X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=b3db4de5e950e08cf84459ad8927426988566b20;hb=ec44bf310ff6aaa0438f486dadc65f2af385d99d;hp=071585785605cd2e3a6d68b2afe41d4c62340512;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 0715857..b3db4de 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -39,6 +39,9 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+
+import junit.extensions.PA;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
@@ -90,9 +93,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     // . codonframes
     //
     //
-    HashMap<String, String> dbtoviewBit = new HashMap<>();
+    Map<String, String> dbtoviewBit = new HashMap<>();
     List<String> keyseq = new ArrayList<>();
-    HashMap<String, File> savedProjects = new HashMap<>();
+    Map<String, File> savedProjects = new HashMap<>();
 
     for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
     {
@@ -186,15 +189,16 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
             if (pass2 == 0)
             { // retrieve and show cross-refs in this thread
-              cra = new CrossRefAction(af, seqs, dna, db);
+              cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
               cra.run();
-              if (cra.getXrefViews().size() == 0)
+              cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+                      "xrefViews");
+              if (cra_views.size() == 0)
               {
                 failedXrefMenuItems.add("No crossrefs retrieved for "
                         + first + " -> " + db);
                 continue;
               }
-              cra_views = cra.getXrefViews();
               assertNucleotide(cra_views.get(0),
                       "Nucleotide panel included proteins for " + first
                               + " -> " + db);
@@ -286,16 +290,18 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
                   if (pass3 == 0)
                   {
-
                     SequenceI[] xrseqs = avp.getAlignment()
                             .getSequencesArray();
                     AlignFrame nextaf = Desktop.getAlignFrameFor(avp
                             .getAlignViewport());
 
-                    cra = new CrossRefAction(nextaf, xrseqs, avp
-                            .getAlignViewport().isNucleotide(), xrefdb);
+                    cra = CrossRefAction.getHandlerFor(xrseqs, avp
+                            .getAlignViewport().isNucleotide(), xrefdb,
+                            nextaf);
                     cra.run();
-                    if (cra.getXrefViews().size() == 0)
+                    cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
+                            cra, "xrefViews");
+                    if (cra_views2.size() == 0)
                     {
                       failedXrefMenuItems
                               .add("No crossrefs retrieved for '"
@@ -303,7 +309,6 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                                       + " via '" + nextaf.getTitle() + "'");
                       continue;
                     }
-                    cra_views2 = cra.getXrefViews();
                     assertNucleotide(cra_views2.get(0),
                             "Nucleotide panel included proteins for '"
                                     + nextxref + "' to " + xrefdb
@@ -541,8 +546,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
    *          viewpanel needs to be called with a distinct xrefpath to ensure
    *          each one's strings are compared)
    */
-  private void stringify(HashMap<String, String> dbtoviewBit,
-          HashMap<String, File> savedProjects, String xrefpath,
+  private void stringify(Map<String, String> dbtoviewBit,
+          Map<String, File> savedProjects, String xrefpath,
           AlignmentViewPanel avp)
   {
     if (savedProjects != null)