From c02741faf92c295a59d36e0422c1791aa74ef025 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 11:19:55 +0100
Subject: [PATCH] JAL-1551 formatting

Conflicts:
	src/MCview/PDBfile.java
---
 src/MCview/PDBfile.java |   24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 19e13e7..20b3171 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,16 +20,21 @@
  */
 package MCview;
 
-import java.io.*;
-import java.util.*;
-import java.util.List;
-import java.awt.*;
-
 import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
+
 public class PDBfile extends jalview.io.AlignFile
 {
   public Vector chains;
@@ -215,7 +220,6 @@ public class PDBfile extends jalview.io.AlignFile
         {
           for (int ai = 0; ai < chainannot.length; ai++)
           {
-
             chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
@@ -224,6 +228,7 @@ public class PDBfile extends jalview.io.AlignFile
       if (processSecondaryStructure)
       {
       if (rna.size() > 0)
+      {
         try
         {
           processPdbFileWithAnnotate3d(rna);
@@ -234,8 +239,10 @@ public class PDBfile extends jalview.io.AlignFile
           x.printStackTrace();
 
         }
+      }
       ;
       if (prot.size() > 0)
+      {
         try
         {
           processPdbFileWithJmol(prot);
@@ -247,6 +254,7 @@ public class PDBfile extends jalview.io.AlignFile
 
         }
       }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -382,7 +390,7 @@ public class PDBfile extends jalview.io.AlignFile
     for (int i = 0; i < chains.size(); i++)
     {
       ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
-              1.0f / (float) i, .4f, 1.0f));
+              1.0f / i, .4f, 1.0f));
     }
   }
 
-- 
1.7.10.2