From 9111e951c482718cebd2748dbfd536b8f8f1c643 Mon Sep 17 00:00:00 2001 From: TZVanaalten Date: Sun, 13 Aug 2017 11:58:35 +0100 Subject: [PATCH] JAL-2629 fix issue where HMM sequences would be too long --- src/jalview/io/FileLoader.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 57fe83e..4f3d026 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -403,7 +403,8 @@ public class FileLoader implements Runnable if (sg != null) { seq.insertCharAt(0, sg.getStartRes(), '-'); - seq.insertCharAt(sg.getEndRes(), alignment.getWidth(), '-'); + seq.insertCharAt(sg.getEndRes(), + alignment.getWidth() - sg.getEndRes(), '-'); SequenceI topSeq = sg.getSequencesInOrder(alignment)[0]; int topIndex = alignment.findIndex(topSeq); alignment.getSequences().add(topIndex, seq); -- 1.7.10.2