From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Oct 2014 08:25:08 +0000 (+0100)
Subject: JAL-1551 formatting
X-Git-Tag: Jalview_2_9~169^2~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fe14748825261a337ae83b2a070c44aac996c666;p=jalview.git

JAL-1551 formatting
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index c9301e8..6055a5b 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -20,15 +20,20 @@
  */
 package MCview;
 
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
 
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 public class PDBChain
 {
   /**
@@ -187,7 +192,9 @@ public class PDBChain
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
                         : ":" + tx.getStatus()));
         if (tx.begin != 0 && tx.end != 0)
+        {
           sq.addSequenceFeature(tx);
+        }
       }
     }
     return features;
@@ -275,7 +282,7 @@ public class PDBChain
       // remains the same as the first atom's resNumber (res)
       while ((resNumber == res) && (i < atoms.size()))
       {
-        resAtoms.addElement((Atom) atoms.elementAt(i));
+        resAtoms.addElement(atoms.elementAt(i));
         i++;
 
         if (i < atoms.size())
@@ -364,7 +371,9 @@ public class PDBChain
     {
       annots[i] = (Annotation) resAnnotation.elementAt(i);
       if (annots[i].value > max)
+      {
         max = annots[i].value;
+      }
       resAnnotation.setElementAt(null, i);
     }
     AlignmentAnnotation tfactorann = new AlignmentAnnotation(
@@ -496,7 +505,7 @@ public class PDBChain
       {
         int prn = mapping.getPDBResNum(k + 1);
 
-        an[k] = new Annotation((float) prn);
+        an[k] = new Annotation(prn);
         if (min == -1)
         {
           min = k;
@@ -516,7 +525,8 @@ public class PDBChain
       }
       sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
               "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
-              an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
+              an, min, max, AlignmentAnnotation.LINE_GRAPH));
+
     }
   }
 }