X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=11fe95e36330a721254024d17bde26b939ecdb4d;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=3fd7541fb25fbb2fa76efe29f634e16b823dca3e;hpb=a6b324e3f5edac3df0b968f0037b1cc8b651598e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 3fd7541..11fe95e 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -20,19 +20,22 @@
  */
 package jalview.ws.dbsources;
 
+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.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
 
@@ -42,6 +45,12 @@ import com.stevesoft.pat.Regex;
  */
 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();
@@ -55,7 +64,6 @@ public class Pdb extends EbiFileRetrievedProxy
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -101,31 +109,41 @@ public class Pdb extends EbiFileRetrievedProxy
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     AlignmentI pdbAlignment = null;
-    Vector result = new Vector();
     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)
     {
@@ -135,7 +153,8 @@ public class Pdb extends EbiFileRetrievedProxy
     {
 
       pdbAlignment = new FormatAdapter().readFile(file,
-              jalview.io.AppletFormatAdapter.FILE, "PDB");
+              jalview.io.AppletFormatAdapter.FILE,
+              StructureImportSettings.getDefaultStructureFileFormat());
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -150,16 +169,16 @@ public class Pdb extends EbiFileRetrievedProxy
               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
             /*
@@ -230,12 +249,12 @@ public class Pdb extends EbiFileRetrievedProxy
   }
 
   /**
-   * obtain human glyoxalase chain A sequence
+   * human glyoxalase
    */
   @Override
   public String getTestQuery()
   {
-    return "1QIPA";
+    return "1QIP";
   }
 
   @Override
@@ -249,4 +268,19 @@ public class Pdb extends EbiFileRetrievedProxy
   {
     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();
+  }
 }