X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=58b69efbb07f9201dec6f1a685f62afd1ee1fa5b;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=8b67ad9d023ec23c3c1cd6cc6f1b7f2ad53f798f;hpb=c7b2143c9cf7c5e05ad63251f7d3910751b16d20;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 8b67ad9..58b69ef 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -55,7 +55,8 @@ public class JmolCommands extends StructureCommandsBase
   private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
           "select *; cartoons off; backbone");
 
-  private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
+  private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+          "zoom 0");
 
   private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
           "select *;color white;");
@@ -113,7 +114,8 @@ public class JmolCommands extends StructureCommandsBase
   }
 
   @Override
-  public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
+  public List<StructureCommandI> colourByResidues(
+          Map<String, Color> colours)
   {
     List<StructureCommandI> cmds = super.colourByResidues(colours);
     cmds.add(0, COLOUR_ALL_WHITE);
@@ -147,7 +149,8 @@ public class JmolCommands extends StructureCommandsBase
           atomSpec.append(" or ");
         }
         first = false;
-        atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
+        atomSpec.append(":").append(tokens[1]).append(" /")
+                .append(tokens[0]);
       }
     }
 
@@ -199,9 +202,11 @@ public class JmolCommands extends StructureCommandsBase
     /*
      * show residues used for superposition as ribbon
      */
-    sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
-    sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
-            .append("cartoons");
+    sb.append("select ")
+            .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
+            .append("|");
+    sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
+            .append(getCommandSeparator()).append("cartoons");
 
     return Arrays.asList(new StructureCommand(sb.toString()));
   }
@@ -228,7 +233,7 @@ public class JmolCommands extends StructureCommandsBase
   @Override
   protected StructureCommandI colourResidues(String atomSpec, Color colour)
   {
-    StringBuilder sb = new StringBuilder(atomSpec.length()+20);
+    StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
     sb.append("select ").append(atomSpec).append(getCommandSeparator())
             .append("color").append(getColourString(colour));
     return new StructureCommand(sb.toString());
@@ -294,8 +299,8 @@ public class JmolCommands extends StructureCommandsBase
   public StructureCommandI loadFile(String file)
   {
     // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
-    return new StructureCommand("load FILES \"" + 
-            Platform.escapeBackslashes(file) + "\"");
+    return new StructureCommand(
+            "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
   }
 
   /**
@@ -434,8 +439,7 @@ public class JmolCommands extends StructureCommandsBase
    * @return
    */
   @Deprecated
-  private static StringBuilder condenseCommand(
-          StringBuilder command,
+  private static StringBuilder condenseCommand(StringBuilder command,
           int pos)
   {