X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=e6d46da5eb51900857bb29c61a6781d49bfe683b;hb=3d1147ffae5fbc5bdb7c80caa9655df656b8e67b;hp=bcf26be04aa16ed8214163f0eee333d28910a94d;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index bcf26be..e6d46da 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -21,9 +21,9 @@ 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
@@ -50,7 +50,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    */
   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)
@@ -88,9 +88,15 @@ 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();
@@ -114,7 +120,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
           // 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("PDB|" + id + "|" + sq.getName());
+          sq.setName(jalview.datamodel.DBRefSource.PDB+"|" + id + "|" + sq.getName());
           // Might need to add more metadata to the PDBEntry object
           // like below
           /*
@@ -143,7 +149,7 @@ 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
     {
@@ -177,4 +183,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return "1QIPA";
   }
 
+  public String getDbName()
+  {
+    return "PDB"; // getDbSource();
+  }
+
 }