Features output for javascript

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 4efab35..ef7f582 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -39,6 +39,75 @@ import jalview.appletgui.FeatureSettings;
  */\r
 public class JalviewLite extends Applet\r
 {\r
+\r
+  ///////////////////////////////////////////\r
+  //The following public methods maybe called\r
+  //externally, eg via javascript in HTML page\r
+  public String getSelectedSequences()\r
+    {\r
+      StringBuffer result = new StringBuffer("");\r
+\r
+      if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
+      {\r
+        SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
+            getSequencesInOrder(\r
+                initialAlignFrame.viewport.getAlignment());\r
+\r
+        for (int i = 0; i < seqs.length; i++)\r
+          result.append(seqs[i].getName() + "¬");\r
+      }\r
+\r
+      return result.toString();\r
+    }\r
+\r
+    public String getAlignment(String format)\r
+    {\r
+      return getAlignment(format, "true");\r
+    }\r
+\r
+    public String getAlignment(String format, String suffix)\r
+    {\r
+      try\r
+      {\r
+        boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+        String reply = new AppletFormatAdapter().formatSequences(format,\r
+            currentAlignFrame.viewport.getAlignment(), seqlimits);\r
+        return reply;\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        ex.printStackTrace();\r
+        return "Error retrieving alignment in " + format + " format. ";\r
+      }\r
+    }\r
+\r
+    public String getFeatures(String format)\r
+    {\r
+      return currentAlignFrame.outputFeatures(false, format);\r
+    }\r
+\r
+    public void loadAlignment(String text, String title)\r
+    {\r
+        Alignment al = null;\r
+        String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);\r
+        try{\r
+          al = new AppletFormatAdapter().readFile(text,\r
+                                                  AppletFormatAdapter.PASTE,\r
+                                                  format);\r
+          if (al.getHeight() > 0)\r
+            new AlignFrame(al, this, title, false);\r
+        }catch(java.io.IOException ex)\r
+        {\r
+          ex.printStackTrace();\r
+        }\r
+   }\r
+\r
+\r
+    ////////////////////////////////////////////////\r
+    ////////////////////////////////////////////////\r
+\r
+\r
     static int lastFrameX = 200;\r
     static int lastFrameY = 200;\r
     boolean fileFound = true;\r
@@ -199,44 +268,7 @@ public class JalviewLite extends Applet
         frame.setVisible(true);\r
     }\r
 \r
-    public String getSelectedSequences()\r
-    {\r
-      StringBuffer result = new StringBuffer("");\r
-\r
-      if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
-      {\r
-        SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
-            getSequencesInOrder(\r
-                initialAlignFrame.viewport.getAlignment());\r
-\r
-        for (int i = 0; i < seqs.length; i++)\r
-          result.append(seqs[i].getName() + "¬");\r
-      }\r
-\r
-      return result.toString();\r
-    }\r
 \r
-    public String getAlignment(String format)\r
-    {\r
-      return getAlignment(format, "true");\r
-    }\r
-\r
-    public String getAlignment(String format, String suffix)\r
-    {\r
-      try\r
-      {\r
-        boolean seqlimits = suffix.equalsIgnoreCase("true");\r
-\r
-        String reply = new AppletFormatAdapter().formatSequences(format,\r
-            currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
-        return reply;\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        ex.printStackTrace();\r
-        return "Error retrieving alignment in " + format + " format. ";\r
-      }\r
-    }\r
 \r
     /**\r
      * This paints the background surrounding the "Launch Jalview button"\r