X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=cd0b8359bb12b2ac03623a05e1c30d3f0c29262a;hb=47aec94b56baa5b666c3189280f4d1d5c7567a95;hp=c9ec3918e3f65231aced553aeaf2cc9372c6ed6d;hpb=9344c308a62c48e2ddedd12247edab74e581c2e7;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index c9ec391..cd0b835 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -40,18 +40,25 @@ 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");
+ //The currentAlignFrame is static, it will change
+ //if and when the user selects a new window
+ static AlignFrame currentAlignFrame;
+
+ //This is the first frame to be displayed, and does not change
+ AlignFrame initialAlignFrame;
+
+ boolean embedded = false;
+
+
/**
* init method for Jalview Applet
*/
public void init()
{
- applet = this;
-
int r = 255;
int g = 255;
int b = 255;
@@ -73,22 +80,34 @@ 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 != null)
+ final JalviewLite applet = this;
+ if(getParameter("embedded")!=null
+ && getParameter("embedded").equalsIgnoreCase("true"))
+ {
+ embedded = true;
+ LoadingThread loader = new LoadingThread(file, 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,
+ applet);
+ loader.start();
+ }
});
}
else
@@ -98,6 +117,7 @@ public class JalviewLite extends Applet
}
}
+
public static void main(String [] args)
{
if(args.length!=1)
@@ -106,62 +126,22 @@ public class JalviewLite extends Applet
System.exit(1);
}
- String format = jalview.io.IdentifyFile.Identify(args[0],"File");
- SequenceI[] sequences = FormatAdapter.readFile(args[0], "File", format);
+ String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);
+ SequenceI[] sequences = null;
+ try{
+ sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
+ }catch(java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
if ( (sequences != null) && (sequences.length > 0))
{
- AlignFrame af = new AlignFrame(new Alignment(sequences), null);
- addFrame(af, args[0], AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
af.statusBar.setText("Successfully loaded file " + args[0]);
}
}
- /**
- * 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)
- {
- if(applet==null)
- {
- System.out.println("Not running as applet - no browser available.");
- }
- else
- {
- try
- {
- applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
-
- /**
- * 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
@@ -183,12 +163,64 @@ 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 getSelectedSequences()
+ {
+ StringBuffer result = new StringBuffer("");
+
+ if(initialAlignFrame.viewport.getSelectionGroup()!=null)
+ {
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
+ getSequencesInOrder(
+ initialAlignFrame.viewport.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ result.append(seqs[i].getName() + "¬");
+ }
+
+ return result.toString();
+ }
+
+ 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"
*
@@ -207,6 +239,15 @@ 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
@@ -214,29 +255,145 @@ 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,
+ JalviewLite _applet)
{
- this.file = file;
- this.protocol = protocol;
- this.format = format;
- this.jlapplet = applet;
+ file = _file;
+ if(inArchive(file))
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ file = addProtocol(file);
+ protocol = AppletFormatAdapter.URL;
+ }
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ applet = _applet;
}
public void run()
{
SequenceI[] sequences = null;
- sequences = FormatAdapter.readFile(file, protocol, format);
-
+ try{
+ sequences = new AppletFormatAdapter().readFile(file, protocol,
+ format);
+ }catch(java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
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,
+ embedded);
+
+
+ initialAlignFrame = currentAlignFrame;
+
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+
+ String treeFile = applet.getParameter("treeFile");
+ if (treeFile != null)
+ {
+ try
+ {
+ if(inArchive(treeFile))
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ treeFile = addProtocol(treeFile);
+ }
+
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol);
+
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ currentAlignFrame.loadTree(fin, treeFile);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ String param = getParameter("features");
+ if (param != null)
+ {
+ if( !inArchive(param) )
+ param = addProtocol( param );
+
+ currentAlignFrame.parseFeaturesFile(param);
+ }
+
+ param = getParameter("annotations");
+ if (param != null)
+ {
+ if( !inArchive(param) )
+ param = addProtocol( param );
+
+ new AnnotationReader().readAnnotationFile(
+ currentAlignFrame.viewport.getAlignment(),
+ param);
+
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0,0);
+
+ }
+
+ param = getParameter("jnetfile");
+ if (param != null)
+ {
+ try
+ {
+ if (inArchive(param))
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ param = addProtocol(param);
+ }
+
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ param, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ currentAlignFrame.viewport.getAlignment(),
+ 0,false); // do not add sequence profile from concise output
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ }
+
+
+ String pdbfile = applet.getParameter("PDBFILE");
+ if(pdbfile!=null)
+ {
+ if( inArchive(pdbfile) )
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ pdbfile = addProtocol(pdbfile);
+ }
+
+ String sequence = applet.getParameter("PDBSEQ");
+
+ if(sequence!=null)
+ {
+ new MCview.AppletPDBViewer(pdbfile, protocol,
+ (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
+ currentAlignFrame.getSeqcanvas());
+ }
+
+ }
}
else
{
@@ -245,5 +402,32 @@ public class JalviewLite extends Applet
repaint();
}
}
+
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ * @param file String
+ * @return boolean
+ */
+ boolean inArchive(String file)
+ {
+ //This might throw a security exception in certain browsers
+ //Netscape Communicator for instance.
+ try{
+ return (getClass().getResourceAsStream("/" + file) != null);
+ }catch(Exception ex)
+ {
+ System.out.println("Exception checking resources: "+file+" "+ex);
+ return false;
+ }
+ }
+
+ String addProtocol(String file)
+ {
+ if (file.indexOf("://") == -1)
+ file = getCodeBase() + file;
+
+ return file;
+ }
+
}
}