X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FGroupingTest.java;h=d5476313b7c74e477b719c6518067d447e636812;hb=91581a29a66a51e9c2f3039fd2df8c8870acd606;hp=3afa6e547f1feb69b843c66d9d12b0ecbc5fb334;hpb=fefc840cd97faf34b69ca387e8a38e3b9c79b92f;p=jalview.git

diff --git a/test/jalview/analysis/GroupingTest.java b/test/jalview/analysis/GroupingTest.java
index 3afa6e5..d547631 100644
--- a/test/jalview/analysis/GroupingTest.java
+++ b/test/jalview/analysis/GroupingTest.java
@@ -26,14 +26,23 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.util.Arrays;
 
 import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class GroupingTest
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
 
   Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
@@ -44,19 +53,27 @@ public class GroupingTest
 
   Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
 
-  SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] { s1,
-      s2 }), "Group1", null, false, false, false, 0, 5);
+  SequenceGroup sg_12 = new SequenceGroup(
+          Arrays.asList(new SequenceI[]
+          { s1, s2 }), "Group1", null, false, false, false, 0, 5);
 
-  SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] { s3,
-      s4, s5 }), "Group2", null, false, false, false, 0, 5);
+  SequenceGroup sg_345 = new SequenceGroup(
+          Arrays.asList(new SequenceI[]
+          { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
 
   AlignmentI alignment = new Alignment(
-          new SequenceI[] { s1, s2, s3, s4, s5 });
+          new SequenceI[]
+          { s1, s2, s3, s4, s5 });
+
+  /*
+   * test for the case where column selections are not added in
+   * left to right order
+   */
+  int[] positions = new int[] { 7, 9, 1 };
 
   @Test(groups = { "Functional" })
   public void testMakeGroupsWithBoth()
   {
-    int[] positions = new int[] { 1, 7, 9 };
     String[] str = new String[alignment.getHeight()];
     int seq = 0;
     for (SequenceI s : alignment.getSequences())
@@ -70,13 +87,9 @@ public class GroupingTest
     }
     SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
             alignment.getSequencesArray(), str,
-            Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+            Arrays.asList(new SequenceGroup[]
+            { sg_12, sg_345 }));
 
-    /*
-     * test for the case where column selections are not added in
-     * left to right order
-     */
-    positions = new int[] { 7, 9, 1 };
     ColumnSelection cs = new ColumnSelection();
     for (int p : positions)
     {
@@ -84,9 +97,10 @@ public class GroupingTest
     }
     SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
             alignment.getSequencesArray(), cs,
-            Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
-    AssertJUnit
-            .assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+            Arrays.asList(new SequenceGroup[]
+            { sg_12, sg_345 }));
+    AssertJUnit.assertEquals(seqgroupsString.length,
+            seqgroupsColSel.length);
     for (int p = 0; p < seqgroupsString.length; p++)
     {
       AssertJUnit.assertEquals(seqgroupsString[p].getName(),