-/**\r
- * \r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.SequenceI;\r
-\r
-import java.io.BufferedInputStream;\r
-import java.io.InputStream;\r
-import java.io.InputStreamReader;\r
-import java.util.Hashtable;\r
-import java.util.Vector;\r
-\r
-import MCview.PDBChain;\r
-import MCview.PDBfile;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.io.FileParse;\r
-import jalview.ws.EBIFetchClient;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
-\r
-/**\r
- * @author JimP\r
- *\r
- */\r
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy\r
-{\r
- public Pdb() {\r
- super();\r
- addDbSourceProperty(DBRefSource.PROTSEQDB);\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
- */\r
- public Regex getAccessionValidator()\r
- {\r
- return new Regex("[1-9][0-9A-Za-z]{3}[ _A-Za-z0-9]?");\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
- public String getDbSource()\r
- {\r
- return DBRefSource.PDB;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\r
- public String getDbVersion()\r
- {\r
- return "0";\r
- }\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
- */\r
- public AlignmentI getSequenceRecords(String queries) throws Exception\r
- {\r
-\r
- Vector result = new Vector();\r
- String chain = null;\r
- String id = null;\r
- if (queries.indexOf(":") > -1)\r
- {\r
- chain = queries.substring(queries.indexOf(":") + 1);\r
- id = queries.substring(0, queries.indexOf(":"));\r
- }\r
- else\r
- {\r
- id = queries;\r
- }\r
- if (queries.length() > 4 && chain == null)\r
- {\r
- chain = queries.substring(4);\r
- id = queries.substring(0, 4);\r
- }\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw")\r
- .getAbsolutePath();\r
- stopQuery();\r
- if (file == null)\r
- {\r
- return null;\r
- }\r
- try\r
- {\r
- \r
- PDBfile pdbfile = new PDBfile(file,\r
- jalview.io.AppletFormatAdapter.FILE);\r
- for (int i = 0; i < pdbfile.chains.size(); i++)\r
- {\r
- if (chain == null\r
- || ((PDBChain) pdbfile.chains.elementAt(i)).id\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
- 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
- // 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
- */\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
- DBRefEntry dbentry = new DBRefEntry(getDbSource(),\r
- getDbVersion(), id + pdbchain.id);\r
- sq.addDBRef(dbentry);\r
- // and add seuqence to the retrieved set\r
- result.addElement(sq.deriveSequence());\r
- }\r
- }\r
-\r
- if (result.size() < 1)\r
- {\r
- throw new Exception("No PDB Records for " + id + " chain "\r
- + ((chain == null) ? " " : chain));\r
- }\r
- } catch (Exception ex) // Problem parsing PDB file\r
- {\r
- stopQuery();\r
- throw (ex);\r
- }\r
-\r
- SequenceI[] results = new SequenceI[result.size()];\r
- for (int i = 0, j = result.size(); i < j; i++)\r
- {\r
- results[i] = (SequenceI) result.elementAt(i);\r
- result.setElementAt(null, i);\r
- }\r
- return new Alignment(results);\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
- */\r
- public boolean isValidReference(String accession)\r
- {\r
- Regex r = getAccessionValidator();\r
- return r.search(accession.trim());\r
- }\r
-\r
- /**\r
- * obtain human glyoxalase chain A sequence\r
- */\r
- public String getTestQuery()\r
- {\r
- return "1QIPA";\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+
+import java.util.Vector;
+
+import MCview.PDBChain;
+import MCview.PDBfile;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.datamodel.AlignmentI;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * @author JimP
+ *
+ */
+public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+{
+ public Pdb()
+ {
+ super();
+ addDbSourceProperty(DBRefSource.PROTSEQDB);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ public String getAccessionSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ public Regex getAccessionValidator()
+ {
+ return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource()
+ */
+ public String getDbSource()
+ {
+ return DBRefSource.PDB;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ public String getDbVersion()
+ {
+ return "0";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+
+ Vector result = new Vector();
+ String chain = null;
+ String id = null;
+ if (queries.indexOf(":") > -1)
+ {
+ chain = queries.substring(queries.indexOf(":") + 1);
+ id = queries.substring(0, queries.indexOf(":"));
+ }
+ else
+ {
+ id = queries;
+ }
+ if (queries.length() > 4 && chain == null)
+ {
+ chain = queries.substring(4, 5);
+ id = queries.substring(0, 4);
+ }
+ if (!isValidReference(id))
+ {
+ System.err.println("Ignoring invalid pdb query: '" + id + "'");
+ stopQuery();
+ return null;
+ }
+ EBIFetchClient ebi = new EBIFetchClient();
+ file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+ stopQuery();
+ if (file == null)
+ {
+ return null;
+ }
+ try
+ {
+
+ PDBfile pdbfile = new PDBfile(file,
+ jalview.io.AppletFormatAdapter.FILE);
+ for (int i = 0; i < pdbfile.chains.size(); i++)
+ {
+ if (chain == null
+ || ((PDBChain) pdbfile.chains.elementAt(i)).id
+ .toUpperCase().equals(chain))
+ {
+ PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
+ // Get the Chain's Sequence - who's dataset includes any special
+ // features added from the PDB file
+ SequenceI sq = pdbchain.sequence;
+ // Specially formatted name for the PDB chain sequences retrieved from
+ // the PDB
+ sq.setName(jalview.datamodel.DBRefSource.PDB + "|" + id + "|"
+ + sq.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" + sq.getStart()
+ * + "-" + sq.getEnd()); sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+ getDbVersion(), id + pdbchain.id);
+ sq.addDBRef(dbentry);
+ // and add seuqence to the retrieved set
+ result.addElement(sq.deriveSequence());
+ }
+ }
+
+ if (result.size() < 1)
+ {
+ throw new Exception("No PDB Records for " + id + " chain "
+ + ((chain == null) ? "' '" : chain));
+ }
+ } catch (Exception ex) // Problem parsing PDB file
+ {
+ stopQuery();
+ throw (ex);
+ }
+
+ SequenceI[] results = new SequenceI[result.size()];
+ for (int i = 0, j = result.size(); i < j; i++)
+ {
+ results[i] = (SequenceI) result.elementAt(i);
+ result.setElementAt(null, i);
+ }
+ return new Alignment(results);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ public boolean isValidReference(String accession)
+ {
+ Regex r = getAccessionValidator();
+ return r.search(accession.trim());
+ }
+
+ /**
+ * obtain human glyoxalase chain A sequence
+ */
+ public String getTestQuery()
+ {
+ return "1QIPA";
+ }
+
+ public String getDbName()
+ {
+ return "PDB"; // getDbSource();
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff