JAL-3210 Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 86b4402..f0f1ca3 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -646,7 +646,7 @@ public class AnnotationFile
 
   String refSeqId = null;
 
-  public boolean annotateAlignmentView(AlignViewportI viewport, String file,
+  public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
           DataSourceType protocol)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
@@ -677,23 +677,23 @@ public class AnnotationFile
   }
 
   public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
-          String file, DataSourceType sourceType)
+          Object file, DataSourceType sourceType)
   {
     BufferedReader in = null;
     try
     {
       if (sourceType == DataSourceType.FILE)
       {
-        in = new BufferedReader(new FileReader(file));
+        in = FileLoader.getBufferedReader(file);
       }
       else if (sourceType == DataSourceType.URL)
       {
-        URL url = new URL(file);
+        URL url = new URL(file.toString());
         in = new BufferedReader(new InputStreamReader(url.openStream()));
       }
       else if (sourceType == DataSourceType.PASTE)
       {
-        in = new BufferedReader(new StringReader(file));
+        in = new BufferedReader(new StringReader(file.toString()));
       }
       else if (sourceType == DataSourceType.CLASSLOADER)
       {