JAL-3692 unit test (J03321), fixes, dbrefs; todo: protein mappings

[jalview.git] / test / MCview / PDBfileTest.java

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 31c3beb..c07c62e 100644 (file)
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -26,21 +26,34 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.structure.StructureImportSettings;
 
 import java.io.IOException;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBfileTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testIsRna()
   {
@@ -70,7 +83,7 @@ public class PDBfileTest
      * Constructor with file path performs parse()
      */
     PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     assertEquals("3W5V", pf.getId());
     // verify no alignment annotations created
@@ -83,6 +96,8 @@ public class PDBfileTest
     assertEquals("D", pf.getChains().get(3).id);
 
     PDBChain chainA = pf.getChains().get(0);
+    SequenceI seqA = pf.getSeqs().get(0);
+
     assertEquals(0, chainA.seqstart); // not set
     assertEquals(0, chainA.seqend); // not set
     assertEquals(18, chainA.sequence.getStart());
@@ -91,8 +106,8 @@ public class PDBfileTest
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, chainA.sequence.getAllPDBEntries().size());
-    PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
+    assertEquals(1, seqA.getAllPDBEntries().size());
+    PDBEntry pdb = seqA.getAllPDBEntries().get(0);
     assertEquals("A", pdb.getChainCode());
     assertEquals("PDB", pdb.getType());
     assertEquals("3W5V", pdb.getId());
@@ -144,7 +159,7 @@ public class PDBfileTest
   public void testParse_withAnnotations_noSS() throws IOException
   {
     PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
     assertEquals(4, anns.length);
@@ -202,7 +217,7 @@ public class PDBfileTest
   public void testParse_withJmol_noAnnotations() throws IOException
   {
     PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     /*
      * alignment annotations _are_ created anyway (in
@@ -232,7 +247,7 @@ public class PDBfileTest
           throws IOException
   {
     PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     /*
      * Alignment annotations for TempFactor, SecStruct, per sequence (chain)
@@ -251,10 +266,10 @@ public class PDBfileTest
     /*
      * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
      */
-    assertEquals("Secondary Structure for 3W5VA", anns[0].description);
-    assertEquals("Secondary Structure for 3W5VB", anns[2].description);
-    assertEquals("Secondary Structure for 3W5VC", anns[4].description);
-    assertEquals("Secondary Structure for 3W5VD", anns[6].description);
+    assertEquals("Secondary Structure for 3w5vA", anns[0].description);
+    assertEquals("Secondary Structure for 3w5vB", anns[2].description);
+    assertEquals("Secondary Structure for 3w5vC", anns[4].description);
+    assertEquals("Secondary Structure for 3w5vD", anns[6].description);
 
     /*
      * Verify SS annotations are linked to respective sequences (chains)
@@ -290,7 +305,7 @@ public class PDBfileTest
     // TODO requires a mock for Annotate3D processing
     // and/or run as an integration test
     PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
   }
 
   /**
@@ -305,4 +320,17 @@ public class PDBfileTest
     pf.addAnnotations(al);
     return al.getAlignmentAnnotation();
   }
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+  }
 }