From 3a2eea48af60359b187c5dd0b95cbd29a64cb62b Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 09:34:15 +0100
Subject: [PATCH] JAL-1551 source formatting

---
 src/jalview/datamodel/AlignmentAnnotation.java |   29 ++++++++++++++++++------
 1 file changed, 22 insertions(+), 7 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 012ecb3..c0d911e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -22,17 +22,13 @@ package jalview.datamodel;
 
 import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
-
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
-import java.util.Map;
 import java.util.Map.Entry;
 
-import fr.orsay.lri.varna.models.rna.RNA;
-
 /**
  * DOCUMENT ME!
  * 
@@ -261,7 +257,8 @@ public class AlignmentAnnotation
       // Check for RNA secondary structure
       {
         // System.out.println(annotations[i].secondaryStructure);
-        // TODO: 2.8.2 should this ss symbol validation check be a function in RNA/ResidueProperties ?
+        // TODO: 2.8.2 should this ss symbol validation check be a function in
+        // RNA/ResidueProperties ?
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
@@ -604,7 +601,9 @@ public class AlignmentAnnotation
   {
     this.label = new String(annotation.label);
     if (annotation.description != null)
+    {
       this.description = new String(annotation.description);
+    }
     this.graphMin = annotation.graphMin;
     this.graphMax = annotation.graphMax;
     this.graph = annotation.graph;
@@ -659,7 +658,7 @@ public class AlignmentAnnotation
           {
             // could optimise this!
             p = (Integer) pos.nextElement();
-            Annotation a = (Annotation) annotation.sequenceMapping.get(p);
+            Annotation a = annotation.sequenceMapping.get(p);
             if (a == null)
             {
               continue;
@@ -702,13 +701,21 @@ public class AlignmentAnnotation
       return;
     }
     if (startRes < 0)
+    {
       startRes = 0;
+    }
     if (startRes >= annotations.length)
+    {
       startRes = annotations.length - 1;
+    }
     if (endRes >= annotations.length)
+    {
       endRes = annotations.length - 1;
+    }
     if (annotations == null)
+    {
       return;
+    }
     Annotation[] temp = new Annotation[endRes - startRes + 1];
     if (startRes < annotations.length)
     {
@@ -870,7 +877,9 @@ public class AlignmentAnnotation
   public void adjustForAlignment()
   {
     if (sequenceRef == null)
+    {
       return;
+    }
 
     if (annotations == null)
     {
@@ -896,7 +905,7 @@ public class AlignmentAnnotation
       {
         position = sequenceRef.findIndex(a) - 1;
 
-        temp[position] = (Annotation) sequenceMapping.get(index);
+        temp[position] = sequenceMapping.get(index);
       }
     }
 
@@ -917,8 +926,10 @@ public class AlignmentAnnotation
       if (annotations[i] == null)
       {
         if (i + 1 < iSize)
+        {
           System.arraycopy(annotations, i + 1, annotations, i, iSize - i
                   - 1);
+        }
         iSize--;
       }
       else
@@ -1056,11 +1067,15 @@ public class AlignmentAnnotation
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] == null)
+        {
           annotations[i] = new Annotation(String.valueOf(gapchar), null,
                   ' ', 0f, null);
+        }
         else if (annotations[i].displayCharacter == null
                 || annotations[i].displayCharacter.equals(" "))
+        {
           annotations[i].displayCharacter = String.valueOf(gapchar);
+        }
       }
     }
   }
-- 
1.7.10.2