Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 54e8379..ae06650 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -21,7 +21,6 @@
 package jalview.datamodel;
 
 import jalview.api.DBRefEntryI;
-import jalview.io.vamsas.Dbref;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 
@@ -29,16 +28,7 @@ import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
 {
-  /*
-   * the mapping to chromosome (genome) is held as an instance with
-   * source = speciesId
-   * version = assemblyId
-   * accessionId = "chromosome:" + chromosomeId
-   * map = mapping from sequence to reference assembly
-   */
-  public static final String CHROMOSOME = "chromosome";
-
-  private String source = "";
+  String source = "";
 
   private String version = "";
   
@@ -49,9 +39,10 @@ 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
    */
   Mapping map = null;
@@ -60,20 +51,37 @@ public class DBRefEntry implements DBRefEntryI
   {
 
   }
-/**
- * 
- * @param source may not be null
- * @param version may be null
- * @param accessionId may be null
- */
+
+  /**
+   * 
+   * @param source
+   *                      may not be null
+   * @param version
+   *                      may be null
+   * @param accessionId
+   *                      may be null
+   */
   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)
@@ -84,13 +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;
   }
 
   /**
@@ -380,16 +389,6 @@ public class DBRefEntry implements DBRefEntryI
   }
 
   /**
-   * Mappings to chromosome are held with accessionId as "chromosome:id"
-   * 
-   * @return
-   */
-  public boolean isChromosome()
-  {
-    return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
-  }
-
-  /**
    * stores the upper-case canonical name of the source for use in
    * Sequence.getPrimaryDBRefs().
    * 
@@ -401,5 +400,21 @@ public class DBRefEntry implements DBRefEntryI
        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;
+  }
 }