Merge branch 'develop' into bug/JAL-2225mapMultipleChains

[jalview.git] / benchmarking / src / main / java / org / jalview / HiddenColumnsBenchmark.java

diff --git a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.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.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.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+
+/*
+ * 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 HiddenColumnsBenchmark 
+{      
+       /*
+        * State with multiple hidden columns and a start position set
+        */
+       @State(Scope.Thread)
+       public static class HiddenColsAndStartState
+       {
+               @Param({"300", "10000", "100000"})
+               public int maxcols;
+               
+               @Param({"1", "50", "90"})
+               public int startpcnt; // position as percentage of maxcols
+               
+               @Param({"1","15","100"})
+               public int hide;
+               
+               HiddenColumns h = new HiddenColumns();
+               Random rand = new Random();
+               
+               public int hiddenColumn;
+               public int visibleColumn;
+       
+               @Setup
+               public void setup()
+               {
+                       rand.setSeed(1234);
+                       int lastcol = 0;
+               while (lastcol < maxcols)
+               {
+                       int count = rand.nextInt(100); 
+                       lastcol += count;
+                       h.hideColumns(lastcol, lastcol+hide);
+                       lastcol+=hide;
+               }
+               
+               // make sure column at start is hidden
+               hiddenColumn = (int)(maxcols * startpcnt/100.0);
+               h.hideColumns(hiddenColumn, hiddenColumn);
+               
+               // and column <hide> after start is visible
+               ColumnSelection sel = new ColumnSelection();
+               h.revealHiddenColumns(hiddenColumn+hide, sel);
+               visibleColumn = hiddenColumn+hide;
+               
+               System.out.println("Maxcols: " + maxcols + " HiddenCol: " + hiddenColumn + " Hide: " + hide);
+               System.out.println("Number of hidden columns: " + h.getSize());
+               }
+       }
+       
+       /* Convention: functions in alphabetical order */
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+       public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
+       {
+               return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
+       }
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+       public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+       {
+               return tstate.h.findColumnPosition(tstate.visibleColumn);
+       }
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+       public List<Integer> benchFindHiddenRegionPositions(HiddenColsAndStartState tstate)
+       {
+               return tstate.h.findHiddenRegionPositions();
+       }
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+       public ArrayList<int[]> benchGetHiddenColumnsCopy(HiddenColsAndStartState tstate)
+       {
+               return tstate.h.getHiddenColumnsCopy();
+       }
+       
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+    public int benchGetSize(HiddenColsAndStartState tstate)
+    {
+               return tstate.h.getSize();
+    }
+
+   @Benchmark
+    @BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchHideCols(HiddenColsAndStartState tstate) 
+    {
+       tstate.h.hideColumns(tstate.visibleColumn,
+                       tstate.visibleColumn+2000); 
+       return tstate.h;
+    }
+   
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+    public boolean benchIsVisible(HiddenColsAndStartState tstate) 
+    {
+       return tstate.h.isVisible(tstate.hiddenColumn); 
+    }
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchReveal(HiddenColsAndStartState tstate) 
+    {
+               ColumnSelection sel = new ColumnSelection();
+       tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
+       return tstate.h;
+    }
+       
+       @Benchmark
+       @BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate) 
+    {
+               ColumnSelection sel = new ColumnSelection();
+       tstate.h.revealAllHiddenColumns(sel);
+       return tstate.h;
+    }
+       
+       
+}
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