From ee1c37b3e5d47128cb71ec2aa51c6e4a69dddbbe Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 20 Apr 2012 16:04:38 +0100 Subject: [PATCH] (JAL-1071) hacked the square matrix that stores the interacting pairs to allow 36 types of base pair rather than 25 (so self-pair interactions can be counted too) --- src/jalview/analysis/StructureFrequency.java | 2 +- src/jalview/renderer/AnnotationRenderer.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 0c9f830..5f85916 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -406,7 +406,7 @@ public class StructureFrequency public static int[] extractProfile(Hashtable hconsensus, boolean ignoreGapsInConsensusCalculation) { - int[] rtnval = new int[52]; // 2*(5*5)+2 + int[] rtnval = new int[74]; // 2*(5*5)+2 int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE); int[][] pairs = (int[][]) hconsensus .get(StructureFrequency.PAIRPROFILE); diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index d063c5b..476d7f7 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -863,7 +863,7 @@ public class AnnotationRenderer * Therefore dc gets length 2, to have space for a basepair instead of * just a single nucleotide */ - if (profl.length == 52) + if (profl.length == 74) { dc = new char[2]; } -- 1.7.10.2