JAL-4134 properly resolve positions in associated aligned sequence for matrix group...

[jalview.git] / src / jalview / gui / TreeCanvas.java

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 2bdfc27..55ce44a 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1148,14 +1148,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (aa != null)
     {
       ContactMatrixI cm = av.getContactMatrix(aa);
+      // generally, we assume cm has 1:1 mapping to annotation row - probably wrong
+      // but.. if
       if (cm instanceof MappableContactMatrixI)
       {
+        int[] pos;
+          // use the mappable's mapping - always the case for PAE Matrices so good
+        // for 2.11.3
         MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
-        int pos[]=mcm.getMappedPositionsFor(rseq, colm+1);
-        if (pos!=null)
+        pos = mcm.getMappedPositionsFor(rseq, colm + 1);
+        // finally, look up the position of the column
+        if (pos != null)
         {
-          offp=rseq.findIndex(pos[0]);
+          offp = rseq.findIndex(pos[0]);
         }
+      } else {
+        offp = colm;
       }
     }
     if (offp<=0)