X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=3c9e6b4e44e75f994d59e21a7a6f626443bd5434;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=cb61cd49f2403c8cc4f3b8894c85f2789a6ffb96;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index cb61cd4..3c9e6b4 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
 
 /**
@@ -83,6 +85,18 @@ public class EBIFetchClient
     throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
 
+  /**
+   * 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)
           throws OutOfMemoryError
   {
@@ -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);