JAL-3730 retry ping before failing; sysout logging changed to Cache.log

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

diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index e9cc9e1..16d16d2 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -1,12 +1,25 @@
+/*
+ * 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.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.GeneLociI;
-import jalview.datamodel.GeneLocus;
-import jalview.datamodel.Mapping;
-import jalview.util.MapList;
-
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -18,6 +31,14 @@ import java.util.Map;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
+import jalview.util.MapList;
+
 /**
  * A client for the Ensembl REST service /map endpoint, to convert from
  * coordinates of one genome assembly to another.
@@ -137,7 +158,7 @@ public class EnsemblMap extends EnsemblRestClient
       return (parseAssemblyMappingResponse(url));
     } catch (Throwable t)
     {
-      System.out.println("Error calling " + url + ": " + t.getMessage());
+      Cache.log.error("Error calling " + url + ": " + t.getMessage());
       return null;
     }
   }
@@ -244,7 +265,7 @@ public class EnsemblMap extends EnsemblRestClient
       return null;
     } catch (Throwable t)
     {
-      System.out.println("Error calling " + url + ": " + t.getMessage());
+      Cache.log.error("Error calling " + url + ": " + t.getMessage());
       return null;
     }
   }