JAL-1645 source formatting and organise imports

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index a352de6..4a50196 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,27 +20,23 @@
  */
 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.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 /**
  * @author JimP
  * 
@@ -144,11 +140,11 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         {
           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();
 
             }
             ;
@@ -193,12 +189,21 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         for (SequenceI pdbcs : toremove)
         {
           pdbfile.deleteSequence(pdbcs);
+          if (pdbcs.getAnnotation() != null)
+          {
+            for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+            {
+              pdbfile.deleteAnnotation(aa);
+            }
+          }
         }
       }
 
       if (pdbfile == null || pdbfile.getHeight() < 1)
       {
-        throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((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