From 59c8d9d6d8d42c579dc5ab6bfc37902ff4bd118f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 20 Nov 2014 14:54:01 +0000 Subject: [PATCH] JAL-1569 rna pair code in secondary structure character of annotation --- src/jalview/datamodel/AlignmentAnnotation.java | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 0207575..8a44535 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -486,11 +486,10 @@ public class AlignmentAnnotation @Override public char charAt(int index) { - String dc; return ((index + offset < 0) || (index + offset) >= max - || annotations[index + offset] == null || (dc = annotations[index - + offset].displayCharacter.trim()).length() < 1) ? '.' : dc - .charAt(0); + || annotations[index + offset] == null || (annotations[index + + offset].secondaryStructure < ' ') ? ' ' + : annotations[index + offset].secondaryStructure); } public String toString() @@ -500,9 +499,8 @@ public class AlignmentAnnotation for (int i = offset; i < mx; i++) { - String dc; - string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter - .trim()).length() < 1) ? '.' : dc.charAt(0); + string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' ' + : annotations[i].secondaryStructure; } return new String(string); } -- 1.7.10.2