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
*
}
}
-
/**
* Answers true if obj is a PDBEntry with the same id and chain code (both
* ignoring case), file, type and properties
{
}
-
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
String filePath)
{
* @param entryType
* @param filePath
*/
- void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+ void init(String pdbId, String chain, PDBEntry.Type entryType,
+ String filePath)
{
this.id = pdbId;
this.type = entryType == null ? null : entryType.toString();
{
if (!DBRefSource.PDB.equals(dbr.getSource()))
{
- throw new IllegalArgumentException("Invalid source: "
- + dbr.getSource());
+ throw new IllegalArgumentException(
+ "Invalid source: " + dbr.getSource());
}
String pdbId = dbr.getAccessionId();
return false; // shouldn't happen
}
- /*
- * id 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
}
/*
*/
String key = newProps.nextElement();
Object value = newEntry.getProperty(key);
+ if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key))
+ {
+ // we never update the fake ID property
+ continue;
+ }
if (!value.equals(getProperty(key)))
{
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