Merge remote-tracking branch 'origin/bug/JAL-2722' into portforward/JAL-2675_2102b1to2103

[jalview.git] / test / jalview / ext / ensembl / EnsemblSeqProxyTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index 2d3948f..aa2c315 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -1,14 +1,36 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
 import jalview.io.FileParse;
 import jalview.io.gff.SequenceOntologyFactory;
@@ -16,6 +38,7 @@ import jalview.io.gff.SequenceOntologyLite;
 
 import java.lang.reflect.Method;
 import java.util.Arrays;
+import java.util.List;
 
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
@@ -23,9 +46,16 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-
 public class EnsemblSeqProxyTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private static final Object[][] allSeqs = new Object[][] {
       {
           new EnsemblProtein(),
@@ -125,14 +155,13 @@ public class EnsemblSeqProxyTest
   }
 
   @Test(dataProvider = "ens_seqs", suiteName = "live")
-  public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
-          throws Exception
+  public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
+          String fastasq) throws Exception
   {
     FileParse fp = proxy.getSequenceReader(Arrays
-            .asList(new String[]
-    { sq }));
+            .asList(new String[] { sq }));
     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
-    FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
+    FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
     Assert.assertEquals(sqs.length, trueSqs.length,
             "Different number of sequences retrieved for query " + sq);
@@ -152,7 +181,7 @@ public class EnsemblSeqProxyTest
               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                       + tr.getSequenceAsString() + "\n" + "Got:"
                       + rseq[0].getSequenceAsString());
-  
+
     }
   }
 
@@ -242,15 +271,22 @@ public class EnsemblSeqProxyTest
     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
-    SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
+    List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
+        sf2, sf3, sf4 });
 
     // sort by start position ascending (forward strand)
     // sf2 and sf3 tie and should not be reordered by sorting
-    EnsemblSeqProxy.sortFeatures(sfs, true);
-    assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+    SequenceFeatures.sortFeatures(sfs, true);
+    assertSame(sfs.get(0), sf2);
+    assertSame(sfs.get(1), sf3);
+    assertSame(sfs.get(2), sf1);
+    assertSame(sfs.get(3), sf4);
 
     // sort by end position descending (reverse strand)
-    EnsemblSeqProxy.sortFeatures(sfs, false);
-    assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+    SequenceFeatures.sortFeatures(sfs, false);
+    assertSame(sfs.get(0), sf1);
+    assertSame(sfs.get(1), sf3);
+    assertSame(sfs.get(2), sf2);
+    assertSame(sfs.get(3), sf4);
   }
-}
\ No newline at end of file
+}