X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=982c399a62b7aeab93cd37ed9cac6bcc679682bb;hb=51728d3951398f9c12d7017c776953f17322cc68;hp=a50ed143888938e947a845a1007f549e719acbee;hpb=5d7968c49365f35b490ca101b838c998df0df675;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index a50ed14..982c399 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -29,12 +29,16 @@ 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.io.File;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -47,9 +51,10 @@ 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;
 
+  private static final int PDB_ID_LENGTH = 4;
 
   public Pdb()
   {
@@ -137,13 +142,19 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
-    String ext = StructureImportSettings.getDefaultStructureFileFormat()
-            .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
+
+    /*
+     * ensure that an mmCIF format structure file is saved with extension.cif,
+     * because the Chimera "open" command recognises this extension
+     */
+    Type pdbFileFormat = StructureImportSettings
+            .getDefaultStructureFileFormat();
+    String ext = pdbFileFormat.getExtension();
+    String fetchFormat = pdbFileFormat.getFormat();
+
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id,
-            StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
-            ext)
-            .getAbsolutePath();
+    File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
+    file = tmpFile.getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -151,10 +162,11 @@ public class Pdb extends EbiFileRetrievedProxy
     }
     try
     {
-
+      // todo get rid of Type and use FileFormatI instead?
+      FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
+              : FileFormat.MMCif;
       pdbAlignment = new FormatAdapter().readFile(file,
-              jalview.io.AppletFormatAdapter.FILE,
-              StructureImportSettings.getDefaultStructureFileFormat());
+              DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -177,8 +189,8 @@ public class Pdb extends EbiFileRetrievedProxy
           {
             // 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());
+            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
+                    + id + SEPARATOR + pdbcs.getName());
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -269,7 +281,6 @@ public class Pdb extends EbiFileRetrievedProxy
     return 0;
   }
 
-
   /**
    * Returns a descriptor for suitable feature display settings with
    * <ul>