X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=a26b9d05b83c26ac560cbbeb3f33fb2dccdc5537;hb=a87f4c6fd568ccf29aaf3af0ad528da442ea921d;hp=b99d642ecc6128158bb6e57445f53696f5ed6319;hpb=ac233160f70bacfd484e371af9433a7ed226ceb4;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index b99d642..a26b9d0 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -28,6 +28,7 @@ import java.applet.*;
import java.awt.*;
import java.awt.event.*;
+import jalview.appletgui.TreePanel;
/**
@@ -40,18 +41,19 @@ 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");
+ static AlignFrame currentAlignFrame;
+ boolean embedded = false;
+
+
/**
* init method for Jalview Applet
*/
public void init()
{
- applet = this;
-
int r = 255;
int g = 255;
int b = 255;
@@ -73,22 +75,39 @@ public class JalviewLite extends Applet
}
}
+ param = getParameter("label");
+ if(param != null)
+ launcher.setLabel(param);
+
this.setBackground(new Color(r, g, b));
file = getParameter("file");
+ if(file.indexOf("://")==-1)
+ file = getCodeBase() + file;
- if (file != null)
+ final JalviewLite applet = this;
+ if(getParameter("embedded")!=null
+ && getParameter("embedded").equalsIgnoreCase("true"))
+ {
+ embedded = true;
+ LoadingThread loader = new LoadingThread(file,
+ "URL",
+ applet);
+ loader.start();
+ }
+ else 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);
- }
+ LoadingThread loader = new LoadingThread(file,
+ "URL",
+ applet);
+ loader.start();
+ }
});
}
else
@@ -98,44 +117,26 @@ public class JalviewLite extends Applet
}
}
- /**
- * 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)
- {
- showURL(url, "HELP");
- }
- public static void showURL(String url, String target)
+ public static void main(String [] args)
+ {
+ if(args.length!=1)
{
- try
- {
- applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+ System.exit(1);
}
+ String format = jalview.io.IdentifyFile.Identify(args[0],"File");
+ SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
- /**
- * 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();
+ 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
*
@@ -156,12 +157,47 @@ public class JalviewLite extends Applet
{
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"
*
@@ -180,6 +216,15 @@ public class JalviewLite extends Applet
g.drawString("Jalview can't open file", 5, 15);
g.drawString("\"" + file + "\"", 5, 30);
}
+ else if(embedded)
+ {
+ g.setColor(Color.black);
+ g.setFont(new Font("Arial", Font.BOLD, 24));
+ g.drawString("Jalview Applet", 50, this.size().height/2 -30);
+ g.drawString("Loading Data...", 50, this.size().height/2);
+ }
+
+
}
class LoadingThread extends Thread
@@ -187,29 +232,100 @@ public class JalviewLite extends Applet
String file;
String protocol;
String format;
- JalviewLite jlapplet;
+ JalviewLite applet;
- public LoadingThread(String file, String protocol, String format,
- JalviewLite applet)
+ public LoadingThread(String file,
+ String protocol,
+ JalviewLite applet)
{
this.file = file;
this.protocol = protocol;
- this.format = format;
- this.jlapplet = applet;
+ format = jalview.io.IdentifyFile.Identify(file, "URL");
+ this.applet = applet;
}
public void run()
{
SequenceI[] sequences = null;
- sequences = FormatAdapter.readFile(file, protocol, format);
+ sequences = new AppletFormatAdapter().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);
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),
+ applet, file);
+ if (embedded)
+ currentAlignFrame.setEmbedded();
+
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+
+ String treeFile = applet.getParameter("treeFile");
+ if (treeFile != null)
+ {
+ if (treeFile.indexOf("://") == -1)
+ treeFile = getCodeBase() + treeFile;
+
+ 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 param = getParameter("features");
+ if (param != null)
+ {
+ if (param.indexOf("://") == -1)
+ param = getCodeBase() + param;
+
+ currentAlignFrame.parseFeaturesFile(param);
+ }
+
+ param = getParameter("annotations");
+ if (param != null)
+ {
+ if (param.indexOf("://") == -1)
+ param = getCodeBase() + param;
+
+ new AnnotationReader().readAnnotationFile(
+ currentAlignFrame.viewport.getAlignment(),
+ param);
+
+ currentAlignFrame.alignPanel.fontChanged();
+ }
+
+
+ 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
{