X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;fp=src%2FMCview%2FPDBChain.java;h=8944f237afb12f9e92c09ac6dd3f18a5ca68ab8c;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=aeb48008f51fa8350fd56f54b6ff7dc3aded716a;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index aeb4800..8944f23 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -98,8 +98,9 @@ public class PDBChain
 
   /**
    * Annotate the residues with their corresponding positions in s1 using the
-   * alignment in as
-   * NOTE: This clears all atom.alignmentMapping values on the structure.
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
+   * 
    * @param as
    * @param s1
    */
@@ -108,8 +109,9 @@ public class PDBChain
     int pdbpos = as.getSeq2Start() - 2;
     int alignpos = s1.getStart() + as.getSeq1Start() - 3;
     // first clear out any old alignmentMapping values:
-    for (Atom atom: (Vector<Atom>) atoms) { 
-      atom.alignmentMapping=-1;
+    for (Atom atom : (Vector<Atom>) atoms)
+    {
+      atom.alignmentMapping = -1;
     }
     // and now trace the alignment onto the atom set.
     for (int i = 0; i < as.astr1.length(); i++)
@@ -247,7 +249,7 @@ public class PDBChain
   {
     int count = 0;
     Object symbol;
-    boolean deoxyn=false;
+    boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
@@ -302,10 +304,13 @@ public class PDBChain
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
         String nucname = tmpat.resName.trim();
-        // use the aaIndex rather than call 'toLower' - which would take a bit more time.
-        deoxyn=nucname.length()==2 && ResidueProperties.aaIndex[nucname.charAt(0)]==ResidueProperties.aaIndex['D'];
+        // use the aaIndex rather than call 'toLower' - which would take a bit
+        // more time.
+        deoxyn = nucname.length() == 2
+                && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
         if (tmpat.name.equalsIgnoreCase("CA")
-                || ResidueProperties.nucleotideIndex[nucname.charAt((deoxyn ? 1 : 0))] == -1)
+                || ResidueProperties.nucleotideIndex[nucname
+                        .charAt((deoxyn ? 1 : 0))] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +