JAL-2110 work in progress

[jalview.git] / test / jalview / ws / SequenceFetcherTest.java

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index a54ce8b..50fb3c0 100644 (file)
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -1,5 +1,6 @@
 package jalview.ws;
 
+import jalview.analysis.CrossRef;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
@@ -105,18 +106,17 @@ public class SequenceFetcherTest
           {
             boolean dna = sp.isDnaCoding();
             // try and find products
-            String types[] = jalview.analysis.CrossRef
-                    .findSequenceXrefTypes(dna, al.getSequencesArray());
+            CrossRef crossRef = new CrossRef(al.getSequencesArray(),
+                    al);
+            List<String> types = crossRef.findXrefSourcesForSequences();
             if (types != null)
             {
               System.out.println("Xref Types for: "
                       + (dna ? "dna" : "prot"));
-              for (int t = 0; t < types.length; t++)
+              for (String source : types)
               {
-                System.out.println("Type: " + types[t]);
-                SequenceI[] prod = jalview.analysis.CrossRef
-                        .findXrefSequences(al.getSequencesArray(), dna,
-                                types[t], null)
+                System.out.println("Type: " + source);
+                SequenceI[] prod = crossRef.findXrefSequences(source)
                         .getSequencesArray();
                 System.out.println("Found "
                         + ((prod == null) ? "no" : "" + prod.length)
@@ -199,8 +199,8 @@ public class SequenceFetcherTest
           // have a bash at finding the products amongst all the retrieved
           // sequences.
           SequenceI[] seqs = al.getSequencesArray();
-          Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
-                  seqs, dna, null, ds);
+          Alignment prodal = new CrossRef(seqs, ds)
+                  .findXrefSequences(null);
           System.out.println("Found "
                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
                   + " products");