-/**\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
* \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.ws.dbsources;\r
\r
\r
/**\r
* @author JimP\r
- *\r
+ * \r
*/\r
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy\r
{\r
- public Pdb() {\r
+ public Pdb()\r
+ {\r
super();\r
addDbSourceProperty(DBRefSource.PROTSEQDB);\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
*/\r
public String getAccessionSeparator()\r
return null;\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
*/\r
public Regex getAccessionValidator()\r
return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getDbSource()\r
*/\r
public String getDbSource()\r
return DBRefSource.PDB;\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getDbVersion()\r
*/\r
public String getDbVersion()\r
{\r
return "0";\r
}\r
- /* (non-Javadoc)\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
*/\r
public AlignmentI getSequenceRecords(String queries) throws Exception\r
}\r
if (queries.length() > 4 && chain == null)\r
{\r
- chain = queries.substring(4,5);\r
+ chain = queries.substring(4, 5);\r
id = queries.substring(0, 4);\r
}\r
if (!isValidReference(id))\r
{\r
- System.err.println("Ignoring invalid pdb query: '"+id+"'");\r
+ System.err.println("Ignoring invalid pdb query: '" + id + "'");\r
stopQuery();\r
return null;\r
}\r
EBIFetchClient ebi = new EBIFetchClient();\r
- file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw")\r
- .getAbsolutePath();\r
+ file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();\r
stopQuery();\r
if (file == null)\r
{\r
}\r
try\r
{\r
- \r
+\r
PDBfile pdbfile = new PDBfile(file,\r
jalview.io.AppletFormatAdapter.FILE);\r
for (int i = 0; i < pdbfile.chains.size(); i++)\r
.toUpperCase().equals(chain))\r
{\r
PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);\r
- // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file\r
+ // Get the Chain's Sequence - who's dataset includes any special\r
+ // features added from the PDB file\r
SequenceI sq = pdbchain.sequence;\r
- // Specially formatted name for the PDB chain sequences retrieved from the PDB\r
- sq.setName(jalview.datamodel.DBRefSource.PDB+"|" + id + "|" + sq.getName());\r
+ // Specially formatted name for the PDB chain sequences retrieved from\r
+ // the PDB\r
+ sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"\r
+ + sq.getName());\r
// Might need to add more metadata to the PDBEntry object\r
// like below\r
/*\r
- * PDBEntry entry = new PDBEntry();\r
- // Construct the PDBEntry\r
- entry.setId(id);\r
- if (entry.getProperty() == null)\r
- entry.setProperty(new Hashtable());\r
- entry.getProperty().put("chains",\r
- pdbchain.id\r
- + "=" + sq.getStart()\r
- + "-" + sq.getEnd());\r
- sq.getDatasetSequence().addPDBId(entry);\r
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry\r
+ * entry.setId(id); if (entry.getProperty() == null)\r
+ * entry.setProperty(new Hashtable());\r
+ * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart()\r
+ * + "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);\r
*/\r
// Add PDB DB Refs\r
- // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
+ // We make a DBRefEtntry because we have obtained the PDB file from a\r
+ // verifiable source\r
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping\r
+ // information\r
DBRefEntry dbentry = new DBRefEntry(getDbSource(),\r
getDbVersion(), id + pdbchain.id);\r
sq.addDBRef(dbentry);\r
return new Alignment(results);\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
*/\r
public boolean isValidReference(String accession)\r
git://source.jalview.org / jalview.git / blobdiff