3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 package jalview.ws.dbsources;
24 import jalview.api.FeatureSettingsModelI;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.DBRefEntry;
28 import jalview.datamodel.DBRefSource;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.PDBEntry.Type;
31 import jalview.datamodel.SequenceI;
32 import jalview.io.DataSourceType;
33 import jalview.io.FileFormat;
34 import jalview.io.FileFormatI;
35 import jalview.io.FormatAdapter;
36 import jalview.io.PDBFeatureSettings;
37 import jalview.structure.StructureImportSettings;
38 import jalview.util.MessageManager;
39 import jalview.ws.ebi.EBIFetchClient;
41 import java.util.ArrayList;
42 import java.util.List;
44 import com.stevesoft.pat.Regex;
50 public class Pdb extends EbiFileRetrievedProxy
52 private static final String SEPARATOR = "|";
54 private static final String COLON = ":";
56 private static final int PDB_ID_LENGTH = 4;
66 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
69 public String getAccessionSeparator()
77 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
80 public Regex getAccessionValidator()
82 return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
88 * @see jalview.ws.DbSourceProxy#getDbSource()
91 public String getDbSource()
93 return DBRefSource.PDB;
99 * @see jalview.ws.DbSourceProxy#getDbVersion()
102 public String getDbVersion()
110 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
113 public AlignmentI getSequenceRecords(String queries) throws Exception
115 AlignmentI pdbAlignment = null;
118 if (queries.indexOf(COLON) > -1)
120 chain = queries.substring(queries.indexOf(COLON) + 1);
121 id = queries.substring(0, queries.indexOf(COLON));
129 * extract chain code if it is appended to the id and we
130 * don't already have one
132 if (queries.length() > PDB_ID_LENGTH && chain == null)
134 chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
135 id = queries.substring(0, PDB_ID_LENGTH);
138 if (!isValidReference(id))
140 System.err.println("Ignoring invalid pdb query: '" + id + "'");
144 Type pdbFileFormat = StructureImportSettings
145 .getDefaultStructureFileFormat();
146 String ext = "." + pdbFileFormat.getExtension();
147 EBIFetchClient ebi = new EBIFetchClient();
148 file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
157 // todo get rid of Type and use FileFormatI instead?
158 // todo get rid of "ext" and just use "tmp"?
159 FileFormatI fileFormat = pdbFileFormat == Type.PDB ? FileFormat.PDB
161 pdbAlignment = new FormatAdapter().readFile(file,
162 DataSourceType.FILE, fileFormat);
163 if (pdbAlignment != null)
165 List<SequenceI> toremove = new ArrayList<SequenceI>();
166 for (SequenceI pdbcs : pdbAlignment.getSequences())
170 for (PDBEntry pid : pdbcs.getAllPDBEntries())
172 if (pid.getFile() == file)
174 chid = pid.getChainCode();
179 || (chid != null && (chid.equals(chain)
180 || chid.trim().equals(chain.trim()) || (chain
181 .trim().length() == 0 && chid.equals("_")))))
183 // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
184 // TODO: suggest simplify naming to 1qip|A as default name defined
185 pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
186 + id + SEPARATOR + pdbcs.getName());
187 // Might need to add more metadata to the PDBEntry object
190 * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
191 * entry.setId(id); if (entry.getProperty() == null)
192 * entry.setProperty(new Hashtable());
193 * entry.getProperty().put("chains", pdbchain.id + "=" +
194 * sq.getStart() + "-" + sq.getEnd());
195 * sq.getDatasetSequence().addPDBId(entry);
198 // We make a DBRefEtntry because we have obtained the PDB file from
201 // JBPNote - PDB DBRefEntry should also carry the chain and mapping
203 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
204 getDbVersion(), (chid == null ? id : id + chid));
206 pdbcs.addDBRef(dbentry);
210 // mark this sequence to be removed from the alignment
211 // - since it's not from the right chain
215 // now remove marked sequences
216 for (SequenceI pdbcs : toremove)
218 pdbAlignment.deleteSequence(pdbcs);
219 if (pdbcs.getAnnotation() != null)
221 for (AlignmentAnnotation aa : pdbcs.getAnnotation())
223 pdbAlignment.deleteAnnotation(aa);
229 if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
231 throw new Exception(MessageManager.formatMessage(
232 "exception.no_pdb_records_for_chain", new String[] { id,
233 ((chain == null) ? "' '" : chain) }));
236 } catch (Exception ex) // Problem parsing PDB file
247 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
250 public boolean isValidReference(String accession)
252 Regex r = getAccessionValidator();
253 return r.search(accession.trim());
260 public String getTestQuery()
266 public String getDbName()
268 return "PDB"; // getDbSource();
278 * Returns a descriptor for suitable feature display settings with
280 * <li>ResNums or insertions features visible</li>
281 * <li>insertions features coloured red</li>
282 * <li>ResNum features coloured by label</li>
283 * <li>Insertions displayed above (on top of) ResNums</li>
287 public FeatureSettingsModelI getFeatureColourScheme()
289 return new PDBFeatureSettings();