2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.dbsources;
21 import jalview.datamodel.Alignment;
22 import jalview.datamodel.DBRefEntry;
23 import jalview.datamodel.DBRefSource;
24 import jalview.datamodel.SequenceI;
26 import java.util.Vector;
28 import MCview.PDBChain;
29 import MCview.PDBfile;
31 import com.stevesoft.pat.Regex;
33 import jalview.datamodel.AlignmentI;
34 import jalview.ws.ebi.EBIFetchClient;
35 import jalview.ws.seqfetcher.DbSourceProxy;
41 public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
46 addDbSourceProperty(DBRefSource.PROTSEQDB);
52 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
54 public String getAccessionSeparator()
56 // TODO Auto-generated method stub
63 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
65 public Regex getAccessionValidator()
67 return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
73 * @see jalview.ws.DbSourceProxy#getDbSource()
75 public String getDbSource()
77 return DBRefSource.PDB;
83 * @see jalview.ws.DbSourceProxy#getDbVersion()
85 public String getDbVersion()
93 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
95 public AlignmentI getSequenceRecords(String queries) throws Exception
98 Vector result = new Vector();
101 if (queries.indexOf(":") > -1)
103 chain = queries.substring(queries.indexOf(":") + 1);
104 id = queries.substring(0, queries.indexOf(":"));
110 if (queries.length() > 4 && chain == null)
112 chain = queries.substring(4, 5);
113 id = queries.substring(0, 4);
115 if (!isValidReference(id))
117 System.err.println("Ignoring invalid pdb query: '" + id + "'");
121 EBIFetchClient ebi = new EBIFetchClient();
122 file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
131 PDBfile pdbfile = new PDBfile(file,
132 jalview.io.AppletFormatAdapter.FILE);
133 for (int i = 0; i < pdbfile.chains.size(); i++)
136 || ((PDBChain) pdbfile.chains.elementAt(i)).id
137 .toUpperCase().equals(chain))
139 PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
140 // Get the Chain's Sequence - who's dataset includes any special
141 // features added from the PDB file
142 SequenceI sq = pdbchain.sequence;
143 // Specially formatted name for the PDB chain sequences retrieved from
145 sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"
147 // Might need to add more metadata to the PDBEntry object
150 * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
151 * entry.setId(id); if (entry.getProperty() == null)
152 * entry.setProperty(new Hashtable());
153 * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart()
154 * + "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);
157 // We make a DBRefEtntry because we have obtained the PDB file from a
159 // JBPNote - PDB DBRefEntry should also carry the chain and mapping
161 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
162 getDbVersion(), id + pdbchain.id);
163 sq.addDBRef(dbentry);
164 // and add seuqence to the retrieved set
165 result.addElement(sq.deriveSequence());
169 if (result.size() < 1)
171 throw new Exception("No PDB Records for " + id + " chain "
172 + ((chain == null) ? "' '" : chain));
174 } catch (Exception ex) // Problem parsing PDB file
180 SequenceI[] results = new SequenceI[result.size()];
181 for (int i = 0, j = result.size(); i < j; i++)
183 results[i] = (SequenceI) result.elementAt(i);
184 result.setElementAt(null, i);
186 return new Alignment(results);
192 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
194 public boolean isValidReference(String accession)
196 Regex r = getAccessionValidator();
197 return r.search(accession.trim());
201 * obtain human glyoxalase chain A sequence
203 public String getTestQuery()
208 public String getDbName()
210 return "PDB"; // getDbSource();