X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=7f8c76ca6430a00149fc412d4a7499b04993f17c;hb=12a2da1bc751ed3612bcd022881bf2b6f73bb975;hp=219008d4567769932b154083dcb8ffefeec6b840;hpb=5730402f9459bf91e9eab40755433bc7c85a326d;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 219008d..7f8c76c 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,40 +1,42 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Vector;
 
-import MCview.PDBChain;
-import MCview.PDBfile;
-
 import com.stevesoft.pat.Regex;
 
-import jalview.datamodel.AlignmentI;
-import jalview.io.FormatAdapter;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 /**
  * @author JimP
  * 
@@ -95,7 +97,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    AlignmentI pdbfile = null;
+    AlignmentI pdbAlignment = null;
     Vector result = new Vector();
     String chain = null;
     String id = null;
@@ -129,19 +131,20 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     try
     {
 
-      pdbfile = new FormatAdapter().readFile(file,
+      pdbAlignment = new FormatAdapter().readFile(file,
               jalview.io.AppletFormatAdapter.FILE, "PDB");
-      if (pdbfile != null)
+      if (pdbAlignment != null)
       {
-        for (SequenceI pdbcs : pdbfile.getSequences())
+        List<SequenceI> toremove = new ArrayList<SequenceI>();
+        for (SequenceI pdbcs : pdbAlignment.getSequences())
         {
           String chid = null;
           // Mapping map=null;
-          for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+          for (PDBEntry pid : pdbcs.getAllPDBEntries())
           {
             if (pid.getFile() == file)
             {
-              chid = (String) pid.getProperty().get("CHAIN");
+              chid = pid.getChainCode();
 
             }
             ;
@@ -177,23 +180,38 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
           }
           else
           {
-            // remove this sequence from the alignment - since it's not from the
-            // right chain
-            pdbfile.deleteSequence(pdbcs);
+            // mark this sequence to be removed from the alignment
+            // - since it's not from the right chain
+            toremove.add(pdbcs);
+          }
+        }
+        // now remove marked sequences
+        for (SequenceI pdbcs : toremove)
+        {
+          pdbAlignment.deleteSequence(pdbcs);
+          if (pdbcs.getAnnotation() != null)
+          {
+            for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+            {
+              pdbAlignment.deleteAnnotation(aa);
+            }
           }
         }
       }
-      if (pdbfile == null || pdbfile.getHeight() < 1)
+
+      if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
       {
-        throw new Exception("No PDB Records for " + id + " chain "
-                + ((chain == null) ? "' '" : chain));
+        throw new Exception(MessageManager.formatMessage(
+                "exception.no_pdb_records_for_chain", new String[] { id,
+                    ((chain == null) ? "' '" : chain) }));
       }
+
     } catch (Exception ex) // Problem parsing PDB file
     {
       stopQuery();
       throw (ex);
     }
-    return pdbfile;
+    return pdbAlignment;
   }
 
   /*
@@ -220,4 +238,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return "PDB"; // getDbSource();
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }