Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[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 11fe95e..982c399 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,3 +1,4 @@
+
 /*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
@@ -28,12 +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;
 
@@ -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>();