X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=6bf701004ffafb344ff363a12828385fb9fcbc6d;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=42127497a3800840fe3d058abfe7441116f1d92d;hpb=bbbad521d82472ce439a6375603694f2137b79dd;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 4212749..6bf7010 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -25,7 +25,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
@@ -61,7 +61,7 @@ public class JmolCommands
     FeatureRenderer fr = viewPanel.getFeatureRenderer();
     FeatureColourFinder finder = new FeatureColourFinder(fr);
     AlignViewportI viewport = viewPanel.getAlignViewport();
-    ColumnSelection cs = viewport.getColumnSelection();
+    HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
     AlignmentI al = viewport.getAlignment();
     List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
 
@@ -110,25 +110,17 @@ public class JmolCommands
                */
               if (!cs.isVisible(r))
               {
-                // col = ColorUtils.darkerThan(col);
                 col = Color.GRAY;
               }
 
-              String newSelcom = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
+              String newSelcom = (mapping[m].getChain() != " "
+                      ? ":" + mapping[m].getChain()
+                      : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
+                      + col.getRed() + "," + col.getGreen() + ","
                       + col.getBlue() + "]";
-              if (command.length() > newSelcom.length()
-                      && command.substring(
-                              command.length() - newSelcom.length())
-                              .equals(newSelcom))
+              if (command.length() > newSelcom.length() && command
+                      .substring(command.length() - newSelcom.length())
+                      .equals(newSelcom))
               {
                 command = JmolCommands.condenseCommand(command, pos);
                 continue;