JAL-1686 @Override and/or TODO added to equals(Object) methods

diff --git a/src/ext/vamsas/ServiceHandle.java b/src/ext/vamsas/ServiceHandle.java
index 442e5f7..83412ea 100755 (executable)
--- a/src/ext/vamsas/ServiceHandle.java
+++ b/src/ext/vamsas/ServiceHandle.java
@@ -128,15 +128,15 @@ public class ServiceHandle implements java.io.Serializable
 
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof ServiceHandle))
+    if (obj == null)
     {
       return false;
     }
-    ServiceHandle other = (ServiceHandle) obj;
-    if (obj == null)
+    if (!(obj instanceof ServiceHandle))
     {
       return false;
     }
+    ServiceHandle other = (ServiceHandle) obj;
     if (this == obj)
     {
       return true;

diff --git a/src/ext/vamsas/ServiceHandles.java b/src/ext/vamsas/ServiceHandles.java
index 45c49d8..5ed466f 100755 (executable)
--- a/src/ext/vamsas/ServiceHandles.java
+++ b/src/ext/vamsas/ServiceHandles.java
@@ -57,15 +57,15 @@ public class ServiceHandles implements java.io.Serializable
 
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof ServiceHandles))
+    if (obj == null)
     {
       return false;
     }
-    ServiceHandles other = (ServiceHandles) obj;
-    if (obj == null)
+    if (!(obj instanceof ServiceHandles))
     {
       return false;
     }
+    ServiceHandles other = (ServiceHandles) obj;
     if (this == obj)
     {
       return true;

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index c3d7ac1..e6a4853 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -20,9 +20,12 @@
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Vector;
 
 /**
  * Routines for approximate Sequence Id resolution by name using string
@@ -258,14 +261,20 @@ public class SequenceIdMatcher
       }
     }
 
+    @Override
     public int hashCode()
     {
       return ((id.length() >= 4) ? id.substring(0, 4).hashCode() : id
               .hashCode());
     }
 
+    @Override
     public boolean equals(Object s)
     {
+      if (s == null)
+      {
+        return false;
+      }
       if (s instanceof SeqIdName)
       {
         return this.equals((SeqIdName) s);

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index bc1d610..54bdf20 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -69,12 +69,20 @@ public class DBRefEntry
             (entry.map == null ? null : new Mapping(entry.map)));
   }
 
-  public boolean equals(DBRefEntry entry)
+  @Override
+  public boolean equals(Object o)
   {
+    // TODO should also override hashCode to ensure equal objects have equal
+    // hashcodes
+    if (o == null || !(o instanceof DBRefEntry))
+    {
+      return false;
+    }
+    DBRefEntry entry = (DBRefEntry) o;
     if (entry == this)
+    {
       return true;
-    if (entry == null)
-      return false;
+    }
     if (equalRef(entry)
             && ((map == null && entry.map == null) || (map != null
                     && entry.map != null && map.equals(entry.map))))
@@ -97,7 +105,9 @@ public class DBRefEntry
       return false;
     }
     if (entry == this)
+    {
       return true;
+    }
     if ((source != null && entry.source != null && source
             .equalsIgnoreCase(entry.source))
             && (accessionId != null && entry.accessionId != null && accessionId

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 59dc8ff..559ae4c 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -348,6 +348,8 @@ public class Mapping
   @Override
   public boolean equals(Object o)
   {
+    // TODO should override Object.hashCode() to ensure that equal objects have
+    // equal hashcodes
     if (o == null || !(o instanceof Mapping))
     {
       return false;
@@ -366,7 +368,7 @@ public class Mapping
     {
       return false;
     }
-    if (map.equals(other.map))
+    if ((map == null && other.map == null) || map.equals(other.map))
     {
       return true;
     }

diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index be52600..2641659 100644 (file)
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -79,6 +79,8 @@ public class MapList
   @Override
   public boolean equals(Object o)
   {
+    // TODO should also override hashCode to ensure equal objects have equal
+    // hashcodes
     if (o == null || !(o instanceof MapList))
     {
       return false;

diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java
index e972068..bbe131d 100644 (file)
--- a/src/jalview/ws/rest/RestServiceDescription.java
+++ b/src/jalview/ws/rest/RestServiceDescription.java
@@ -77,6 +77,7 @@ public class RestServiceDescription
     this.gapCharacter = gapCharacter;
   }
 
+  @Override
   public boolean equals(Object o)
   {
     if (o == null || !(o instanceof RestServiceDescription))

diff --git a/src/uk/ac/ebi/picr/model/CrossReference.java b/src/uk/ac/ebi/picr/model/CrossReference.java
index aef2ca9..498a47b 100644 (file)
--- a/src/uk/ac/ebi/picr/model/CrossReference.java
+++ b/src/uk/ac/ebi/picr/model/CrossReference.java
@@ -244,15 +244,22 @@ public class CrossReference implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof CrossReference))
+    {
       return false;
+    }
     CrossReference other = (CrossReference) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -285,6 +292,11 @@ public class CrossReference implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  /**
+   * hashCode designed to ensure that if two instances satisfy o1.equals(o2)
+   * then they have the same hashcode.
+   */
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/uk/ac/ebi/picr/model/UPEntry.java b/src/uk/ac/ebi/picr/model/UPEntry.java
index 0390d48..c94bf15 100644 (file)
--- a/src/uk/ac/ebi/picr/model/UPEntry.java
+++ b/src/uk/ac/ebi/picr/model/UPEntry.java
@@ -198,15 +198,22 @@ public class UPEntry implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof UPEntry))
+    {
       return false;
+    }
     UPEntry other = (UPEntry) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -236,6 +243,7 @@ public class UPEntry implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/uk/ac/ebi/www/Data.java b/src/uk/ac/ebi/www/Data.java
index b12de70..2020fc9 100755 (executable)
--- a/src/uk/ac/ebi/www/Data.java
+++ b/src/uk/ac/ebi/www/Data.java
@@ -52,17 +52,18 @@ public class Data implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof Data))
+    if (obj == null)
     {
       return false;
     }
-    Data other = (Data) obj;
-    if (obj == null)
+    if (!(obj instanceof Data))
     {
       return false;
     }
+    Data other = (Data) obj;
     if (this == obj)
     {
       return true;
@@ -84,6 +85,7 @@ public class Data implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/uk/ac/ebi/www/InputParams.java b/src/uk/ac/ebi/www/InputParams.java
index 189c7f6..fe1c70c 100755 (executable)
--- a/src/uk/ac/ebi/www/InputParams.java
+++ b/src/uk/ac/ebi/www/InputParams.java
@@ -220,17 +220,18 @@ public class InputParams implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof InputParams))
+    if (obj == null)
     {
       return false;
     }
-    InputParams other = (InputParams) obj;
-    if (obj == null)
+    if (!(obj instanceof InputParams))
     {
       return false;
     }
+    InputParams other = (InputParams) obj;
     if (this == obj)
     {
       return true;
@@ -274,6 +275,7 @@ public class InputParams implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/uk/ac/ebi/www/WSFile.java b/src/uk/ac/ebi/www/WSFile.java
index 9199353..210de76 100755 (executable)
--- a/src/uk/ac/ebi/www/WSFile.java
+++ b/src/uk/ac/ebi/www/WSFile.java
@@ -52,17 +52,18 @@ public class WSFile implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof WSFile))
+    if (obj == null)
     {
       return false;
     }
-    WSFile other = (WSFile) obj;
-    if (obj == null)
+    if (!(obj instanceof WSFile))
     {
       return false;
     }
+    WSFile other = (WSFile) obj;
     if (this == obj)
     {
       return true;
@@ -84,6 +85,7 @@ public class WSFile implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/Alignment.java b/src/vamsas/objects/simple/Alignment.java
index 9bff9cf..9d47b6a 100755 (executable)
--- a/src/vamsas/objects/simple/Alignment.java
+++ b/src/vamsas/objects/simple/Alignment.java
@@ -103,15 +103,22 @@ public class Alignment extends vamsas.objects.simple.Object implements
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof Alignment))
+    {
       return false;
+    }
     Alignment other = (Alignment) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -131,6 +138,7 @@ public class Alignment extends vamsas.objects.simple.Object implements
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/JpredResult.java b/src/vamsas/objects/simple/JpredResult.java
index 9db8cfe..cc7cc67 100755 (executable)
--- a/src/vamsas/objects/simple/JpredResult.java
+++ b/src/vamsas/objects/simple/JpredResult.java
@@ -79,17 +79,18 @@ public class JpredResult extends vamsas.objects.simple.Result implements
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof JpredResult))
+    if (obj == null)
     {
       return false;
     }
-    JpredResult other = (JpredResult) obj;
-    if (obj == null)
+    if (!(obj instanceof JpredResult))
     {
       return false;
     }
+    JpredResult other = (JpredResult) obj;
     if (this == obj)
     {
       return true;
@@ -111,6 +112,7 @@ public class JpredResult extends vamsas.objects.simple.Result implements
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/MsaResult.java b/src/vamsas/objects/simple/MsaResult.java
index 30a5414..49fa4a7 100755 (executable)
--- a/src/vamsas/objects/simple/MsaResult.java
+++ b/src/vamsas/objects/simple/MsaResult.java
@@ -58,20 +58,20 @@ public class MsaResult extends vamsas.objects.simple.Result implements
     this.msa = msa;
   }
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof MsaResult))
+    if (obj == null)
     {
       return false;
     }
-
-    MsaResult other = (MsaResult) obj;
-
-    if (obj == null)
+    if (!(obj instanceof MsaResult))
     {
       return false;
     }
 
+    MsaResult other = (MsaResult) obj;
+
     if (this == obj)
     {
       return true;
@@ -93,6 +93,7 @@ public class MsaResult extends vamsas.objects.simple.Result implements
     return _equals;
   }
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/Msfalignment.java b/src/vamsas/objects/simple/Msfalignment.java
index 573eb96..90370f0 100755 (executable)
--- a/src/vamsas/objects/simple/Msfalignment.java
+++ b/src/vamsas/objects/simple/Msfalignment.java
@@ -78,17 +78,18 @@ public class Msfalignment implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof Msfalignment))
+    if (obj == null)
     {
       return false;
     }
-    Msfalignment other = (Msfalignment) obj;
-    if (obj == null)
+    if (!(obj instanceof Msfalignment))
     {
       return false;
     }
+    Msfalignment other = (Msfalignment) obj;
     if (this == obj)
     {
       return true;
@@ -110,6 +111,7 @@ public class Msfalignment implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/Object.java b/src/vamsas/objects/simple/Object.java
index 23eedec..7e79e6a 100755 (executable)
--- a/src/vamsas/objects/simple/Object.java
+++ b/src/vamsas/objects/simple/Object.java
@@ -29,15 +29,21 @@ public abstract class Object implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof Object))
-      return false;
-    Object other = (Object) obj;
     if (obj == null)
+    {
+      return false;
+    }
+    if (!(obj instanceof Object))
+    {
       return false;
+    }
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -51,6 +57,7 @@ public abstract class Object implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/Result.java b/src/vamsas/objects/simple/Result.java
index 18293f5..87f0a48 100755 (executable)
--- a/src/vamsas/objects/simple/Result.java
+++ b/src/vamsas/objects/simple/Result.java
@@ -288,15 +288,22 @@ public class Result implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof Result))
+    {
       return false;
+    }
     Result other = (Result) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -322,6 +329,7 @@ public class Result implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/Secstructpred.java b/src/vamsas/objects/simple/Secstructpred.java
index 77fdd34..349c21e 100755 (executable)
--- a/src/vamsas/objects/simple/Secstructpred.java
+++ b/src/vamsas/objects/simple/Secstructpred.java
@@ -57,15 +57,15 @@ public class Secstructpred implements java.io.Serializable
 
   public synchronized boolean equals(java.lang.Object obj)
   {
-    if (!(obj instanceof Secstructpred))
+    if (obj == null)
     {
       return false;
     }
-    Secstructpred other = (Secstructpred) obj;
-    if (obj == null)
+    if (!(obj instanceof Secstructpred))
     {
       return false;
     }
+    Secstructpred other = (Secstructpred) obj;
     if (this == obj)
     {
       return true;

diff --git a/src/vamsas/objects/simple/SeqSearchResult.java b/src/vamsas/objects/simple/SeqSearchResult.java
index 98d1d21..8ef8f7c 100644 (file)
--- a/src/vamsas/objects/simple/SeqSearchResult.java
+++ b/src/vamsas/objects/simple/SeqSearchResult.java
@@ -127,15 +127,22 @@ public class SeqSearchResult extends vamsas.objects.simple.Result implements
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof SeqSearchResult))
+    {
       return false;
+    }
     SeqSearchResult other = (SeqSearchResult) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -157,6 +164,7 @@ public class SeqSearchResult extends vamsas.objects.simple.Result implements
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/Sequence.java b/src/vamsas/objects/simple/Sequence.java
index 28dc9eb..8eb7208 100755 (executable)
--- a/src/vamsas/objects/simple/Sequence.java
+++ b/src/vamsas/objects/simple/Sequence.java
@@ -78,15 +78,22 @@ public class Sequence implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof Sequence))
+    {
       return false;
+    }
     Sequence other = (Sequence) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -104,6 +111,7 @@ public class Sequence implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/SequenceSet.java b/src/vamsas/objects/simple/SequenceSet.java
index 2c43f96..d5a269b 100755 (executable)
--- a/src/vamsas/objects/simple/SequenceSet.java
+++ b/src/vamsas/objects/simple/SequenceSet.java
@@ -55,15 +55,22 @@ public class SequenceSet implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof SequenceSet))
+    {
       return false;
+    }
     SequenceSet other = (SequenceSet) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -78,6 +85,7 @@ public class SequenceSet implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)

diff --git a/src/vamsas/objects/simple/WsJobId.java b/src/vamsas/objects/simple/WsJobId.java
index 3419899..eb04dcf 100755 (executable)
--- a/src/vamsas/objects/simple/WsJobId.java
+++ b/src/vamsas/objects/simple/WsJobId.java
@@ -78,15 +78,22 @@ public class WsJobId implements java.io.Serializable
 
   private java.lang.Object __equalsCalc = null;
 
+  @Override
   public synchronized boolean equals(java.lang.Object obj)
   {
+    if (obj == null)
+    {
+      return false;
+    }
     if (!(obj instanceof WsJobId))
+    {
       return false;
+    }
     WsJobId other = (WsJobId) obj;
-    if (obj == null)
-      return false;
     if (this == obj)
+    {
       return true;
+    }
     if (__equalsCalc != null)
     {
       return (__equalsCalc == obj);
@@ -103,6 +110,7 @@ public class WsJobId implements java.io.Serializable
 
   private boolean __hashCodeCalc = false;
 
+  @Override
   public synchronized int hashCode()
   {
     if (__hashCodeCalc)