2.08, not 2.07

[jalview.git] / src / jalview / io / AnnotationReader.java

diff --git a/src/jalview/io/AnnotationReader.java b/src/jalview/io/AnnotationReader.java
index 9c6dc49..4325dae 100755 (executable)
--- a/src/jalview/io/AnnotationReader.java
+++ b/src/jalview/io/AnnotationReader.java
@@ -13,18 +13,25 @@ public class AnnotationReader
 \r
     try\r
     {\r
-\r
       BufferedReader in = null;\r
-      try{\r
-        URL url = new URL(file);\r
-        in = new BufferedReader(new InputStreamReader(url.openStream()));\r
+      java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
+      if (is != null)\r
+      {\r
+        in = new BufferedReader(new java.io.InputStreamReader(is));\r
       }\r
-      catch(java.net.MalformedURLException ex)\r
+      else\r
       {\r
-        in = new BufferedReader(new FileReader(file));\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
+        {\r
+          in = new BufferedReader(new FileReader(file));\r
+        }\r
       }\r
 \r
-\r
       String line, label, description, token;\r
       int graphStyle, index;\r
       SequenceI refSeq = null;\r
@@ -262,7 +269,7 @@ public class AnnotationReader
       colour = ucs.findColour("A");\r
     }\r
 \r
-    annotation.addGraphLine(new GraphLine(value, label, colour));\r
+    annotation.setThreshold(new GraphLine(value, label, colour));\r
 \r
   }\r
 }\r