public void CompressByIdentity(string fastaDB, double Identity, string saveDB = null)
{
if (Identity > 1)
{
throw new Exception("Maximum allowed identity = 1");
}
MyFastaSequences = new PatternTools.FastaParser.FastaFileParser();
MyFastaSequences.ParseFile(new StreamReader(fastaDB), false, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
CompressByIdentity(MyFastaSequences, Identity, saveDB);
}
public ResultPckg2 RunFullAnalysisMAlginer()
{
DateTime start = DateTime.Now;
PrepareDeNovoRegistries();
FastaFileParser ffp = new FastaFileParser();
Console.WriteLine("Parsing database");
ffp.ParseFile(new StreamReader(Arguments.DataBaseFile), false, DBTypes.IDSpaceDescription);
Console.WriteLine("Generating byte sequences");
ffp.IncludeByteSequences();
MResultPckg = AlignMAlign(ffp.MyItems, deNovoRegistryList);
Console.Write("Benchmarking: " + (DateTime.Now - start).TotalSeconds + " seconds");
return(MResultPckg);
}
public void LoadFastaDB(string db, bool eliminateReverse)
{
fastaParser.MyItems.Clear();
fastaParser.ParseFile(new StreamReader(db), true, DBTypes.IDSpaceDescription);
fastaParser.DBName = db;
}
