JAL-3438 spotless for 2.11.2.0

[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..176b21d 100644 (file)
--- a/src/jalview/ext/htsjdk/VCFReader.java
+++ b/src/jalview/ext/htsjdk/VCFReader.java
@@ -1,7 +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.htsjdk;
 
-import jalview.bin.Cache;
-
 import java.io.Closeable;
 import java.io.File;
 import java.io.IOException;
@@ -10,6 +28,7 @@ import htsjdk.samtools.util.CloseableIterator;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import jalview.bin.Console;
 
 /**
  * A thin wrapper for htsjdk classes to read either plain, or compressed, or
@@ -28,10 +47,12 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   private VCFFileReader reader;
 
   /**
-   * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
+   * Constructor given a raw or compressed VCF file or a (csi or tabix) index
+   * file
    * <p>
-   * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of these
-   * extensions gives a valid file path, open as indexed, else as unindexed.
+   * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of
+   * these extensions gives a valid file path, open as indexed, else as
+   * unindexed.
    * 
    * @param f
    * @throws IOException
@@ -65,7 +86,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
     }
     else
     {
-      Cache.log.error("File not found: " + filePath);
+      Console.error("File not found: " + filePath);
     }
   }
 
@@ -134,8 +155,8 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
           final String chrom, final int start, final int end)
   {
     final CloseableIterator<VariantContext> it = reader.iterator();
-    
-    return new CloseableIterator<>()
+
+    return new CloseableIterator<VariantContext>()
     {
       boolean atEnd = false;