Uses of Class
com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix
Package | Description |
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com.compomics.util.experiment.biology.variants |
Experiment classes related to variants.
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com.compomics.util.gui.variants.aa_substitutions |
GUI classes relative to amino acid substitution.
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com.compomics.util.parameters.identification.advanced |
Advanced Identification parameters.
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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 AaSubstitutionMatrix
AaSubstitutionMatrix. allSubstitutions
Substitution matrix allowing all substitutions.static AaSubstitutionMatrix[]
AaSubstitutionMatrix. defaultMutationMatrices
Returns the implemented default substitution matrices.static AaSubstitutionMatrix
AaSubstitutionMatrix. noSubstitution
Empty substitution matrix.static AaSubstitutionMatrix
AaSubstitutionMatrix. singleBaseSubstitution
Substitution matrix allowing for a single base substitution.static AaSubstitutionMatrix
AaSubstitutionMatrix. synonymousVariant
Substitution matrix grouping synonymous amino acids.static AaSubstitutionMatrix
AaSubstitutionMatrix. transitionsSingleBaseSubstitution
Substitution matrix allowing for a single base transition variant.static 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 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.