From 2d3be0b3f26fa3e35480976cd5a90a5562d43dcf Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 27 Jun 2017 14:03:09 +0100 Subject: [PATCH] JAL-2602 check for null or empty description when copying consensus --- src/jalview/gui/AlignViewport.java | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 86e1144..288f261 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -34,6 +34,7 @@ import jalview.commands.CommandI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; @@ -330,15 +331,18 @@ public class AlignViewport extends AlignmentViewport implements StringBuffer seqs = new StringBuffer(); for (int i = 0; i < consensus.annotations.length; i++) { - if (consensus.annotations[i] != null) + Annotation annotation = consensus.annotations[i]; + if (annotation != null) { - if (consensus.annotations[i].description.charAt(0) == '[') + String description = annotation.description; + if (description != null && description.startsWith("[")) { - seqs.append(consensus.annotations[i].description.charAt(1)); + // consensus is a tie - just pick the first one + seqs.append(description.charAt(1)); } else { - seqs.append(consensus.annotations[i].displayCharacter); + seqs.append(annotation.displayCharacter); } } } -- 1.7.10.2