From a9f80616357f04492852a963a610f98657c63533 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 21 Apr 2014 16:06:30 +0100 Subject: [PATCH] JAL-1484 always update the dataset sequence if 'trimDatasetSeqs' option is not set. --- src/jalview/ws/DBRefFetcher.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index d742eaa..84eba02 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -658,6 +658,11 @@ public class DBRefFetcher implements Runnable // unknownSequences.remove(sequence); int absEnd = absStart + nonGapped.length(); absStart += 1; + if (!trimDatasetSeqs) { + // insert full length sequence from record + sequence.setSequence(entry.getSequenceAsString()); + sequence.setStart(entry.getStart()); + } if (updateRefFrame) { // finally, update local sequence reference frame if we're allowed @@ -665,9 +670,6 @@ public class DBRefFetcher implements Runnable // just fix start/end sequence.setStart(absStart); sequence.setEnd(absEnd); - } else { - // insert full length sequence from record - sequence.setSequence(entry.getSequenceAsString()); } // search for alignment sequences to update coordinate frame for for (int alsq = 0; alsq < alseqs.length; alsq++) -- 1.7.10.2