JAL-793 added ability to visualise raw BioJSON in the exported HTML using facebox

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

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 76b83ba..f652035 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -533,9 +533,9 @@ public class StockholmFile extends AlignFile
           }
           else
           {
-            throw new IOException(MessageManager.formatMessage(
-                    "exception.error_parsing_line", new String[]
-                    { line }));
+            // throw new IOException(MessageManager.formatMessage(
+            // "exception.error_parsing_line", new String[] { line }));
+            System.err.println(">> missing annotation: " + line);
           }
         }
         else if (annType.equals("GC"))
@@ -978,6 +978,7 @@ public class StockholmFile extends AlignFile
             {
               feature = ds.getSequenceFeatures()[0].type;
             }
+            // ?bug - feature may still have previous loop value
             String key = type2id(feature);
 
             if (key == null)