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.preferences |
Utilities preferences classes.
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Modifier and Type | Field and Description |
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static AaSubstitutionMatrix |
AaSubstitutionMatrix.allSubstitutions
Substitution matrix allowing all substitutions.
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static AaSubstitutionMatrix[] |
AaSubstitutionMatrix.defaultMutationMatrices
Returns the implemented default substitution matrices.
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static AaSubstitutionMatrix |
AaSubstitutionMatrix.noSubstitution
Empty substitution matrix.
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static AaSubstitutionMatrix |
AaSubstitutionMatrix.singleBaseSubstitution
Substitution matrix allowing for a single base substitution.
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static AaSubstitutionMatrix |
AaSubstitutionMatrix.synonymousVariant
Substitution matrix grouping synonymous amino acids.
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static AaSubstitutionMatrix |
AaSubstitutionMatrix.transitionsSingleBaseSubstitution
Substitution matrix allowing for a single base transition variant.
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static AaSubstitutionMatrix |
AaSubstitutionMatrix.transversalSingleBaseSubstitution
Substitution matrix allowing for a single base transversion variant.
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Modifier and Type | Method and Description |
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void |
AaSubstitutionMatrix.add(AaSubstitutionMatrix otherMatrix)
Adds the content of a substitution matrix in this matrix.
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boolean |
AaSubstitutionMatrix.isSameAs(AaSubstitutionMatrix aaSubstitutionMatrix)
Indicates whether the given AaSubstitutionMatrix is the same as this one.
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Modifier and Type | Method and Description |
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void |
AaSubstitutionMatrixTableModel.setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
Sets the substitution matrix to display.
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Constructor and Description |
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AaSubstitutionMatrixTableModel(AaSubstitutionMatrix aaSubstitutionMatrix,
boolean editable)
Constructor.
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Modifier and Type | Method and Description |
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AaSubstitutionMatrix |
PeptideVariantsPreferences.getAaSubstitutionMatrix()
Returns the amino acid substitution matrix to use.
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Modifier and Type | Method and Description |
---|---|
void |
PeptideVariantsPreferences.setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
Sets the amino acid substitution matrix to use.
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