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 (executable)
--- 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());\r
 \r
           seq = viewport.alignment.getSequenceAt(index);\r
-          start = seq.findIndex(start) - 1;\r
-          end = seq.findIndex(end) - 1;\r
 \r
           type = st.nextToken();\r
 \r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3319b33..5778a7e 100755 (executable)
--- 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());\r
 \r
           seq = viewport.alignment.getSequenceAt(index);\r
-          start = seq.findIndex(start) - 1;\r
-          end = seq.findIndex(end) - 1;\r
 \r
           type = st.nextToken();\r
 \r
@@ -2606,6 +2604,7 @@ public boolean parseGroupsFile(String file)
     }\r
     catch (Exception ex)\r
     {\r
+      ex.printStackTrace();\r
       System.out.println("Error parsing groups file: " + ex);\r
       return false;\r
     }\r