Merge branch 'bug/JAL-3760_protsTreatedAsNucleotides' into releases/Release_2_11_1_Branch

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

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index ff745ac..533c0af 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -30,18 +30,29 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TaylorColourScheme;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
+import java.util.List;
 import java.util.Vector;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBChainTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   PDBChain c;
 
   final Atom a1 = new Atom(1f, 2f, 3f);
@@ -56,7 +67,7 @@ public class PDBChainTest
   public void setUp()
   {
     System.out.println("setup");
-    StructureViewSettings.setShowSeqFeatures(true);
+    StructureImportSettings.setShowSeqFeatures(true);
     c = new PDBChain("1GAQ", "A");
   }
 
@@ -80,7 +91,7 @@ public class PDBChainTest
     a3.resName = "ASP";
     a3.resNumber = 41;
 
-    Vector<Bond> v = new Vector<Bond>();
+    Vector<Bond> v = new Vector<>();
     v.add(new Bond(a1, a2));
     v.add(new Bond(a2, a3));
     v.add(new Bond(a3, a1));
@@ -223,7 +234,7 @@ public class PDBChainTest
   @Test(groups = { "Functional" })
   public void testMakeResidueList_noAnnotation()
   {
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     c.isNa = true;
     atoms.add(makeAtom(4, "N", "MET"));
@@ -248,19 +259,19 @@ public class PDBChainTest
     /*
      * check sequence features
      */
-    SequenceFeature[] sfs = c.sequence.getSequenceFeatures();
-    assertEquals(3, sfs.length);
-    assertEquals("RESNUM", sfs[0].type);
-    assertEquals("MET:4 1gaqA", sfs[0].description);
-    assertEquals(4, sfs[0].begin);
-    assertEquals(4, sfs[0].end);
-    assertEquals("RESNUM", sfs[0].type);
-    assertEquals("LYS:5 1gaqA", sfs[1].description);
-    assertEquals(5, sfs[1].begin);
-    assertEquals(5, sfs[1].end);
-    assertEquals("LEU:6 1gaqA", sfs[2].description);
-    assertEquals(6, sfs[2].begin);
-    assertEquals(6, sfs[2].end);
+    List<SequenceFeature> sfs = c.sequence.getSequenceFeatures();
+    assertEquals(3, sfs.size());
+    assertEquals("RESNUM", sfs.get(0).type);
+    assertEquals("MET:4 1gaqA", sfs.get(0).description);
+    assertEquals(4, sfs.get(0).begin);
+    assertEquals(4, sfs.get(0).end);
+    assertEquals("RESNUM", sfs.get(0).type);
+    assertEquals("LYS:5 1gaqA", sfs.get(1).description);
+    assertEquals(5, sfs.get(1).begin);
+    assertEquals(5, sfs.get(1).end);
+    assertEquals("LEU:6 1gaqA", sfs.get(2).description);
+    assertEquals(6, sfs.get(2).begin);
+    assertEquals(6, sfs.get(2).end);
   }
 
   private Atom makeAtom(int resnum, String name, String resname)
@@ -281,7 +292,7 @@ public class PDBChainTest
   @Test(groups = { "Functional" })
   public void testMakeResidueList_withTempFactor()
   {
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
     atoms.get(atoms.size() - 1).tfactor = 1f;
@@ -296,7 +307,7 @@ public class PDBChainTest
     atoms.add(makeAtom(5, "CA", "LYS"));
     atoms.get(atoms.size() - 1).tfactor = 9f;
     atoms.add(makeAtom(6, "O", "LEU"));
-    atoms.get(atoms.size() - 1).tfactor = 4f;
+    atoms.get(atoms.size() - 1).tfactor = -4f;
     atoms.add(makeAtom(6, "N", "LEU"));
     atoms.get(atoms.size() - 1).tfactor = 5f;
     atoms.add(makeAtom(6, "CA", "LEU"));
@@ -309,7 +320,7 @@ public class PDBChainTest
 
     /*
      * Verify annotations; note the tempFactor is read from the first atom in
-     * each residue i.e. we expect values 1, 7, 4 for the residues
+     * each residue i.e. we expect values 1, 7, -4 for the residues
      */
     AlignmentAnnotation[] ann = c.sequence.getAnnotation();
     assertEquals(1, ann.length);
@@ -317,12 +328,12 @@ public class PDBChainTest
     assertEquals("Temperature Factor for 1gaqA", ann[0].description);
     assertSame(c.sequence, ann[0].sequenceRef);
     assertEquals(AlignmentAnnotation.LINE_GRAPH, ann[0].graph);
-    assertEquals(0f, ann[0].graphMin, 0.001f);
+    assertEquals(-4f, ann[0].graphMin, 0.001f);
     assertEquals(7f, ann[0].graphMax, 0.001f);
     assertEquals(3, ann[0].annotations.length);
     assertEquals(1f, ann[0].annotations[0].value, 0.001f);
     assertEquals(7f, ann[0].annotations[1].value, 0.001f);
-    assertEquals(4f, ann[0].annotations[2].value, 0.001f);
+    assertEquals(-4f, ann[0].annotations[2].value, 0.001f);
   }
 
   /**
@@ -333,7 +344,7 @@ public class PDBChainTest
   public void testMakeCaBondList()
   {
     c.isNa = true;
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
     atoms.add(makeAtom(4, "CA", "MET"));
@@ -364,7 +375,7 @@ public class PDBChainTest
   public void testMakeCaBondList_nucleotide()
   {
     c.isNa = false;
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "G"));
     atoms.add(makeAtom(4, "P", "G"));
@@ -395,7 +406,7 @@ public class PDBChainTest
   @Test(groups = { "Functional" })
   public void testMakeExactMapping()
   {
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
     atoms.add(makeAtom(4, "CA", "MET"));