JAL-1894 update year/version in copyright

[jalview.git] / test / jalview / structure / Mapping.java

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 74dddb4..5397c48 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -1,14 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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.structure;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import MCview.PDBfile;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
@@ -17,6 +31,12 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
+
 public class Mapping
 {
 
@@ -27,7 +47,7 @@ public class Mapping
    * 115 in PDB Res Numbering secondary structure numbers in jmol seem to be in
    * msd numbering, not pdb res numbering.
    */
-  @Test(enabled = false)
+  @Test(groups = { "Functional" }, enabled = false)
   public void pdbEntryPositionMap() throws Exception
   {
     Assert.fail("This test intentionally left to fail");
@@ -43,15 +63,12 @@ public class Mapping
       // original numbers taken from
       // http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html
       // these are in numbering relative to the subsequence above
-      int coils[] =
-      { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
-      { 303, 315 }, sheets[] = new int[]
-      { 267, 268, 269, 270 };
+      int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
+      { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
 
       StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-      PDBfile pmap = ssm.setMapping(true, new SequenceI[]
-      { uprot }, new String[]
-      { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
+      PDBfile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+              new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
               jalview.io.FormatAdapter.FILE);
       assertTrue(pmap != null);
       SequenceI protseq = pmap.getSeqsAsArray()[0];
@@ -109,7 +126,7 @@ public class Mapping
     }
   }
 
-  @Test(enabled = false)
+  @Test(groups = { "Functional" }, enabled = false)
   public void testPDBentryMapping() throws Exception
   {
     Assert.fail("This test intentionally left to fail");
@@ -121,8 +138,7 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
-    PDBfile pde = ssm.setMapping(true, new SequenceI[]
-    { sq }, new String[]
+    PDBfile pde = ssm.setMapping(true, new SequenceI[] { sq }, new String[]
     { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
@@ -194,8 +210,7 @@ public class Mapping
             Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
             assertEquals("Non-equivalent annotation element at " + p + "("
                     + rseqpos + ")" + " expected at " + fpos + " (alIndex "
-                    + tanpos + ")",
-                    a == null ? a : a.toString(),
+                    + tanpos + ")", a == null ? a : a.toString(),
                     b == null ? b : b.toString());
             System.out.print("(" + a + "|" + b + ")");
           }
@@ -210,7 +225,7 @@ public class Mapping
    * transform
    * 
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void mapFer1From3W5V() throws Exception
   {
     AlignFrame seqf = new FileLoader(false)
@@ -219,9 +234,8 @@ public class Mapping
                     FormatAdapter.PASTE, "FASTA");
     SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[]
-    { newseq }, new String[]
-    { null }, "examples/3W5V.pdb",
+    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+            new String[] { null }, "examples/3W5V.pdb",
             jalview.io.FormatAdapter.FILE);
     if (pmap == null)
     {
@@ -233,7 +247,7 @@ public class Mapping
    * compare reference annotation for imported pdb sequence to identical
    * seuqence with transferred annotation from mapped pdb file
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
     AlignFrame ref = new FileLoader(false)
@@ -248,9 +262,8 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     ssm.setProcessSecondaryStructure(true);
     ssm.setAddTempFacAnnot(true);
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[]
-    { newseq }, new String[]
-    { null }, "test/jalview/ext/jmol/1QCF.pdb",
+    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+            new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
             jalview.io.FormatAdapter.FILE);
     assertTrue(pmap != null);
     assertEquals("Original and copied sequence of different lengths.",