From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 7 Jul 2013 11:39:43 +0000 (+0100)
Subject: JAL-583 refactor todo about separating code to construct Jmol superposition from... 
X-Git-Tag: Jalview_2_9~229^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b664e416bc329636167a511e42e2410abb59782f;p=jalview.git

JAL-583 refactor todo about separating code to construct Jmol superposition from the code that obtains the atom matching used to construct the expression
---

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 4ac247c..db1162e 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -469,6 +469,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
           }
         }
       }
+      
+      // TODO: consider bailing if nmatched less than 4 because superposition
+      // not
+      // well defined.
+      // TODO: refactor superposable position search (above) from jmol selection
+      // construction (below)
+
       String[] selcom = new String[files.length];
       int nmatched = 0;
       // generate select statements to select regions to superimpose structures
@@ -534,11 +541,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
           }
         }
       }
-      // TODO: consider bailing if nmatched less than 4 because superposition
-      // not
-      // well defined.
-      // TODO: refactor superposable position search (above) from jmol selection
-      // construction (below)
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
         if (pdbfnum == refStructure)