formatting

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 35e0ea5..a76a27e 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -28,37 +28,43 @@ import jalview.datamodel.*;
 
 public class StructureSelectionManager
 {
-  static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
+  static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
 
   StructureMapping[] mappings;
 
   /**
    * debug function - write all mappings to stdout
    */
-  public void reportMapping() {\r
-    if (mappings==null)\r
-    {\r
-      System.err.println("reportMapping: No PDB/Sequence mappings.");\r
-    }else{\r
-      System.err.println("reportMapping: There are "+mappings.length+" mappings.");\r
-      for (int m=0;m<mappings.length;m++)\r
-      {\r
-        System.err.println("mapping "+m+" : "+mappings[m].pdbfile);\r
-      }\r
-    }\r
-  }\r
+  public void reportMapping()
+  {
+    if (mappings == null)
+    {
+      System.err.println("reportMapping: No PDB/Sequence mappings.");
+    }
+    else
+    {
+      System.err.println("reportMapping: There are " + mappings.length
+              + " mappings.");
+      for (int m = 0; m < mappings.length; m++)
+      {
+        System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
+      }
+    }
+  }
+
   Hashtable mappingData = new Hashtable();
 
-  public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
+  public static StructureSelectionManager getStructureSelectionManager(
+          StructureSelectionManagerProvider context)
   {
     if (instances == null)
     {
-      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+      instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
     }
-    StructureSelectionManager instance=instances.get(context);
-    if (instance==null)
+    StructureSelectionManager instance = instances.get(context);
+    if (instance == null)
     {
-      instances.put(context, instance=new StructureSelectionManager());
+      instances.put(context, instance = new StructureSelectionManager());
     }
     return instance;
   }
@@ -96,6 +102,7 @@ public class StructureSelectionManager
 
   /**
    * register a listener for alignment sequence mouseover events
+   * 
    * @param svl
    */
   public void addStructureViewerListener(Object svl)
@@ -152,7 +159,7 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-    
+
     String targetChain;
     for (int s = 0; s < sequence.length; s++)
     {
@@ -190,7 +197,8 @@ public class StructureSelectionManager
       for (int i = 0; i < pdb.chains.size(); i++)
       {
         PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
-        if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
+        if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+                && !infChain)
         {
           continue; // don't try to map chains don't match.
         }
@@ -249,7 +257,8 @@ public class StructureSelectionManager
 
       // allocate enough slots to store the mapping from positions in
       // sequence[s] to the associated chain
-      int[][] mapping = new int[sequence[s].findPosition(sequence[s].getLength()) + 2][2];
+      int[][] mapping = new int[sequence[s].findPosition(sequence[s]
+              .getLength()) + 2][2];
       int resNum = -10000;
       int index = 0;
 
@@ -295,15 +304,16 @@ public class StructureSelectionManager
     listeners.removeElement(svl);
     if (svl instanceof SequenceListener)
     {
-      for (int i=0;i<listeners.size();i++)
+      for (int i = 0; i < listeners.size(); i++)
       {
         if (listeners.elementAt(i) instanceof StructureListener)
         {
-          ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+          ((StructureListener) listeners.elementAt(i))
+                  .releaseReferences(svl);
         }
       }
     }
-      
+
     if (pdbfiles == null)
     {
       return;
@@ -349,7 +359,7 @@ public class StructureSelectionManager
 
   public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
   {
-    if (listeners==null)
+    if (listeners == null)
     {
       // old or prematurely sent event
       return;
@@ -398,7 +408,7 @@ public class StructureSelectionManager
         }
       }
     }
-    if (results!=null)
+    if (results != null)
     {
       for (int i = 0; i < listeners.size(); i++)
       {
@@ -433,8 +443,8 @@ public class StructureSelectionManager
     int atomNo = 0;
     for (int i = 0; i < listeners.size(); i++)
     {
-      Object listener=listeners.elementAt(i);
-      if (listener==source)
+      Object listener = listeners.elementAt(i);
+      if (listener == source)
       {
         continue;
       }
@@ -498,12 +508,10 @@ public class StructureSelectionManager
           }
           if (hasSequenceListeners)
           {
-            ((SequenceListener) listener)
-                    .highlightSequence(results);
+            ((SequenceListener) listener).highlightSequence(results);
           }
         }
-        else if (listener instanceof VamsasListener
-                && !handlingVamsasMo)
+        else if (listener instanceof VamsasListener && !handlingVamsasMo)
         {
           // DEBUG
           // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
@@ -511,11 +519,12 @@ public class StructureSelectionManager
           // index);
           // pass the mouse over and absolute position onto the
           // VamsasListener(s)
-          ((VamsasListener) listener).mouseOver(seq,
-                  indexpos, source);
+          ((VamsasListener) listener).mouseOver(seq, indexpos, source);
         }
-        else if(listener instanceof SecondaryStructureListener){
-               ((SecondaryStructureListener) listener).mouseOverSequence(seq,indexpos);
+        else if (listener instanceof SecondaryStructureListener)
+        {
+          ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+                  indexpos);
         }
       }
     }
@@ -744,19 +753,21 @@ public class StructureSelectionManager
       }
     }
   }
-  
-  Vector<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
-  public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes,
-          int endRes, int startSeq, int endSeq)
+
+  Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
+
+  public synchronized void sendViewPosition(
+          jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+          int startSeq, int endSeq)
   {
 
     if (view_listeners != null && view_listeners.size() > 0)
     {
-      Enumeration<AlignmentViewPanelListener> listeners = view_listeners.elements();
+      Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+              .elements();
       while (listeners.hasMoreElements())
       {
-        AlignmentViewPanelListener slis = listeners
-                .nextElement();
+        AlignmentViewPanelListener slis = listeners.nextElement();
         if (slis != source)
         {
           slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
@@ -765,39 +776,41 @@ public class StructureSelectionManager
       }
     }
   }
-  
 
-  public void finalize() throws Throwable {
-    if (listeners!=null) {
+  public void finalize() throws Throwable
+  {
+    if (listeners != null)
+    {
       listeners.clear();
-      listeners=null;
+      listeners = null;
     }
-    if (mappingData!=null)
+    if (mappingData != null)
     {
       mappingData.clear();
-      mappingData=null;
+      mappingData = null;
     }
-    if (sel_listeners!=null)
+    if (sel_listeners != null)
     {
       sel_listeners.clear();
-      sel_listeners=null;
+      sel_listeners = null;
     }
-    if (view_listeners!=null)
+    if (view_listeners != null)
     {
       view_listeners.clear();
-      view_listeners=null;
+      view_listeners = null;
     }
-    mappings=null;
-    seqmappingrefs=null;
+    mappings = null;
+    seqmappingrefs = null;
   }
 
   /**
    * release all references associated with this manager provider
+   * 
    * @param jalviewLite
    */
   public static void release(StructureSelectionManagerProvider jalviewLite)
   {
-//    synchronized (instances)
+    // synchronized (instances)
     {
       if (instances == null)
       {