From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 24 Jan 2007 17:29:20 +0000 (+0000)
Subject: Features output for javascript
X-Git-Tag: Release_2_3~450
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7159dfadb2622541b1b39251cabef7e0655ce2b8;p=jalview.git

Features output for javascript
---

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 4efab35..ef7f582 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -39,6 +39,75 @@ import jalview.appletgui.FeatureSettings;
  */
 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 String getFeatures(String format)
+    {
+      return currentAlignFrame.outputFeatures(false, format);
+    }
+
+    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;
@@ -199,44 +268,7 @@ 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"