JAL-2778 Sequence width benchmark

diff --git a/benchmarking/src/main/java/org/jalview/SeqWidthBenchmark.java b/benchmarking/src/main/java/org/jalview/SeqWidthBenchmark.java
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+/*
+ * 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;
+
+import org.jalview.HiddenColumnsBenchmark.HiddenColsAndStartState;
+import org.openjdk.jmh.annotations.Benchmark;
+import org.openjdk.jmh.annotations.BenchmarkMode;
+import org.openjdk.jmh.annotations.Fork;
+import org.openjdk.jmh.annotations.Measurement;
+import org.openjdk.jmh.annotations.Mode;
+import org.openjdk.jmh.annotations.Setup;
+import org.openjdk.jmh.annotations.State;
+import org.openjdk.jmh.annotations.Warmup;
+import org.openjdk.jmh.annotations.Scope;
+import org.openjdk.jmh.annotations.Param;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Random;
+import java.util.concurrent.TimeUnit;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+/*
+ * A class to benchmark hidden columns performance
+ */
+@Warmup(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
+@Measurement(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
+@Fork(1)
+public class SeqWidthBenchmark {
+
+       /*
+        * State with multiple hidden columns and a start position set
+        */
+       @State(Scope.Thread)
+       public static class AlignmentState
+       {
+               @Param({"100", "1000", "10000", "100000"})
+               public int numSeqs;
+               
+               Random rand = new Random();
+               
+               AlignmentI al;
+               
+               @Setup
+               public void setup()
+               {
+                       rand.setSeed(1234);
+                       
+                       SequenceI[] seqs = new Sequence[numSeqs];
+                   for (int i = 0; i < numSeqs; i++)
+                   {
+                     int count = rand.nextInt(10000); 
+                     StringBuilder aas = new StringBuilder();
+                     for (int j=0; j<count; j++)
+                     {
+                        aas.append("a");
+                     }
+
+                     seqs[i] = new Sequence("Sequence" + i, aas.toString());
+                   }
+                       al = new Alignment(seqs);
+               }
+       }
+       
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+       public int benchSeqGetWidth(AlignmentState tstate)
+       {
+               return tstate.al.getWidth();
+       }
+       
+}