JAL-1861 bugfix to allow parsing of stockholm files with missing annotations

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 6490d28..f652035 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -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"))