JAL-2335 filterNonStandardResidues configurable for jabaws clients

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 0aae38f..982c399 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -38,9 +38,9 @@ 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;
-import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
 
@@ -142,12 +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)
     {
@@ -155,9 +162,9 @@ public class Pdb extends EbiFileRetrievedProxy
     }
     try
     {
-      // convert Type.PDB/MMCIF to FileFormat.PDB/MMCIF
-      // todo get rid of Type?
-      FileFormatI fileFormat = FileFormat.valueOf(pdbFileFormat.toString());
+      // todo get rid of Type and use FileFormatI instead?
+      FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
+              : FileFormat.MMCif;
       pdbAlignment = new FormatAdapter().readFile(file,
               DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)