From de6f16e01ddb7846dc67f8f7a71ed6862d7aa986 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 13 May 2016 16:08:10 +0100 Subject: [PATCH] JAL-2103 propagate inserts only used for reconstructing profile view, currently --- src/jalview/ws/jws1/JPredWSUtils.java | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/src/jalview/ws/jws1/JPredWSUtils.java b/src/jalview/ws/jws1/JPredWSUtils.java index afdd21f..42f0268 100644 --- a/src/jalview/ws/jws1/JPredWSUtils.java +++ b/src/jalview/ws/jws1/JPredWSUtils.java @@ -205,32 +205,22 @@ public class JPredWSUtils { al.setDataset(null); } - if (fullAlignment != null) - { - // map gapMap from positions in visible sequence to positions in - // original sequence - if (predMap != null) - { - - } - } jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq, true, predMap); SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps. if (fullAlignment == null) { alignToProfileSeq(al, profileseq); - } - if (fullAlignment == null && predMap != null) - { - // Adjust input view for gaps - // propagate insertions into profile - alcsel = ColumnSelection.propagateInsertions(profileseq, al, - input); + if (predMap != null) + { + // Adjust input view for gaps + // propagate insertions into profile + alcsel = ColumnSelection.propagateInsertions(profileseq, al, + input); + } } } } - // transfer to dataset for (AlignmentAnnotation alant : al.getAlignmentAnnotation()) { -- 1.7.10.2