X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fgff%2FExonerateHelperTest.java;fp=test%2Fjalview%2Fio%2Fgff%2FExonerateHelperTest.java;h=825af240aee3dc8d241447e0a86ee06e8945a6c2;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=dbacceb1c82f855d671991bbb0069898da4c700c;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git

diff --git a/test/jalview/io/gff/ExonerateHelperTest.java b/test/jalview/io/gff/ExonerateHelperTest.java
index dbacceb..825af24 100644
--- a/test/jalview/io/gff/ExonerateHelperTest.java
+++ b/test/jalview/io/gff/ExonerateHelperTest.java
@@ -35,8 +35,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -44,10 +45,19 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class ExonerateHelperTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = "Functional")
   public void testGetMappingType()
   {
@@ -258,19 +268,20 @@ public class ExonerateHelperTest
   {
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(
-            "examples/testdata/exonerateseqs.fa", FormatAdapter.FILE);
-
+            "examples/testdata/exonerateseqs.fa",
+            DataSourceType.FILE);
+  
     af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
-            FormatAdapter.FILE, null, null);
-
+            DataSourceType.FILE, null, null);
+  
     /*
      * verify one mapping to a dummy sequence, one to a real one
      */
-    List<AlignedCodonFrame> mappings = af.getViewport().getAlignment()
-            .getDataset().getCodonFrames();
+    List<AlignedCodonFrame> mappings = af
+            .getViewport().getAlignment().getDataset().getCodonFrames();
     assertEquals(2, mappings.size());
     Iterator<AlignedCodonFrame> iter = mappings.iterator();
-
+  
     // first mapping is to dummy sequence
     AlignedCodonFrame mapping = iter.next();
     Mapping[] mapList = mapping.getProtMappings();
@@ -281,7 +292,7 @@ public class ExonerateHelperTest
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+  
     // second mapping is to a sequence in the alignment
     mapping = iter.next();
     mapList = mapping.getProtMappings();
@@ -290,23 +301,23 @@ public class ExonerateHelperTest
             .findName("DDB_G0280897");
     assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
     assertEquals(1, mapping.getdnaToProt().length);
-
+  
     // 143 in protein should map to codon [11270, 11269, 11268] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
     assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+  
     // 182 in protein should map to codon [11153, 11152, 11151] in dna
     mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
     assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-
+  
     // and the reverse mapping:
     mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
     assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-
+  
     // 11150 in dna should _not_ map to protein
     mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
     assertNull(mappedRegion);
-
+  
     // similarly 183 in protein should _not_ map to dna
     mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
     assertNull(mappedRegion);