X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=a5775592fe0e9893b21f0ba153bc87f522101871;hb=9c66e390c2195d640a50bb645655c12158454f1e;hp=2f3464be0c7af6ec58d6e186019ec2ffc88803c2;hpb=4e1d9a661070768f2b74a8ef7925c38372ee83d6;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 2f3464b..a577559 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -307,6 +307,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * 'matched' array will hold 'true' for visible alignment columns where
        * all sequences have a residue with a mapping to the PDB structure
        */
+      // TODO could use a BitSet for matched
       boolean matched[] = new boolean[alignment.getWidth()];
       for (int m = 0; m < matched.length; m++)
       {
@@ -352,6 +353,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
        * generate select statements to select regions to superimpose structures
        */
       {
+        // TODO extract method to construct selection statements
         for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
         {
           String chainCd = ":" + structures[pdbfnum].chain;
@@ -449,6 +451,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
       if (selectioncom.length() > 0)
       {
+        // TODO is performing selectioncom redundant here? is done later on
         // System.out.println("Select regions:\n" + selectioncom.toString());
         evalStateCommand("select *; cartoons off; backbone; select ("
                 + selectioncom.toString() + "); cartoons; ");