X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=37dfdbf14057f4184b9fdf36a5ee5183d8976fdf;hb=ea1b74357e517baef19ef6f862bc7775f7a7804e;hp=12ed4e0503e1a3ef260817085687105612fca011;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 12ed4e0..37dfdbf 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,39 +1,70 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import java.util.Hashtable;
 
 public class PDBEntry
 {
-  String file;
+  private String file;
 
-  String type;
+  private String type;
 
-  String id;
+  private String id;
 
-  Hashtable properties;
+  private String chainCode;
+
+  public enum Type
+  {
+    // TODO is FILE needed; if not is this needed or can we
+    // use FileFormatI for PDB, MMCIF?
+    PDB("pdb", "xml"), MMCIF("mmcif", "mmcif"), FILE("?", "?");
+    String ext;
+
+    String format;
+
+    private Type(String fmt, String ex)
+    {
+      format = fmt;
+      ext = ex;
+    }
+
+    public String getFormat()
+    {
+      return format;
+    }
+    public String getExtension()
+    {
+      return ext;
+    }
+  }
+
+  Hashtable<String, String> properties;
 
   /*
    * (non-Javadoc)
    * 
    * @see java.lang.Object#equals(java.lang.Object)
    */
+  @Override
   public boolean equals(Object obj)
   {
     if (obj == null || !(obj instanceof PDBEntry))
@@ -41,28 +72,61 @@ public class PDBEntry
       return false;
     }
     if (obj == this)
+    {
       return true;
+    }
     PDBEntry o = (PDBEntry) obj;
-    return (file == o.file || (file != null && o.file != null && o.file
-            .equals(file)))
-            && (type == o.type || (type != null && o.type != null && o.type
-                    .equals(type)))
+    return (type == o.type || (type != null && o.type != null && o.type
+            .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)));
+
   }
 
+  /**
+   * Default constructor
+   */
   public PDBEntry()
   {
   }
 
+  /**
+   * Constructor given file path and PDB id.
+   * 
+   * @param filePath
+   */
+  // public PDBEntry(String filePath, String pdbId)
+  // {
+  // this.file = filePath;
+  // this.id = pdbId;
+  // }
+
+  public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
+          String filePath)
+  {
+    this.id = pdbId;
+    this.chainCode = chain;
+    this.type = type == null ? null : type.toString();
+    this.file = filePath;
+  }
+
+  /**
+   * Copy constructor.
+   * 
+   * @param entry
+   */
   public PDBEntry(PDBEntry entry)
   {
     file = entry.file;
     type = entry.type;
     id = entry.id;
+    chainCode = entry.chainCode;
     if (entry.properties != null)
     {
       properties = (Hashtable) entry.properties.clone();
@@ -79,9 +143,14 @@ public class PDBEntry
     return file;
   }
 
-  public void setType(String type)
+  public void setType(String t)
+  {
+    this.type = t;
+  }
+
+  public void setType(PDBEntry.Type type)
   {
-    this.type = type;
+    this.type = type == null ? null : type.toString();
   }
 
   public String getType()
@@ -104,9 +173,24 @@ public class PDBEntry
     this.properties = property;
   }
 
-  public Hashtable getProperty()
+  public Hashtable<String, String> getProperty()
   {
     return properties;
   }
 
+  public String getChainCode()
+  {
+    return chainCode;
+  }
+
+  public void setChainCode(String chainCode)
+  {
+    this.chainCode = chainCode;
+  }
+
+  @Override
+  public String toString()
+  {
+    return id;
+  }
 }