X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=6b02022c61ac1ec1b9bc33577e0200889da48b7a;hb=10dfe2a100d53e45c4a9d23ce3957fa68de35046;hp=00476d619c774dab65c3762ff3f390ead3473af8;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 00476d6..6b02022 100755
--- 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.getBuffereReader(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)
       {
@@ -968,7 +968,7 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              hidden.hideInsertionsFor(sr);
+              hidden.hideList(sr.getInsertions());
             }
           }
           modified = true;