From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 13 Feb 2006 15:26:40 +0000 (+0000)
Subject: Parsing features file - dont adjust for alignment position
X-Git-Tag: Root_VamJalview_2_07b+~150
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc6f7ebe59c148e62cd9f1947d9ba30638db2980;p=jalview.git

Parsing features file - dont adjust for alignment position
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 01bea4d..96dc64b 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -184,8 +184,6 @@ public class AlignFrame extends Frame implements ActionListener,
           end = Integer.parseInt(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
 
           type = st.nextToken();
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3319b33..5778a7e 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2586,8 +2586,6 @@ public boolean parseGroupsFile(String file)
           end = Integer.parseInt(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
 
           type = st.nextToken();
 
@@ -2606,6 +2604,7 @@ public boolean parseGroupsFile(String file)
     }
     catch (Exception ex)
     {
+      ex.printStackTrace();
       System.out.println("Error parsing groups file: " + ex);
       return false;
     }