Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / ws / dbsources / EmblFlatfileSource.java

diff --git a/src/jalview/ws/dbsources/EmblFlatfileSource.java b/src/jalview/ws/dbsources/EmblFlatfileSource.java
index 6694a52..93c4ad6 100644 (file)
--- a/src/jalview/ws/dbsources/EmblFlatfileSource.java
+++ b/src/jalview/ws/dbsources/EmblFlatfileSource.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.ws.dbsources;
 
 import java.util.Locale;
@@ -7,13 +27,14 @@ import java.io.IOException;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.EmblFlatFile;
 import jalview.io.FileParse;
+import jalview.util.Platform;
 import jalview.ws.ebi.EBIFetchClient;
 
 /**
@@ -24,7 +45,7 @@ import jalview.ws.ebi.EBIFetchClient;
  */
 public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
 {
-  private static final Regex ACCESSION_REGEX = null;
+  private static Regex ACCESSION_REGEX = null;
 
   @Override
   public String getDbVersion()
@@ -79,7 +100,8 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
     try
     {
       reply = dbFetch.fetchDataAsFile(
-              dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
+              dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null,
+              "gz");
     } catch (Exception e)
     {
       stopQuery();
@@ -109,8 +131,7 @@ public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
 
       if (al == null)
       {
-        Cache.log.error(
-                "No record found for '" + dbName + ":" + query + "'");
+        Console.error("No record found for '" + dbName + ":" + query + "'");
       }
     }