Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef

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

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 7a9b553..76ca69b 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;
@@ -25,7 +26,7 @@ public class SequenceFetcherTest
     // assertions
 
     AlignmentI ds = null;
-    Vector noProds = new Vector();
+    Vector<Object[]> noProds = new Vector<Object[]>();
     String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
             + "With no arguments, all DbSources will be queried with their test Accession number.\n"
             + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
@@ -105,18 +106,19 @@ public class SequenceFetcherTest
           {
             boolean dna = sp.isDnaCoding();
             // try and find products
-            String types[] = jalview.analysis.CrossRef
-                    .findSequenceXrefTypes(dna, al.getSequencesArray());
+            List<String> types = CrossRef.findXrefSourcesForSequences(dna,
+                    al.getSequencesArray(), null);
             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]);
+                System.out.println("Type: " + source);
                 SequenceI[] prod = jalview.analysis.CrossRef
                         .findXrefSequences(al.getSequencesArray(), dna,
-                                types[t]).getSequencesArray();
+                                source, null)
+                        .getSequencesArray();
                 System.out.println("Found "
                         + ((prod == null) ? "no" : "" + prod.length)
                         + " products");
@@ -184,11 +186,11 @@ public class SequenceFetcherTest
       }
       if (noProds.size() > 0)
       {
-        Enumeration ts = noProds.elements();
+        Enumeration<Object[]> ts = noProds.elements();
         while (ts.hasMoreElements())
   
         {
-          Object[] typeSq = (Object[]) ts.nextElement();
+          Object[] typeSq = ts.nextElement();
           boolean dna = (typeSq.length > 1);
           AlignmentI al = (AlignmentI) typeSq[0];
           System.out.println("Trying getProducts for "