merge of SIFTs Branch

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 0581845..0b1fb6d 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -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
    */
@@ -98,7 +101,8 @@ 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)
     {
@@ -108,63 +112,59 @@ public class DBRefEntry
     {
       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
-   */
+
   public Mapping getMap()
   {
     return map;
@@ -194,8 +194,33 @@ public class DBRefEntry
             + ((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;
+  }
 }