JAL-3863 mark first accession retrieved from Uniprot as the canonical accession

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index f557ff8..ae06650 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -39,6 +39,8 @@ public class DBRefEntry implements DBRefEntryI
   int sourceKey = Integer.MIN_VALUE;
 
   String canonicalSourceName;
+  
+  boolean isCanonicalAccession;
 
   /*
    * maps from associated sequence to the database sequence's coordinate system
@@ -61,12 +63,25 @@ public class DBRefEntry implements DBRefEntryI
    */
   public DBRefEntry(String source, String version, String accessionId)
   {
-    this(source, version, accessionId, null);
+    this(source, version, accessionId, null,false);
   }
 
   /**
    * 
    * @param source
+   *                      may not be null
+   * @param version
+   *                      may be null
+   * @param accessionId
+   *                      may be null
+   */
+  public DBRefEntry(String source, String version, String accessionId, Mapping map)
+  {
+    this(source, version, accessionId, map,false);
+  }
+  /**
+   * 
+   * @param source
    *          canonical source (turned to uppercase; cannot be null)
    * @param version
    *          (source dependent version string or null)
@@ -77,13 +92,14 @@ public class DBRefEntry implements DBRefEntryI
    *          numbering or null)
    */
   public DBRefEntry(String source, String version, String accessionId,
-          Mapping map)
+          Mapping map,boolean isCanonical)
   {
        
     this.source = source.toUpperCase();
     setVersion(version);
     this.accessionId = accessionId;
     this.map = map;
+    this.isCanonicalAccession=isCanonical;
   }
 
   /**
@@ -383,4 +399,22 @@ public class DBRefEntry implements DBRefEntryI
   public String getCanonicalSourceName() {
        return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
   }
+
+  /**
+   * 
+   * @param canonical
+   */
+  public void setCanonical(boolean canonical)
+  {
+    isCanonicalAccession = canonical;
+  }
+  /**
+   * 
+   * @return true if this is the primary canonical accession for the database source
+   */
+  public boolean isCanonical()
+  {
+    // TODO Auto-generated method stub
+    return isCanonicalAccession;
+  }
 }