X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=6a6ccd0f7d1904425a7e9dc0476d4f4d088da187;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=69f0d68e54410f2cf8be31ccafefbe6bdad47393;hpb=33d29753b74b33be28fef39da85fc9fbb256f6c8;p=jalview.git

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 69f0d68..6a6ccd0 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -1,63 +1,205 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 jalview.util.CaseInsensitiveString;
+
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.Hashtable;
 
 public class PDBEntry
 {
-  String file;
-  String type;
-  String id;
-  Hashtable properties;
 
-  /* (non-Javadoc)
-   * @see java.lang.Object#equals(java.lang.Object)
+  /**
+   * constant for storing chain code in properties table
+   */
+  private static final String CHAIN_ID = "chain_code";
+
+  private Hashtable<String, Object> properties;
+
+  private static final int PDB_ID_LENGTH = 4;
+
+  private String file;
+
+  private String type;
+
+  private String id;
+
+  public enum Type
+  {
+    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));
+    }
+  }
+
+
+  /**
+   * Answers true if obj is a PDBEntry with the same id and chain code (both
+   * ignoring case), file, type and properties
    */
+  @Override
   public boolean equals(Object obj)
   {
-    if (obj==null || !(obj instanceof PDBEntry))
+    if (obj == null || !(obj instanceof PDBEntry))
     {
-        return false;
+      return false;
     }
-    if (obj==this)
+    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)))
-    && (id==o.id || (id!=null && o.id!=null && o.id.equalsIgnoreCase(id)))
-    && (properties==o.properties || (properties!=null && o.properties!=null && properties.equals(o.properties)));
+
+    /*
+     * note that chain code is stored as a property wrapped by a 
+     * CaseInsensitiveString, so we are in effect doing a 
+     * case-insensitive comparison of chain codes
+     */
+    boolean idMatches = id == o.id
+            || (id != null && id.equalsIgnoreCase(o.id));
+    boolean fileMatches = file == o.file
+            || (file != null && file.equals(o.file));
+    boolean typeMatches = type == o.type
+            || (type != null && type.equals(o.type));
+    if (idMatches && fileMatches && typeMatches)
+    {
+      return properties == o.properties
+              || (properties != null && properties.equals(o.properties));
+    }
+    return false;
   }
+
+  /**
+   * Default constructor
+   */
   public PDBEntry()
-  {}
-  public PDBEntry(PDBEntry entry) {
+  {
+  }
+
+  /**
+   * 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)
+  {
+    init(pdbId, chain, type, filePath);
+  }
+
+  /**
+   * @param pdbId
+   * @param chain
+   * @param entryType
+   * @param filePath
+   */
+  void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+  {
+    this.id = pdbId;
+    this.type = entryType == null ? null : entryType.toString();
+    this.file = filePath;
+    setChainCode(chain);
+  }
+
+  /**
+   * Copy constructor.
+   * 
+   * @param entry
+   */
+  public PDBEntry(PDBEntry entry)
+  {
     file = entry.file;
     type = entry.type;
     id = entry.id;
-    if (entry.properties!=null)
+    if (entry.properties != null)
+    {
+      properties = (Hashtable<String, Object>) entry.properties.clone();
+    }
+  }
+
+  /**
+   * Make a PDBEntry from a DBRefEntry. The accession code is used for the PDB
+   * id, but if it is 5 characters in length, the last character is removed and
+   * set as the chain code instead.
+   * 
+   * @param dbr
+   */
+  public PDBEntry(DBRefEntry dbr)
+  {
+    if (!DBRefSource.PDB.equals(dbr.getSource()))
+    {
+      throw new IllegalArgumentException("Invalid source: "
+              + dbr.getSource());
+    }
+
+    String pdbId = dbr.getAccessionId();
+    String chainCode = null;
+    if (pdbId.length() == PDB_ID_LENGTH + 1)
     {
-      properties = (Hashtable) entry.properties.clone();
+      char chain = pdbId.charAt(PDB_ID_LENGTH);
+      if (('a' <= chain && chain <= 'z') || ('A' <= chain && chain <= 'Z'))
+      {
+        pdbId = pdbId.substring(0, PDB_ID_LENGTH);
+        chainCode = String.valueOf(chain);
+      }
     }
+    init(pdbId, chainCode, null, null);
   }
-  public void setFile(String file)
+
+  public void setFile(String f)
   {
-    this.file = file;
+    this.file = f;
   }
 
   public String getFile()
@@ -65,9 +207,14 @@ 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()
@@ -85,14 +232,211 @@ 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 == 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 (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)
+  {
+    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;
+  }
+
+  /**
+   * Answers true if this object is either equivalent to, or can be 'improved'
+   * by, the given entry.
+   * <p>
+   * If newEntry has the same id (ignoring case), and doesn't have a conflicting
+   * file spec or chain code, then update this entry from its file and/or chain
+   * code.
+   * 
+   * @param newEntry
+   * @return true if modifications were made
+   */
+  public boolean updateFrom(PDBEntry newEntry)
+  {
+    if (this.equals(newEntry))
+    {
+      return true;
+    }
+
+    String newId = newEntry.getId();
+    if (newId == null || getId() == null)
+    {
+      return false; // shouldn't happen
+    }
+
+    /*
+     * id has to match (ignoring case)
+     */
+    if (!getId().equalsIgnoreCase(newId))
+    {
+      return false;
+    }
+
+    /*
+     * Don't update if associated with different structure files
+     */
+    String newFile = newEntry.getFile();
+    if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+    {
+      return false;
+    }
+
+    /*
+     * Don't update if associated with different chains (ignoring case)
+     */
+    String newChain = newEntry.getChainCode();
+    if (newChain != null && newChain.length() > 0 && getChainCode() != null
+            && getChainCode().length() > 0
+            && !getChainCode().equalsIgnoreCase(newChain))
+    {
+      return false;
+    }
+
+    /*
+     * set file path if not already set
+     */
+    String newType = newEntry.getType();
+    if (getFile() == null && newFile != null)
+    {
+      setFile(newFile);
+      setType(newType);
+    }
+
+    /*
+     * set file type if new entry has it and we don't
+     * (for the case where file was not updated)
+     */
+    if (getType() == null && newType != null)
+    {
+      setType(newType);
+    }
+
+    /*
+     * set chain if not already set (we excluded differing 
+     * chains earlier) (ignoring case change only)
+     */
+    if (newChain != null && newChain.length() > 0
+            && !newChain.equalsIgnoreCase(getChainCode()))
+    {
+      setChainCode(newChain);
+    }
+
+    /*
+     * copy any new or modified properties
+     */
+    Enumeration<String> newProps = newEntry.getProperties();
+    while (newProps.hasMoreElements())
+    {
+      /*
+       * copy properties unless value matches; this defends against changing
+       * the case of chain_code which is wrapped in a CaseInsensitiveString
+       */
+      String key = newProps.nextElement();
+      Object value = newEntry.getProperty(key);
+      if (!value.equals(getProperty(key)))
+      {
+        setProperty(key, value);
+      }
+    }
+    return true;
+  }
 }