JAL-2952 set negative TempFactor values as AlignmentAnnotation.graphMin

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 29b994e..904a860 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -45,11 +45,11 @@ public class PDBChain
 
   public String id;
 
-  public Vector<Bond> bonds = new Vector<Bond>();
+  public Vector<Bond> bonds = new Vector<>();
 
-  public Vector<Atom> atoms = new Vector<Atom>();
+  public Vector<Atom> atoms = new Vector<>();
 
-  public Vector<Residue> residues = new Vector<Residue>();
+  public Vector<Residue> residues = new Vector<>();
 
   public int offset;
 
@@ -343,12 +343,13 @@ public class PDBChain
     boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuilder seq = new StringBuilder(256);
-    Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
-    Vector<Annotation> resAnnotation = new Vector<Annotation>();
-    int i, iSize = atoms.size() - 1;
+    Vector<SequenceFeature> resFeatures = new Vector<>();
+    Vector<Annotation> resAnnotation = new Vector<>();
+    int iSize = atoms.size() - 1;
     int resNumber = -1;
     char insCode = ' ';
-    for (i = 0; i <= iSize; i++)
+
+    for (int i = 0; i <= iSize; i++)
     {
       Atom tmp = atoms.elementAt(i);
       resNumber = tmp.resNumber;
@@ -362,7 +363,7 @@ public class PDBChain
         offset = resNumber;
       }
 
-      Vector<Atom> resAtoms = new Vector<Atom>();
+      Vector<Atom> resAtoms = new Vector<>();
       // Add atoms to a vector while the residue number
       // remains the same as the first atom's resNumber (res)
       while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
@@ -469,7 +470,8 @@ public class PDBChain
 
     if (StructureImportSettings.isShowSeqFeatures())
     {
-      for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+      iSize = resFeatures.size();
+      for (int i = 0; i < iSize; i++)
       {
         sequence.addSequenceFeature(resFeatures.elementAt(i));
         resFeatures.setElementAt(null, i);
@@ -478,20 +480,20 @@ public class PDBChain
     if (visibleChainAnnotation)
     {
       Annotation[] annots = new Annotation[resAnnotation.size()];
-      float max = 0;
-      for (i = 0, iSize = annots.length; i < iSize; i++)
+      float max = 0f;
+      float min = 0f;
+      iSize = annots.length;
+      for (int i = 0; i < iSize; i++)
       {
         annots[i] = resAnnotation.elementAt(i);
-        if (annots[i].value > max)
-        {
-          max = annots[i].value;
-        }
+        max = Math.max(max, annots[i].value);
+        min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
 
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
               "Temperature Factor", "Temperature Factor for " + pdbid + id,
-              annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+              annots, min, max, AlignmentAnnotation.LINE_GRAPH);
       tfactorann.setSequenceRef(sequence);
       sequence.addAlignmentAnnotation(tfactorann);
     }

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"));