safer copy constructor

[jalview.git] / src / jalview / datamodel / DBRefEntry.java

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 8bbb5f7..b6c3192 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -32,32 +32,62 @@ 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;
   }
   public DBRefEntry(DBRefEntry entry)
   {
-    this(new String(entry.source), new String(entry.version), new String(entry.accessionId), new Mapping(entry.map));
+    this((entry.source==null ? "" : new String(entry.source)), 
+            (entry.version==null ? "" : new String(entry.version)),
+            (entry.accessionId==null ? "" : new String(entry.accessionId)),
+            (entry.map==null ? null : new Mapping(entry.map)));
   }
   public boolean equals(DBRefEntry entry) {
       if (entry==this)
           return true;
       if (entry==null)
           return false;
-      if ((source!=null && entry.source!=null && source.equals(entry.source))
-          &&
-          (accessionId!=null && entry.accessionId!=null && accessionId.equals(entry.accessionId))
-          &&
-          (version!=null && entry.version!=null && version.equals(entry.version))
-          &&
+      if (equalRef(entry)
+              &&
           ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
               return true;
           }
       return false;
   }
+  /**
+   * test for similar DBRef attributes, except for the map object.
+   * @param entry 
+   * @return true if source, accession and version are equal with those of entry
+   */
+  public boolean equalRef(DBRefEntry entry)
+  {
+    if (entry==null)
+    {
+      return false;
+    }
+    if (entry==this)
+      return true;
+    if ((source!=null && entry.source!=null && source.equalsIgnoreCase(entry.source))
+            &&
+            (accessionId!=null && entry.accessionId!=null && accessionId.equalsIgnoreCase(entry.accessionId))
+            &&
+            (version!=null && entry.version!=null && version.equalsIgnoreCase(entry.version))
+            )
+    {
+      return true;
+    }
+    return false;
+  }
   public String getSource()
   {
     return source;
@@ -104,7 +134,6 @@ public void setMap(Mapping map) {
 }
 public boolean hasMap()
 {
-  // TODO Auto-generated method stub
   return map!=null;
 }
 /**