X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=d42157b3e70c2821a18e04f1302bf8bd0c9d5405;hb=e601d78bc7762386f570e346a803684c43a66ff1;hp=5eb4d2bd6d427abb5103b620cb98af5800d97aff;hpb=60dde97e0115909c22d4b6dff689a061e497e36d;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5eb4d2b..d42157b 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -117,7 +117,18 @@ public class AppletFormatAdapter
   AlignFile afile = null;
 
   String inFile;
-
+  /**
+   * character used to write newlines 
+   */
+  protected String newline = System.getProperty("line.separator");
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+  public String getNewlineString()
+  {
+    return newline;
+  }
   /**
    * check that this format is valid for reading
    * 
@@ -441,7 +452,7 @@ public class AppletFormatAdapter
         throw new Exception(
                 "Implementation error: Unknown file format string");
       }
-
+      afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
 
       afile.setSeqs(alignment.getSequencesArray());