JAL-2110 remove hardwired detection of search context from the dataset ‘isNucleotide...

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

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index d7058d0..4e08430 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;
@@ -7,7 +8,6 @@ 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 +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"
@@ -106,18 +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(dna);
             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, new ArrayList<SequenceI>())
+                System.out.println("Type: " + source);
+                SequenceI[] prod = crossRef.findXrefSequences(source, dna)
                         .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 "
@@ -200,8 +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, new ArrayList<SequenceI>());
+          Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null,
+                  dna);
           System.out.println("Found "
                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
                   + " products");