JAL-2106 DBRefEntry.isPrimary() minimal test & implementation

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index a641b1b..6a48da7 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -22,6 +22,8 @@ package jalview.datamodel;
 
 import jalview.api.DBRefEntryI;
 
+import java.util.Arrays;
+
 public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
@@ -279,5 +281,45 @@ public class DBRefEntry implements DBRefEntryI
   public String toString()
   {
     return getSrcAccString();
+
+  @Override
+  public boolean isPrimary()
+  {
+    /*
+     * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.  
+     */
+    if (map != null)
+    {
+      if (map.getTo() != null)
+      {
+        return false;
+      }
+      if (map.getMap().getFromRatio() != map.getMap().getToRatio()
+              || map.getMap().getFromRatio() != 1)
+      {
+        return false;
+      }
+    }
+    if (version == null)
+    {
+      // no version string implies the reference has not been verified at all.
+      return false;
+    }
+    // tricky - this test really needs to search the sequence's set of dbrefs to
+    // see if there is a primary reference that derived this reference.
+    String ucv = version.toUpperCase();
+    for (String primsrc : Arrays.asList(DBRefSource.allSources()))
+    {
+      if (ucv.startsWith(primsrc.toUpperCase()))
+      {
+        // by convention, many secondary references inherit the primary
+        // reference's
+        // source string as a prefix for any version information from the
+        // secondary reference.
+        return false;
+      }
+    }
+    return true;
+  }
   }
 }