From 301974b9fb0b89dbe5a931371084fc2936905f38 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 22 Jan 2008 16:14:54 +0000 Subject: [PATCH] ensured that seqeunce feature shift takes into account start position difference w.r.t. db seqeunce --- src/jalview/ws/DBRefFetcher.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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); } } } -- 1.7.10.2