X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=engine%2Fcompbio%2Fengine%2FFilePuller.java;h=98a44bcb39a96170c068eb7d4c1aa4d4d8b2a67f;hb=09a35ddd6973ae31086ca96b1455e379e73198a8;hp=d04083815cc579b8cebc567f6bba74a9303cf6a1;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

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();
-    }
 
 }