JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...

[jalview.git] / src / jalview / ext / htsjdk / VCFReader.java

diff --git a/src/jalview/ext/htsjdk/VCFReader.java b/src/jalview/ext/htsjdk/VCFReader.java
index 3e7fbc2..508d609 100644 (file)
--- a/src/jalview/ext/htsjdk/VCFReader.java
+++ b/src/jalview/ext/htsjdk/VCFReader.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.htsjdk;
 
 import jalview.bin.Cache;
@@ -65,7 +85,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
     }
     else
     {
-      Cache.log.error("File not found: " + filePath);
+      Cache.error("File not found: " + filePath);
     }
   }
 
@@ -135,7 +155,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   {
     final CloseableIterator<VariantContext> it = reader.iterator();
     
-    return new CloseableIterator<>()
+    return new CloseableIterator<VariantContext>()
     {
       boolean atEnd = false;