From 75836e49226d034ba50dfec18ab75f8bf4f0b242 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 19 Jan 2007 15:51:12 +0000
Subject: [PATCH] Need to know protocol to load anntotations

---
 src/jalview/io/AnnotationFile.java |   32 +++++++++++++++++++-------------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 749d2a7..2291f39 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -164,28 +164,34 @@ public class AnnotationFile
     return text.toString();
   }
 
-  public boolean readAnnotationFile(AlignmentI al, String file)
+  public boolean readAnnotationFile(AlignmentI al,
+                                    String file,
+                                    String protocol)
   {
     try
     {
       BufferedReader in = null;
-      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-      if (is != null)
+      if (protocol.equals(AppletFormatAdapter.FILE))
       {
-        in = new BufferedReader(new java.io.InputStreamReader(is));
+        in = new BufferedReader(new FileReader(file));
       }
-      else
+      else if (protocol.equals(AppletFormatAdapter.URL))
       {
-        try
-        {
-          URL url = new URL(file);
-          in = new BufferedReader(new InputStreamReader(url.openStream()));
-        }
-        catch (java.net.MalformedURLException ex)
+        URL url = new URL(file);
+        in = new BufferedReader(new InputStreamReader(url.openStream()));
+      }
+     else if (protocol.equals(AppletFormatAdapter.PASTE))
+      {
+        in = new BufferedReader(new StringReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      {
+        java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+        if (is != null)
         {
-          in = new BufferedReader(new FileReader(file));
+          in = new BufferedReader(new java.io.InputStreamReader(is));
         }
-      }
+    }
 
       String line, label, description, token;
       int graphStyle, index;
-- 
1.7.10.2