/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.util.CaseInsensitiveString;
+import java.util.Collections;
+import java.util.Enumeration;
import java.util.Hashtable;
public class PDBEntry
{
+
+ /**
+ * 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;
+ /**
+ * property set when id is a 'manufactured' identifier from the structure data's filename
+ */
+ private static final String FAKED_ID = "faked_pdbid";
+ /**
+ * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+ */
+ private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
+
private String file;
private String type;
public enum Type
{
- PDB, MMCIF, FILE;
+ // TODO is FILE needed; if not is this enum needed, or can we
+ // use FileFormatI for PDB, MMCIF?
+ PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?");
+
+ /*
+ * file extension for cached structure file; must be one that
+ * is recognised by Chimera 'open' command
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+ */
+ String ext;
+
+ /*
+ * format specifier used in dbfetch request
+ * @see http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#pdb
+ */
+ String format;
+
+ private Type(String fmt, String ex)
+ {
+ format = fmt;
+ ext = ex;
+ }
+
+ public String getFormat()
+ {
+ return format;
+ }
+
+ public String getExtension()
+ {
+ return ext;
+ }
+
/**
* case insensitive matching for Type enum
*
}
/**
- * constant for storing chain code in properties table
- */
- private static final String CHAIN_ID = "chain_code";
-
- Hashtable properties;
-
- /**
* Answers true if obj is a PDBEntry with the same id and chain code (both
* ignoring case), file, type and properties
*/
{
}
- /**
- * 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)
{
/**
* @param pdbId
* @param chain
- * @param type
+ * @param entryType
* @param filePath
*/
- void init(String pdbId, String chain, PDBEntry.Type type, String filePath)
+ void init(String pdbId, String chain, PDBEntry.Type entryType,
+ String filePath)
{
this.id = pdbId;
- this.type = type == null ? null : type.toString();
+ this.type = entryType == null ? null : entryType.toString();
this.file = filePath;
setChainCode(chain);
}
id = entry.id;
if (entry.properties != null)
{
- properties = (Hashtable) entry.properties.clone();
+ properties = (Hashtable<String, Object>) entry.properties.clone();
}
}
{
if (!DBRefSource.PDB.equals(dbr.getSource()))
{
- throw new IllegalArgumentException("Invalid source: "
- + dbr.getSource());
+ throw new IllegalArgumentException(
+ "Invalid source: " + dbr.getSource());
}
String pdbId = dbr.getAccessionId();
init(pdbId, chainCode, null, null);
}
- 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();
}
/**
: 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 (properties == null)
+ if (chainCode == null)
{
- if (chainCode == null)
- {
- // nothing to do.
- return;
- }
- properties = new Hashtable();
+ deleteProperty(CHAIN_ID);
}
- if (chainCode == null)
+ else
{
- properties.remove(CHAIN_ID);
- return;
+ setProperty(CHAIN_ID, new CaseInsensitiveString(chainCode));
}
- // update property for non-null chainCode
- properties.put(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
}
/**
+ * 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>
* @param newEntry
* @return true if modifications were made
*/
- protected boolean updateFrom(PDBEntry newEntry)
+ public boolean updateFrom(PDBEntry newEntry)
{
if (this.equals(newEntry))
{
return false; // shouldn't happen
}
- /*
- * id (less any chain code) has to match (ignoring case)
- */
- if (!getId().equalsIgnoreCase(newId))
- {
- return false;
- }
+ boolean idMatches = getId().equalsIgnoreCase(newId);
/*
* Don't update if associated with different structure files
*/
String newFile = newEntry.getFile();
- if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+ if (newFile != null && getFile() != null)
{
- return false;
+ 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
+ if (!newEntry.fakedPDBId() && !isAuthoritative())
+ {
+ return false;
+ } // otherwise we can update
+ }
+ }
+ }
+ else
+ {
+ // one has data, one doesn't ..
+ if (!idMatches)
+ {
+ return false;
+ } // otherwise maybe can update
}
/*
}
/*
- * copy any new properties; notice this may include chain_code,
- * but we excluded differing chain codes earlier
+ * copy any new or modified properties
*/
- if (newEntry.getProperty() != null)
+ Enumeration<String> newProps = newEntry.getProperties();
+ while (newProps.hasMoreElements())
{
- if (properties == null)
+ /*
+ * 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 (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key))
{
- properties = new Hashtable();
+ // we never update the fake ID property
+ continue;
}
- for (Object p : newEntry.getProperty().keySet())
+ if (!value.equals(getProperty(key)))
{
- /*
- * copy properties unless value matches; this defends against changing
- * the case of chain_code which is wrapped in a CaseInsensitiveString
- */
- Object value = newEntry.getProperty().get(p);
- if (!value.equals(properties.get(p)))
- {
- properties.put(p, newEntry.getProperty().get(p));
- }
+ setProperty(key, value);
}
}
return true;
}
+
+ public void setAuthoritative(boolean isAuthoritative)
+ {
+ setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
+ }
+
+ /**
+ *
+ * @return true if the identifier should be preferred over any identifiers
+ * embedded in the structure data
+ */
+ public boolean isAuthoritative()
+ {
+ if (_hasProperty(AUTHORITATIVE_ID))
+ {
+ return ((Boolean)getProperty(AUTHORITATIVE_ID));
+ }
+ return false;
+ }
+
+ /**
+ * set when Jalview has manufactured the ID using a local filename
+ * @return
+ */
+ public boolean fakedPDBId()
+ {
+ if (_hasProperty(FAKED_ID))
+ {
+ return true;
+ }
+ return false;
+ }
+ public void setFakedPDBId(boolean faked)
+ {
+ if (faked)
+ {
+ setProperty(FAKED_ID, Boolean.TRUE);
+ }
+ else
+ {
+ if (properties!=null) {
+ properties.remove(FAKED_ID);
+ }
+ }
+ }
+
+ 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff