Merge branch 'releases/Release_2_10_4_Branch' into develop

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

diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index defcdbc..533c0af 100644 (file)
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -91,7 +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));
@@ -234,7 +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"));
@@ -292,7 +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;
@@ -307,7 +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"));
@@ -320,7 +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);
@@ -328,12 +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);
   }
 
   /**
@@ -344,7 +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"));
@@ -375,7 +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"));
@@ -406,7 +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"));