JAL-2344 use ".cif" for saved mmCIF file (and refactor fetch as file)

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 40edc73..f108fc2 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -151,7 +151,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     {
       EBIFetchClient ebi = new EBIFetchClient();
       String query = "pdb:" + pdbentry.getId();
-      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml")
+      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "xml")
               .getAbsolutePath());
 
       if (pdbentry.getFile() != null)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 97fb08d..8debacf 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -46,11 +46,21 @@ public class PDBEntry
 
   public enum Type
   {
-    // TODO is FILE needed; if not is this needed or can we
+    // TODO is FILE needed; if not is this enum needed, or can we
     // use FileFormatI for PDB, MMCIF?
-    PDB("pdb", "xml"), MMCIF("mmcif", "mmcif"), FILE("?", "?");
+    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+
+    /*
+     * file extension for cached structure file; must be one that
+     * is recognised by Chimera 'open' command
+     * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+     */
     String ext;
 
+    /*
+     * format specifier used in dbfetch request
+     * @see http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#pdb
+     */
     String format;
 
     private Type(String fmt, String ex)

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index b139574..b2fb808 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -64,7 +64,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     {
       reply = dbFetch.fetchDataAsFile(
               emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
-              ".xml");
+              "xml");
     } catch (Exception e)
     {
       stopQuery();

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 68dda88..982c399 100644 (file)
--- 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)
     {
@@ -155,8 +163,7 @@ 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,
               DataSourceType.FILE, fileFormat);

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index b6f53cd..3afe8ec 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -165,7 +165,7 @@ public class Uniprot extends DbSourceProxyImpl
       // uniprotxml parameter required since december 2007
       // uniprotkb dbname changed introduced december 2008
       File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
-              ".xml");
+              "xml");
       Vector<UniprotEntry> entries = getUniprotEntries(new FileReader(file));
 
       if (entries != null)

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index f6928c4..3e8c55e 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -91,7 +91,7 @@ public class EBIFetchClient
    * @param format
    *          the format wanted
    * @param extension
-   *          for the temporary file to hold response
+   *          for the temporary file to hold response (without separator)
    * @return the file holding the response
    * @throws OutOfMemoryError
    */
@@ -102,7 +102,7 @@ public class EBIFetchClient
     File outFile = null;
     try
     {
-      outFile = File.createTempFile("jalview", ext);
+      outFile = File.createTempFile("jalview", "." + ext);
       outFile.deleteOnExit();
       fetchData(ids, format, outFile);
       if (outFile.length() == 0)