JAL-2755 find gene loci for fetched xrefs where possible

[jalview.git] / test / jalview / io / CrossRef2xmlTests.java

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 9e24262..b3db4de 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -31,12 +31,17 @@ import jalview.gui.CrossRefAction;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
 
 import java.io.File;
 import java.io.IOException;
 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;
@@ -68,6 +73,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     List<String> failedDBRetr = new ArrayList<>();
     List<String> failedXrefMenuItems = new ArrayList<>();
     List<String> failedProjectRecoveries = new ArrayList<>();
+    // only search for ensembl or Uniprot crossrefs
+    List<String> limit=Arrays.asList(new String[] {
+        DBRefUtils.getCanonicalName("ENSEMBL"), 
+        DBRefUtils.getCanonicalName("Uniprot")});
     // for every set of db queries
     // retrieve db query
     // verify presence of expected xrefs
@@ -84,12 +93,11 @@ 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[][] { { "ENSEMBL", "ENSG00000157764" },
-    { "UNIPROT", "P01731" } })
+    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
     {
       // pass counters - 0 - first pass, 1 means retrieve project rather than
       // perform action
@@ -162,7 +170,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
         ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
                 seqs, dataset).findXrefSourcesForSequences(dna);
-
+        filterDbRefs(ptypes, limit);
+        
         // start of pass2: retrieve each cross-ref for fetched or restored
         // project.
         do // first cross ref and recover crossref loop
@@ -180,15 +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);
@@ -280,16 +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 '"
@@ -297,7 +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
@@ -436,6 +447,25 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     }
   }
 
+  private void filterDbRefs(List<String> ptypes, List<String> limit)
+  {
+    if (limit != null)
+    {
+      int p = 0;
+      while (ptypes.size() > p)
+      {
+        if (!limit.contains(ptypes.get(p)))
+        {
+          ptypes.remove(p);
+        }
+        else
+        {
+          p++;
+        }
+      }
+    }
+  }
+
   /**
    * wrapper to trap known defect for AH002001 testcase
    * 
@@ -516,8 +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)