X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=7c2d2909274363e60b8ff57fc973c369aff834b5;hb=6c96743ff6c65895e4b96523d0e3d05f6dc3cb01;hp=db792e270fd7d6042eac33df4b026f84cc00ad3f;hpb=0e90e35fa87e18e80a340f982110b03c5eccc503;p=jalview.git

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index db792e2..7c2d290 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -20,23 +20,62 @@
  */
 package jalview.datamodel;
 
+import jalview.util.CaseInsensitiveString;
+
+import java.util.Collections;
+import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Map.Entry;
 
 public class PDBEntry
 {
+
+  /**
+   * constant for storing chain code in properties table
+   */
+  private static final String CHAIN_ID = "chain_code";
+
+  Hashtable<String, Object> properties;
+
   private String file;
 
   private String type;
 
   private String id;
 
-  private String chainCode;
-
   public enum Type
   {
-    PDB, 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));
+    }
   }
-  Hashtable properties;
+
 
   /*
    * (non-Javadoc)
@@ -55,18 +94,14 @@ public class PDBEntry
       return true;
     }
     PDBEntry o = (PDBEntry) obj;
-    return
-    (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)));
-    
+
   }
 
   /**
@@ -86,14 +121,14 @@ public class PDBEntry
   // 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;
+    setChainCode(chain);
   }
 
   /**
@@ -106,16 +141,15 @@ public class PDBEntry
     file = entry.file;
     type = entry.type;
     id = entry.id;
-    chainCode = entry.chainCode;
     if (entry.properties != null)
     {
-      properties = (Hashtable) entry.properties.clone();
+      properties = (Hashtable<String, Object>) entry.properties.clone();
     }
   }
 
-  public void setFile(String file)
+  public void setFile(String f)
   {
-    this.file = file;
+    this.file = f;
   }
 
   public String getFile()
@@ -127,6 +161,7 @@ public class PDBEntry
   {
     this.type = t;
   }
+
   public void setType(PDBEntry.Type type)
   {
     this.type = type == null ? null : type.toString();
@@ -147,24 +182,154 @@ public class PDBEntry
     return id;
   }
 
-  public void setProperty(Hashtable property)
+  public void setProperty(String key, Object value)
   {
-    this.properties = property;
+    if (this.properties == null)
+    {
+      this.properties = new Hashtable<String, Object>();
+    }
+    properties.put(key, value);
   }
 
-  public Hashtable getProperty()
+  public Object getProperty(String key)
   {
-    return properties;
+    return properties == null ? null : properties.get(key);
   }
 
+  /**
+   * Returns an enumeration of the keys of this object's properties (or an empty
+   * enumeration if it has no properties)
+   * 
+   * @return
+   */
+  public Enumeration<String> getProperties()
+  {
+    if (properties == null)
+    {
+      return Collections.emptyEnumeration();
+    }
+    return properties.keys();
+  }
+
+  /**
+   * 
+   * @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();
   }
 
+  /**
+   * Sets a non-case-sensitive property for the given chain code. Two PDBEntry
+   * objects which differ only in the case of their chain code are considered
+   * equal. This avoids duplication of objects in lists of PDB ids.
+   * 
+   * @param chainCode
+   */
   public void setChainCode(String chainCode)
   {
-    this.chainCode = chainCode;
+    if (chainCode == null)
+    {
+      deleteProperty(CHAIN_ID);
+    }
+    else
+    {
+      setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode));
+    }
+  }
+
+  /**
+   * Deletes the property with the given key, and returns the deleted value (or
+   * null)
+   */
+  Object deleteProperty(String key)
+  {
+    Object result = null;
+    if (properties != null)
+    {
+      result = properties.remove(key);
+    }
+    return result;
+  }
+
+  @Override
+  public String toString()
+  {
+    return id;
+  }
+
+  /**
+   * Getter provided for Castor binding only. Application code should call
+   * getProperty() or getProperties() instead.
+   * 
+   * @deprecated
+   * @see #getProperty(String)
+   * @see #getProperties()
+   * @see jalview.ws.dbsources.Uniprot#getUniprotEntries
+   * @return
+   */
+  @Deprecated
+  public Hashtable<String, Object> getProps()
+  {
+    return properties;
+  }
+
+  /**
+   * Setter provided for Castor binding only. Application code should call
+   * setProperty() instead.
+   * 
+   * @deprecated
+   * @return
+   */
+  @Deprecated
+  public void setProps(Hashtable<String, Object> props)
+  {
+    properties = props;
   }
 
+  /**
+   * update entry with details from another entry concerning the same PDB
+   * ID/file spec.
+   * 
+   * @param newEntry
+   * @return true if modifications were made
+   */
+  public boolean updateFrom(PDBEntry newEntry)
+  {
+    boolean modified = false;
+
+    if (getFile() == null)
+    {
+      // update file and type of file
+      modified = newEntry.getFile() != null;
+      setFile(newEntry.getFile());
+    }
+    if (newEntry.getType() != null && newEntry.getFile() != null
+            && newEntry.getFile().equals(getFile()))
+    {
+      setType(newEntry.getType());
+    }
+    if (getChainCode() == null
+            || (getChainCode() != null && getChainCode().length() == 0 && newEntry
+                    .getChainCode() != null))
+    {
+      modified |= (getChainCode() == null || !newEntry.getChainCode()
+              .equals(getChainCode()));
+      setChainCode(newEntry.getChainCode());
+    }
+    if (newEntry.properties != null)
+    {
+      for (Entry<String, Object> entry : newEntry.properties.entrySet())
+      {
+        if (!entry.getValue().equals(getProperty(entry.getKey())))
+        {
+          modified = true;
+        }
+        setProperty(entry.getKey(), entry.getValue());
+      }
+    }
+    return modified;
+  }
 }