From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 18 Aug 2015 15:17:28 +0000 (+0100)
Subject: JAL-1861 bugfix to allow parsing of stockholm files with missing annotations
X-Git-Tag: Release_2_10_0~532
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8db8d34d6839742068935c364b790de72dc3bc94;p=jalview.git

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
--- 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"))