X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=bb5c1659441b805e9db85eef87060b1b80091083;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=68dda8862ff7240c56d012e4b47ef6f41445e1d1;hpb=2b6a2fdd887521f16ec777aab3126d6209f2a0a6;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 68dda88..bb5c165 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -38,6 +38,7 @@ 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;
 
@@ -141,12 +142,19 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
+
+    /*
+     * 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 ext = pdbFileFormat.getExtension();
+    String fetchFormat = pdbFileFormat.getFormat();
+
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
-            .getAbsolutePath();
+    File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
+    file = tmpFile.getAbsolutePath();
     stopQuery();
     if (file == null)
     {
@@ -155,10 +163,9 @@ public class Pdb extends EbiFileRetrievedProxy
     try
     {
       // 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
+      FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
               : FileFormat.MMCif;
-      pdbAlignment = new FormatAdapter().readFile(file,
+      pdbAlignment = new FormatAdapter().readFile(tmpFile,
               DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)
       {
@@ -175,15 +182,14 @@ public class Pdb extends EbiFileRetrievedProxy
 
             }
           }
-          if (chain == null
-                  || (chid != null && (chid.equals(chain)
-                          || chid.trim().equals(chain.trim()) || (chain
-                          .trim().length() == 0 && chid.equals("_")))))
+          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());
+            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+                    + SEPARATOR + pdbcs.getName());
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -229,8 +235,8 @@ public class Pdb extends EbiFileRetrievedProxy
       if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
       {
         throw new Exception(MessageManager.formatMessage(
-                "exception.no_pdb_records_for_chain", new String[] { id,
-                    ((chain == null) ? "' '" : chain) }));
+                "exception.no_pdb_records_for_chain", new String[]
+                { id, ((chain == null) ? "' '" : chain) }));
       }
 
     } catch (Exception ex) // Problem parsing PDB file