Need to know protocol to load anntotations

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