From 3343930d6c04059a817920c77c9b78a0b7f33525 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 Dec 2014 10:40:59 +0000
Subject: [PATCH] JAL-1619 refactorings: Map, StringBuilder, Override

---
 src/jalview/datamodel/AlignmentAnnotation.java |   33 +++++++++++++-----------
 1 file changed, 18 insertions(+), 15 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e137225..0d99155 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,9 +27,8 @@ import jalview.analysis.WUSSParseException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Enumeration;
 import java.util.HashMap;
-import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
@@ -155,7 +154,7 @@ public class AlignmentAnnotation
   /**
    * map of positions in the associated annotation
    */
-  public java.util.Hashtable<Integer, Annotation> sequenceMapping;
+  private Map<Integer, Annotation> sequenceMapping;
 
   /** DOCUMENT ME!! */
   public float graphMin;
@@ -499,6 +498,7 @@ public class AlignmentAnnotation
               : annotations[index + offset].secondaryStructure);
     }
 
+    @Override
     public String toString()
     {
       char[] string = new char[max - offset];
@@ -710,12 +710,13 @@ public class AlignmentAnnotation
       if (annotation.sequenceMapping != null)
       {
         Integer p = null;
-        sequenceMapping = new Hashtable();
-        Enumeration pos = annotation.sequenceMapping.keys();
-        while (pos.hasMoreElements())
+        sequenceMapping = new HashMap<Integer, Annotation>();
+        Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+                .iterator();
+        while (pos.hasNext())
         {
           // could optimise this!
-          p = (Integer) pos.nextElement();
+          p = pos.next();
           Annotation a = annotation.sequenceMapping.get(p);
           if (a == null)
           {
@@ -789,11 +790,11 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Hashtable newmapping = new Hashtable();
-        Enumeration e = sequenceMapping.keys();
-        while (e.hasMoreElements())
+        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Iterator<Integer> e = sequenceMapping.keySet().iterator();
+        while (e.hasNext())
         {
-          Integer pos = (Integer) e.nextElement();
+          Integer pos = e.next();
           if (pos.intValue() >= spos && pos.intValue() <= epos)
           {
             newmapping.put(pos, sequenceMapping.get(pos));
@@ -836,9 +837,10 @@ public class AlignmentAnnotation
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String toString()
   {
-    StringBuffer buffer = new StringBuffer();
+    StringBuilder buffer = new StringBuilder(256);
 
     for (int i = 0; i < annotations.length; i++)
     {
@@ -911,7 +913,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new java.util.Hashtable();
+    sequenceMapping = new HashMap<Integer, Annotation>();
 
     int seqPos;
 
@@ -1223,7 +1225,7 @@ public class AlignmentAnnotation
             .getTo() == sq.getDatasetSequence()) : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Hashtable<Integer, Annotation> mapForsq = new Hashtable();
+    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1275,7 +1277,8 @@ public class AlignmentAnnotation
   {
     if (mapping != null)
     {
-      Hashtable<Integer, Annotation> old = sequenceMapping, remap = new Hashtable<Integer, Annotation>();
+      Map<Integer, Annotation> old = sequenceMapping;
+      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
       int index = -1;
       for (int mp[] : mapping)
       {
-- 
1.7.10.2