From d06d69a4dfa079d588636737c40ca5868731e273 Mon Sep 17 00:00:00 2001
From: James Procter <jprocter@ls30857.local>
Date: Fri, 5 Jun 2015 11:08:08 +0100
Subject: [PATCH] JAL-1551 formatting

---
 src/jalview/analysis/Conservation.java |   20 ++++++++++++-------
 src/jalview/gui/AlignmentPanel.java    |   33 ++++++++++++++++----------------
 2 files changed, 29 insertions(+), 24 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 1aa29e0..76323bc 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,10 +20,16 @@
  */
 package jalview.analysis;
 
-import java.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * Calculates conservation values for a given set of sequences
@@ -108,7 +114,7 @@ public class Conservation
     {
       for (s = 0; s < sSize; s++)
       {
-        sarray[s] = (SequenceI) sequences.get(s);
+        sarray[s] = sequences.get(s);
         if (sarray[s].getLength() > maxLength)
         {
           maxLength = sarray[s].getLength();
@@ -274,7 +280,7 @@ public class Conservation
                 resultHash.put(type, ht.get("-"));
               }
             }
-            else if (((Integer) resultHash.get(type)).equals((Integer) ht
+            else if (((Integer) resultHash.get(type)).equals(ht
                     .get(res)) == false)
             {
               resultHash.put(type, new Integer(-1));
@@ -373,7 +379,7 @@ public class Conservation
     {
       gapcons = countConsNGaps(i);
       totGaps = gapcons[1];
-      pgaps = ((float) totGaps * 100) / (float) sequences.length;
+      pgaps = ((float) totGaps * 100) / sequences.length;
       consSymbs[i-start]=new String();
       
       if (percentageGaps > pgaps)
@@ -679,7 +685,7 @@ public class Conservation
 
       if (Character.isDigit(c))
       {
-        value = (int) (c - '0');
+        value = c - '0';
       }
       else if (c == '*')
       {
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 5bc46f4..9dd00c0 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,6 +20,21 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
@@ -41,21 +56,6 @@ import java.util.List;
 
 import javax.swing.SwingUtilities;
 
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.math.AlignmentDimension;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -828,8 +828,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment()
-            .getAlignmentAnnotation(),
+    sorter.sort(getAlignment().getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
     repaint();
 
-- 
1.7.10.2