/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
private JTextArea textArea;
- int lines = 0;
-
- int lim = 1000;
-
- 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 PrintStream stdout = System.out;
+ private final PrintStream stdout = System.out, stderr = System.err;
- private final PrintStream stderr = System.err;
+ private PipedInputStream pin = new PipedInputStream();
- private final PipedInputStream pin = new PipedInputStream();
+ private PipedInputStream pin2 = new PipedInputStream();
- private final PipedInputStream pin2 = new PipedInputStream();
+ private StringBuffer displayPipe = new StringBuffer();
Thread errorThrower; // just for testing (Throws an Exception at this Console
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 = new JTextArea();
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)
+ if (redirect)
{
- textArea.append("Couldn't redirect STDOUT to this console\n"
- + io.getMessage());
- } catch (SecurityException se)
- {
- textArea.append("Couldn't redirect STDOUT to this console\n"
- + se.getMessage());
+ redirectStreams();
}
-
- try
- {
- 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)
+ else
{
- 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 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");
*/
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_");
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);
}
public synchronized void windowClosed(WindowEvent evt)
{
frame.setVisible(false);
+ closeConsoleGui();
+ }
+
+ private void closeConsoleGui()
+ {
+ updateConsole = false;
if (parent == null)
{
public synchronized void windowClosing(WindowEvent evt)
{
frame.setVisible(false); // default behaviour of JFrame
+ closeConsoleGui();
+
// frame.dispose();
}
{
while (Thread.currentThread() == reader)
{
- if (pin.available()==0)
- {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)
+ {
+ }
+ }
+
while (pin.available() != 0)
{
String input = this.readLine(pin);
stdout.print(input);
- textArea.append(input);
+ long time = System.nanoTime();
+ appendToTextArea(input);
+ // stderr.println("Time taken to stdout append:\t"
+ // + (System.nanoTime() - time) + " ns");
// lines++;
}
if (quit)
return;
- trimBuffer(false);
}
while (Thread.currentThread() == reader2)
{
- if (pin2.available()==0) {
- try
- {
- this.wait(100);
- } catch (InterruptedException ie)
+ if (pin2.available() == 0)
{
- }
+ try
+ {
+ this.wait(100);
+ if (pin2.available() == 0)
+ {
+ trimBuffer(false);
+ }
+ } catch (InterruptedException ie)
+ {
+ }
}
while (pin2.available() != 0)
{
String input = this.readLine(pin2);
stderr.print(input);
- textArea.append(input);
+ long time = System.nanoTime();
+ appendToTextArea(input);
+ // stderr.println("Time taken to stderr append:\t"
+ // + (System.nanoTime() - time) + " ns");
// lines++;
}
if (quit)
return;
- trimBuffer(false);
+ }
+ 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.getMessage());
- lines += 2;
+ // Need to uncomment this to ensure that line tally is synched.
+ // lines += 2;
stderr.println("Console reports an Internal error.\nThe error is: "
+ e);
}
}
}
+ 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)
{
- // trim the buffer
- if (clear || lines > lim)
+ if (header == null && textArea.getLineCount() > 5)
{
try
{
- if (lines > 5)
+ 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
{
- // minimum length for truncation/clearing
- String header = textArea.getText(0, textArea.getLineEndOffset(5))
- + "\n..Truncated..\n"; // keep first 5 lines for startup info
- int truncate;
if (!clear)
{
- truncate = textArea.getLineEndOffset(lines - lim - 7);
- textArea.setText(header
- + textArea.getText(truncate, textArea.getText()
- .length()
- - truncate));
+ 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();
}
-
- } catch (Exception e)
- {
- e.printStackTrace();
+ // lines = textArea.getLineCount();
}
- lines = textArea.getLineCount();
}
}
byte b[] = new byte[available];
in.read(b);
input = input + new String(b, 0, b.length);
- while ((lp = input.indexOf("\n", lp + 1)) > -1)
- {
- lines++;
- }
+ // 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;
}
frame.setVisible(selected);
if (selected == true)
{
+ redirectStreams();
+ updateConsole = true;
frame.toFront();
}
+ else
+ {
+ unredirectStreams();
+ updateConsole = false;
+ }
}
public Rectangle 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