/// <summary>
/// Initializes a new instance of the SimilarityMatrix class
/// Constructs one of the standard similarity matrices.
/// </summary>
/// <param name="matrixId">
/// Matrix to load, BLOSUM and PAM currently supported.
/// The enum StandardSimilarityMatrices contains list of available matrices.
/// </param>
public SimilarityMatrix(StandardSimilarityMatrix matrixId)
{
// MoleculeType.Protein for BLOSUM and PAM series supported matrices
MoleculeType moleculeType = MoleculeType.Protein;
string matrixText = null;
switch (matrixId)
{
case StandardSimilarityMatrix.Blosum45:
matrixText = SimilarityMatrixResources.Blosum45;
break;
case StandardSimilarityMatrix.Blosum50:
matrixText = SimilarityMatrixResources.Blosum50;
break;
case StandardSimilarityMatrix.Blosum62:
matrixText = SimilarityMatrixResources.Blosum62;
break;
case StandardSimilarityMatrix.Blosum80:
matrixText = SimilarityMatrixResources.Blosum80;
break;
case StandardSimilarityMatrix.Blosum90:
matrixText = SimilarityMatrixResources.Blosum90;
break;
case StandardSimilarityMatrix.Pam250:
matrixText = SimilarityMatrixResources.Pam250;
break;
case StandardSimilarityMatrix.Pam30:
matrixText = SimilarityMatrixResources.Pam30;
break;
case StandardSimilarityMatrix.Pam70:
matrixText = SimilarityMatrixResources.Pam70;
break;
case StandardSimilarityMatrix.AmbiguousDna:
matrixText = SimilarityMatrixResources.AmbiguousDna;
moleculeType = MoleculeType.DNA;
break;
case StandardSimilarityMatrix.AmbiguousRna:
matrixText = SimilarityMatrixResources.AmbiguousRna;
moleculeType = MoleculeType.RNA;
break;
case StandardSimilarityMatrix.DiagonalScoreMatrix:
matrixText = SimilarityMatrixResources.DiagonalScoreMatrix;
break;
}
using (TextReader reader = new StringReader(matrixText))
{
LoadFromStream(reader, moleculeType);
}
}
/// <summary>
/// Initializes a new instance of the SimilarityMatrix class
/// Constructs one of the standard similarity matrices.
/// </summary>
/// <param name="matrixId">
/// Matrix to load, BLOSUM and PAM currently supported.
/// The enum StandardSimilarityMatrices contains list of available matrices.
/// </param>
public SimilarityMatrix(StandardSimilarityMatrix matrixId)
{
// MoleculeType.Protein for BLOSUM and PAM series supported matrices
IAlphabet moleculeType = Alphabets.Protein;
string matrixText = null;
switch (matrixId)
{
case StandardSimilarityMatrix.Blosum45:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM45.txt";
break;
case StandardSimilarityMatrix.Blosum50:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM50.txt";
break;
case StandardSimilarityMatrix.Blosum62:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM62.txt";
break;
case StandardSimilarityMatrix.Blosum80:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM80.txt";
break;
case StandardSimilarityMatrix.Blosum90:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM90.txt";
break;
case StandardSimilarityMatrix.Pam250:
matrixText = "Bio.SimilarityMatrices.Resources.PAM250.txt";
break;
case StandardSimilarityMatrix.Pam30:
matrixText = "Bio.SimilarityMatrices.Resources.PAM30.txt";
break;
case StandardSimilarityMatrix.Pam70:
matrixText = "Bio.SimilarityMatrices.Resources.PAM70.txt";
break;
case StandardSimilarityMatrix.AmbiguousDna:
matrixText = "Bio.SimilarityMatrices.Resources.AmbiguousDNA.txt";
moleculeType = Alphabets.DNA;
break;
case StandardSimilarityMatrix.AmbiguousRna:
matrixText = "Bio.SimilarityMatrices.Resources.AmbiguousRNA.txt";
moleculeType = Alphabets.RNA;
break;
case StandardSimilarityMatrix.DiagonalScoreMatrix:
matrixText = "Bio.SimilarityMatrices.Resources.DiagonalScoreMatrix.txt";
break;
case StandardSimilarityMatrix.EDnaFull:
matrixText = "Bio.SimilarityMatrices.Resources.EDNAFull.txt";
moleculeType = Alphabets.AmbiguousDNA;
break;
}
Stream stream = typeof(SimilarityMatrix).GetTypeInfo().Assembly.GetManifestResourceStream(matrixText);
if (stream == null)
throw new Exception("Could not locate SimilarityMatrix " + matrixText + " in resources.");
using (TextReader reader = new StreamReader(stream))
{
LoadFromStream(reader, moleculeType);
}
}
/// <summary>
/// Initializes a new instance of the SimilarityMatrix class
/// Constructs one of the standard similarity matrices.
/// </summary>
/// <param name="matrixId">
/// Matrix to load, BLOSUM and PAM currently supported.
/// The enum StandardSimilarityMatrices contains list of available matrices.
/// </param>
public SimilarityMatrix(StandardSimilarityMatrix matrixId)
{
// MoleculeType.Protein for BLOSUM and PAM series supported matrices
IAlphabet moleculeType = Alphabets.Protein;
string matrixText = null;
switch (matrixId)
{
case StandardSimilarityMatrix.Blosum45:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM45.txt";
break;
case StandardSimilarityMatrix.Blosum50:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM50.txt";
break;
case StandardSimilarityMatrix.Blosum62:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM62.txt";
break;
case StandardSimilarityMatrix.Blosum80:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM80.txt";
break;
case StandardSimilarityMatrix.Blosum90:
matrixText = "Bio.SimilarityMatrices.Resources.BLOSUM90.txt";
break;
case StandardSimilarityMatrix.Pam250:
matrixText = "Bio.SimilarityMatrices.Resources.PAM250.txt";
break;
case StandardSimilarityMatrix.Pam30:
matrixText = "Bio.SimilarityMatrices.Resources.PAM30.txt";
break;
case StandardSimilarityMatrix.Pam70:
matrixText = "Bio.SimilarityMatrices.Resources.PAM70.txt";
break;
case StandardSimilarityMatrix.Pam1:
matrixText = "Bio.SimilarityMatrices.Resources.PAM1.txt";
break;
case StandardSimilarityMatrix.Conservative:
matrixText = "Bio.SimilarityMatrices.Resources.Conservative.txt";
break;
case StandardSimilarityMatrix.radical:
matrixText = "Bio.SimilarityMatrices.Resources.radical.txt";
break;
case StandardSimilarityMatrix.Conservative_Only_By_Side:
matrixText = "Bio.SimilarityMatrices.Resources.Conservative_Only_By_Side.txt";
break;
case StandardSimilarityMatrix.radical_Only_By_Side:
matrixText = "Bio.SimilarityMatrices.Resources.radical_Only_By_Side.txt";
break;
case StandardSimilarityMatrix.AmbiguousDna:
matrixText = "Bio.SimilarityMatrices.Resources.AmbiguousDNA.txt";
moleculeType = Alphabets.DNA;
break;
case StandardSimilarityMatrix.AmbiguousRna:
matrixText = "Bio.SimilarityMatrices.Resources.AmbiguousRNA.txt";
moleculeType = Alphabets.RNA;
break;
case StandardSimilarityMatrix.DiagonalScoreMatrix:
matrixText = "Bio.SimilarityMatrices.Resources.DiagonalScoreMatrix.txt";
break;
case StandardSimilarityMatrix.EDnaFull:
matrixText = "Bio.SimilarityMatrices.Resources.EDNAFull.txt";
moleculeType = Alphabets.AmbiguousDNA;
break;
case StandardSimilarityMatrix.Silent:
matrixText = "Bio.SimilarityMatrices.Resources.Silent.txt";
break;
}
Assembly H = typeof(SimilarityMatrix).GetTypeInfo().Assembly;
H.GetManifestResourceStream(matrixText);
Stream stream = typeof(SimilarityMatrix).GetTypeInfo().Assembly.GetManifestResourceStream(matrixText);
if (stream == null)
{
throw new Exception("Could not locate SimilarityMatrix " + matrixText + " in resources.");
}
using (TextReader reader = new StreamReader(stream))
{
LoadFromStream(reader, moleculeType);
}
}
