From cc6f7ebe59c148e62cd9f1947d9ba30638db2980 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 13 Feb 2006 15:26:40 +0000 Subject: [PATCH] Parsing features file - dont adjust for alignment position --- src/jalview/appletgui/AlignFrame.java | 2 -- src/jalview/gui/AlignFrame.java | 3 +-- 2 files changed, 1 insertion(+), 4 deletions(-) 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; } -- 1.7.10.2