X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=7586856ab95c47b59c996e6e041b2f72304ed7f9;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=07df2c4512dfd12ca6680cd27bec416f70a39684;hpb=fefbeb6a7ff8cdce3580749e016bf7980e76679c;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 07df2c4..7586856 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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 <http://www.gnu.org/licenses/>.
  */
 package jalview.ws.dbsources;
 
@@ -21,22 +35,25 @@ import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;
 import jalview.io.FileParse;
-import jalview.ws.DbSourceProxy;
-import jalview.ws.DbSourceProxyImpl;
-import jalview.ws.EBIFetchClient;
+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() {
+  public Pdb()
+  {
     super();
     addDbSourceProperty(DBRefSource.PROTSEQDB);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -45,15 +62,19 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
   {
-    return new Regex("[1-9][0-9A-Za-z]{3}[ _A-Za-z0-9]?");
+    return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   public String getDbSource()
@@ -61,14 +82,19 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return DBRefSource.PDB;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
   {
     return "0";
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
@@ -88,12 +114,17 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     }
     if (queries.length() > 4 && chain == null)
     {
-      chain = queries.substring(4);
+      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();
+    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -101,7 +132,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     }
     try
     {
-      
+
       PDBfile pdbfile = new PDBfile(file,
               jalview.io.AppletFormatAdapter.FILE);
       for (int i = 0; i < pdbfile.chains.size(); i++)
@@ -111,27 +142,27 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
                         .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
+          // 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());
+          // 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);
+           * 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
+          // 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);
@@ -143,7 +174,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
       if (result.size() < 1)
       {
         throw new Exception("No PDB Records for " + id + " chain "
-                + ((chain == null) ? " " : chain));
+                + ((chain == null) ? "' '" : chain));
       }
     } catch (Exception ex) // Problem parsing PDB file
     {
@@ -160,7 +191,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return new Alignment(results);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
@@ -177,4 +210,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return "1QIPA";
   }
 
+  public String getDbName()
+  {
+    return "PDB"; // getDbSource();
+  }
+
 }