From 5961bc45666de0159c3d3529abf0aad680e29a5d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 13 May 2016 16:06:06 +0100 Subject: [PATCH] JAL-2103 always remove gaps from input sequence, then add in hidden regions if recovering full-width alignment --- src/jalview/ws/jws1/JPredWSUtils.java | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/src/jalview/ws/jws1/JPredWSUtils.java b/src/jalview/ws/jws1/JPredWSUtils.java index 2d562e9..afdd21f 100644 --- a/src/jalview/ws/jws1/JPredWSUtils.java +++ b/src/jalview/ws/jws1/JPredWSUtils.java @@ -168,18 +168,23 @@ public class JPredWSUtils MessageManager .getString("error.implementation_error_invalid_msa_index_for_job")); } + // // + // Uses RemoveGapsCommand + // // + new jalview.commands.RemoveGapsCommand( + MessageManager.getString("label.remove_gaps"), + new SequenceI[] { sqs[msaIndex] }, currentView); if (fullAlignment == null) { - // // - // Uses RemoveGapsCommand - // // - new jalview.commands.RemoveGapsCommand( - MessageManager.getString("label.remove_gaps"), - new SequenceI[] { sqs[msaIndex] }, currentView); - + // just replace trimmed sequence in prediction profile with full + // length sequence SequenceI profileseq = al.getSequenceAt(FirstSeq); profileseq.setSequence(sqs[msaIndex].getSequenceAsString()); } + else + { + insertHiddenResidues(al, '.', predMap, sqs[msaIndex]); + } } if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash( -- 1.7.10.2