Merge branch 'releases/Release_2_10_Branch' into develop

[jalview.git] / src / jalview / ext / ensembl / EnsemblRestClient.java

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 30dcee8..b7b1985 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.io.FileParse;
@@ -52,10 +72,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
 
   private static final Regex TRANSCRIPT_REGEX = new Regex(
-            "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+          "(ENS)([A-Z]{3}|)T[0-9]{11}$");
 
   private static final Regex GENE_REGEX = new Regex(
-            "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+          "(ENS)([A-Z]{3}|)G[0-9]{11}$");
 
   static
   {
@@ -207,7 +227,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
           throws IOException
   {
     URL url = getUrl(ids);
-  
+
     BufferedReader reader = getHttpResponse(url, ids);
     if (reader == null)
     {
@@ -233,7 +253,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   {
     // long now = System.currentTimeMillis();
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
-  
+
     /*
      * POST method allows multiple queries in one request; it is supported for
      * sequence queries, but not for overlap
@@ -253,9 +273,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     {
       writePostBody(connection, ids);
     }
-  
+
     int responseCode = connection.getResponseCode();
-  
+
     if (responseCode != 200)
     {
       /*
@@ -272,7 +292,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     // + (System.currentTimeMillis() - now) + "ms to fetch");
 
     checkRateLimits(connection);
-  
+
     BufferedReader reader = null;
     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
     return reader;
@@ -325,7 +345,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       // remaining, limit, reset));
     }
   }
-  
+
   /**
    * Rechecks if Ensembl is responding, unless the last check was successful and
    * the retest interval has not yet elapsed. Returns true if Ensembl is up,