From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 7 Jan 2015 17:57:43 +0000 (+0000)
Subject: JAL-1483 source formatting
X-Git-Tag: Jalview_2_9~123^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aca60fdee290e47c3102c8ef118bb76801fb40ba;p=jalview.git

JAL-1483 source formatting
---

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index f08a436..099400e 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -867,12 +867,12 @@ public class NJTree
     {
       System.out
               .println("Leaf = " + ((SequenceI) node.element()).getName());
-      System.out.println("Dist " + ((SequenceNode) node).dist);
+      System.out.println("Dist " + node.dist);
       System.out.println("Boot " + node.getBootstrap());
     }
     else
     {
-      System.out.println("Dist " + ((SequenceNode) node).dist);
+      System.out.println("Dist " + node.dist);
       printNode((SequenceNode) node.left());
       printNode((SequenceNode) node.right());
     }
@@ -893,11 +893,11 @@ public class NJTree
 
     if ((node.left() == null) && (node.right() == null))
     {
-      float dist = ((SequenceNode) node).dist;
+      float dist = node.dist;
 
       if (dist > maxDistValue)
       {
-        maxdist = (SequenceNode) node;
+        maxdist = node;
         maxDistValue = dist;
       }
     }
@@ -1099,9 +1099,9 @@ public class NJTree
               + ((SequenceI) node.element()).getName());
     }
 
-    System.out.println(" dist = " + ((SequenceNode) node).dist + " "
-            + ((SequenceNode) node).count + " "
-            + ((SequenceNode) node).height);
+    System.out.println(" dist = " + node.dist + " "
+            + node.count + " "
+            + node.height);
   }
 
   /**
@@ -1147,13 +1147,13 @@ public class NJTree
       SequenceNode l = (SequenceNode) node.left();
       SequenceNode r = (SequenceNode) node.right();
 
-      ((SequenceNode) node).count = l.count + r.count;
-      ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+      node.count = l.count + r.count;
+      node.ycount = (l.ycount + r.ycount) / 2;
     }
     else
     {
-      ((SequenceNode) node).count = 1;
-      ((SequenceNode) node).ycount = ycount++;
+      node.count = 1;
+      node.ycount = ycount++;
     }
     _lycount--;
   }
@@ -1292,7 +1292,9 @@ public class NJTree
   {
     for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
             .transform((BinaryNode) nodes.nextElement()))
+    {
       ;
+    }
   }
 }
 
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 9530dd1..655e182 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -219,8 +219,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       {
         int start, end;
         SequenceI[] seqs;
-        boolean selview = (av.getSelectionGroup() != null)
-                && (av.getSelectionGroup().getSize() > 1);
+        boolean selview = av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() > 1;
         AlignmentView seqStrings = av.getAlignmentView(selview);
         if (!selview)
         {