JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / test / jalview / structures / models / AAStructureBindingModelTest.java

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 3354e38..9c5657e 100644 (file)
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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;
@@ -57,14 +77,13 @@ public class AAStructureBindingModelTest
   /**
    * Set up test conditions with three aligned sequences,
    */
- @BeforeMethod(alwaysRun = true)
+  @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];
@@ -73,20 +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)
     {
@@ -97,17 +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)
       {
@@ -116,10 +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(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testFindSuperposableResidues()
   {
     SuperposeData[] structs = new SuperposeData[al.getHeight()];
@@ -150,7 +168,7 @@ public class AAStructureBindingModelTest
     assertTrue(matched[5]);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testFindSuperposableResidues_hiddenColumn()
   {
     SuperposeData[] structs = new SuperposeData[al.getHeight()];