Merge branch 'develop' into features/filetypeEnum

[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 0d590b0..757ab83 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
@@ -26,9 +27,14 @@ 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.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;
 
@@ -53,8 +59,6 @@ public class Pdb extends EbiFileRetrievedProxy
 
   public static final String FEATURE_RES_NUM = "RESNUM";
 
-  private static String currentDefaultFomart = DBRefSource.PDB;
-
   /*
    * (non-Javadoc)
    * 
@@ -132,11 +136,11 @@ public class Pdb extends EbiFileRetrievedProxy
       stopQuery();
       return null;
     }
-    String ext = getCurrentDefaultFomart().equalsIgnoreCase("mmcif") ? ".cif"
-            : ".xml";
+    Type pdbFileFormat = StructureImportSettings
+            .getDefaultStructureFileFormat();
+    String ext = "." + pdbFileFormat.getExtension();
     EBIFetchClient ebi = new EBIFetchClient();
-    file = ebi.fetchDataAsFile("pdb:" + id,
-            getCurrentDefaultFomart().toLowerCase(), ext)
+    file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
             .getAbsolutePath();
     stopQuery();
     if (file == null)
@@ -145,10 +149,11 @@ 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());
       pdbAlignment = new FormatAdapter().readFile(file,
-              jalview.io.AppletFormatAdapter.FILE,
-              getCurrentDefaultFomart());
+              DataSourceType.FILE, fileFormat);
       if (pdbAlignment != null)
       {
         List<SequenceI> toremove = new ArrayList<SequenceI>();
@@ -243,12 +248,12 @@ public class Pdb extends EbiFileRetrievedProxy
   }
 
   /**
-   * obtain human glyoxalase chain A sequence
+   * human glyoxalase
    */
   @Override
   public String getTestQuery()
   {
-    return "1QIPA";
+    return "1QIP";
   }
 
   @Override
@@ -263,15 +268,6 @@ public class Pdb extends EbiFileRetrievedProxy
     return 0;
   }
 
-  public static String getCurrentDefaultFomart()
-  {
-    return currentDefaultFomart;
-  }
-
-  public static void setCurrentDefaultFomart(String currentDefaultFomart)
-  {
-    Pdb.currentDefaultFomart = currentDefaultFomart;
-  }
 
   /**
    * Returns a descriptor for suitable feature display settings with