From ae2aad01e22e7b6e300bbbd7c3a1ef15ec022b9f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 21 Nov 2014 08:55:38 +0000 Subject: [PATCH 1/1] JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA structure with one call to .isValidStructure() --- src/jalview/datamodel/AlignmentAnnotation.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 8a44535..c77cbdb 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -75,9 +75,10 @@ public class AlignmentAnnotation public SequenceFeature[] _rnasecstr = null; /** - * position of annotation resulting in invalid WUSS parsing or -1 + * position of annotation resulting in invalid WUSS parsing or -1. -2 means + * there was no RNA structure in this annotation */ - private long invalidrnastruc = -1; + private long invalidrnastruc = -2; /** * Updates the _rnasecstr field Determines the positions that base pair and @@ -141,8 +142,8 @@ public class AlignmentAnnotation annotations[_rnasecstr[x].getBegin()].value = val; annotations[_rnasecstr[x].getEnd()].value = val; - annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val; - annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val; + // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val; + // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val; } } /** -- 1.7.10.2