public void CompressByIdentity(FastaFileParser myFastaFileParser, double Identity, string saveDB = null)
{
if (Identity > 1)
{
throw new Exception("Maximum allowed identity = 1");
}
MyFastaSequences = myFastaFileParser;
Console.WriteLine("The original DB has " + MyFastaSequences.MyItems.Count + " sequences.");
MyFastaSequences.MyItems.Sort((a, b) => a.Sequence.Length.CompareTo(b.Sequence.Length));
Console.WriteLine("Converting sequences to byte array.");
MyFastaSequences.IncludeByteSequences();
Console.WriteLine("Finished converting to byte array.");
MAligner.Aligner ma = new Aligner();
ConcurrentDictionary <FastaItem, List <FastaItem> > toExclude = new ConcurrentDictionary <FastaItem, List <FastaItem> >(); //The ID to exlclude and the items it matches
ParallelOptions options = new ParallelOptions();
options.MaxDegreeOfParallelism = Environment.ProcessorCount * 2;
Console.WriteLine("Limiting number of threads to {0}.", options.MaxDegreeOfParallelism);
int eliminated = 0;
int count = 0;
Parallel.For(0, MyFastaSequences.MyItems.Count - 1, options, i =>
//for (int i = 0; i < fp.MyItems.Count - 1; i++)
{
Interlocked.Increment(ref count);
Console.WriteLine("Testing sequence no {0} ", count);
//Determine speed;
int speed = 1;
if (MyFastaSequences.MyItems[i].Sequence.Length >= 6)
{
speed = (int)Math.Round((double)MyFastaSequences.MyItems[i].Sequence.Length / 6) + 1;
}
List <FastaItem> matching = new List <FastaItem>();
for (int j = i + 1; j < MyFastaSequences.MyItems.Count; j++)
{
//i is peptide, j is protein
int identity = ma.IDScore(MyFastaSequences.MyItems[i].SequenceInBytes, MyFastaSequences.MyItems[j].SequenceInBytes, speed);
double approximateIdentityPercentage = (double)identity / ((double)MyFastaSequences.MyItems[i].SequenceInBytes.Length / (double)speed);
if (approximateIdentityPercentage >= Identity * 0.75)
{
int identityFull = ma.IDScore(MyFastaSequences.MyItems[i].SequenceInBytes, MyFastaSequences.MyItems[j].SequenceInBytes, 1);
double identityPercentage = (double)identityFull / (double)MyFastaSequences.MyItems[i].SequenceInBytes.Length;
if (identityPercentage >= Identity)
{
matching.Add(MyFastaSequences.MyItems[j]);
}
}
}
if (matching.Count > 0)
{
toExclude.TryAdd(MyFastaSequences.MyItems[i], matching);
Interlocked.Increment(ref eliminated);
Console.WriteLine("Sequences eliminated {0} ", eliminated);
}
}
);
//Reduce the DB
Console.WriteLine();
Console.WriteLine("Reducing DB.");
List <FastaItem> holders = toExclude.Keys.ToList();
holders.Sort((a, b) => a.Sequence.Length.CompareTo(b.Sequence.Length));
foreach (KeyValuePair <FastaItem, List <FastaItem> > kvp in toExclude)
{
foreach (FastaItem fiMatches in kvp.Value)
{
fiMatches.Description += " Includes: " + kvp.Key.SequenceIdentifier;
}
}
//Eliminate sequences from original DB
MyFastaSequences.MyItems = MyFastaSequences.MyItems.Except(holders).ToList();
Console.WriteLine("Sequences eliminated: " + eliminated + " | " + "DB size with " + Identity + ": " + ((count + 1) - eliminated) + " | " + "DB Size: " + (count + 1));
if (saveDB != null)
{
MyFastaSequences.SaveDB(saveDB);
Console.WriteLine("Done saving DB to disk");
}
}
