From 24e0210e437c1dcfd36dd0080613327284c76b8e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Sep 2016 13:13:46 +0100
Subject: [PATCH] JAL-1803 chainCode moved onto property hashtable as
 chain_code

---
 src/jalview/datamodel/PDBEntry.java |   92 +++++++++++++++++++++++++++++++----
 1 file changed, 82 insertions(+), 10 deletions(-)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 1c7df49..673c12a 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -30,13 +30,69 @@ public class PDBEntry
 
   private String id;
 
-  private String chainCode;
-
   public enum Type
   {
-    PDB, MMCIF, FILE
+    PDB, MMCIF, FILE;
+    /**
+     * case insensitive matching for Type enum
+     * 
+     * @param value
+     * @return
+     */
+    public static Type getType(String value)
+    {
+      for (Type t : Type.values())
+      {
+        if (t.toString().equalsIgnoreCase(value))
+        {
+          return t;
+        }
+      }
+      return null;
+    }
+
+    /**
+     * case insensitive equivalence for strings resolving to PDBEntry type
+     * 
+     * @param t
+     * @return
+     */
+    public boolean matches(String t)
+    {
+      return (this.toString().equalsIgnoreCase(t));
+    }
   }
 
+  public final class ChainId
+  {
+    String chainId;
+
+    public ChainId(String chainId)
+    {
+      this.chainId = chainId;
+    }
+
+    @Override
+    public String toString()
+    {
+      return chainId;
+    }
+
+    @Override
+    public boolean equals(Object o){
+      if (o==null)
+      {
+        return false;
+      }
+      return chainId.equalsIgnoreCase(o.toString());
+    }
+  }
+
+  /**
+   * constant for storing chain code in properties table
+   */
+  private static final String CHAIN_ID = "chain_code";
+
   Hashtable properties;
 
   /*
@@ -60,9 +116,6 @@ public class PDBEntry
             .equals(type)))
             && (id == o.id || (id != null && o.id != null && o.id
                     .equalsIgnoreCase(id)))
-            && (chainCode == o.chainCode || (chainCode != null
-                    && o.chainCode != null && o.chainCode
-                      .equalsIgnoreCase(chainCode)))
             && (properties == o.properties || (properties != null
                     && o.properties != null && properties
                       .equals(o.properties)));
@@ -91,9 +144,9 @@ public class PDBEntry
           String filePath)
   {
     this.id = pdbId;
-    this.chainCode = chain;
     this.type = type == null ? null : type.toString();
     this.file = filePath;
+    setChainCode(chain);
   }
 
   /**
@@ -106,7 +159,6 @@ public class PDBEntry
     file = entry.file;
     type = entry.type;
     id = entry.id;
-    chainCode = entry.chainCode;
     if (entry.properties != null)
     {
       properties = (Hashtable) entry.properties.clone();
@@ -158,14 +210,34 @@ public class PDBEntry
     return properties;
   }
 
+  /**
+   * 
+   * @return null or a string for associated chain IDs
+   */
   public String getChainCode()
   {
-    return chainCode;
+    return (properties == null || properties.get(CHAIN_ID) == null) ? null
+            : properties.get(CHAIN_ID).toString();
   }
 
   public void setChainCode(String chainCode)
   {
-    this.chainCode = chainCode;
+    if (properties == null)
+    {
+      if (chainCode == null)
+      {
+        // nothing to do.
+        return;
+      }
+      properties = new Hashtable();
+    }
+    if (chainCode == null)
+    {
+      properties.remove(CHAIN_ID);
+      return;
+    }
+    // update property for non-null chainCode
+    properties.put(CHAIN_ID, new ChainId(chainCode));
   }
 
   @Override
-- 
1.7.10.2