X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=53642b530103bcb9c4ec61fd704da87481857cf8;hb=884952b9d0bf7e07ff8c8f70ed1601bfe20ac554;hp=2151fc410a303590b5637376388aea11647c5c68;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 2151fc4..53642b5 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,13 @@
  */
 package jalview.datamodel;
 
-public class DBRefEntry
+import jalview.api.DBRefEntryI;
+
+public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
 
+  private int startRes, endRes;
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
@@ -34,6 +37,7 @@ public class DBRefEntry
 
   }
 
+
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -60,21 +64,30 @@ public class DBRefEntry
     this.map = map;
   }
 
-  public DBRefEntry(DBRefEntry entry)
+  public DBRefEntry(DBRefEntryI entry)
   {
-    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)));
+    this((entry.getSource() == null ? "" : new String(entry.getSource())),
+            (entry.getVersion() == null ? "" : new String(
+                    entry.getVersion())),
+            (entry.getAccessionId() == null ? "" : new String(
+                    entry.getAccessionId())),
+            (entry.getMap() == null ? null : new Mapping(entry.getMap())));
   }
 
-  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))))
@@ -90,71 +103,71 @@ public class DBRefEntry
    * @param entry
    * @return true if source, accession and version are equal with those of entry
    */
-  public boolean equalRef(DBRefEntry entry)
+  @Override
+  public boolean equalRef(DBRefEntryI 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)))
+    }
+    if (entry != null
+            && (source != null && entry.getSource() != null && source
+                    .equalsIgnoreCase(entry.getSource()))
+            && (accessionId != null && entry.getAccessionId() != null && accessionId
+                    .equalsIgnoreCase(entry.getAccessionId()))
+            && (version != null && entry.getVersion() != null && version
+                    .equalsIgnoreCase(entry.getVersion())))
     {
       return true;
     }
     return false;
   }
 
+  @Override
   public String getSource()
   {
     return source;
   }
 
+  @Override
   public String getVersion()
   {
     return version;
   }
 
+  @Override
   public String getAccessionId()
   {
     return accessionId;
   }
 
-  /**
-   * @param accessionId
-   *          the accessionId to set
-   */
+
+  @Override
   public void setAccessionId(String accessionId)
   {
     this.accessionId = accessionId;
   }
 
-  /**
-   * @param source
-   *          the source to set
-   */
+
+  @Override
   public void setSource(String source)
   {
     this.source = source;
   }
 
-  /**
-   * @param version
-   *          the version to set
-   */
+
+  @Override
   public void setVersion(String version)
   {
     this.version = version;
   }
 
-  /**
-   * @return the map
-   */
+
+  @Override
   public Mapping getMap()
   {
     return map;
@@ -183,4 +196,34 @@ public class DBRefEntry
     return ((source != null) ? source : "") + ":"
             + ((accessionId != null) ? accessionId : "");
   }
+
+  @Override
+  public String toString()
+  {
+    return getSrcAccString();
+  }
+
+  @Override
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  @Override
+  public void setStartRes(int startRes)
+  {
+    this.startRes = startRes;
+  }
+
+  @Override
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  @Override
+  public void setEndRes(int endRes)
+  {
+    this.endRes = endRes;
+  }
 }