X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=11fe95e36330a721254024d17bde26b939ecdb4d;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=af8676f57ec7631e2447ac5d435e8653dee8f0f5;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index af8676f..11fe95e 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,49 +1,59 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.
  * 
  * 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.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.FormatAdapter;
+import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureImportSettings;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
 
-import java.util.Vector;
-
-import MCview.PDBChain;
-import MCview.PDBfile;
+import java.util.ArrayList;
+import java.util.List;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.datamodel.AlignmentI;
-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);
   }
 
   /*
@@ -51,9 +61,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -62,6 +72,7 @@ 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]?)");
@@ -72,6 +83,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.PDB;
@@ -82,6 +94,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
+  @Override
   public String getDbVersion()
   {
     return "0";
@@ -92,34 +105,45 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-
-    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;
     }
+    String ext = StructureImportSettings.getDefaultStructureFileFormat()
+            .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+    file = ebi.fetchDataAsFile(
+            "pdb:" + id,
+            StructureImportSettings.getDefaultStructureFileFormat()
+                    .toLowerCase(), ext).getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -128,62 +152,88 @@ 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++)
+      pdbAlignment = new FormatAdapter().readFile(file,
+              jalview.io.AppletFormatAdapter.FILE,
+              StructureImportSettings.getDefaultStructureFileFormat());
+      if (pdbAlignment != null)
       {
-        if (chain == null
-                || ((PDBChain) pdbfile.chains.elementAt(i)).id
-                        .toUpperCase().equals(chain))
+        List<SequenceI> toremove = new ArrayList<SequenceI>();
+        for (SequenceI pdbcs : pdbAlignment.getSequences())
         {
-          PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
-          // 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());
-          // 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);
-           */
-          // 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
-          DBRefEntry dbentry = new DBRefEntry(getDbSource(),
-                  getDbVersion(), id + pdbchain.id);
-          sq.addDBRef(dbentry);
-          // and add seuqence to the retrieved set
-          result.addElement(sq.deriveSequence());
+          String chid = null;
+          // Mapping map=null;
+          for (PDBEntry pid : pdbcs.getAllPDBEntries())
+          {
+            if (pid.getFile() == file)
+            {
+              chid = pid.getChainCode();
+
+            }
+          }
+          if (chain == null
+                  || (chid != null && (chid.equals(chain)
+                          || chid.trim().equals(chain.trim()) || (chain
+                          .trim().length() == 0 && chid.equals("_")))))
+          {
+            // 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
+            /*
+             * 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
+            DBRefEntry dbentry = new DBRefEntry(getDbSource(),
+                    getDbVersion(), (chid == null ? id : id + chid));
+            // dbentry.setMap()
+            pdbcs.addDBRef(dbentry);
+          }
+          else
+          {
+            // 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 (result.size() < 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);
     }
-
-    SequenceI[] results = new SequenceI[result.size()];
-    for (int i = 0, j = result.size(); i < j; i++)
-    {
-      results[i] = (SequenceI) result.elementAt(i);
-      result.setElementAt(null, i);
-    }
-    return new Alignment(results);
+    return pdbAlignment;
   }
 
   /*
@@ -191,6 +241,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     Regex r = getAccessionValidator();
@@ -198,13 +249,15 @@ 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();
@@ -215,4 +268,19 @@ 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();
+  }
 }