X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;fp=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=da784208d9aceae920bc2fe9b3ff82c40db8afc5;hb=2e9e0527943d0c42a6059ebbb8e7e69346c38206;hp=5e209e6569970c260d95410ebd1c853e4b0a37b0;hpb=e4843176d8337fc165c1b93ae6c161cb29521f6d;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5e209e6..da78420 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -147,6 +147,20 @@ public class AppletFormatAdapter
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {
+    if (alignFile == null)
+    {
+      prepareFileReader(file, sourceType, fileFormat);
+    }
+    else
+    {
+      alignFile.parse();
+    }
+    return buildAlignmentFromFile();
+  }
+  
+  public void prepareFileReader(String file, DataSourceType sourceType,
+          FileFormatI fileFormat) throws IOException
+  {
     this.inFile = file;
     try
     {
@@ -176,10 +190,9 @@ public class AppletFormatAdapter
       }
       else
       {
-        // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
         alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
       }
-      return buildAlignmentFromFile();
+      return;
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -200,7 +213,7 @@ public class AppletFormatAdapter
           // Possible sequence is just residues with no label
           alignFile = new FastaFile(">UNKNOWN\n" + inFile,
                   DataSourceType.PASTE);
-          return buildAlignmentFromFile();
+          return;
 
         } catch (Exception ex)
         {