JAL-1705 reworked AlignmentUtils.makeCdsAlignment and associated code

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

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index d7058d0..a54ce8b 100644 (file)
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -7,7 +7,6 @@ import jalview.datamodel.SequenceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -26,7 +25,7 @@ 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"
@@ -117,7 +116,7 @@ public class SequenceFetcherTest
                 System.out.println("Type: " + types[t]);
                 SequenceI[] prod = jalview.analysis.CrossRef
                         .findXrefSequences(al.getSequencesArray(), dna,
-                                types[t], null, new ArrayList<SequenceI>())
+                                types[t], null)
                         .getSequencesArray();
                 System.out.println("Found "
                         + ((prod == null) ? "no" : "" + prod.length)
@@ -186,11 +185,11 @@ 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 "
@@ -201,7 +200,7 @@ public class SequenceFetcherTest
           // sequences.
           SequenceI[] seqs = al.getSequencesArray();
           Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
-                  seqs, dna, null, ds, new ArrayList<SequenceI>());
+                  seqs, dna, null, ds);
           System.out.println("Found "
                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
                   + " products");