X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=b4adf07ddeb02a296809c104d1670b03b374b268;hb=848bef9fdc243cfab564acb0b82fc7ee3bcffe9f;hp=bd5abb0dcb55b1452306424ddc9de63fb12b8d99;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index bd5abb0..b4adf07 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -16,126 +16,294 @@
* 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;
+import jalview.appletgui.TreePanel;
+
+/**
+ * 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;
+ boolean fileFound = true;
+ String file = "No file";
+ Button launcher = new Button("Start Jalview");
+
+ static AlignFrame currentAlignFrame;
+
+
+ /**
+ * 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);
- }
- });
+ 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;
+ }
+ }
+
+ param = getParameter("label");
+ if(param != null)
+ launcher.setLabel(param);
+
+ this.setBackground(new Color(r, g, b));
+
+
+ param = getParameter("features");
+ if(param!=null)
+ {
+ if(param.indexOf("://")==-1)
+ param = getCodeBase() + param;
+ }
+ final String featuresFile = param;
+
+ file = getParameter("file");
+ final JalviewLite applet = this;
+ if (file != null)
+ {
+ add(launcher);
+ if(file.indexOf("://")==-1)
+ file = getCodeBase() + file;
+
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String format = jalview.io.IdentifyFile.Identify(file,
+ "URL");
+ LoadingThread loader = new LoadingThread(file,
+ "URL",
+ format,
+ featuresFile,
+ applet);
+ loader.start();
+ }
+ });
+ }
+ 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()
+
+
+ public static void main(String [] args)
{
- public void windowClosing(WindowEvent e)
+ if(args.length!=1)
{
- frame.dispose();
+ System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+ System.exit(1);
}
- });
- 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();
- }
- }
- }
-}
+ String format = jalview.io.IdentifyFile.Identify(args[0],"File");
+ SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
+
+ if ( (sequences != null) && (sequences.length > 0))
+ {
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
+ af.statusBar.setText("Successfully loaded file " + args[0]);
+ }
+ }
+
+
+ /**
+ * 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)
+ {
+ if(currentAlignFrame == frame)
+ {
+ currentAlignFrame = null;
+ }
+ lastFrameX -=40;
+ lastFrameY-=40;
+ frame.setMenuBar(null);
+ frame.dispose();
+ }
+ public void windowActivated(WindowEvent e)
+ {
+ if(frame instanceof AlignFrame)
+ currentAlignFrame = (AlignFrame)frame;
+ }
+
+ });
+ frame.setVisible(true);
+ }
+
+ public String getAlignment(String format)
+ {
+ return getAlignment(format, "true");
+ }
+
+ public String getAlignment(String format, String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);
+ return reply;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+ /**
+ * 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;
+ String featuresFile;
+ JalviewLite applet;
+
+ public LoadingThread(String file,
+ String protocol,
+ String format,
+ String features,
+ JalviewLite applet)
+ {
+ this.file = file;
+ this.protocol = protocol;
+ this.format = format;
+ featuresFile = features;
+ this.applet = applet;
+ }
+
+ public void run()
+ {
+ SequenceI[] sequences = null;
+ sequences = new AppletFormatAdapter().readFile(file, protocol, format);
+
+ if ((sequences != null) && (sequences.length > 0))
+ {
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),
+ applet, file);
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+ if(featuresFile!=null)
+ currentAlignFrame.parseFeaturesFile(featuresFile);
+
+ String treeFile = applet.getParameter("treeFile");
+ if (treeFile != null)
+ {
+ try
+ {
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+ getCodeBase() + treeFile, "URL");
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ TreePanel tp = null;
+ tp = new TreePanel(currentAlignFrame.viewport,
+ currentAlignFrame.viewport.getAlignment().getSequences(),
+ fin, "FromFile", applet.getCodeBase() + treeFile);
+ addFrame(tp, treeFile, 600, 500);
+ currentAlignFrame.addTreeMenuItem(tp, treeFile);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+
+ String pdbfile = applet.getParameter("PDBFILE");
+ if(pdbfile!=null)
+ {
+ if(pdbfile.indexOf("://")==-1)
+ pdbfile = getCodeBase() + pdbfile;
+
+ String sequence = applet.getParameter("PDBSEQ");
+
+ if(sequence!=null)
+ {
+ new MCview.AppletPDBViewer(pdbfile, "URL",
+ (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
+ currentAlignFrame.getSeqcanvas());
+ }
+
+ }
+ }
+ else
+ {
+ fileFound = false;
+ remove(launcher);
+ repaint();
+ }
+ }
+ }
+}