added facility for sending non-fatal warnings back to caller.

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index eb10375..f4f765c 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -37,6 +37,7 @@ public class FileParse
   protected BufferedReader dataIn=null;
   protected String errormessage="UNITIALISED SOURCE";
   protected boolean error=true;
+  protected String warningMessage=null;
   /**
    * size of readahead buffer used for when initial stream position is marked.
    */
@@ -206,4 +207,18 @@ public class FileParse
       throw new IOException("Implementation Error: Reset called for invalid source.");
     }
   }
+  /**
+   * 
+   * @return true if there is a warning for the user
+   */
+  public boolean hasWarningMessage() {
+    return (warningMessage!=null && warningMessage.length()>0);
+  }
+  /**
+   * 
+   * @return empty string or warning message about file that was just parsed.
+   */
+  public String getWarningMessage() {
+    return warningMessage;
+  }
 }