X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=071585785605cd2e3a6d68b2afe41d4c62340512;hb=44be050a48b372e5e29c74a0b838c73269501e0e;hp=eaf1e791eb55e4faec5e5ffada2c099c3b332771;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index eaf1e79..0715857 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -31,10 +31,12 @@ 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;
 
@@ -65,10 +67,13 @@ 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 +90,11 @@ 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>();
+    HashMap<String, String> dbtoviewBit = new HashMap<>();
+    List<String> keyseq = new ArrayList<>();
+    HashMap<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
@@ -140,7 +144,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           Desktop.instance.closeAll_actionPerformed(null);
           // recover stored project
           af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
-                  .get(first).toString(), FormatAdapter.FILE);
+                  .get(first).toString(), DataSourceType.FILE);
           System.out.println("Recovered view for '" + first + "' from '"
                   + savedProjects.get(first).toString() + "'");
           dna = af.getViewport().getAlignment().isNucleotide();
@@ -163,7 +167,8 @@ 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
@@ -176,7 +181,7 @@ 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)
@@ -213,7 +218,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
               // recover stored project
               AlignFrame af2 = new FileLoader(false)
                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
-                              .toString(), FormatAdapter.FILE);
+                              .toString(), DataSourceType.FILE);
               System.out.println("Recovered view for '" + nextxref
                       + "' from '" + savedProjects.get(nextxref).toString()
                       + "'");
@@ -237,7 +242,7 @@ 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)
             {
@@ -274,7 +279,7 @@ 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 + "}";
@@ -324,7 +329,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     AlignFrame af2 = new FileLoader(false)
                             .LoadFileWaitTillLoaded(
                                     savedProjects.get(nextnextxref)
-                                            .toString(), FormatAdapter.FILE);
+                                            .toString(),
+                                    DataSourceType.FILE);
                     System.out.println("Recovered view for '"
                             + nextnextxref + "' from '"
                             + savedProjects.get(nextnextxref).toString()
@@ -436,6 +442,25 @@ 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
    * 
@@ -479,7 +504,7 @@ 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())
     {