From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 23 May 2016 10:47:35 +0000 (+0100)
Subject: JAL-2113 tidy variable naming / javadoc
X-Git-Tag: Release_2_10_0~196^2~2^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eaa8cc6ff032ac14e2bd96ee3bd27e80cfa74a25;p=jalview.git

JAL-2113 tidy variable naming / javadoc
---

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index dd3cc16..1dff32f 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -116,28 +116,32 @@ public class EBIFetchClient
     return outFile;
   }
 
-  String[] fetchData(String ids, String f, File outFile)
+  /**
+   * Fetches queries and either saves the response to a file or returns as
+   * string data
+   * 
+   * @param ids
+   * @param format
+   * @param outFile
+   * @return
+   * @throws OutOfMemoryError
+   */
+  String[] fetchData(String ids, String format, File outFile)
           throws OutOfMemoryError
   {
-    String[] rslts = new String[0];
     StringBuilder querystring = new StringBuilder(ids.length());
-    String db = parseIds(ids, querystring);
-    if (db == null)
+    String database = parseIds(ids, querystring);
+    if (database == null)
     {
       System.err.println("Invalid Query string : '" + ids + "'");
       System.err.println("Should be of form 'dbname:q1;q2;q3;q4'");
       return null;
     }
-    String[] rslt = fetchBatch(querystring.toString(), db, f, outFile);
-    if (rslt != null)
-    {
-      String[] nrslts = new String[rslt.length + rslts.length];
-      System.arraycopy(rslts, 0, nrslts, 0, rslts.length);
-      System.arraycopy(rslt, 0, nrslts, rslts.length, rslt.length);
-      rslts = nrslts;
-    }
 
-    return (rslts.length == 0 ? null : rslts);
+    // note: outFile is currently always specified, so return value is null
+    String[] rslt = fetchBatch(querystring.toString(), database, format, outFile);
+
+    return (rslt != null && rslt.length > 0 ? rslt : null);
   }
 
   /**
@@ -179,11 +183,22 @@ public class EBIFetchClient
     return database;
   }
 
-  String[] fetchBatch(String ids, String dbPath, String format,
+  /**
+   * Fetches queries and either saves the response to a file or (if no file
+   * specified) returns as string data
+   * 
+   * @param ids
+   * @param database
+   * @param format
+   * @param outFile
+   * @return
+   * @throws OutOfMemoryError
+   */
+  String[] fetchBatch(String ids, String database, String format,
           File outFile) throws OutOfMemoryError
   {
     // long time = System.currentTimeMillis();
-    String url = buildUrl(ids, dbPath, format);
+    String url = buildUrl(ids, database, format);
 
     try
     {
@@ -215,8 +230,7 @@ public class EBIFetchClient
       }
     } catch (OutOfMemoryError er)
     {
-
-      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + dbPath
+      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
               + ":\n" + ids);
       throw er;
     } catch (Exception ex)
@@ -227,7 +241,7 @@ public class EBIFetchClient
         return null;
       }
       System.err.println("Unexpected exception when retrieving from "
-              + dbPath
+              + database
               + "\nQuery was : '" + ids + "'");
       ex.printStackTrace(System.err);
       return null;