X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=b99d642ecc6128158bb6e57445f53696f5ed6319;hb=6f4eaccaaabb743c27589d4107439caeb490ac3e;hp=1ce20661064e6374bf7a59259ba5fb6bcd52c1af;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 1ce2066..b99d642 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,122 +1,222 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* 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 program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
package jalview.bin;
+import jalview.appletgui.AlignFrame;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
import java.applet.*;
+
import java.awt.*;
import java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.appletgui.AlignFrame;
+
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision$
+ */
public class JalviewLite extends Applet
{
- static int lastFrameX = 200;
- static int lastFrameY = 200;
- static Applet applet;
- boolean fileFound = true;
- String file = "No file";
- Button launcher = new Button("Start Jalview");
-
- public void init()
- {
- applet = this;
- this.setBackground(Color.white);
-
- file = getParameter("file");
- if (file != null)
+ static int lastFrameX = 200;
+ static int lastFrameY = 200;
+ static Applet applet;
+ boolean fileFound = true;
+ String file = "No file";
+ Button launcher = new Button("Start Jalview");
+
+ /**
+ * init method for Jalview Applet
+ */
+ public void init()
{
- add(launcher);
- file = applet.getCodeBase() + file;
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- String format = jalview.io.IdentifyFile.Identify( file, "URL");
- LoadFile(file, "URL", format);
- }
- });
+ applet = this;
+
+ int r = 255;
+ int g = 255;
+ int b = 255;
+ String param = getParameter("RGB");
+
+ if (param != null)
+ {
+ try
+ {
+ r = Integer.parseInt(param.substring(0, 2), 16);
+ g = Integer.parseInt(param.substring(2, 4), 16);
+ b = Integer.parseInt(param.substring(4, 6), 16);
+ }
+ catch (Exception ex)
+ {
+ r = 255;
+ g = 255;
+ b = 255;
+ }
+ }
+
+ this.setBackground(new Color(r, g, b));
+
+ file = getParameter("file");
+
+ if (file != null)
+ {
+ add(launcher);
+ file = applet.getCodeBase() + file;
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String format = jalview.io.IdentifyFile.Identify(file,
+ "URL");
+ LoadFile(file, "URL", format);
+ }
+ });
+ }
+ else
+ {
+ file = "NO FILE";
+ fileFound = false;
+ }
}
- else
- {
- file = "NO FILE";
- fileFound = false;
- }
- }
-
-
- public static void showURL(String url)
- {
- try{
- applet.getAppletContext().showDocument(new java.net.URL(url), "HELP_WINDOW");
- }catch(Exception ex){}
- }
-
- public void LoadFile(String file, String protocol, String format)
- {
- LoadingThread loader = new LoadingThread(file, protocol, format, this);
- loader.start();
- }
-
- public static void addFrame(final Frame frame, String title, int width, int height)
- {
- frame.setLocation(lastFrameX,lastFrameY);
- lastFrameX+=40; lastFrameY+=40;
- frame.setSize(width,height);
- frame.setTitle(title);
- frame.addWindowListener(new WindowAdapter()
+
+ /**
+ * Displays the given URL in a new browser window
+ *
+ * @param url URL to display in browser window.
+ *
New window will be named "HELP_WINDOW"
+ */
+ public static void showURL(String url)
{
- public void windowClosing(WindowEvent e)
+ showURL(url, "HELP");
+ }
+
+ public static void showURL(String url, String target)
{
- frame.dispose();
+ try
+ {
+ applet.getAppletContext().showDocument(new java.net.URL(url),
+ target);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
}
- });
- frame.setVisible(true);
- }
-
-
- public void paint(Graphics g)
- {
- if(!fileFound)
- {
- g.setColor(new Color(200,200,200));
- g.setColor(Color.cyan);
- g.fillRect(0,0,getSize().width, getSize().height);
- g.setColor(Color.red);
- g.drawString("Jalview can't open file", 5, 15);
- g.drawString("\""+ file+"\"", 5, 30);
- }
- }
-
- class LoadingThread extends Thread
- {
- String file, protocol, format;
- JalviewLite jlapplet;
-
- public LoadingThread(String file, String protocol, String format, JalviewLite applet)
- {
- this.file = file;
- this.protocol = protocol;
- this.format = format;
- this.jlapplet = applet;
- }
- public void run()
- {
- SequenceI [] sequences = null;
- sequences = FormatAdapter.readFile(file, protocol, format);
-
- if (sequences != null && sequences.length>0)
- {
- AlignFrame af = new AlignFrame(new Alignment(sequences), jlapplet );
- addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
- af.statusBar.setText("Successfully loaded file " + file);
- }
- else
- {
- fileFound = false;
- remove(launcher);
- repaint();
- }
- }
- }
-}
+ /**
+ * Starts a new LoadingThread for loading an alignment file
+ *
+ * @param file file name including full path to file
+ * @param protocol file or URL or paste
+ * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview
+ */
+ public void LoadFile(String file, String protocol, String format)
+ {
+ LoadingThread loader = new LoadingThread(file, protocol, format, this);
+ loader.start();
+ }
+
+ /**
+ * Initialises and displays a new java.awt.Frame
+ *
+ * @param frame java.awt.Frame to be displayed
+ * @param title title of new frame
+ * @param width width if new frame
+ * @param height height of new frame
+ */
+ public static void addFrame(final Frame frame, String title, int width,
+ int height)
+ {
+ frame.setLocation(lastFrameX, lastFrameY);
+ lastFrameX += 40;
+ lastFrameY += 40;
+ frame.setSize(width, height);
+ frame.setTitle(title);
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ frame.dispose();
+ }
+ });
+ frame.setVisible(true);
+ }
+
+ /**
+ * This paints the background surrounding the "Launch Jalview button"
+ *
+ *
If file given in parameter not found, displays error message
+ *
+ * @param g graphics context
+ */
+ public void paint(Graphics g)
+ {
+ if (!fileFound)
+ {
+ g.setColor(new Color(200, 200, 200));
+ g.setColor(Color.cyan);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setColor(Color.red);
+ g.drawString("Jalview can't open file", 5, 15);
+ g.drawString("\"" + file + "\"", 5, 30);
+ }
+ }
+
+ class LoadingThread extends Thread
+ {
+ String file;
+ String protocol;
+ String format;
+ JalviewLite jlapplet;
+
+ public LoadingThread(String file, String protocol, String format,
+ JalviewLite applet)
+ {
+ this.file = file;
+ this.protocol = protocol;
+ this.format = format;
+ this.jlapplet = applet;
+ }
+
+ public void run()
+ {
+ SequenceI[] sequences = null;
+ sequences = FormatAdapter.readFile(file, protocol, format);
+
+ if ((sequences != null) && (sequences.length > 0))
+ {
+ AlignFrame af = new AlignFrame(new Alignment(sequences),
+ jlapplet);
+ addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+ af.statusBar.setText("Successfully loaded file " + file);
+ }
+ else
+ {
+ fileFound = false;
+ remove(launcher);
+ repaint();
+ }
+ }
+ }
+}