From 33d29753b74b33be28fef39da85fc9fbb256f6c8 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 21 Dec 2007 14:59:49 +0000
Subject: [PATCH] equivalence for transferring/updating references

---
 src/jalview/datamodel/DBRefEntry.java |   11 +++++++++--
 src/jalview/datamodel/PDBEntry.java   |   17 +++++++++++++++++
 2 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 03445cd..7491da2 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -32,8 +32,15 @@ public class DBRefEntry
   {
     this(source, version, accessionId, null);
   }
+  /**
+   * 
+   * @param source canonical source (uppercase only)
+   * @param version (source dependent version string)
+   * @param accessionId (source dependent accession number string)
+   * @param map (mapping from local sequence numbering to source accession numbering)
+   */
   public DBRefEntry(String source, String version, String accessionId, Mapping map) {
-    this.source = source;
+    this.source = source.toUpperCase();
     this.version = version;
     this.accessionId = accessionId;
     this.map = map;
@@ -67,7 +74,7 @@ public class DBRefEntry
     }
     if (entry==this)
       return true;
-    if ((source!=null && entry.source!=null && source.equals(entry.source))
+    if ((source!=null && entry.source!=null && source.equalsIgnoreCase(entry.source))
             &&
             (accessionId!=null && entry.accessionId!=null && accessionId.equalsIgnoreCase(entry.accessionId))
             &&
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 7cd6a80..69f0d68 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -27,6 +27,23 @@ public class PDBEntry
   String id;
   Hashtable properties;
 
+  /* (non-Javadoc)
+   * @see java.lang.Object#equals(java.lang.Object)
+   */
+  public boolean equals(Object obj)
+  {
+    if (obj==null || !(obj instanceof PDBEntry))
+    {
+        return false;
+    }
+    if (obj==this)
+      return true;
+    PDBEntry o = (PDBEntry) obj;
+    return (file==o.file || (file!=null && o.file!=null && o.file.equals(file)))
+    && (type==o.type || (type!=null && o.type!=null && o.type.equals(type)))
+    && (id==o.id || (id!=null && o.id!=null && o.id.equalsIgnoreCase(id)))
+    && (properties==o.properties || (properties!=null && o.properties!=null && properties.equals(o.properties)));
+  }
   public PDBEntry()
   {}
   public PDBEntry(PDBEntry entry) {
-- 
1.7.10.2