JAL-2418 source formatting

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 3ae7593..00446f2 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -79,7 +79,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   private List<String> chainNames = new ArrayList<String>();
 
   private Hashtable<String, String> chainFile = new Hashtable<String, String>();
-  
+
   /*
    * Object through which we talk to Chimera
    */
@@ -172,8 +172,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       if (getSsm() != null)
       {
         getSsm().addStructureViewerListener(this);
-        // ssm.addSelectionListener(this);
-        refreshGUI();
       }
       return true;
     } catch (Exception q)
@@ -194,7 +192,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param protocol
    */
   public JalviewChimeraBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
     super(ssm, pdbentry, sequenceIs, protocol);
     viewer = new ChimeraManager(new StructureManager(true));
@@ -243,8 +242,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       viewer.startListening(chimeraListener.getUri());
     } catch (BindException e)
     {
-      System.err.println("Failed to start Chimera listener: "
-              + e.getMessage());
+      System.err.println(
+              "Failed to start Chimera listener: " + e.getMessage());
     }
   }
 
@@ -265,8 +264,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     for (String chain : toshow)
     {
       int modelNumber = getModelNoForChain(chain);
-      String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
-              + chain.split(":")[1];
+      String showChainCmd = modelNumber == -1 ? ""
+              : modelNumber + ":." + chain.split(":")[1];
       if (!first)
       {
         cmd.append(",");
@@ -291,7 +290,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void closeViewer(boolean closeChimera)
   {
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     if (closeChimera)
     {
       viewer.exitChimera();
@@ -342,7 +341,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           int[] _refStructure, HiddenColumns[] _hiddenCols)
   {
     StringBuilder allComs = new StringBuilder(128);
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
 
     if (!waitForFileLoad(files))
     {
@@ -517,8 +516,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
         if (debug)
         {
           System.out.println("Select regions:\n" + selectioncom.toString());
-          System.out.println("Superimpose command(s):\n"
-                  + command.toString());
+          System.out.println(
+                  "Superimpose command(s):\n" + command.toString());
         }
         allComs.append("~display all; chain @CA|P; ribbon ")
                 .append(selectioncom.toString())
@@ -579,7 +578,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * to the Chimera command 'list models type molecule', see
      * ChimeraManager.getModelList().
      */
-    List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+    List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
     boolean hasSubModels = maps != null && maps.size() > 1;
     return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
   }
@@ -598,8 +597,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       return true;
     }
 
-    boolean launched = viewer.launchChimera(StructureManager
-            .getChimeraPaths());
+    boolean launched = viewer
+            .launchChimera(StructureManager.getChimeraPaths());
     if (launched)
     {
       startChimeraProcessMonitor();
@@ -743,19 +742,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
-
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public synchronized String[] getPdbFile()
+  public synchronized String[] getStructureFiles()
   {
     if (viewer == null)
     {
       return new String[0];
     }
 
-    return chimeraMaps.keySet().toArray(
-            modelFileNames = new String[chimeraMaps.size()]);
+    return chimeraMaps.keySet()
+            .toArray(modelFileNames = new String[chimeraMaps.size()]);
   }
 
   /**
@@ -839,7 +837,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * Parse model number, residue and chain for each selected position,
      * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
      */
-    List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
+    List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
+            selection);
 
     /*
      * Broadcast the selection (which may be empty, if the user just cleared all
@@ -934,12 +933,13 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
             false);
     for (String resName : residueSet)
     {
-      char res = resName.length() == 3 ? ResidueProperties
-              .getSingleCharacterCode(resName) : resName.charAt(0);
+      char res = resName.length() == 3
+              ? ResidueProperties.getSingleCharacterCode(resName)
+              : resName.charAt(0);
       Color col = cs.findColour(res, 0, null, null, 0f);
       command.append("color " + col.getRed() / normalise + ","
-              + col.getGreen() / normalise + "," + col.getBlue()
-              / normalise + " ::" + resName + ";");
+              + col.getGreen() / normalise + "," + col.getBlue() / normalise
+              + " ::" + resName + ";");
     }
 
     sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
@@ -985,7 +985,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /**
    * Send the Chimera 'background solid <color>" command.
    * 
-   * @see https 
+   * @see https
    *      ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
    *      .html
    * @param col
@@ -996,8 +996,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     viewerCommandHistory(false);
     double normalise = 255D;
     final String command = "background solid " + col.getRed() / normalise
-            + "," + col.getGreen() / normalise + "," + col.getBlue()
-            / normalise + ";";
+            + "," + col.getGreen() / normalise + ","
+            + col.getBlue() / normalise + ";";
     viewer.sendChimeraCommand(command, false);
     viewerCommandHistory(true);
   }
@@ -1102,7 +1102,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     // TODO refactor as required to pull up to an interface
     AlignmentI alignment = avp.getAlignment();
 
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return 0;
@@ -1150,9 +1150,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       sendAsynchronousCommand("open cmd:" + path, null);
     } catch (IOException e)
     {
-      System.err
-              .println("Sending commands to Chimera via file failed with "
-                      + e.getMessage());
+      System.err.println("Sending commands to Chimera via file failed with "
+              + e.getMessage());
     }
   }
 
@@ -1290,7 +1289,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     return CHIMERA_FEATURE_GROUP;
   }
 
-
   public Hashtable<String, String> getChainFile()
   {
     return chainFile;