X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=89c01679f49945c95ee43c145bc819f0f776e06c;hb=3ab14ac58b3829f6f83353eb3e600cf9152d83bc;hp=09e87013484837b26038173afea1de51deac5861;hpb=829c30f2ba9994a71e18db7dc652cbd11a9c8846;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 09e8701..89c0167 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.FeatureSettings;
 
 
 /**
@@ -38,6 +39,96 @@ import java.awt.event.*;
  */
 public class JalviewLite extends Applet
 {
+
+  ///////////////////////////////////////////
+  //The following public methods maybe called
+  //externally, eg via javascript in HTML page
+
+  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(), seqlimits);
+        return reply;
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+        return "Error retrieving alignment in " + format + " format. ";
+      }
+    }
+
+    public void loadAnnotation(String annotation)
+    {
+      if (new AnnotationFile().readAnnotationFile(
+          currentAlignFrame.getAlignViewport().getAlignment(), annotation,
+          AppletFormatAdapter.PASTE))
+      {
+        currentAlignFrame.alignPanel.fontChanged();
+        currentAlignFrame.alignPanel.setScrollValues(0, 0);
+      }
+      else
+      {
+        currentAlignFrame.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+      }
+    }
+
+    public String getFeatures(String format)
+    {
+      return currentAlignFrame.outputFeatures(false, format);
+    }
+
+    public String getAnnotation()
+    {
+      return currentAlignFrame.outputAnnotations(false);
+    }
+
+    public void loadAlignment(String text, String title)
+    {
+        Alignment al = null;
+        String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
+        try{
+          al = new AppletFormatAdapter().readFile(text,
+                                                  AppletFormatAdapter.PASTE,
+                                                  format);
+          if (al.getHeight() > 0)
+            new AlignFrame(al, this, title, false);
+        }catch(java.io.IOException ex)
+        {
+          ex.printStackTrace();
+        }
+   }
+
+    ////////////////////////////////////////////////
+    ////////////////////////////////////////////////
+
+
+
     static int lastFrameX = 200;
     static int lastFrameY = 200;
     boolean fileFound = true;
@@ -142,16 +233,16 @@ public class JalviewLite extends Applet
 
       String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);
 
-      SequenceI[] sequences = null;
+     Alignment al = null;
      try{
-       sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
+       al = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
      }catch(java.io.IOException ex)
      {
        ex.printStackTrace();
      }
-      if ( (sequences != null) && (sequences.length > 0))
+      if ( (al != null) && (al.getHeight() > 0))
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
+        AlignFrame af = new AlignFrame(al, null, args[0], false);
         af.statusBar.setText("Successfully loaded file " + args[0]);
       }
     }
@@ -177,6 +268,8 @@ public class JalviewLite extends Applet
             {
                 public void windowClosing(WindowEvent e)
                 {
+                  if(frame instanceof AlignFrame)
+                    ((AlignFrame)frame).closeMenuItem_actionPerformed();
                     if(currentAlignFrame == frame)
                     {
                       currentAlignFrame = null;
@@ -196,44 +289,7 @@ public class JalviewLite extends Applet
         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"
@@ -257,8 +313,8 @@ public class JalviewLite extends Applet
         {
           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);
+          g.drawString("Jalview Applet", 50, this.getSize().height/2 -30);
+          g.drawString("Loading Data...", 50, this.getSize().height/2);
         }
 
 
@@ -293,17 +349,17 @@ public class JalviewLite extends Applet
 
         public void run()
         {
-            SequenceI[] sequences = null;
+            Alignment al = null;
             try{
-              sequences = new AppletFormatAdapter().readFile(file, protocol,
+              al = new AppletFormatAdapter().readFile(file, protocol,
                   format);
             }catch(java.io.IOException ex)
             {
               ex.printStackTrace();
             }
-            if ((sequences != null) && (sequences.length > 0))
+            if ((al != null) && (al.getHeight() > 0))
             {
-              currentAlignFrame = new AlignFrame(new Alignment(sequences),
+              currentAlignFrame = new AlignFrame(al,
                                                  applet,
                                                  file,
                                                  embedded);
@@ -360,7 +416,7 @@ public class JalviewLite extends Applet
               if(param !=null && param.equalsIgnoreCase("true"))
               {
                 currentAlignFrame.viewport.showSequenceFeatures(true);
-                currentAlignFrame.featureSettings_actionPerformed();
+                new FeatureSettings(currentAlignFrame.alignPanel);
               }
 
              param = getParameter("annotations");
@@ -371,7 +427,8 @@ public class JalviewLite extends Applet
 
                new AnnotationFile().readAnnotationFile(
                    currentAlignFrame.viewport.getAlignment(),
-                   param);
+                   param,
+                   protocol);
 
                currentAlignFrame.alignPanel.fontChanged();
                currentAlignFrame.alignPanel.setScrollValues(0,0);
@@ -404,22 +461,22 @@ public class JalviewLite extends Applet
              }
 
 
-                String pdbfile = applet.getParameter("PDBFILE");
-                if(pdbfile!=null)
+                param = getParameter("PDBFILE");
+                if(param!=null)
                 {
-                  if( inArchive(pdbfile) )
+                  if( inArchive(param) )
                     protocol = AppletFormatAdapter.CLASSLOADER;
                   else
                   {
                     protocol = AppletFormatAdapter.URL;
-                    pdbfile = addProtocol(pdbfile);
+                    param = addProtocol(param);
                   }
 
                   String sequence = applet.getParameter("PDBSEQ");
 
                   if(sequence!=null)
                   {
-                    new MCview.AppletPDBViewer(pdbfile, protocol,
+                    new MCview.AppletPDBViewer(param, protocol,
                                                (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
                                                currentAlignFrame.getSeqcanvas());
                   }