X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=cb9e656e35ff8e78eb78a898e6f5aa8ddff8b5cd;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=420957766603a9955eaa9ab95f4579c9a3794fa0;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 4209577..cb9e656 100644
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -1,12 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.structures.models;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
-import java.util.Arrays;
-import java.util.List;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -19,6 +35,12 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel.SuperposeData;
 
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 /**
  * Unit tests for non-abstract methods of abstract base class
  * 
@@ -55,14 +77,13 @@ public class AAStructureBindingModelTest
   /**
    * Set up test conditions with three aligned sequences,
    */
-  @BeforeMethod
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     SequenceI seq1 = new Sequence("1YCS", "-VPSQK");
     SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
     SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
-    al = new Alignment(new SequenceI[]
-    { seq1, seq2, seq3 });
+    al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
     al.setDataset(null);
 
     PDBEntry[] pdbFiles = new PDBEntry[3];
@@ -71,20 +92,17 @@ public class AAStructureBindingModelTest
     pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "1OOT.pdb");
     String[][] chains = new String[3][];
     SequenceI[][] seqs = new SequenceI[3][];
-    seqs[0] = new SequenceI[]
-    { seq1 };
-    seqs[1] = new SequenceI[]
-    { seq2 };
-    seqs[2] = new SequenceI[]
-    { seq3 };
+    seqs[0] = new SequenceI[] { seq1 };
+    seqs[1] = new SequenceI[] { seq2 };
+    seqs[2] = new SequenceI[] { seq3 };
     StructureSelectionManager ssm = new StructureSelectionManager();
 
-    ssm.setMapping(new SequenceI[]
-    { seq1 }, null, PDB_1, AppletFormatAdapter.PASTE);
-    ssm.setMapping(new SequenceI[]
-    { seq2 }, null, PDB_2, AppletFormatAdapter.PASTE);
-    ssm.setMapping(new SequenceI[]
-    { seq3 }, null, PDB_3, AppletFormatAdapter.PASTE);
+    ssm.setMapping(new SequenceI[] { seq1 }, null, PDB_1,
+            AppletFormatAdapter.PASTE);
+    ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
+            AppletFormatAdapter.PASTE);
+    ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
+            AppletFormatAdapter.PASTE);
 
     testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
     {
@@ -95,17 +113,19 @@ public class AAStructureBindingModelTest
          * fudge 'filenames' to match those generated when PDBFile parses PASTE
          * data
          */
-        return new String[]
-        { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
+        return new String[] { "INLINE1YCS", "INLINE3A6S", "INLINE1OOT" };
       }
+
       @Override
       public void updateColours(Object source)
       {
       }
+
       @Override
       public void releaseReferences(Object svl)
       {
       }
+
       @Override
       public void highlightAtoms(List<AtomSpec> atoms)
       {
@@ -114,10 +134,10 @@ public class AAStructureBindingModelTest
   }
 
   /**
-   * Verify that the method determines that columns 2, 5 and 6 of the aligment
+   * Verify that the method determines that columns 2, 5 and 6 of the alignment
    * are alignable in structure
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testFindSuperposableResidues()
   {
     SuperposeData[] structs = new SuperposeData[al.getHeight()];
@@ -148,7 +168,7 @@ public class AAStructureBindingModelTest
     assertTrue(matched[5]);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testFindSuperposableResidues_hiddenColumn()
   {
     SuperposeData[] structs = new SuperposeData[al.getHeight()];