From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 May 2013 13:12:15 +0000 (+0100)
Subject: JAL-1070 - [ not a real patch ] - include offending line number and content in output... 
X-Git-Tag: Jalview_2_9~249^2~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3a737f9769e1d0abbf973730b4f240c4abd5f475;p=jalview.git

JAL-1070 - [ not a real patch ] - include offending line number and content in output when an Alignment annotation file parsing exception stacktraces to stderr
---

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 45e6c47..a94bd3c 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -579,14 +579,19 @@ public class AnnotationFile
     {
       ex.printStackTrace();
       System.out.println("Problem reading annotation file: " + ex);
+      if (nlinesread>0) {
+        System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ...");
+      }
       return false;
     }
     return false;
   }
-
+  long nlinesread=0;
+  String lastread="";
   public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
           throws Exception
   {
+    nlinesread = 0;
     boolean modified = false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
@@ -631,6 +636,7 @@ public class AnnotationFile
       boolean jvAnnotationFile = false;
       while ((line = in.readLine()) != null)
       {
+        nlinesread++;lastread = new String(line);
         if (line.indexOf("#") == 0)
         {
           continue;
@@ -651,6 +657,7 @@ public class AnnotationFile
 
       while ((line = in.readLine()) != null)
       {
+        nlinesread++;lastread = new String(line);
         if (line.indexOf("#") == 0
                 || line.indexOf("JALVIEW_ANNOTATION") > -1
                 || line.length() == 0)