JAL-1645 source formatting and organise imports

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 729780c..b464c94 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -231,10 +231,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void superposeStructures(AlignmentI alignment, int refStructure,
           ColumnSelection hiddenCols)
   {
-    superposeStructures(new AlignmentI[]
-    { alignment }, new int[]
-    { refStructure }, new ColumnSelection[]
-    { hiddenCols });
+    superposeStructures(new AlignmentI[] { alignment },
+            new int[] { refStructure },
+            new ColumnSelection[] { hiddenCols });
   }
 
   /**
@@ -458,8 +457,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
                 + selectioncom.toString() + "); cartoons; ");
         // selcom.append("; ribbons; ");
         String cmdString = command.toString();
-        System.out
-.println("Superimpose command(s):\n" + cmdString);
+        System.out.println("Superimpose command(s):\n" + cmdString);
 
         evalStateCommand(cmdString);
       }
@@ -516,7 +514,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     AlignmentI alignment = alignmentv.getAlignment();
 
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+            files, sr, fr, alignment))
     {
       for (String cbyseq : cpdbbyseq.commands)
       {
@@ -536,10 +535,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           String[] files, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
   {
-    return JmolCommands
-            .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
-                    fr,
-                    alignment);
+    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+            getSequence(), sr, fr, alignment);
   }
 
   /**
@@ -592,8 +589,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     // TODO: verify atomIndex is selecting correct model.
     // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
-    int colour = viewer.ms.at[atomIndex]
-            .atomPropertyInt(T.color);
+    int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
     return new Color(colour);
   }
 
@@ -891,8 +887,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         pdbfilename = modelFileNames[_mp];
         if (pdbfilename == null)
         {
-          pdbfilename = new File(
-                  viewer.ms.getModelFileName(mnumber))
+          pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
                   .getAbsolutePath();
         }
 
@@ -1135,8 +1130,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
                 + ".0", "PDB");
       }
-        // search pdbentries and sequences to find correct pdbentry for this
-        // model
+      // search pdbentries and sequences to find correct pdbentry for this
+      // model
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
@@ -1460,4 +1455,3 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     showConsole(false);
   }
 }
-