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 ec5855f..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;
@@ -65,10 +70,13 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   public void testRetrieveAndShowCrossref() throws Exception
   {
 
-    List<String> failedDBRetr = new ArrayList<String>();
-    List<String> failedXrefMenuItems = new ArrayList<String>();
-    List<String> failedProjectRecoveries = new ArrayList<String>();
-
+    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
@@ -85,12 +93,11 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     // . codonframes
     //
     //
-    HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
-    List<String> keyseq = new ArrayList<String>();
-    HashMap<String, File> savedProjects = new HashMap<String, File>();
+    Map<String, String> dbtoviewBit = new HashMap<>();
+    List<String> keyseq = new ArrayList<>();
+    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
@@ -163,7 +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
@@ -176,20 +184,21 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             // build next key so we an retrieve all views
             String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
             // perform crossref action, or retrieve stored project
-            List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+            List<AlignmentViewPanel> cra_views = new ArrayList<>();
             CrossRefAction cra = null;
 
             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);
@@ -237,7 +246,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
               }
             }
-            HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+            HashMap<String, List<String>> xrptypes = new HashMap<>();
             // first save/verify views.
             for (AlignmentViewPanel avp : cra_views)
             {
@@ -274,23 +283,25 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
                 for (String xrefdb : xrptypes.get(nextxref))
                 {
-                  List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+                  List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
                   int q = 0;
                   String nextnextxref = nextxref + " -> " + xrefdb + "{"
                           + q + "}";
 
                   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 '"
@@ -298,7 +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
@@ -437,6 +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
    * 
@@ -480,7 +509,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   private void assertType(boolean expectProtein,
           AlignmentViewPanel alignmentViewPanel, String message)
   {
-    List<SequenceI> nonType = new ArrayList<SequenceI>();
+    List<SequenceI> nonType = new ArrayList<>();
     for (SequenceI sq : alignmentViewPanel.getAlignViewport()
             .getAlignment().getSequences())
     {
@@ -517,8 +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)