JAL-1919 code improvement to make PDB sequence fetcher file format configurable....

[jalview.git] / src / jalview / ws / ebi / EBIFetchClient.java

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 074b76c..468b7f0 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,30 +1,36 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.ebi;
 
+import jalview.util.MessageManager;
+
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.StringTokenizer;
 
 /**
@@ -54,7 +60,7 @@ public class EBIFetchClient
   public String[] getSupportedDBs()
   {
     // TODO - implement rest call for dbfetch getSupportedDBs
-    throw new Error("Not yet implemented");
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
 
   /**
@@ -65,7 +71,7 @@ public class EBIFetchClient
   public String[] getSupportedFormats()
   {
     // TODO - implement rest call for dbfetch getSupportedFormats
-    throw new Error("Not yet implemented");
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
 
   /**
@@ -76,16 +82,28 @@ public class EBIFetchClient
   public String[] getSupportedStyles()
   {
     // TODO - implement rest call for dbfetch getSupportedStyles
-    throw new Error("Not yet implemented");
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
 
-  public File fetchDataAsFile(String ids, String f, String s)
+  /**
+   * Send an HTTP fetch request to EBI and save the reply in a temporary file.
+   * 
+   * @param ids
+   *          the query formatted as db:query1;query2;query3
+   * @param f
+   *          the format wanted
+   * @param s
+   *          - unused parameter
+   * @return the file holding the response
+   * @throws OutOfMemoryError
+   */
+  public File fetchDataAsFile(String ids, String f, String s, String ext)
           throws OutOfMemoryError
   {
     File outFile = null;
     try
     {
-      outFile = File.createTempFile("jalview", ".xml");
+      outFile = File.createTempFile("jalview", ext);
       outFile.deleteOnExit();
       fetchData(ids, f, s, outFile);
       if (outFile.length() == 0)
@@ -107,7 +125,7 @@ public class EBIFetchClient
    * @param f
    *          raw/xml
    * @param s
-   *          ?
+   *          not used - remove?
    * 
    * @return Raw string array result of query set
    */
@@ -176,7 +194,7 @@ public class EBIFetchClient
               + db.toLowerCase() + "/" + ids.toLowerCase()
               + (f != null ? "/" + f : ""));
 
-      BufferedInputStream is = new BufferedInputStream(rcall.openStream());
+      InputStream is = new BufferedInputStream(rcall.openStream());
       if (outFile != null)
       {
         FileOutputStream fio = new FileOutputStream(outFile);
@@ -193,7 +211,7 @@ public class EBIFetchClient
       {
         BufferedReader br = new BufferedReader(new InputStreamReader(is));
         String rtn;
-        ArrayList<String> arl = new ArrayList<String>();
+        List<String> arl = new ArrayList<String>();
         while ((rtn = br.readLine()) != null)
         {
           arl.add(rtn);
@@ -219,10 +237,9 @@ public class EBIFetchClient
       return null;
     } finally
     {
-      //System.err.println("Took " + (System.currentTimeMillis() - time)
-      //        / 1000 + " secs for one call.");
+      // System.err.println("Took " + (System.currentTimeMillis() - time)
+      // / 1000 + " secs for one call.");
     }
     return null;
   }
 }
-