public static _Queue getQueue(int maxMemory, int timeLimitInHours) { 
-		if(timeLimitInHours==0) { 
+	public static _Queue getQueue(int maxMemory, int timeLimitInHours) {
+		if (timeLimitInHours == 0) {
 			return getQueueByMemoryRequirements(maxMemory);
-		} else { 
-			if(timeLimitInHours<=SHORT_TIME_LIMIT) { 
-				if(maxMemory<=FIRST_MEMORY_LIMIT) { 
+		} else {
+			if (timeLimitInHours <= SHORT_TIME_LIMIT) {
+				if (maxMemory <= FIRST_MEMORY_LIMIT) {
 					return DEVEL;
-				}else if(maxMemory<=MAX_MEMORY_LIMIT){ 
+				} else if (maxMemory <= MAX_MEMORY_LIMIT) {
 					return BIGINT;
-				} else { 
-					throw new UnsupportedOperationException("Cluster does not support tasks requiring more than 30000M of memory");
+				} else {
+					throw new UnsupportedOperationException(
+							"Cluster does not support tasks requiring more than 30000M of memory");
 				}
-			} else { 
+			} else {
 				// timeLimit > 8
-				if(timeLimitInHours <= LONG_TIME_LIMIT && maxMemory <=FIRST_MEMORY_LIMIT) { 
-					return PRIBIT64; 
-				} else if( maxMemory<= MAX_MEMORY_LIMIT){ 
+				if (timeLimitInHours <= LONG_TIME_LIMIT
+						&& maxMemory <= FIRST_MEMORY_LIMIT) {
+					return PRIBIT64;
+				} else if (maxMemory <= MAX_MEMORY_LIMIT) {
 					return BIGMEM;
-				} else { 
-					throw new UnsupportedOperationException("Cluster does not support tasks requiring more than 30000M of memory");
+				} else {
+					throw new UnsupportedOperationException(
+							"Cluster does not support tasks requiring more than 30000M of memory");
 				}
 			}
 		}
 	}
-	
-	public _Queue getQueue(String queueName) { 
-		switch(this) { 
-		case DEVEL: 
-			if ( queueName.equals(DEVEL.toString())) {  
-				return DEVEL;
-			}
-			break;
-		case PRIBIT64: 
-			if ( queueName.equals(PRIBIT64.toString())) {  
-				return PRIBIT64;
-			}
-			break;
-		case BIT64: 
-			if ( queueName.equals(BIT64.toString())) {  
-				return BIT64;
-			}
-			break;
-		case BIGMEM: 
-			if ( queueName.equals(BIGMEM.toString())) {  
-				return BIGMEM;
-			}
-			break;
-		case BIGINT: 
-			if ( queueName.equals(BIGINT.toString())) {  
-				return BIGINT;
-			}
-			break; 
+
+	public _Queue getQueue(String queueName) {
+		switch (this) {
+			case DEVEL :
+				if (queueName.equals(DEVEL.toString())) {
+					return DEVEL;
+				}
+				break;
+			case PRIBIT64 :
+				if (queueName.equals(PRIBIT64.toString())) {
+					return PRIBIT64;
+				}
+				break;
+			case BIT64 :
+				if (queueName.equals(BIT64.toString())) {
+					return BIT64;
+				}
+				break;
+			case BIGMEM :
+				if (queueName.equals(BIGMEM.toString())) {
+					return BIGMEM;
+				}
+				break;
+			case BIGINT :
+				if (queueName.equals(BIGINT.toString())) {
+					return BIGINT;
+				}
+				break;
 		}
 		// such queue appears to be not defined in the system!
-		return null; 
+		return null;
 	}
 
 }
diff --git a/engine/compbio/engine/cluster/dundee/_QueueConstraints.java b/engine/compbio/engine/cluster/dundee/_QueueConstraints.java
index 2f69728..637136f 100644
--- a/engine/compbio/engine/cluster/dundee/_QueueConstraints.java
+++ b/engine/compbio/engine/cluster/dundee/_QueueConstraints.java
@@ -17,14 +17,15 @@
  */
 package compbio.engine.cluster.dundee;
 
-public final class _QueueConstraints {
+@Deprecated
+final class _QueueConstraints {
 
-	private _QueueConstraints() {} 
+	private _QueueConstraints() {
+	}
 
 	public static final int SHORT_TIME_LIMIT = 8;
-	public static final int LONG_TIME_LIMIT = 24; 
+	public static final int LONG_TIME_LIMIT = 24;
 	public static final int FIRST_MEMORY_LIMIT = 14000;
-	public static final int MAX_MEMORY_LIMIT = 30000;	
-
+	public static final int MAX_MEMORY_LIMIT = 30000;
 
 }
diff --git a/engine/compbio/engine/conf/PropertyHelperManager.java b/engine/compbio/engine/conf/PropertyHelperManager.java
index 939e5fe..fb35362 100644
--- a/engine/compbio/engine/conf/PropertyHelperManager.java
+++ b/engine/compbio/engine/conf/PropertyHelperManager.java
@@ -23,8 +23,6 @@ import java.io.IOException;
 import java.net.URISyntaxException;
 import java.net.URL;
 
-import javax.naming.ConfigurationException;
-
 import org.apache.log4j.Logger;
 
 import compbio.util.PropertyHelper;
@@ -52,7 +50,7 @@ public final class PropertyHelperManager {
 	 * 
 	 * Try 1 - succeed.
 	 * 
-	 * @return
+	 * @return an instance
 	 */
 	public static PropertyHelper getPropertyHelper() {
 		if (ph == null) {
@@ -91,8 +89,9 @@ public final class PropertyHelperManager {
 	 * binaries WEB-INF classes compbio engine conf If the structure changes it
 	 * must be reflected in this method
 	 * 
-	 * @return
-	 * @throws ConfigurationException
+	 * @return the local path
+	 * @throws RuntimeException
+	 *             if cannot determine the local path
 	 */
 	public static String getLocalPath() {
 		String clname = PropertyHelperManager.class.getSimpleName();
diff --git a/engine/compbio/engine/conf/RunnerConfigMarshaller.java b/engine/compbio/engine/conf/RunnerConfigMarshaller.java
index 570b43c..4fbd3a0 100644
--- a/engine/compbio/engine/conf/RunnerConfigMarshaller.java
+++ b/engine/compbio/engine/conf/RunnerConfigMarshaller.java
@@ -60,8 +60,8 @@ public class RunnerConfigMarshaller<T> {
 			throws JAXBException {
 
 		if (classes != null) {
-			List<Class<?>> classesList = new ArrayList<Class<?>>(Arrays
-					.asList(classes));
+			List<Class<?>> classesList = new ArrayList<Class<?>>(
+					Arrays.asList(classes));
 			classesList.add(rootClass);
 			ctx = JAXBContext.newInstance(classesList.toArray(new Class<?>[0]));
 		} else {
@@ -109,7 +109,7 @@ public class RunnerConfigMarshaller<T> {
 
 	/**
 	 * 
-	 * @return
+	 * @return validator instance
 	 * @throws SAXException
 	 */
 	public static Validator getValidator(String schemafile) throws SAXException {
@@ -182,8 +182,8 @@ public class RunnerConfigMarshaller<T> {
 		}
 		JAXBContext ctx = null;
 		if (classes != null) {
-			List<Class<?>> classesList = new ArrayList<Class<?>>(Arrays
-					.asList(classes));
+			List<Class<?>> classesList = new ArrayList<Class<?>>(
+					Arrays.asList(classes));
 			classesList.add(resultElemType);
 			ctx = JAXBContext.newInstance(classesList.toArray(new Class<?>[0]));
 		} else {
diff --git a/engine/compbio/engine/conf/_Key.java b/engine/compbio/engine/conf/_Key.java
index 67343c7..a40abf3 100644
--- a/engine/compbio/engine/conf/_Key.java
+++ b/engine/compbio/engine/conf/_Key.java
@@ -22,6 +22,7 @@ import javax.management.openmbean.InvalidKeyException;
 
 import compbio.util.Util;
 
+@Deprecated
 public final class _Key {
 
 	public final static String DELIM = "#";
diff --git a/engine/compbio/engine/local/AsyncLocalRunner.java b/engine/compbio/engine/local/AsyncLocalRunner.java
index cfc2916..d269aad 100644
--- a/engine/compbio/engine/local/AsyncLocalRunner.java
+++ b/engine/compbio/engine/local/AsyncLocalRunner.java
@@ -47,10 +47,9 @@ public final class AsyncLocalRunner implements AsyncExecutor {
 				.getTask(jobId);
 		// The job has already finished or cancelled.
 		if (future == null) {
-			log
-					.debug("Did not find future for local job "
-							+ jobId
-							+ " will not cancel it. Perhaps it has finished or cancelled already.");
+			log.debug("Did not find future for local job "
+					+ jobId
+					+ " will not cancel it. Perhaps it has finished or cancelled already.");
 			return false;
 		}
 		LocalEngineUtil.cancelJob(future, getWorkDirectory(jobId));
@@ -88,7 +87,7 @@ public final class AsyncLocalRunner implements AsyncExecutor {
 	/**
 	 * 
 	 * @param jobId
-	 * @return
+	 * @return true if all files were removed, false otherwise
 	 */
 	@Override
 	public boolean cleanup(String jobId) {
diff --git a/engine/compbio/engine/local/LocalExecutorService.java b/engine/compbio/engine/local/LocalExecutorService.java
index 04a0bd5..cbed001 100644
--- a/engine/compbio/engine/local/LocalExecutorService.java
+++ b/engine/compbio/engine/local/LocalExecutorService.java
@@ -50,7 +50,7 @@ public final class LocalExecutorService extends ThreadPoolExecutor {
 	 * This method returns the single instance of CachedThreadPoolExecutor which
 	 * it cashes internally
 	 * 
-	 * @return
+	 * @return the instance
 	 */
 	public synchronized static LocalExecutorService getExecutor() {
 		if (INSTANCE == null) {
diff --git a/engine/compbio/engine/local/_TrackingExecutor.java b/engine/compbio/engine/local/_TrackingExecutor.java
index 5204049..ac0f848 100644
--- a/engine/compbio/engine/local/_TrackingExecutor.java
+++ b/engine/compbio/engine/local/_TrackingExecutor.java
@@ -37,9 +37,11 @@ import java.util.concurrent.TimeUnit;
  * TODO it may be better to persists task from different place
  * 
  * @author pvtroshin
- * @Date October 2009
+ * @version 1.0 October 2009
+ * @deprecated
  */
-public class _TrackingExecutor extends AbstractExecutorService {
+@Deprecated
+class _TrackingExecutor extends AbstractExecutorService {
 
 	private final ExecutorService executor;
 
diff --git a/runner/compbio/runner/_NativeSpecHelper.java b/runner/compbio/runner/_NativeSpecHelper.java
index 6f4125f..57ec660 100644
--- a/runner/compbio/runner/_NativeSpecHelper.java
+++ b/runner/compbio/runner/_NativeSpecHelper.java
@@ -21,6 +21,7 @@ import java.net.UnknownServiceException;
 
 import compbio.engine.cluster.dundee._Queue;
 
+@Deprecated
 public class _NativeSpecHelper {
 
 	int maxCalculationTime;
diff --git a/runner/compbio/runner/_SkeletalCommandBuilder.java b/runner/compbio/runner/_SkeletalCommandBuilder.java
index c8f1373..3767ffb 100644
--- a/runner/compbio/runner/_SkeletalCommandBuilder.java
+++ b/runner/compbio/runner/_SkeletalCommandBuilder.java
@@ -27,8 +27,10 @@ import compbio.engine.client.RunConfiguration;
 import compbio.metadata.Limit;
 import compbio.metadata.LimitsManager;
 
-public abstract class _SkeletalCommandBuilder implements
-		Executable<_SkeletalCommandBuilder> {
+@Deprecated
+public abstract class _SkeletalCommandBuilder
+		implements
+			Executable<_SkeletalCommandBuilder> {
 
 	String tmpDirectory;
 	String name;
@@ -109,11 +111,11 @@ public abstract class _SkeletalCommandBuilder implements
 		// TODO Auto-generated method stub
 		return null;
 	}
-	
+
 	@Override
 	public String getClusterJobSettings() {
 		// TODO Auto-generated method stub
-		return null; 
+		return null;
 	}
 
 }
diff --git a/runner/compbio/runner/msa/Muscle.java b/runner/compbio/runner/msa/Muscle.java
index e627462..54c7732 100644
--- a/runner/compbio/runner/msa/Muscle.java
+++ b/runner/compbio/runner/msa/Muscle.java
@@ -50,7 +50,6 @@ public class Muscle extends SkeletalExecutable<Muscle> {
 	 * 
 	 * -clwstrict - write output in clustal format
 	 * 
-	 * @param workDirectory
 	 */
 	public Muscle() {
 		/*
diff --git a/runner/compbio/runner/msa/Probcons.java b/runner/compbio/runner/msa/Probcons.java
index 3d0f86a..532ba30 100644
--- a/runner/compbio/runner/msa/Probcons.java
+++ b/runner/compbio/runner/msa/Probcons.java
@@ -43,8 +43,6 @@ public class Probcons extends SkeletalExecutable<Probcons>
 	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
 
 	/**
-	 * 
-	 * @param workDirectory
 	 */
 	public Probcons() {
 		addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));
diff --git a/runner/compbio/runner/msa/Tcoffee.java b/runner/compbio/runner/msa/Tcoffee.java
index 0c76d21..645b994 100644
--- a/runner/compbio/runner/msa/Tcoffee.java
+++ b/runner/compbio/runner/msa/Tcoffee.java
@@ -37,7 +37,8 @@ import compbio.runner.Util;
 import compbio.util.PropertyHelper;
 
 public class Tcoffee extends SkeletalExecutable<Tcoffee>
-		implements PipedExecutable<Tcoffee> {
+		implements
+			PipedExecutable<Tcoffee> {
 
 	private static Logger log = Logger.getLogger(Tcoffee.class);
 
@@ -58,8 +59,6 @@ public class Tcoffee extends SkeletalExecutable<Tcoffee>
 	private final static String ncorePrm = "-n_core";
 
 	/**
-	 * 
-	 * @param workDirectory
 	 */
 	public Tcoffee() {
 		super(KEY_VALUE_SEPARATOR);
@@ -128,12 +127,11 @@ public class Tcoffee extends SkeletalExecutable<Tcoffee>
 			int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
 			if (cpunum != 0) {
 				setNCore(cpunum);
-			} 
+			}
 		}
 		return super.getParameters(provider);
 	}
 
-
 	@SuppressWarnings("unchecked")
 	@Override
 	public Class<Tcoffee> getType() {
diff --git a/webservices/compbio/data/msa/RegistryWS.java b/webservices/compbio/data/msa/RegistryWS.java
index e06d58e..faaea67 100644
--- a/webservices/compbio/data/msa/RegistryWS.java
+++ b/webservices/compbio/data/msa/RegistryWS.java
@@ -49,7 +49,7 @@ public interface RegistryWS extends JABAService {
 	 * tested or tested less then a one second ago.
 	 * 
 	 * @param service
-	 * @return
+	 * @return when last time tested
 	 */
 	int getLastTested(Services service);
 	/**
diff --git a/webservices/compbio/ws/server/GenericMetadataService.java b/webservices/compbio/ws/server/GenericMetadataService.java
index 61d9393..c094283 100644
--- a/webservices/compbio/ws/server/GenericMetadataService.java
+++ b/webservices/compbio/ws/server/GenericMetadataService.java
@@ -113,7 +113,7 @@ public abstract class GenericMetadataService<T> {
 	 * 
 	 * @param jobId
 	 * @param position
-	 * @return
+	 * @return ChunkHolder
 	 */
 	public ChunkHolder pullExecStatistics(String jobId, long position) {
 		// Execution stat is not supported
diff --git a/webservices/compbio/ws/server/SimpleWSPublisher.java b/webservices/compbio/ws/server/SimpleWSPublisher.java
index 3230317..3e3a34b 100644
--- a/webservices/compbio/ws/server/SimpleWSPublisher.java
+++ b/webservices/compbio/ws/server/SimpleWSPublisher.java
@@ -28,46 +28,47 @@ import javax.xml.ws.Endpoint;
  * @author pvtroshin
  * @date October 2009
  */
+@Deprecated
 public class SimpleWSPublisher {
 
-    public SimpleWSPublisher(Object exec, String context) {
+	public SimpleWSPublisher(Object exec, String context) {
 
-    }
+	}
 
-    public static void main(String[] args) {
-	if (args.length != 2) {
-	    System.out.println("Usage: ");
-	    System.out.println("SimpleWSPublisher context class");
-	    System.out
-		    .println("where context is a context name, the name after the address by "
-			    + "which web service can be called e.g. Clustal "
-			    + " and class is a web service implementation class");
+	public static void main(String[] args) {
+		if (args.length != 2) {
+			System.out.println("Usage: ");
+			System.out.println("SimpleWSPublisher context class");
+			System.out
+					.println("where context is a context name, the name after the address by "
+							+ "which web service can be called e.g. Clustal "
+							+ " and class is a web service implementation class");
 
+		}
+		String context = args[0];
+		String clazzName = args[1];
+		try {
+			Class<?> clazz = Class.forName(clazzName);
+			if (!clazz.isAnnotationPresent(WebService.class)) {
+				System.out.println("Can only start web services. "
+						+ "Please check whether the class provided is "
+						+ "annotated with Webservice annotation");
+				System.exit(1);
+			}
+			Endpoint.publish("http://127.0.0.1:7979/" + context,
+					clazz.newInstance());
+		} catch (InstantiationException e) {
+			e.printStackTrace();
+			System.exit(1);
+		} catch (IllegalAccessException e) {
+			e.printStackTrace();
+			System.exit(1);
+		} catch (ClassNotFoundException e) {
+			e.printStackTrace();
+			System.exit(1);
+		} catch (IllegalArgumentException e) {
+			e.printStackTrace();
+			System.exit(1);
+		}
 	}
-	String context = args[0];
-	String clazzName = args[1];
-	try {
-	    Class<?> clazz = Class.forName(clazzName);
-	    if (!clazz.isAnnotationPresent(WebService.class)) {
-		System.out.println("Can only start web services. "
-			+ "Please check whether the class provided is "
-			+ "annotated with Webservice annotation");
-		System.exit(1);
-	    }
-	    Endpoint.publish("http://127.0.0.1:7979/" + context, clazz
-		    .newInstance());
-	} catch (InstantiationException e) {
-	    e.printStackTrace();
-	    System.exit(1);
-	} catch (IllegalAccessException e) {
-	    e.printStackTrace();
-	    System.exit(1);
-	} catch (ClassNotFoundException e) {
-	    e.printStackTrace();
-	    System.exit(1);
-	} catch (IllegalArgumentException e) {
-	    e.printStackTrace();
-	    System.exit(1);
-	}
-    }
 }