Class PeptideVariantsParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters
- All Implemented Interfaces:
Serializable
public class PeptideVariantsParameters extends ExperimentObject
Preferences for the allowed variants in peptide sequences.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
PeptideVariantsParameters.VariantType
Enum indicating all three variant types -
Field Summary
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Constructor Summary
Constructors Constructor Description PeptideVariantsParameters()
Constructor. -
Method Summary
Modifier and Type Method Description AaSubstitutionMatrix
getAaSubstitutionMatrix()
Returns the amino acid substitution matrix to use.HashMap<String,ArrayList<SNPElement>>
getFixedVariants()
returns the fixed variantsint
getnAaDeletions()
Returns the number of amino acid deletions allowed.int
getnAaInsertions()
Returns the number of amino acid insertions allowed.int
getnAaSubstitutions()
Returns the number of amino acid substitutions allowed.int
getnAaSwap()
Returns the number of amino acid swaps allowed.static PeptideVariantsParameters
getNoVariantPreferences()
Returns the preferences corresponding to no variants allowed.int
getnVariants()
Returns the total number of variants allowed.String
getShortDescription()
Returns a short description of the parameters.PeptideVariantsParameters.VariantType
getVariantType()
Returns whether the specific variant count limitations should be used.boolean
isSameAs(PeptideVariantsParameters peptideVariantsPreferences)
Indicates whether another peptide variant preferences is the same as this one.void
setAaSubstitutionMatrix(AaSubstitutionMatrix aaSubstitutionMatrix)
Sets the amino acid substitution matrix to use.void
setFixedVariants(HashMap<String,ArrayList<SNPElement>> fixedVariants)
sets the fixed variantsvoid
setnAaDeletions(int nAaDeletions)
Sets the number of amino acid deletions allowed.void
setnAaInsertions(int nAaInsertions)
Sets the number of amino acid insertions allowed.void
setnAaSubstitutions(int nAaSubstitutions)
Sets the number of amino acid substitutions allowed.void
setnAaSwap(int nAaSwap)
Sets the number of amino acid swaps allowed.void
setnVariants(int nVariants)
Sets the total number of variants allowed.void
setVatiantType(PeptideVariantsParameters.VariantType variantType)
Sets whether the specific variant count limitations should be used.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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PeptideVariantsParameters
public PeptideVariantsParameters()Constructor.
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Method Details
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getnAaDeletions
public int getnAaDeletions()Returns the number of amino acid deletions allowed.- Returns:
- the number of amino acid deletions allowed
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setnAaDeletions
public void setnAaDeletions(int nAaDeletions)Sets the number of amino acid deletions allowed.- Parameters:
nAaDeletions
- the number of amino acid deletions allowed
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getnAaInsertions
public int getnAaInsertions()Returns the number of amino acid insertions allowed.- Returns:
- the number of amino acid insertions allowed
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setnAaInsertions
public void setnAaInsertions(int nAaInsertions)Sets the number of amino acid insertions allowed.- Parameters:
nAaInsertions
- the number of amino acid insertions allowed
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getnAaSubstitutions
public int getnAaSubstitutions()Returns the number of amino acid substitutions allowed.- Returns:
- the number of amino acid substitutions allowed
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setnAaSubstitutions
public void setnAaSubstitutions(int nAaSubstitutions)Sets the number of amino acid substitutions allowed.- Parameters:
nAaSubstitutions
- the number of amino acid substitutions allowed
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getnAaSwap
public int getnAaSwap()Returns the number of amino acid swaps allowed.- Returns:
- the number of amino acid swaps allowed
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setnAaSwap
public void setnAaSwap(int nAaSwap)Sets the number of amino acid swaps allowed.- Parameters:
nAaSwap
- the number of amino acid swaps allowed
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getAaSubstitutionMatrix
Returns the amino acid substitution matrix to use.- Returns:
- the amino acid substitution matrix to use
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setAaSubstitutionMatrix
Sets the amino acid substitution matrix to use.- Parameters:
aaSubstitutionMatrix
- the amino acid substitution matrix to use
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getVariantType
Returns whether the specific variant count limitations should be used.- Returns:
- a boolean indicating whether the specific variant count limitations should be used
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setVatiantType
Sets whether the specific variant count limitations should be used.- Parameters:
variantType
- a boolean indicating whether the specific variant count limitations should be used
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getnVariants
public int getnVariants()Returns the total number of variants allowed.- Returns:
- the total number of variants allowed
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setnVariants
public void setnVariants(int nVariants)Sets the total number of variants allowed.- Parameters:
nVariants
- the total number of variants allowed
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isSameAs
Indicates whether another peptide variant preferences is the same as this one.- Parameters:
peptideVariantsPreferences
- the other preferences- Returns:
- whether another peptide variant preferences is the same as this one
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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getNoVariantPreferences
Returns the preferences corresponding to no variants allowed.- Returns:
- the preferences corresponding to no variants allowed
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getFixedVariants
returns the fixed variants- Returns:
- fixed variants dictionary
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setFixedVariants
sets the fixed variants- Parameters:
fixedVariants
- fixed variants dictionary
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