///Commenting out for now as part of .NET 4 upgrade
//public static string WriteToCSV(this IntArray x, string filename)
//{
// string fullFileName = ShoUtils.GetCSVFilename(filename);
// ShoNS.IO.DlmWriter.dlmwrite(fullFileName, ",", x);
// return fullFileName;
//}
//public static string WriteToCSVNoDate(this IntArray x, string filename)
//{
// string fullFileName = ShoUtils.GetCSVFilenameNoDate(filename);
// ShoNS.IO.DlmWriter.dlmwrite(fullFileName, ",", x);
// return fullFileName;
//}
/// <summary>
/// Gives similar functionality to Matlab's [sortVal,sortIn]=sort(x), except that it is more
/// general in that it allows one to sort any vector of values and not just those in x, by
/// the ordering imposed by x.
/// </summary>
/// <param name="x">list of values to sort</param>
/// <param name="sortedInd">Outputs the sorted values</param>
/// <returns>The indexes of the sorted values</returns>
public static IntArray SortWithInd(this IntArray x, out IntArray sortedInd)
{
Helper.CheckCondition(x.IsVector());
x = x.ToVector();
//ensures that if the values are all tied, the ordering does not change
//if (x.Unique().Length == 1 && x.Unique()[0]==0)
//{
// sortedInd = ShoUtils.MakeRangeInt(0, x.Length-1);
// return x;
//}
if (!x.IsEmpty())
{
Helper.CheckCondition(x.IsVector());
x = x.ToVector();
Array tmp1 = x.ToList().ToArray();
Array tmp2 = Enumerable.Range(0, x.size1).ToArray();
Array.Sort(tmp1, tmp2);
sortedInd = IntArray.From(tmp2);
IntArray sortedVals = IntArray.From(tmp1);
return(sortedVals);
}
else
{
sortedInd = new IntArray(0);
return(x);
}
}
/// <summary>
/// Given a 1D matrix (a vector), permute it's entries
/// </summary>
/// <param name="x"></param>
/// <returns></returns>
public static IntArray RandomPermutation(this IntArray x, Random rand)
{
Helper.CheckCondition(x.IsVector(), "method only takes vectors not matrixes");
List <int> xList = x.ToList();
//Random myRand = new Random();
xList.ShuffleInPlace(rand);
return(IntArray.From(xList));
}
/// <summary>
/// Called from constructor to initialize instance values
/// </summary>
private void Initialize()
{
// Determine the read lengths of the input data and store maximum read length
this.ReadLengths = IntArray.From(this.DetermineReadLengths());
this.Count = this.ReadLengths.Count;
if (this.Count == 0)
{
throw new ArgumentOutOfRangeException("Zero sequence records were processed");
}
this.SymbolCountByPositionTable = new Dictionary <byte, int[]>();
// Determine the alphabet of this input file
this.Alphabet = this.Sequences.FirstOrDefault().Alphabet;
this.GCContentByPositionArray = new DoubleArray((int)ReadLengthMax);
this.GCContentBySequenceArray = new DoubleArray((int)Count);
}
public static IntArray Unique(this IntArray x)
{
return(IntArray.From(x.Distinct().ToList()));
}
