JAL-1551 format and tidy

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

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index a99f172..7d2ceac 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -33,11 +33,12 @@ import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class PDBfile extends jalview.io.AlignFile
 {
-  public Vector chains;
+  public Vector<PDBChain> chains;
 
   public String id;
 
@@ -181,15 +182,15 @@ public class PDBfile extends jalview.io.AlignFile
       }
       for (int i = 0; i < chains.size(); i++)
       {
-        SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+        SequenceI dataset = chains.elementAt(i).sequence;
         dataset.setName(id + "|" + dataset.getName());
         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         entry.setProperty(new Hashtable());
-        if (((PDBChain) chains.elementAt(i)).id != null)
+        if (chains.elementAt(i).id != null)
         {
           entry.getProperty().put("CHAIN",
-                  ((PDBChain) chains.elementAt(i)).id);
+                  chains.elementAt(i).id);
         }
         if (inFile != null)
         {
@@ -406,7 +407,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).makeResidueList();
+      chains.elementAt(i).makeResidueList();
     }
   }
 
@@ -414,7 +415,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).makeCaBondList();
+      chains.elementAt(i).makeCaBondList();
     }
   }
 
@@ -422,9 +423,9 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      if (((PDBChain) chains.elementAt(i)).id.equals(id))
+      if (chains.elementAt(i).id.equals(id))
       {
-        return (PDBChain) chains.elementAt(i);
+        return chains.elementAt(i);
       }
     }
 
@@ -435,7 +436,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChargeColours();
+      chains.elementAt(i).setChargeColours();
     }
   }
 
@@ -443,7 +444,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+      chains.elementAt(i).setChainColours(cs);
     }
   }
 
@@ -451,7 +452,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+      chains.elementAt(i).setChainColours(Color.getHSBColor(
               1.0f / i, .4f, 1.0f));
     }
   }