JAL-845 refinements + tests for making mappings between alignments

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 47bd7bc..eed2d7e 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -583,6 +583,49 @@ public class CrossRef
   }
 
   /**
+   * Returns true if either sequence has a cross-reference to the other
+   * 
+   * @param seq1
+   * @param seq2
+   * @return
+   */
+  public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)
+  {
+    return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1);
+  }
+
+  /**
+   * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
+   * that sequence name is structured as Source|AccessId.
+   * 
+   * @param seq1
+   * @param seq2
+   * @return
+   */
+  public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)
+  {
+    if (seq1 == null || seq2 == null)
+    {
+      return false;
+    }
+    String name = seq2.getName();
+    final DBRefEntry[] xrefs = seq1.getDBRef();
+    if (xrefs != null)
+    {
+      for (DBRefEntry xref : xrefs)
+      {
+        String xrefName = xref.getSource() + "|" + xref.getAccessionId();
+        // case-insensitive test, consistent with DBRefEntry.equalRef()
+        if (xrefName.equalsIgnoreCase(name))
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  /**
    * precalculate different products that can be found for seqs in dataset and
    * return them.
    *