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;
{
// TODO is FILE needed; if not is this enum needed, or can we
// use FileFormatI for PDB, MMCIF?
- PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+ PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif", "bcif"),
+ FILE("?", "?");
/*
* file extension for cached structure file; must be one that
// 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;
+ if (!newEntry.fakedPDBId() && !isAuthoritative())
+ {
+ return false;
+ } // otherwise we 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));