X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=b432dff58ffaaab1c266cbb5aaa226665541c84e;hb=74aab3b256df66c0dc8785c349565c191d3ef0f8;hp=087a78f61ab3aebef8272255612e555451e2aa32;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 087a78f..b432dff 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,218 +1,212 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-package jalview.ws.dbsources;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-
-import java.io.BufferedInputStream;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import MCview.PDBChain;
-import MCview.PDBfile;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.AlignmentI;
-import jalview.io.FileParse;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-/**
- * @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();
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+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();
+ }
+
+}