X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=68dda8862ff7240c56d012e4b47ef6f41445e1d1;hb=2b6a2fdd887521f16ec777aab3126d6209f2a0a6;hp=76e8351066a5f737661176f615ef6cd18d763d8d;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 76e8351..68dda88 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,3 +1,4 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
@@ -20,38 +21,43 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.datamodel.Alignment;
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureImportSettings;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
 
 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
  * 
  */
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+public class Pdb extends EbiFileRetrievedProxy
 {
+  private static final String SEPARATOR = "|";
+
+  private static final String COLON = ":";
+
+  private static final int PDB_ID_LENGTH = 4;
+
   public Pdb()
   {
     super();
-    addDbSourceProperty(DBRefSource.PROTSEQDB);
   }
 
   /*
@@ -59,9 +65,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -70,6 +76,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
     return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
@@ -80,6 +87,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.PDB;
@@ -90,6 +98,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
+  @Override
   public String getDbVersion()
   {
     return "0";
@@ -100,34 +109,44 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    AlignmentI pdbfile = null;
-    Vector result = new Vector();
+    AlignmentI pdbAlignment = null;
     String chain = null;
     String id = null;
-    if (queries.indexOf(":") > -1)
+    if (queries.indexOf(COLON) > -1)
     {
-      chain = queries.substring(queries.indexOf(":") + 1);
-      id = queries.substring(0, queries.indexOf(":"));
+      chain = queries.substring(queries.indexOf(COLON) + 1);
+      id = queries.substring(0, queries.indexOf(COLON));
     }
     else
     {
       id = queries;
     }
-    if (queries.length() > 4 && chain == null)
+
+    /*
+     * extract chain code if it is appended to the id and we
+     * don't already have one
+     */
+    if (queries.length() > PDB_ID_LENGTH && chain == null)
     {
-      chain = queries.substring(4, 5);
-      id = queries.substring(0, 4);
+      chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
+      id = queries.substring(0, PDB_ID_LENGTH);
     }
+
     if (!isValidReference(id))
     {
       System.err.println("Ignoring invalid pdb query: '" + id + "'");
       stopQuery();
       return null;
     }
+    Type pdbFileFormat = StructureImportSettings
+            .getDefaultStructureFileFormat();
+    String ext = "." + pdbFileFormat.getExtension();
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
+            .getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -135,33 +154,36 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     }
     try
     {
-
-      pdbfile = new FormatAdapter().readFile(file,
-              jalview.io.AppletFormatAdapter.FILE, "PDB");
-      if (pdbfile != null)
+      // todo get rid of Type and use FileFormatI instead?
+      // todo get rid of "ext" and just use "tmp"?
+      FileFormatI fileFormat = pdbFileFormat == Type.PDB ? FileFormat.PDB
+              : FileFormat.MMCif;
+      pdbAlignment = new FormatAdapter().readFile(file,
+              DataSourceType.FILE, fileFormat);
+      if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
-        for (SequenceI pdbcs : pdbfile.getSequences())
+        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();
 
             }
-            ;
-
           }
           if (chain == null
                   || (chid != null && (chid.equals(chain)
                           || chid.trim().equals(chain.trim()) || (chain
                           .trim().length() == 0 && chid.equals("_")))))
           {
-            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
-                    + "|" + pdbcs.getName());
+            // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+            // TODO: suggest simplify naming to 1qip|A as default name defined
+            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
+                    + id + SEPARATOR + pdbcs.getName());
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -193,20 +215,22 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         // now remove marked sequences
         for (SequenceI pdbcs : toremove)
         {
-          pdbfile.deleteSequence(pdbcs);
-          if (pdbcs.getAnnotation()!=null)
+          pdbAlignment.deleteSequence(pdbcs);
+          if (pdbcs.getAnnotation() != null)
           {
-            for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+            for (AlignmentAnnotation aa : pdbcs.getAnnotation())
             {
-              pdbfile.deleteAnnotation(aa);
+              pdbAlignment.deleteAnnotation(aa);
             }
           }
         }
       }
 
-      if (pdbfile == null || pdbfile.getHeight() < 1)
+      if (pdbAlignment == null || pdbAlignment.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
@@ -214,7 +238,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
       stopQuery();
       throw (ex);
     }
-    return pdbfile;
+    return pdbAlignment;
   }
 
   /*
@@ -222,6 +246,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     Regex r = getAccessionValidator();
@@ -229,13 +254,15 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
   }
 
   /**
-   * obtain human glyoxalase chain A sequence
+   * human glyoxalase
    */
+  @Override
   public String getTestQuery()
   {
-    return "1QIPA";
+    return "1QIP";
   }
 
+  @Override
   public String getDbName()
   {
     return "PDB"; // getDbSource();
@@ -246,4 +273,19 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
   {
     return 0;
   }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }