From a79d9d9c5d2e79f5d86bb7fcabf897a34d48dd13 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 24 Nov 2014 16:01:33 +0000 Subject: [PATCH] JAL-1595 annotation score is total number of rna helices --- src/jalview/datamodel/AlignmentAnnotation.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index c77cbdb..e137225 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -119,6 +119,7 @@ public class AlignmentAnnotation private void _markRnaHelices() { + int mxval = 0; // Figure out number of helices // Length of rnasecstr is the number of pairs of positions that base pair // with each other in the secondary structure @@ -134,6 +135,10 @@ public class AlignmentAnnotation try { val = Integer.valueOf(_rnasecstr[x].getFeatureGroup()); + if (mxval < val) + { + mxval = val; + } } catch (NumberFormatException q) { } @@ -145,6 +150,7 @@ public class AlignmentAnnotation // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val; // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val; } + setScore(mxval); } /** * map of positions in the associated annotation -- 1.7.10.2