private static void Main(string[] args)
{
if (args.Length != 4)
{
Console.Out.Write("参数不正确");
return;
}
int cycleLengthThreshold = 20; //环长度
int dustLengthThreshold = 20;
string infile = args[0];
string outdir = args[1];
if (!Directory.Exists(outdir))
{
Directory.CreateDirectory(outdir);
}
cycleLengthThreshold = int.Parse(args[2]);
dustLengthThreshold = int.Parse(args[3]);
//步数15
int simplificationSteps = 15;
IGraphTool graphTool = new GraphTool(); //创建图池子
ABruijnGraph aBruijnGraph = new ABruijnGraph(graphTool); //AB图
IDataReader dataReader = new SyntenyDataReader(infile, ' ');
IDataWriter dataWriter = new SyntenyDataWriter(outdir + "/synteny.txt", ' ', outdir + "/sequenceColor.txt", infile,
outdir + "/modifiedSequence.txt");
IColorTracker colorTracker = new ColorTracker(); //颜色标记
ISequenceSmother smother = new SequenceSmother(2, cycleLengthThreshold); //序列平滑
ISyntenyFinder syntenyFinder = new SyntenyFinder(dataReader, dataWriter, aBruijnGraph, smother, colorTracker); //核心函数
syntenyFinder.Run(cycleLengthThreshold, 2, 3, simplificationSteps, true, dustLengthThreshold, outdir);
}
private static void Main(string[] args)
{
int cycleLengthThreshold = 30; //环长度
string infile = INFILE;
string outdir = OUTDIR;
int dustLengthThreshold = 8;
int simplificationSteps = 15; //步数15
IGraphTool graphTool = new GraphTool(); //创建图池子
ABruijnGraph aBruijnGraph = new ABruijnGraph(graphTool); //AB图
IDataReader dataReader = new SyntenyDataReader(infile, ' ');
IDataWriter dataWriter = new SyntenyDataWriter(outdir + "/synteny.txt", ' ', outdir + "/sequenceColor.txt", infile,
outdir + "/modifiedSequence.txt");
IColorTracker colorTracker = new ColorTracker(); //颜色标记
ISequenceSmother smother = new SequenceSmother(2, cycleLengthThreshold); //序列平滑
ISyntenyFinder syntenyFinder = new SyntenyFinder(dataReader, dataWriter, aBruijnGraph, smother, colorTracker); //核心函数
syntenyFinder.Run(cycleLengthThreshold, 2, 3, simplificationSteps, true, dustLengthThreshold, outdir);
}