merge

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index e4cc336..8e3e086 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -4,6 +4,10 @@ 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;
@@ -11,6 +15,8 @@ import java.util.Set;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import MCview.PDBfile;
+
 public class StructureSelectionManagerTest
 {
   private StructureSelectionManager ssm;
@@ -72,4 +78,46 @@ 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());
+  }
 }