JAL-1264 remove broken applet build dependencies

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 6f0125d..b78afeb 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -37,6 +37,7 @@ import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
@@ -282,7 +283,7 @@ public class AlignmentUtils
          * many-to-many, as that would risk mixing species with similar cDNA
          * sequences.
          */
-        if (xrefsOnly && !CrossRef.haveCrossRef(aaSeq, cdnaSeq))
+        if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq))
         {
           continue;
         }
@@ -1212,4 +1213,49 @@ public class AlignmentUtils
       }
     }
   }
+
+  /**
+   * 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)
+  {
+    // Note: moved here from class CrossRef as the latter class has dependencies
+    // not availability to the applet's classpath
+    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;
+  }
 }