X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=eee4fc7c34fbda5d3867b1e3ea5b0f6d195e05bb;hb=c8d150be394e2acf91a600a588492b44aa172052;hp=68769761536f1f23e37a6545cdaa2f7b8a95db22;hpb=03c446f178b6a0b61ad33cb219398132d640fbef;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 6876976..eee4fc7 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;
 
 
 /**
@@ -89,6 +88,20 @@ 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"))
@@ -262,7 +275,12 @@ public class JalviewLite extends Applet
                              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
             {
@@ -290,13 +308,18 @@ public class JalviewLite extends Applet
                                                  file,
                                                  embedded);
 
+              if(protocol==jalview.io.AppletFormatAdapter.PASTE)
+                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
 
               initialAlignFrame = currentAlignFrame;
 
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
 
-                String treeFile = applet.getParameter("treeFile");
+                String treeFile = applet.getParameter("tree");
+                if(treeFile==null)
+                  treeFile = applet.getParameter("treeFile");
+
                 if (treeFile != null)
                 {
                   try
@@ -330,7 +353,14 @@ 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");
@@ -339,7 +369,7 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )
                   param = addProtocol( param );
 
-               new AnnotationReader().readAnnotationFile(
+               new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
                    param);
 
@@ -348,6 +378,31 @@ public class JalviewLite extends Applet
 
              }
 
+             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)