/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.io;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.core.util.InputStreamProvider;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
/** The "Sandbox" style of organizing files is to have a directory structure like below, i.e. the files are organized into
* <ul>
* <li>directory with two characters, based on the two middle characters of a PDB ID</li>
* <li>directory of PDB ID</li>
* <li>several files that are available for this PDB ID</li>
* </ul>
*
* <pre>
a1/2a1v/2a1v.cif.gz
a1/2a1v/2a1v.dssp.gz
a1/2a1v/2a1v.pdb-250.jpg.gz
a1/2a1v/2a1v.pdb-500.jpg.gz
a1/2a1v/2a1v.pdb-65.jpg.gz
a1/2a1v/2a1v.pdb-80.jpg.gz
a1/2a1v/2a1v.pdb1-250.jpg.gz
a1/2a1v/2a1v.pdb1-500.jpg.gz
a1/2a1v/2a1v.pdb1-65.jpg.gz
a1/2a1v/2a1v.pdb1-80.jpg.gz
a1/2a1v/2a1v.pdb1.gz
a1/2a1v/2a1v.stride.gz
a1/2a1v/2a1v.xml.gz
a1/2a1v/pdb2a1v.ent.gz
a1/2a1v/r2a1vsf.ent.gz
a1/2a1w/2a1w-deriv.cif.gz
a1/2a1w/2a1w-extatom.xml.gz
a1/2a1w/2a1w-noatom.xml.gz
a1/2a1w/2a1w.cif.gz
a1/2a1w/2a1w.dssp.gz
a1/2a1w/2a1w.pdb-250.jpg.gz
a1/2a1w/2a1w.pdb-500.jpg.gz
a1/2a1w/2a1w.pdb-65.jpg.gz
a1/2a1w/2a1w.pdb-80.jpg.gz
a1/2a1w/2a1w.pdb1-250.jpg.gz
a1/2a1w/2a1w.pdb1-500.jpg.gz
a1/2a1w/2a1w.pdb1-65.jpg.gz
a1/2a1w/2a1w.pdb1-80.jpg.gz
a1/2a1w/2a1w.pdb1.gz
a1/2a1w/2a1w.pdb2-250.jpg.gz
a1/2a1w/2a1w.pdb2-500.jpg.gz
a1/2a1w/2a1w.pdb2-65.jpg.gz
a1/2a1w/2a1w.pdb2-80.jpg.gz
a1/2a1w/2a1w.pdb2.gz
a1/2a1w/2a1w.pdb3-250.jpg.gz
a1/2a1w/2a1w.pdb3-500.jpg.gz
a1/2a1w/2a1w.pdb3-65.jpg.gz
a1/2a1w/2a1w.pdb3-80.jpg.gz
a1/2a1w/2a1w.pdb3.gz
a1/2a1w/2a1w.pdb4-250.jpg.gz
a1/2a1w/2a1w.pdb4-500.jpg.gz
a1/2a1w/2a1w.pdb4-65.jpg.gz
a1/2a1w/2a1w.pdb4-80.jpg.gz
a1/2a1w/2a1w.pdb4.gz
a1/2a1w/2a1w.pdb5-250.jpg.gz
a1/2a1w/2a1w.pdb5-500.jpg.gz
a1/2a1w/2a1w.pdb5-65.jpg.gz
a1/2a1w/2a1w.pdb5-80.jpg.gz
a1/2a1w/2a1w.pdb5.gz
a1/2a1w/2a1w.pdb6-250.jpg.gz
a1/2a1w/2a1w.pdb6-500.jpg.gz
a1/2a1w/2a1w.pdb6-65.jpg.gz
a1/2a1w/2a1w.pdb6-80.jpg.gz
a1/2a1w/2a1w.pdb6.gz
a1/2a1w/2a1w.stride.gz
a1/2a1w/2a1w.xml.gz
a1/2a1w/pdb2a1w.ent.gz
a1/2a1w/r2a1wsf.ent.gz
a1/2a1x/2a1x-deriv.cif.gz
a1/2a1x/2a1x-extatom.xml.gz
a1/2a1x/2a1x-noatom.xml.gz
</pre>
*
*
* @author Andreas Prlic
*
*
*@ since3.2
*/
public class SandboxStyleStructureProvider implements StructureProvider {
FileParsingParameters params ;
String path;
public static final String fileSeparator = System.getProperty("file.separator");
public SandboxStyleStructureProvider() {
params = new FileParsingParameters();
UserConfiguration config = new UserConfiguration();
setPath(config.getPdbFilePath());
}
/** directory where to find PDB files */
public void setPath(String p){
path = p ;
if ( ! (path.endsWith(fileSeparator) ) )
path = path + fileSeparator;
}
@Override
public Structure getStructureById(String pdbId) throws IOException,StructureException {
if (pdbId == null || pdbId.length()< 4)
throw new StructureException("This does not look like a valid PDB ID! (" + pdbId + ")");
pdbId = pdbId.toLowerCase();
String middle = pdbId.substring(1,3).toLowerCase();
File f = new File(path + fileSeparator + middle + fileSeparator + pdbId + fileSeparator + "pdb" + pdbId + ".ent.gz");
if (! f.exists()){
}
InputStreamProvider isp = new InputStreamProvider();
InputStream inputStream = isp.getInputStream(f);
PDBFileParser pdbpars = new PDBFileParser();
pdbpars.setFileParsingParameters(params);
Structure struc = pdbpars.parsePDBFile(inputStream) ;
return struc ;
// something is wrong with the file!
// it probably should be downloaded again...
// TODO: add auto-download functionality...
}
@Override
public void setFileParsingParameters(FileParsingParameters params) {
this.params = params;
}
@Override
public FileParsingParameters getFileParsingParameters() {
return params;
}
/** Returns a list of all PDB IDs that are available in this installation
*
* @return a list of PDB IDs
*/
public List<String> getAllPDBIDs() throws IOException{
File f = new File(path);
if ( ! f.isDirectory())
throw new IOException("Path " + path + " is not a directory!");
String[] dirName = f.list();
List<String>pdbIds = new ArrayList<String>();
for (String dir : dirName) {
File d2= new File(f,dir);
if ( ! d2.isDirectory())
continue;
String[] pdbDirs = d2.list();
for (String pdbId : pdbDirs) {
if ( ! pdbIds.contains(pdbId))
pdbIds.add(pdbId);
}
}
return pdbIds;
}
}