/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * 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.
+ * This file is part of Jalview.
*
- * 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.
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.io.*;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GraphicsEnvironment;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.IOException;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
import org.apache.log4j.SimpleLayout;
/**
- * Simple Jalview Java Console. Version 1 - allows viewing of console output after desktop is created.
- * Acquired with thanks from RJHM's site http://www.comweb.nl/java/Console/Console.html
- * A simple Java Console for your application (Swing version)
- * Requires Java 1.1.5 or higher
- * Disclaimer the use of this source is at your own risk.
- * Permision to use and distribute into your own applications
- * RJHM van den Bergh , rvdb@comweb.nl
+ * Simple Jalview Java Console. Version 1 - allows viewing of console output
+ * after desktop is created. Acquired with thanks from RJHM's site
+ * http://www.comweb.nl/java/Console/Console.html A simple Java Console for your
+ * application (Swing version) Requires Java 1.1.5 or higher Disclaimer the use
+ * of this source is at your own risk. Permision to use and distribute into your
+ * own applications RJHM van den Bergh , rvdb@comweb.nl
*/
public class Console extends WindowAdapter implements WindowListener,
private JTextArea textArea;
- private Thread reader;
+ /*
+ * unused - tally and limit for lines in console window int lines = 0;
+ *
+ * int lim = 1000;
+ */
+ int byteslim = 102400, bytescut = 76800; // 100k and 75k cut point.
- private Thread reader2;
+ private Thread reader, reader2, textAppender;
private boolean quit;
- private final PipedInputStream pin = new PipedInputStream();
+ private final PrintStream stdout = System.out, stderr = System.err;
+
+ private PipedInputStream pin = new PipedInputStream();
- private final PipedInputStream pin2 = new PipedInputStream();
+ private PipedInputStream pin2 = new PipedInputStream();
+ private StringBuffer displayPipe = new StringBuffer();
Thread errorThrower; // just for testing (Throws an Exception at this Console
+
// are we attached to some parent Desktop
Desktop parent = null;
+
public Console()
{
// create all components and add them
private void initConsole(boolean visible)
{
+ initConsole(visible, true);
+ }
+
+ /**
+ *
+ * @param visible
+ * - open the window
+ * @param redirect
+ * - redirect std*
+ */
+ private void initConsole(boolean visible, boolean redirect)
+ {
// CutAndPasteTransfer cpt = new CutAndPasteTransfer();
- //textArea = cpt.getTextArea();
+ // textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
- JButton button = new JButton("clear");
+ JButton button = new JButton(MessageManager.getString("action.clear"));
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
BorderLayout.CENTER);
frame.getContentPane().add(button, BorderLayout.SOUTH);
frame.setVisible(visible);
-
+ updateConsole = visible;
frame.addWindowListener(this);
button.addActionListener(this);
-
- try
- {
- PipedOutputStream pout = new PipedOutputStream(this.pin);
- System.setOut(new PrintStream(pout, true));
- } catch (java.io.IOException io)
- {
- textArea.append("Couldn't redirect STDOUT to this console\n"
- + io.getMessage());
- } catch (SecurityException se)
+ if (redirect)
{
- textArea.append("Couldn't redirect STDOUT to this console\n"
- + se.getMessage());
+ redirectStreams();
}
-
- try
+ else
{
- PipedOutputStream pout2 = new PipedOutputStream(this.pin2);
- System.setErr(new PrintStream(pout2, true));
- } catch (java.io.IOException io)
- {
- textArea.append("Couldn't redirect STDERR to this console\n"
- + io.getMessage());
- } catch (SecurityException se)
- {
- textArea.append("Couldn't redirect STDERR to this console\n"
- + se.getMessage());
+ unredirectStreams();
}
-
quit = false; // signals the Threads that they should exit
// Starting two seperate threads to read from the PipedInputStreams
reader2 = new Thread(this);
reader2.setDaemon(true);
reader2.start();
+ // and a thread to append text to the textarea
+ textAppender = new Thread(this);
+ textAppender.setDaemon(true);
+ textAppender.start();
+ }
+
+ PipedOutputStream pout = null, perr = null;
+
+ public void redirectStreams()
+ {
+ if (pout == null)
+ {
+ try
+ {
+ pout = new PipedOutputStream(this.pin);
+ System.setOut(new PrintStream(pout, true));
+ } catch (java.io.IOException io)
+ {
+ textArea.append("Couldn't redirect STDOUT to this console\n"
+ + io.getMessage());
+ io.printStackTrace(stderr);
+ } catch (SecurityException se)
+ {
+ textArea.append("Couldn't redirect STDOUT to this console\n"
+ + se.getMessage());
+ se.printStackTrace(stderr);
+ }
+
+ try
+ {
+ perr = new PipedOutputStream(this.pin2);
+ System.setErr(new PrintStream(perr, true));
+ } catch (java.io.IOException io)
+ {
+ textArea.append("Couldn't redirect STDERR to this console\n"
+ + io.getMessage());
+ io.printStackTrace(stderr);
+ } catch (SecurityException se)
+ {
+ textArea.append("Couldn't redirect STDERR to this console\n"
+ + se.getMessage());
+ se.printStackTrace(stderr);
+ }
+ }
}
- public void test() {
+
+ public void unredirectStreams()
+ {
+ if (pout != null)
+ {
+ try
+ {
+ System.setOut(stdout);
+ pout.flush();
+ pout.close();
+ pin = new PipedInputStream();
+ pout = null;
+ } catch (java.io.IOException io)
+ {
+ textArea.append("Couldn't unredirect STDOUT to this console\n"
+ + io.getMessage());
+ io.printStackTrace(stderr);
+ } catch (SecurityException se)
+ {
+ textArea.append("Couldn't unredirect STDOUT to this console\n"
+ + se.getMessage());
+ se.printStackTrace(stderr);
+ }
+
+ try
+ {
+ System.setErr(stderr);
+ perr.flush();
+ perr.close();
+ pin2 = new PipedInputStream();
+ perr = null;
+ } catch (java.io.IOException io)
+ {
+ textArea.append("Couldn't unredirect STDERR to this console\n"
+ + io.getMessage());
+ io.printStackTrace(stderr);
+ } catch (SecurityException se)
+ {
+ textArea.append("Couldn't unredirect STDERR to this console\n"
+ + se.getMessage());
+ se.printStackTrace(stderr);
+ }
+ }
+ }
+
+ public void test()
+ {
// testing part
// you may omit this part for your application
- //
-
+ //
+
System.out.println("Hello World 2");
System.out.println("All fonts available to Graphic2D:\n");
GraphicsEnvironment ge = GraphicsEnvironment
{
JFrame frame = new JFrame(string);
frame.setName(string);
- if (x==-1)
+ if (x == -1)
x = (int) (i / 2);
- if (y==-1)
+ if (y == -1)
y = (int) (j / 2);
frame.setBounds(x, y, i, j);
return frame;
*/
public Console(Desktop desktop)
{
+ this(desktop, true);
+ }
+
+ /**
+ * attach a console to the desktop - the desktop will open it if requested.
+ *
+ * @param desktop
+ * @param showjconsole
+ * - if true, then redirect stdout immediately
+ */
+ public Console(Desktop desktop, boolean showjconsole)
+ {
parent = desktop;
// window name - get x,y,width, height possibly scaled
Rectangle bounds = desktop.getLastKnownDimensions("JAVA_CONSOLE_");
- if (bounds==null)
+ if (bounds == null)
+ {
+ frame = initFrame("Jalview Java Console", desktop.getWidth() / 2,
+ desktop.getHeight() / 4, desktop.getX(), desktop.getY());
+ }
+ else
{
- frame = initFrame("Jalview Java Console", desktop.getWidth() / 2,
- desktop.getHeight() / 4,desktop.getX(),desktop.getY());
- } else {
- frame = initFrame("Jalview Java Console", bounds.width, bounds.height, bounds.x, bounds.y);
+ frame = initFrame("Jalview Java Console", bounds.width,
+ bounds.height, bounds.x, bounds.y);
}
// desktop.add(frame);
initConsole(false);
JalviewAppender jappender = new JalviewAppender();
jappender.setLayout(new SimpleLayout());
- jappender.setTextArea(textArea);
+ JalviewAppender.setTextArea(textArea);
org.apache.log4j.Logger.getRootLogger().addAppender(jappender);
}
public synchronized void stopConsole()
{
quit = true;
- this.notifyAll(); // stop all threads
- try
- {
- reader.join(10);
- pin.close();
- } catch (Exception e)
+ this.notifyAll();
+ /*
+ * reader.notify(); reader2.notify(); if (errorThrower!=null)
+ * errorThrower.notify(); // stop all threads if (textAppender!=null)
+ * textAppender.notify();
+ */
+ if (pout != null)
{
+ try
+ {
+ reader.join(10);
+ pin.close();
+ } catch (Exception e)
+ {
+ }
+ try
+ {
+ reader2.join(10);
+ pin2.close();
+ } catch (Exception e)
+ {
+ }
+ try
+ {
+ textAppender.join(10);
+ } catch (Exception e)
+ {
+ }
}
- try
- {
- reader2.join(10);
- pin2.close();
- } catch (Exception e)
+ if (!frame.isVisible())
{
+ frame.dispose();
}
-// System.exit(0);
+ // System.exit(0);
}
public synchronized void windowClosed(WindowEvent evt)
{
frame.setVisible(false);
+ closeConsoleGui();
+ }
+
+ private void closeConsoleGui()
+ {
+ updateConsole = false;
if (parent == null)
{
stopConsole();
- } else {
+ }
+ else
+ {
parent.showConsole(false);
}
}
public synchronized void windowClosing(WindowEvent evt)
{
frame.setVisible(false); // default behaviour of JFrame
-// frame.dispose();
+ closeConsoleGui();
+
+ // frame.dispose();
}
public synchronized void actionPerformed(ActionEvent evt)
{
- textArea.setText("");
+ trimBuffer(true);
+ // textArea.setText("");
}
public synchronized void run()
{
while (Thread.currentThread() == reader)
{
- try
- {
- this.wait(100);
- } catch (InterruptedException ie)
+ if (pin == null || pin.available() == 0)
{
+ try
+ {
+ this.wait(100);
+ if (pin.available() == 0)
+ {
+ trimBuffer(false);
+ }
+ } catch (InterruptedException ie)
+ {
+ }
}
- if (pin.available() != 0)
+
+ while (pin.available() != 0)
{
String input = this.readLine(pin);
- textArea.append(input);
+ stdout.print(input);
+ long time = System.nanoTime();
+ appendToTextArea(input);
+ // stderr.println("Time taken to stdout append:\t"
+ // + (System.nanoTime() - time) + " ns");
+ // lines++;
}
if (quit)
return;
while (Thread.currentThread() == reader2)
{
- try
- {
- this.wait(100);
- } catch (InterruptedException ie)
+ if (pin2.available() == 0)
{
+ try
+ {
+ this.wait(100);
+ if (pin2.available() == 0)
+ {
+ trimBuffer(false);
+ }
+ } catch (InterruptedException ie)
+ {
+ }
}
- if (pin2.available() != 0)
+ while (pin2.available() != 0)
{
String input = this.readLine(pin2);
- textArea.append(input);
+ stderr.print(input);
+ long time = System.nanoTime();
+ appendToTextArea(input);
+ // stderr.println("Time taken to stderr append:\t"
+ // + (System.nanoTime() - time) + " ns");
+ // lines++;
}
if (quit)
return;
}
+ while (Thread.currentThread() == textAppender)
+ {
+ if (updateConsole)
+ {
+ // check string buffer - if greater than console, clear console and
+ // replace with last segment of content, otherwise, append all to
+ // content.
+ long count;
+ while (displayPipe.length() > 0)
+ {
+ count = 0;
+ StringBuffer tmp = new StringBuffer(), replace;
+ synchronized (displayPipe)
+ {
+ replace = displayPipe;
+ displayPipe = tmp;
+ }
+ // simply append whole buffer
+ textArea.append(replace.toString());
+ count += replace.length();
+ if (count > byteslim)
+ {
+ trimBuffer(false);
+ }
+ }
+ if (displayPipe.length() == 0)
+ {
+ try
+ {
+ this.wait(100);
+ if (displayPipe.length() == 0)
+ {
+ trimBuffer(false);
+ }
+ } catch (InterruptedException e)
+ {
+ }
+ ;
+ }
+ }
+ else
+ {
+ try
+ {
+ this.wait(100);
+ } catch (InterruptedException e)
+ {
+
+ }
+ }
+ if (quit)
+ {
+ return;
+ }
+
+ }
} catch (Exception e)
{
textArea.append("\nConsole reports an Internal error.");
- textArea.append("The error is: " + e);
+ textArea.append("The error is: " + e.getMessage());
+ // Need to uncomment this to ensure that line tally is synched.
+ // lines += 2;
+ stderr.println("Console reports an Internal error.\nThe error is: "
+ + e);
}
// just for testing (Throw a Nullpointer after 1 second)
{
}
throw new NullPointerException(
- "Application test: throwing an NullPointerException It should arrive at the console");
+ MessageManager.getString("exception.application_test_npe"));
+ }
+ }
+
+ private void appendToTextArea(final String input)
+ {
+ if (updateConsole == false)
+ {
+ // do nothing;
+ return;
+ }
+ long time = System.nanoTime();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ displayPipe.append(input); // change to stringBuffer
+ // displayPipe.flush();
+
+ }
+ });
+ // stderr.println("Time taken to Spawnappend:\t" + (System.nanoTime() -
+ // time)
+ // + " ns");
+ }
+
+ private String header = null;
+
+ private boolean updateConsole = false;
+
+ private synchronized void trimBuffer(boolean clear)
+ {
+ if (header == null && textArea.getLineCount() > 5)
+ {
+ try
+ {
+ header = textArea.getText(0, textArea.getLineStartOffset(5))
+ + "\nTruncated...\n";
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ // trim the buffer
+ int tlength = textArea.getDocument().getLength();
+ if (header != null)
+ {
+ if (clear || (tlength > byteslim))
+ {
+ try
+ {
+ if (!clear)
+ {
+ long time = System.nanoTime();
+ textArea.replaceRange(header, 0, tlength - bytescut);
+ // stderr.println("Time taken to cut:\t"
+ // + (System.nanoTime() - time) + " ns");
+ }
+ else
+ {
+ textArea.setText(header);
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ // lines = textArea.getLineCount();
+ }
}
}
throws IOException
{
String input = "";
+ int lp = -1;
do
{
int available = in.available();
byte b[] = new byte[available];
in.read(b);
input = input + new String(b, 0, b.length);
+ // counts lines - we don't do this for speed.
+ // while ((lp = input.indexOf("\n", lp + 1)) > -1)
+ // {
+ // lines++;
+ // }
} while (!input.endsWith("\n") && !input.endsWith("\r\n") && !quit);
return input;
}
public static void main(String[] arg)
{
new Console().test(); // create console with not reference
-
+
}
public void setVisible(boolean selected)
frame.setVisible(selected);
if (selected == true)
{
+ redirectStreams();
+ updateConsole = true;
frame.toFront();
- }
+ }
+ else
+ {
+ unredirectStreams();
+ updateConsole = false;
+ }
}
public Rectangle getBounds()
{
- if (frame!=null)
+ if (frame != null)
{
return frame.getBounds();
}
return null;
}
+
+ /**
+ * set the banner that appears at the top of the console output
+ *
+ * @param string
+ */
+ public void setHeader(String string)
+ {
+ header = string;
+ if (header.charAt(header.length() - 1) != '\n')
+ {
+ header += "\n";
+ }
+ textArea.insert(header, 0);
+ }
+
+ /**
+ * get the banner
+ *
+ * @return
+ */
+ public String getHeader()
+ {
+ return header;
+ }
}
git://source.jalview.org / jalview.git / blobdiff