X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=3dff67975023fbd4bf4d4330e580142aa000319e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=8da15259b71de201e48d9e034630cb9939b9b0c4;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 8da1525..3dff679 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,180 +1,218 @@
-/**
- * 
- */
-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.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);
-      id = queries.substring(0, 4);
-    }
-    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";
-  }
-
-}
+/*
+ * 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;
+  }
+}