*/
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)
.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)));
String filePath)
{
this.id = pdbId;
- this.chainCode = chain;
this.type = type == null ? null : type.toString();
this.file = filePath;
+ setChainCode(chain);
}
/**
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()
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff