+
+ /**
+ * 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
+ }
+
+ boolean idMatches = getId().equalsIgnoreCase(newId);
+
+ /*
+ * Don't update if associated with different structure files
+ */
+ String newFile = newEntry.getFile();
+ if (newFile != null && getFile() != null)
+ {
+ if (!newFile.equals(getFile()))
+ {
+ return false;
+ }
+ else
+ {
+ // files match.
+ if (!idMatches)
+ {
+ // this shouldn't happen, but could do if the id from the
+ // file is not the same as the id from the authority that provided
+ // the file
+ return false;
+ }
+ }
+ }
+ else
+ {
+ // one has data, one doesn't ..
+ if (!idMatches)
+ {
+ return false;
+ } // otherwise maybe can update
+ }
+
+ /*
+ * 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;
+ }
+
+ private boolean _hasProperty(final String key)
+ {
+ return (properties != null && properties.containsKey(key));
+ }
+
+ private static final String RETRIEVE_FROM = "RETRIEVE_FROM";
+
+ private static final String PROVIDER = "PROVIDER";
+
+ private static final String MODELPAGE = "PROVIDERPAGE";
+
+ /**
+ * Permanent URI for retrieving the original structure data
+ *
+ * @param urlStr
+ */
+ public void setRetrievalUrl(String urlStr)
+ {
+ setProperty(RETRIEVE_FROM, urlStr);
+ }
+
+ public boolean hasRetrievalUrl()
+ {
+ return _hasProperty(RETRIEVE_FROM);
+ }
+
+ /**
+ * get the Permanent URI for retrieving the original structure data
+ */
+ public String getRetrievalUrl()
+ {
+ return (String) getProperty(RETRIEVE_FROM);
+ }
+
+ /**
+ * Data provider name - from 3D Beacons
+ *
+ * @param provider
+ */
+ public void setProvider(String provider)
+ {
+ setProperty(PROVIDER, provider);
+ }
+
+ /**
+ * Get Data provider name - from 3D Beacons
+ *
+ */
+ public String getProvider()
+ {
+ return (String) getProperty(PROVIDER);
+ }
+
+ /**
+ * Permanent URI for retrieving the original structure data
+ *
+ * @param urlStr
+ */
+ public void setProviderPage(String urlStr)
+ {
+ setProperty(MODELPAGE, urlStr);
+ }
+
+ /**
+ * get the Permanent URI for retrieving the original structure data
+ */
+ public String getProviderPage()
+ {
+ return (String) getProperty(MODELPAGE);
+ }
+
+ public boolean hasProviderPage()
+ {
+ return _hasProperty(MODELPAGE);
+ }
+
+ public boolean hasProvider()
+ {
+ return _hasProperty(PROVIDER);
+ }