From 0e757329af383623b687f00e0a474bc7273b61f3 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 18 Jan 2011 17:40:53 +0000
Subject: [PATCH] javadoc

---
 src/MCview/PDBChain.java |   17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 779b4f0..92a573c 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -66,18 +66,22 @@ public class PDBChain
     this.pdbid = pdbid.toLowerCase();
     this.id = id;
   }
+
   /**
-   * character used to write newlines 
+   * character used to write newlines
    */
   protected String newline = System.getProperty("line.separator");
+
   public void setNewlineString(String nl)
   {
     newline = nl;
   }
+
   public String getNewlineString()
   {
     return newline;
   }
+
   public String print()
   {
     String tmp = "";
@@ -92,6 +96,14 @@ public class PDBChain
     return tmp;
   }
 
+  /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as
+   * 
+   * @param as
+   * @param s1
+   * @return last position in s1 for the last position in the chain
+   */
   public void makeExactMapping(AlignSeq as, SequenceI s1)
   {
     int pdbpos = as.getSeq2Start() - 2;
@@ -286,7 +298,8 @@ public class PDBChain
       if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
       {
         String nucname = tmpat.resName.trim();
-        if (tmpat.name.equalsIgnoreCase("CA") || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
+        if (tmpat.name.equalsIgnoreCase("CA")
+                || ResidueProperties.nucleotideIndex[nucname.charAt(0)] == -1)
         {
           seq.append("X");
           // System.err.println("PDBReader:Null aa3Hash for " +
-- 
1.7.10.2