Uses of Class
org.biojava.bio.alignment.SubstitutionMatrix

Packages that use SubstitutionMatrix
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
 

Uses of SubstitutionMatrix in org.biojava.bio.alignment
 

Fields in org.biojava.bio.alignment declared as SubstitutionMatrix
protected  SubstitutionMatrix NeedlemanWunsch.subMatrix
           
 

Methods in org.biojava.bio.alignment that return SubstitutionMatrix
 SubstitutionMatrix SubstitutionMatrix.normalizeMatrix()
          With this method you can get a "normalized" SubstitutionMatrix object; however, since this implementation uses an int matrix, the normalized matrix will be scaled by ten.
 

Methods in org.biojava.bio.alignment with parameters of type SubstitutionMatrix
 void NeedlemanWunsch.setSubstitutionMatrix(SubstitutionMatrix matrix)
          Sets the substitution matrix to be used to the specified one.
 

Constructors in org.biojava.bio.alignment with parameters of type SubstitutionMatrix
NeedlemanWunsch(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix subMat)
          Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.
SmithWaterman(double match, double replace, double insert, double delete, double gapExtend, SubstitutionMatrix matrix)
          Constructs the new SmithWaterman alignment object.