From: jprocter <Jim Procter>
Date: Tue, 22 Jan 2008 16:14:54 +0000 (+0000)
Subject: ensured that seqeunce feature shift takes into account start position difference... 
X-Git-Tag: Release_2_4~147
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=301974b9fb0b89dbe5a931371084fc2936905f38;p=jalview.git

ensured that seqeunce feature shift takes into account start position difference w.r.t. db seqeunce
---

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index c2d7ad5..ba6d57f 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -438,13 +438,14 @@ public class DBRefFetcher implements Runnable
             SequenceFeature[] sf = sequence.getSequenceFeatures();
             int start = sequence.getStart();
             int end = sequence.getEnd();
+            int startShift = 1-absStart-start; // how much the features are to be shifted by
             for (int sfi = 0; sfi < sf.length; sfi++)
             {
               if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
               {
                 // shift feature along by absstart
-                sf[sfi].setBegin(sf[sfi].getBegin() + absStart);
-                sf[sfi].setEnd(sf[sfi].getEnd() + absStart);
+                sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
+                sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
               }
             }
           }