JAL-2629 update spike branch to latest

[jalview.git] / src / MCview / PDBChain.java

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);
     }