JAL-2662 Tidy

diff --git a/.gitignore b/.gitignore
index bfd5da9..2a55560 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,5 @@
 .gitattributes
 TESTNG
 /jalviewApplet.jar
+/benchmarking/lib
+*.class
\ No newline at end of file

diff --git a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
index ffeb613..2518494 100644 (file)
--- a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
+++ b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
@@ -1,32 +1,22 @@
 /*
- * Copyright (c) 2014, Oracle America, Inc.
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *
- *  * Redistributions of source code must retain the above copyright notice,
- *    this list of conditions and the following disclaimer.
- *
- *  * Redistributions in binary form must reproduce the above copyright
- *    notice, this list of conditions and the following disclaimer in the
- *    documentation and/or other materials provided with the distribution.
- *
- *  * Neither the name of Oracle nor the names of its contributors may be used
- *    to endorse or promote products derived from this software without
- *    specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
- * THE POSSIBILITY OF SUCH DAMAGE.
+ * 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 org.jalview;
@@ -40,6 +30,9 @@ import java.util.Random;
 
 import jalview.datamodel.HiddenColumns;
 
+/*
+ * A class to benchmark hidden columns performance
+ */
 public class HiddenColumnsBenchmark 
 {
        @State(Scope.Thread)
@@ -67,7 +60,9 @@ public class HiddenColumnsBenchmark
                }
     }
        
-       
+       /*
+        * isVisible benchmarking
+        */
     @Benchmark
     public boolean benchIsVisibleLastCol(ThreadState tstate) 
     {