From 0d742b24efde18a6c179affad234793dc2136ae1 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 10 Oct 2006 14:10:35 +0000 Subject: [PATCH] Calculate alWidth earlier --- src/jalview/gui/AlignViewport.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 743c8dd..7d02e14 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -280,9 +280,11 @@ public class AlignViewport { long t = System.currentTimeMillis(); + int alWidth = alignment.getWidth(); + Conservation cons = new jalview.analysis.Conservation("All", jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); + alignment.getSequences(), 0, alWidth -1); cons.calculate(); cons.verdict(false, ConsPercGaps); @@ -295,7 +297,7 @@ public class AlignViewport System.out.println("Conservation took " + (System.currentTimeMillis() - t) + "ms"); - int alWidth = alignment.getWidth(); + String sequence = cons.getConsSequence().getSequence(); float minR; float minG; -- 1.7.10.2