From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 22 May 2023 15:05:17 +0000 (+0100)
Subject: JAL-4134 efficiency improvement
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=279c6495df1a0de231600a2d283098c7411c4730;p=jalview.git

JAL-4134 efficiency improvement
---

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index f6b842d..bb028bf 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1160,6 +1160,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       return;
     }
 
+    // TODO - sort indices for faster lookup
+    ColumnSelection cs = av.getColumnSelection();
+    HiddenColumns hc = av.getAlignment().getHiddenColumns();
+    ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
+    MappableContactMatrixI mcm = null;
+    int offp;
+    if (cm instanceof MappableContactMatrixI)
+    {
+      mcm = (MappableContactMatrixI) cm;
+    }
     for (BinaryNode bn : l)
     {
       int colm = -1;
@@ -1171,15 +1181,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       {
         continue;
       }
-      // TODO - sort indices for faster lookup
-      ColumnSelection cs = av.getColumnSelection();
-      HiddenColumns hc = av.getAlignment().getHiddenColumns();
-      ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
-      MappableContactMatrixI mcm = null;
-      int offp;
-      if (cm instanceof MappableContactMatrixI)
+      if (mcm!=null)
       {
-        mcm = (MappableContactMatrixI) cm;
         int[] seqpos = mcm.getMappedPositionsFor(
                 tp.assocAnnotation.sequenceRef, colm);
         if (seqpos == null)