Uses of Class
com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix

Packages that use AaSubstitutionMatrix

Package	Description
com.compomics.util.experiment.biology.variants	Experiment classes related to variants.
com.compomics.util.gui.variants.aa_substitutions	GUI classes relative to amino acid substitution.
com.compomics.util.parameters.identification.advanced	Advanced Identification parameters.

Uses of AaSubstitutionMatrix in com.compomics.util.experiment.biology.variants

Fields in com.compomics.util.experiment.biology.variants declared as AaSubstitutionMatrix

Modifier and Type	Field	Description
static final AaSubstitutionMatrix	AaSubstitutionMatrix.allSubstitutions	Substitution matrix allowing all substitutions.
static final AaSubstitutionMatrix[]	AaSubstitutionMatrix.defaultMutationMatrices	Returns the implemented default substitution matrices.
static final AaSubstitutionMatrix	AaSubstitutionMatrix.noSubstitution	Empty substitution matrix.
static final AaSubstitutionMatrix	AaSubstitutionMatrix.singleBaseSubstitution	Substitution matrix allowing for a single base substitution.
static final AaSubstitutionMatrix	AaSubstitutionMatrix.synonymousVariant	Substitution matrix grouping synonymous amino acids.
static final AaSubstitutionMatrix	AaSubstitutionMatrix.transitionsSingleBaseSubstitution	Substitution matrix allowing for a single base transition variant.
static final AaSubstitutionMatrix	AaSubstitutionMatrix.transversalSingleBaseSubstitution	Substitution matrix allowing for a single base transversion variant.

Methods in com.compomics.util.experiment.biology.variants with parameters of type AaSubstitutionMatrix

Modifier and Type	Method	Description
void	AaSubstitutionMatrix.add(AaSubstitutionMatrix otherMatrix)	Adds the content of a substitution matrix in this matrix.
boolean	AaSubstitutionMatrix.isSameAs(AaSubstitutionMatrix aaSubstitutionMatrix)	Indicates whether the given AaSubstitutionMatrix is the same as this one.

Uses of AaSubstitutionMatrix in com.compomics.util.gui.variants.aa_substitutions

Methods in com.compomics.util.gui.variants.aa_substitutions with parameters of type AaSubstitutionMatrix

Modifier and Type	Method	Description
void	AaSubstitutionMatrixTableModel.setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)	Sets the substitution matrix to display.

Constructors in com.compomics.util.gui.variants.aa_substitutions with parameters of type AaSubstitutionMatrix

Modifier	Constructor	Description
	AaSubstitutionMatrixTableModel(AaSubstitutionMatrix aaSubstitutionMatrix, boolean editable)	Constructor.

Uses of AaSubstitutionMatrix in com.compomics.util.parameters.identification.advanced

Methods in com.compomics.util.parameters.identification.advanced that return AaSubstitutionMatrix

Modifier and Type	Method	Description
AaSubstitutionMatrix	PeptideVariantsParameters.getAaSubstitutionMatrix()	Returns the amino acid substitution matrix to use.

Methods in com.compomics.util.parameters.identification.advanced with parameters of type AaSubstitutionMatrix

Modifier and Type	Method	Description
void	PeptideVariantsParameters.setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)	Sets the amino acid substitution matrix to use.