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 cb61cd4..468b7f0 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -26,9 +26,11 @@ 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;
 
 /**
@@ -83,13 +85,25 @@ public class EBIFetchClient
     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)
@@ -111,7 +125,7 @@ public class EBIFetchClient
    * @param f
    *          raw/xml
    * @param s
-   *          ?
+   *          not used - remove?
    * 
    * @return Raw string array result of query set
    */
@@ -180,7 +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);
@@ -197,7 +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);