From 5f8a96e101d9e8bd2a35767588398ace4f3022ad Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 14 Nov 2010 14:58:04 +0000
Subject: [PATCH] import annotation file from datasource

---
 src/jalview/io/AnnotationFile.java |   32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ef2673a..3459517 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -461,13 +461,9 @@ public class AnnotationFile
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
-    String groupRef = null;
-    Hashtable groupRefRows = new Hashtable();
-
-    Hashtable autoAnnots = new Hashtable();
+    BufferedReader in = null;
     try
     {
-      BufferedReader in = null;
       if (protocol.equals(AppletFormatAdapter.FILE))
       {
         in = new BufferedReader(new FileReader(file));
@@ -489,7 +485,28 @@ public class AnnotationFile
           in = new BufferedReader(new java.io.InputStreamReader(is));
         }
       }
+      if (in != null)
+      {
+        return parseAnnotationFrom(al, in);
+      }
 
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Problem reading annotation file: " + ex);
+      return false;
+    }
+    return false;
+  }
+
+  public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
+          throws Exception
+  {
+    String groupRef = null;
+    Hashtable groupRefRows = new Hashtable();
+
+    Hashtable autoAnnots = new Hashtable();
+    {
       String line, label, description, token;
       int graphStyle, index;
       int refSeqIndex = 1;
@@ -826,11 +843,6 @@ public class AnnotationFile
         }
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-      System.out.println("Problem reading annotation file: " + ex);
-      return false;
     }
     return true;
   }
-- 
1.7.10.2