private IEnumerable <SequenceAndOffset> SequencesWithOffsetNoCleavage()
{
List <byte> buf = null;
var curOffset = 0L;
var offset = -1L;
foreach (var residue in FastaDatabase.Characters())
{
++offset;
if (residue == FastaDatabaseConstants.Delimiter)
{
if (buf != null && buf.Count > 0)
{
yield return(new SequenceAndOffset(buf.ToArray(), curOffset));
}
//if (buf != null && buf.Count > 0) yield return new SequenceAndOffset(Encoding.GetString(buf.ToArray()), curOffset);
buf = new List <byte>();
curOffset = offset;
}
else
{
if (buf != null)
{
buf.Add(residue);
}
}
}
}
public void TestSequenceEnumerationParallel2()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
var sw = new System.Diagnostics.Stopwatch();
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002216_235ACCEA.fasta";
var db = new FastaDatabase(dbFile);
db.Read();
var indexedDb = new IndexedDatabase(db);
var arr = db.Characters().ToArray();
sw.Start();
//var annotationsAndOffsets = indexedDb.AnnotationsAndOffsetsNoEnzyme(7, 30);
// var num = annotationsAndOffsets.AsParallel().LongCount(annotationsAndOffset => annotationsAndOffset.Annotation.IndexOf('W') >= 0);
//var num = annotationsAndOffsets.LongCount(annotationsAndOffset => annotationsAndOffset.Annotation.IndexOf('W') >= 0);
//var num = arr.AsParallel().Where(c => c == 'W').LongCount();
var num = 0;
var sum = 0L;
//foreach (var c in arr)
for (var a = 0; a < arr.Length; a++)
{
var c = arr[a];
for (var i = 0; i < c * 10000; i++) sum += i;
// Interlocked.Increment(ref num);
if (++num == 1000) break;
}
Console.WriteLine("NumPeptides: {0}", sum);
sw.Stop();
Console.WriteLine(@"{0:f4} sec", sw.Elapsed.TotalSeconds);
}
public void TestSumParallel()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
//var array = Enumerable.Range(0, short.MaxValue).ToArray();
const string dbFile = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\MSPathFinderT\ID_002216_235ACCEA.fasta";
var db = new FastaDatabase(dbFile);
db.Read();
//var indexedDb = new IndexedDatabase(db);
//indexedDb.Read();
//var peptides = indexedDb.AnnotationsAndOffsetsNoEnzyme(7, 30);
var charArray = db.Characters().Select(c => (int)c);
// Test methods.
Console.WriteLine(SumAsParallel(charArray));
Console.WriteLine(SumDefault(charArray));
const int m = 100;
var s1 = Stopwatch.StartNew();
for (var i = 0; i < m; i++)
{
SumDefault(charArray);
}
s1.Stop();
var s2 = Stopwatch.StartNew();
for (var i = 0; i < m; i++)
{
SumAsParallel(charArray);
}
s2.Stop();
Console.WriteLine((s1.Elapsed.TotalMilliseconds * 1000000 /
m).ToString("0.00 ns"));
Console.WriteLine((s2.Elapsed.TotalMilliseconds * 1000000 /
m).ToString("0.00 ns"));
Console.Read();
}
