From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 30 Aug 2017 16:48:55 +0000 (+0100)
Subject: JAL-2694 formatting
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=968af817beecb629eb8bb0c34901e3080bcd9794;p=jalview.git

JAL-2694 formatting
---

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 83a055e..9020ed4 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -66,7 +66,7 @@ public class StructureSelectionManager
 
   static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
 
-  private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
+  private List<StructureMapping> mappings = new ArrayList<>();
 
   private boolean processSecondaryStructure = false;
 
@@ -83,11 +83,11 @@ public class StructureSelectionManager
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
-  private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> seqmappings = new ArrayList<>();
 
-  private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+  private List<CommandListener> commandListeners = new ArrayList<>();
 
-  private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
+  private List<SelectionListener> sel_listeners = new ArrayList<>();
 
   /**
    * @return true if will try to use external services for processing secondary
@@ -175,9 +175,9 @@ public class StructureSelectionManager
    * map between the PDB IDs (or structure identifiers) used by Jalview and the
    * absolute filenames for PDB data that corresponds to it
    */
-  Map<String, String> pdbIdFileName = new HashMap<String, String>();
+  Map<String, String> pdbIdFileName = new HashMap<>();
 
-  Map<String, String> pdbFileNameId = new HashMap<String, String>();
+  Map<String, String> pdbFileNameId = new HashMap<>();
 
   public void registerPDBFile(String idForFile, String absoluteFile)
   {
@@ -228,7 +228,7 @@ public class StructureSelectionManager
     }
     if (instances == null)
     {
-      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
+      instances = new java.util.IdentityHashMap<>();
     }
     StructureSelectionManager instance = instances.get(context);
     if (instance == null)
@@ -724,7 +724,7 @@ public class StructureSelectionManager
             .getMappingFromS1(false);
     maxChain.transferRESNUMFeatures(seq, null);
 
-    HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+    HashMap<Integer, int[]> mapping = new HashMap<>();
     int resNum = -10000;
     int index = 0;
     char insCode = ' ';
@@ -780,7 +780,7 @@ public class StructureSelectionManager
      * Remove mappings to the closed listener's PDB files, but first check if
      * another listener is still interested
      */
-    List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
+    List<String> pdbs = new ArrayList<>(Arrays.asList(pdbfiles));
 
     StructureListener sl;
     for (int i = 0; i < listeners.size(); i++)
@@ -801,7 +801,7 @@ public class StructureSelectionManager
      */
     if (pdbs.size() > 0)
     {
-      List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+      List<StructureMapping> tmp = new ArrayList<>();
       for (StructureMapping sm : mappings)
       {
         if (!pdbs.contains(sm.pdbfile))
@@ -995,7 +995,7 @@ public class StructureSelectionManager
       return;
     }
     int atomNo;
-    List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+    List<AtomSpec> atoms = new ArrayList<>();
     for (StructureMapping sm : mappings)
     {
       if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
@@ -1103,7 +1103,7 @@ public class StructureSelectionManager
 
   public StructureMapping[] getMapping(String pdbfile)
   {
-    List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+    List<StructureMapping> tmp = new ArrayList<>();
     for (StructureMapping sm : mappings)
     {
       if (sm.pdbfile.equals(pdbfile))
@@ -1263,7 +1263,7 @@ public class StructureSelectionManager
     }
   }
 
-  Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+  Vector<AlignmentViewPanelListener> view_listeners = new Vector<>();
 
   public synchronized void sendViewPosition(
           jalview.api.AlignmentViewPanel source, int startRes, int endRes,