From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 19 Feb 2016 16:59:42 +0000 (+0000)
Subject: JAL-1705 updated for change to CrossRef signature
X-Git-Tag: Release_2_10_0~296^2~22^2~2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=3e16aae83055354f09b0f9560686d035a5f2e5aa

JAL-1705 updated for change to CrossRef signature
---

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 7a9b553..d7058d0 100644
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -7,6 +7,7 @@ import jalview.datamodel.SequenceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -116,7 +117,8 @@ public class SequenceFetcherTest
                 System.out.println("Type: " + types[t]);
                 SequenceI[] prod = jalview.analysis.CrossRef
                         .findXrefSequences(al.getSequencesArray(), dna,
-                                types[t]).getSequencesArray();
+                                types[t], null, new ArrayList<SequenceI>())
+                        .getSequencesArray();
                 System.out.println("Found "
                         + ((prod == null) ? "no" : "" + prod.length)
                         + " products");
@@ -199,7 +201,7 @@ public class SequenceFetcherTest
           // sequences.
           SequenceI[] seqs = al.getSequencesArray();
           Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
-                  seqs, dna, null, ds);
+                  seqs, dna, null, ds, new ArrayList<SequenceI>());
           System.out.println("Found "
                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
                   + " products");
diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index fae5778..b9e209f 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -179,8 +179,8 @@ public class DbRefFetcherTest
     assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
             .getMap().getWidth(), 3);
     AlignmentI sprods = CrossRef.findXrefSequences(
-            alsq.getSequencesArray(), true, dr[0].getSource(),
-            alsq.getDataset());
+            alsq.getSequencesArray(), true, dr[0].getSource(), alsq,
+            new ArrayList<SequenceI>());
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);