X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=081efa66b3b39840e796e0aff4864823efa7d6e7;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=858c391371a1ff9f65b53925898e0c887e01fb97;hpb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 858c391..081efa6 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -28,7 +28,6 @@ import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import jalview.appletgui.TreePanel;
 
 
 /**
@@ -89,14 +88,26 @@ public class JalviewLite extends Applet
 
         file = getParameter("file");
 
+        if(file==null)
+        {
+          //Maybe the sequences are added as parameters
+          StringBuffer data = new StringBuffer("PASTE");
+          int i=1;
+          while( (file=getParameter("sequence"+i))!=null)
+          {
+            data.append(file.toString()+"\n");
+            i++;
+          }
+          if(data.length()>5)
+            file = data.toString();
+        }
+
         final JalviewLite applet = this;
         if(getParameter("embedded")!=null
            && getParameter("embedded").equalsIgnoreCase("true"))
         {
           embedded = true;
-          LoadingThread loader = new LoadingThread(file,
-                            AppletFormatAdapter.URL,
-                            applet);
+          LoadingThread loader = new LoadingThread(file, applet);
           loader.start();
         }
         else if (file != null)
@@ -108,7 +119,6 @@ public class JalviewLite extends Applet
                     public void actionPerformed(ActionEvent e)
                     {
                         LoadingThread loader = new LoadingThread(file,
-                            AppletFormatAdapter.URL,
                             applet);
                         loader.start();
                       }
@@ -141,7 +151,7 @@ public class JalviewLite extends Applet
      }
       if ( (sequences != null) && (sequences.length > 0))
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
+        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
         af.statusBar.setText("Successfully loaded file " + args[0]);
       }
     }
@@ -262,15 +272,21 @@ public class JalviewLite extends Applet
         JalviewLite applet;
 
         public LoadingThread(String _file,
-                             String _protocol,
                              JalviewLite _applet)
         {
             file = _file;
-            if(inArchive(file))
+            if(file.startsWith("PASTE"))
+            {
+              file = file.substring(5);
+              protocol = AppletFormatAdapter.PASTE;
+            }
+            else if(inArchive(file))
               protocol = AppletFormatAdapter.CLASSLOADER;
             else
-              protocol = _protocol;
-
+            {
+              file = addProtocol(file);
+              protocol = AppletFormatAdapter.URL;
+            }
             format = new jalview.io.IdentifyFile().Identify(file, protocol);
             applet = _applet;
         }
@@ -288,17 +304,21 @@ public class JalviewLite extends Applet
             if ((sequences != null) && (sequences.length > 0))
             {
               currentAlignFrame = new AlignFrame(new Alignment(sequences),
-                                                 applet, file);
+                                                 applet,
+                                                 file,
+                                                 embedded);
 
-              initialAlignFrame = currentAlignFrame;
+              if(protocol==jalview.io.AppletFormatAdapter.PASTE)
+                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
 
-              if (embedded)
-                currentAlignFrame.setEmbedded();
+              initialAlignFrame = currentAlignFrame;
 
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
 
-                String treeFile = applet.getParameter("treeFile");
+                String treeFile = applet.getParameter("tree");
+                if(treeFile==null)
+                  applet.getParameter("treeFile");
                 if (treeFile != null)
                 {
                   try
@@ -317,12 +337,7 @@ public class JalviewLite extends Applet
 
                     if (fin.getTree() != null)
                     {
-                      TreePanel tp = null;
-                      tp = new TreePanel(currentAlignFrame.viewport,
-                                         currentAlignFrame.viewport.getAlignment().getSequences(),
-                                         fin, "FromFile", treeFile);
-                      addFrame(tp, treeFile, 600, 500);
-                      currentAlignFrame.addTreeMenuItem(tp, treeFile);
+                      currentAlignFrame.loadTree(fin, treeFile);
                     }
                   }
                   catch (Exception ex)
@@ -337,7 +352,14 @@ public class JalviewLite extends Applet
                 if( !inArchive(param) )
                   param = addProtocol( param );
 
-                currentAlignFrame.parseFeaturesFile(param);
+                currentAlignFrame.parseFeaturesFile(param, protocol);
+              }
+
+              param = getParameter("showFeatureSettings");
+              if(param !=null && param.equalsIgnoreCase("true"))
+              {
+                currentAlignFrame.viewport.showSequenceFeatures(true);
+                currentAlignFrame.featureSettings_actionPerformed();
               }
 
              param = getParameter("annotations");
@@ -346,11 +368,38 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().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();
+               }
              }
 
 
@@ -391,7 +440,15 @@ public class JalviewLite extends Applet
          */
         boolean inArchive(String file)
         {
-          return ( getClass().getResourceAsStream("/" + file) != null );
+          //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)