From cff3462c5aecd2344485f26214e4a086091c03b8 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 22 Aug 2017 22:13:07 +0100
Subject: [PATCH] JAL-2681 cross-ref selection for targeted debugging

---
 test/jalview/io/CrossRef2xmlTests.java |   31 ++++++++++++++++++++++++++++---
 1 file changed, 28 insertions(+), 3 deletions(-)

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 9e24262..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;
 
@@ -68,6 +70,10 @@ 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
@@ -88,8 +94,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     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
@@ -162,7 +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
@@ -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
    * 
-- 
1.7.10.2