2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.dbsources;
23 import jalview.datamodel.AlignmentAnnotation;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.datamodel.DBRefSource;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.io.AppletFormatAdapter;
30 import jalview.io.FormatAdapter;
31 import jalview.util.MessageManager;
32 import jalview.ws.ebi.EBIFetchClient;
33 import jalview.ws.seqfetcher.DbSourceProxy;
35 import java.util.ArrayList;
36 import java.util.List;
37 import java.util.Vector;
39 import com.stevesoft.pat.Regex;
45 public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
50 addDbSourceProperty(DBRefSource.PROTSEQDB);
56 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
58 public String getAccessionSeparator()
60 // TODO Auto-generated method stub
67 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
69 public Regex getAccessionValidator()
71 return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
77 * @see jalview.ws.DbSourceProxy#getDbSource()
79 public String getDbSource()
81 return DBRefSource.PDB;
87 * @see jalview.ws.DbSourceProxy#getDbVersion()
89 public String getDbVersion()
97 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
99 public AlignmentI getSequenceRecords(String queries) throws Exception
101 AlignmentI pdbfile = null;
102 Vector result = new Vector();
105 if (queries.indexOf(":") > -1)
107 chain = queries.substring(queries.indexOf(":") + 1);
108 id = queries.substring(0, queries.indexOf(":"));
114 if (queries.length() > 4 && chain == null)
116 chain = queries.substring(4, 5);
117 id = queries.substring(0, 4);
119 if (!isValidReference(id))
121 System.err.println("Ignoring invalid pdb query: '" + id + "'");
125 EBIFetchClient ebi = new EBIFetchClient();
126 file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
135 pdbfile = new FormatAdapter().readFile(file,
136 AppletFormatAdapter.FILE, "PDB");
139 List<SequenceI> toremove = new ArrayList<SequenceI>();
140 for (SequenceI pdbcs : pdbfile.getSequences())
144 for (PDBEntry pid : pdbcs.getPDBId())
146 if (pid.getFile() == file)
148 chid = pid.getChainCode();
155 || (chid != null && (chid.equals(chain)
156 || chid.trim().equals(chain.trim()) || (chain
157 .trim().length() == 0 && chid.equals("_")))))
159 pdbcs.setName(DBRefSource.PDB + "|" + id
160 + "|" + pdbcs.getName());
161 // Might need to add more metadata to the PDBEntry object
164 * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
165 * entry.setId(id); if (entry.getProperty() == null)
166 * entry.setProperty(new Hashtable());
167 * entry.getProperty().put("chains", pdbchain.id + "=" +
168 * sq.getStart() + "-" + sq.getEnd());
169 * sq.getDatasetSequence().addPDBId(entry);
172 // We make a DBRefEtntry because we have obtained the PDB file from
175 // JBPNote - PDB DBRefEntry should also carry the chain and mapping
177 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
178 getDbVersion(), (chid == null ? id : id + chid));
180 pdbcs.addDBRef(dbentry);
184 // mark this sequence to be removed from the alignment
185 // - since it's not from the right chain
189 // now remove marked sequences
190 for (SequenceI pdbcs : toremove)
192 pdbfile.deleteSequence(pdbcs);
193 if (pdbcs.getAnnotation()!=null)
195 for (AlignmentAnnotation aa: pdbcs.getAnnotation())
197 pdbfile.deleteAnnotation(aa);
203 if (pdbfile == null || pdbfile.getHeight() < 1)
205 throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
208 } catch (Exception ex) // Problem parsing PDB file
219 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
221 public boolean isValidReference(String accession)
223 Regex r = getAccessionValidator();
224 return r.search(accession.trim());
228 * obtain human glyoxalase chain A sequence
230 public String getTestQuery()
235 public String getDbName()
237 return "PDB"; // getDbSource();