JAL-3210 Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 54e8379..f557ff8 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 = "";
   
@@ -50,8 +40,7 @@ public class DBRefEntry implements DBRefEntryI
 
   String canonicalSourceName;
 
-
-  /**
+  /*
    * maps from associated sequence to the database sequence's coordinate system
    */
   Mapping map = null;
@@ -60,12 +49,16 @@ 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);
@@ -380,16 +373,6 @@ 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().
    * 
@@ -400,6 +383,4 @@ public class DBRefEntry implements DBRefEntryI
   public String getCanonicalSourceName() {
        return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
   }
-
-
 }