/*
- * 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;
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.TearDown;
+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 ThreadState
+ 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();
- int MAXCOLS = 100000;
Random rand = new Random();
+
+ public int hiddenColumn;
+ public int visibleColumn;
@Setup
public void setup()
{
rand.setSeed(1234);
- for (int i=0; i<MAXCOLS; ++i)
+ int lastcol = 0;
+ while (lastcol < maxcols)
{
- int col = rand.nextInt(MAXCOLS);
- h.hideColumns(col, col+1);
+ 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());
}
+ }
- @TearDown
- public void tearDown()
- {
-
- }
- }
+ /* Convention: functions in alphabetical order */
+/* @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
+ }
- @Benchmark
- public boolean benchIsVisibleLastCol(ThreadState tstate)
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+ {
+ return tstate.h.findColumnPosition(tstate.visibleColumn);
+ }
+
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public int benchGetSize(HiddenColsAndStartState tstate)
{
- return tstate.h.isVisible(tstate.MAXCOLS - 3);
+ return tstate.h.getSize();
}
-
- @Benchmark
- public boolean benchIsVisibleFirstCol(ThreadState tstate)
+*/
+ @Benchmark
+ @BenchmarkMode({Mode.Throughput})
+ public HiddenColumns benchHideCols(HiddenColsAndStartState tstate)
{
- return tstate.h.isVisible(1);
+ 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;
+ }
+ */
+
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff