JAL-1925 update source version in license

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index e4cc336..52b1323 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -1,9 +1,33 @@
+/*
+ * 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.structure;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -11,17 +35,19 @@ import java.util.Set;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import MCview.PDBfile;
+
 public class StructureSelectionManagerTest
 {
   private StructureSelectionManager ssm;
 
- @BeforeMethod(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     ssm = new StructureSelectionManager();
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRegisterMapping()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
@@ -45,7 +71,7 @@ public class StructureSelectionManagerTest
     assertTrue(ssm.seqmappings.contains(acf2));
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRegisterMappings()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
@@ -72,4 +98,45 @@ public class StructureSelectionManagerTest
     assertTrue(ssm.seqmappings.contains(acf2));
     assertTrue(ssm.seqmappings.contains(acf3));
   }
+
+  /**
+   * Verify that RESNUM sequence features are present after creating a PDB
+   * mapping
+   */
+  @Test(groups = { "Functional" })
+  public void testSetMapping_seqFeatures()
+  {
+    SequenceI seq = new Sequence(
+            "1GAQ|B",
+            "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
+    StructureSelectionManager sm = new StructureSelectionManager();
+    sm.setProcessSecondaryStructure(true);
+    sm.setAddTempFacAnnot(true);
+    PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
+            new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+    assertTrue(pmap != null);
+
+    assertEquals(3, pmap.getSeqs().size());
+    assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
+    assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
+    assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());
+
+    /*
+     * Verify a RESNUM sequence feature in the PDBfile sequence
+     */
+    SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
+    assertEquals("RESNUM", sf.getType());
+    assertEquals("1gaq", sf.getFeatureGroup());
+    assertEquals("GLU:  19  1gaqA", sf.getDescription());
+
+    /*
+     * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
+     * sequence
+     */
+    StructureMapping map = sm.getMapping("examples/1gaq.txt")[0];
+    sf = map.sequence.getSequenceFeatures()[0];
+    assertEquals("RESNUM", sf.getType());
+    assertEquals("1gaq", sf.getFeatureGroup());
+    assertEquals("ALA:   1  1gaqB", sf.getDescription());
+  }
 }