Merge branch 'JAL-1755_npe_groupconsensus' into develop

[jalview.git] / test / jalview / io / AnnotatedPDBFileInputTest.java

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 7e99409..ef88ca5 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -4,38 +4,47 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
 
 import java.io.File;
-import java.util.Vector;
 
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+
 public class AnnotatedPDBFileInputTest
 {
 
   AlignmentI al;
 
-  String pdbStr = "examples/2GIS.pdb";
+  String pdbStr = "examples/1gaq.txt";
 
   String pdbId;
 
   @Before
   public void setup() throws Exception
   {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
-            .get(0)).getId();
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getPDBId()
+            .get(0).getId();
   }
 
   @Test
@@ -68,11 +77,53 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
       }
     }
   }
 
+  /**
+   * Check sequence features have been added
+   */
+  @Test
+  public void checkPDBSequenceFeatures()
+  {
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    StructureMapping[] mappings = ssm.getMapping("1gaq");
+    // suspect we really want to make assertions on sequence features
+    // in these mappings' sequencess
+    /*
+     * 1GAQ/A
+     */
+    SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
+    assertEquals(296, sf.length);
+    assertEquals("RESNUM", sf[0].getType());
+    assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+    assertEquals("RESNUM", sf[295].getType());
+    assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+
+    /*
+     * 1GAQ/B
+     */
+    sf = al.getSequenceAt(1).getSequenceFeatures();
+    assertEquals(98, sf.length);
+    assertEquals("RESNUM", sf[0].getType());
+    assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+    assertEquals("RESNUM", sf[97].getType());
+    assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+
+    /*
+     * 1GAQ/C
+     */
+    sf = al.getSequenceAt(2).getSequenceFeatures();
+    assertEquals(296, sf.length);
+    assertEquals("RESNUM", sf[0].getType());
+    assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+    assertEquals("RESNUM", sf[295].getType());
+    assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+  }
+
   @Test
   public void checkAnnotationWiring()
   {
@@ -126,7 +177,7 @@ public class AnnotatedPDBFileInputTest
   public void testJalviewProjectRelocationAnnotation() throws Exception
   {
 
-    String inFile = "examples/2GIS.pdb";
+    String inFile = "examples/1gaq.txt";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
@@ -148,7 +199,7 @@ public class AnnotatedPDBFileInputTest
       }
       assertNotNull(sq.getPDBId());
       assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-      for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+      for (PDBEntry pdbentry : sq.getPDBId())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());
@@ -160,7 +211,7 @@ public class AnnotatedPDBFileInputTest
                   && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
           {
             exists = true;
-            if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
+            if (MCview.PDBfile.isCalcIdForFile(ana,
                     pdbentry.getId()))
             {
               found = true;