*/
package jalview.datamodel;
-import jalview.util.CaseInsensitiveString;
-
import java.util.Collections;
import java.util.Enumeration;
import java.util.Hashtable;
+import jalview.util.CaseInsensitiveString;
+
public class PDBEntry
{
private static final int PDB_ID_LENGTH = 4;
+ private static final String FAKED_ID = "faked_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
{
}
+ /**
+ * Entry point when file is not known and fileType may be string
+ * @param pdbId
+ * @param chain may be null
+ * @param fileType "pdb", "mmcif", or "bcif"; null defaults to mmcif
+ */
+ public PDBEntry(String pdbId, String chain, String fileType) {
+ this.id = pdbId.toLowerCase();
+ setChainCode(chain); // I note that PDB Chains ARE case-sensitive now
+ if (fileType == null)
+ fileType = "mmcif";
+ switch (fileType.toLowerCase()) {
+ case "pdb":
+ this.type = Type.PDB.toString();
+ break;
+ case "mmcif":
+ this.type = Type.MMCIF.toString();
+ break;
+ default:
+ case "bcif":
+ System.out.println("format " + fileType + " has not been implemented; using mmCIF");
+ this.type = Type.MMCIF.toString();
+ break;
+ }
+ }
+
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
String filePath)
{
return id;
}
+ /**
+ * TODO
+ *
+ * @param key "protocol"
+ * @param value
+ */
public void setProperty(String key, Object value)
{
if (this.properties == null)
// 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())
+ {
+ return false;
+ } // otherwise we can update
}
}
}
*/
String key = newProps.nextElement();
Object value = newEntry.getProperty(key);
+ if (FAKED_ID.equals(key))
+ {
+ // we never update the fake ID property
+ continue;
+ }
if (!value.equals(getProperty(key)))
{
setProperty(key, value);
return true;
}
+ /**
+ * 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));