JAL-4090 JAL-1551 spotlessApply

[jalview.git] / src / jalview / gui / StructureViewerBase.java

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 085be71..bd757e8 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -90,8 +90,9 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
-   * Singleton list of all (open) instances of structureViewerBase
-   * TODO: JAL-3362 - review and adopt the swingJS-safe singleton pattern so each structure viewer base instance is kept to its own JalviewJS parent
+   * Singleton list of all (open) instances of structureViewerBase TODO:
+   * JAL-3362 - review and adopt the swingJS-safe singleton pattern so each
+   * structure viewer base instance is kept to its own JalviewJS parent
    */
   private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
 
@@ -607,7 +608,8 @@ public abstract class StructureViewerBase extends GStructureViewer
       chainMenu.add(menuItem);
     }
   }
-  void setHetatmMenuItems(Map<String,String> hetatmNames)
+
+  void setHetatmMenuItems(Map<String, String> hetatmNames)
   {
     hetatmMenu.removeAll();
     if (hetatmNames == null || hetatmNames.isEmpty())
@@ -616,7 +618,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       return;
     }
     hetatmMenu.setVisible(true);
-    allHetatmBeingSelected=false;
+    allHetatmBeingSelected = false;
     JMenuItem allMenuItem = new JMenuItem(
             MessageManager.getString("label.all"));
     JMenuItem noneMenuItem = new JMenuItem(
@@ -624,46 +626,52 @@ public abstract class StructureViewerBase extends GStructureViewer
     allMenuItem.addActionListener(new ActionListener()
     {
       @Override
-      public void actionPerformed(ActionEvent e) {
+      public void actionPerformed(ActionEvent e)
       {
-        allHetatmBeingSelected=true;
-        // Toggle state of everything - on
-        for (int i = 0; i < hetatmMenu.getItemCount(); i++)
         {
-          if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+          allHetatmBeingSelected = true;
+          // Toggle state of everything - on
+          for (int i = 0; i < hetatmMenu.getItemCount(); i++)
           {
-            ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+            if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            {
+              ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+            }
           }
+          allHetatmBeingSelected = false;
+          showSelectedHetatms();
         }
-        allHetatmBeingSelected=false;
-        showSelectedHetatms();
       }
-      }});
+    });
 
     noneMenuItem.addActionListener(new ActionListener()
     {
       @Override
-      public void actionPerformed(ActionEvent e) {
+      public void actionPerformed(ActionEvent e)
       {
-        allHetatmBeingSelected=true;
-        // Toggle state of everything off
-        for (int i = 0; i < hetatmMenu.getItemCount(); i++)
         {
-          if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+          allHetatmBeingSelected = true;
+          // Toggle state of everything off
+          for (int i = 0; i < hetatmMenu.getItemCount(); i++)
           {
-            ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(false);
+            if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+            {
+              ((JCheckBoxMenuItem) hetatmMenu.getItem(i))
+                      .setSelected(false);
+            }
           }
+          allHetatmBeingSelected = false;
+          showSelectedHetatms();
         }
-        allHetatmBeingSelected=false;
-        showSelectedHetatms();
       }
-      }});
+    });
     hetatmMenu.add(noneMenuItem);
     hetatmMenu.add(allMenuItem);
 
     for (Map.Entry<String, String> chain : hetatmNames.entrySet())
     {
-      JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(), false);
+      JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(),
+              false);
       menuItem.setToolTipText(chain.getValue());
       menuItem.addItemListener(new ItemListener()
       {
@@ -671,7 +679,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         public void itemStateChanged(ItemEvent evt)
         {
           if (!allHetatmBeingSelected)
-          { 
+          {
             // update viewer only when we were clicked, not programmatically
             // checked/unchecked
             showSelectedHetatms();
@@ -1237,6 +1245,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
     getBinding().showChains(toshow);
   }
+
   /**
    * Display selected hetatms in viewer
    */
@@ -1256,6 +1265,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
     getBinding().showHetatms(toshow);
   }
+
   /**
    * Tries to fetch a PDB file and save to a temporary local file. Returns the
    * saved file path if successful, or null if not.
@@ -1459,12 +1469,15 @@ public abstract class StructureViewerBase extends GStructureViewer
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     // jmb = null;
-    
-    try {
+
+    try
+    {
       svbs.remove(this);
     } catch (Throwable t)
     {
-      Console.info("Unexpected exception when deregistering structure viewer",t);
+      Console.info(
+              "Unexpected exception when deregistering structure viewer",
+              t);
     }
     dispose();
   }