Class DigestionParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.search.DigestionParameters
- All Implemented Interfaces:
Serializable
public class DigestionParameters extends ExperimentObject
This class groups the parameters for the digestion of proteins.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
DigestionParameters.CleavageParameter
Enum for the different types of digestion.static class
DigestionParameters.Specificity
Enum for the different types of enzyme specificity. -
Field Summary
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Constructor Summary
Constructors Constructor Description DigestionParameters()
Constructor for empty parameters. -
Method Summary
Modifier and Type Method Description void
addEnzyme(Enzyme enzyme)
Adds an enzyme.void
clear()
Clears the parameters.void
clearEnzymes()
Clears the enzymes set including specificity and missed cleavages.static DigestionParameters
clone(DigestionParameters digestionParameters)
Clones the given parameters.DigestionParameters.CleavageParameter
getCleavageParameter()
Returns the cleavage parameters.static DigestionParameters
getDefaultParameters()
Returns default digestion parameters.ArrayList<Enzyme>
getEnzymes()
Returns the enzymes used for digestion in a list.String
getMyriMatchFormat()
Get the MyriMatch enzyme format.Integer
getnMissedCleavages(String enzymeName)
Returns the number of allowed missed cleavages for the given enzyme.String
getShortDescription()
Returns a short description of the parameters.DigestionParameters.Specificity
getSpecificity(String enzymeName)
Returns the expected specificity of the given enzyme.String
getXTandemFormat()
Get the X!Tandem enzyme format.boolean
hasEnzymes()
Returns a boolean indicating whether enzyme settings were set.boolean
isSameAs(DigestionParameters otherDigestionParameters)
Returns a boolean indicating whether these digestion parameters are the same as the given other parameters.void
setCleavageParameter(DigestionParameters.CleavageParameter cleavageParameter)
Sets the cleavage parameters.void
setEnzymes(ArrayList<Enzyme> enzymes)
Sets the enzymes used for digestion.void
setnMissedCleavages(String enzymeName, int enzymeMissedCleavages)
Sets the number of allowed missed cleavages.void
setSpecificity(String enzymeName, DigestionParameters.Specificity enzymeSpecificity)
Sets the expected specificity of the enzyme.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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DigestionParameters
public DigestionParameters()Constructor for empty parameters.
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Method Details
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clone
Clones the given parameters.- Parameters:
digestionParameters
- the parameters to clone- Returns:
- a new object containing the same parameters
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getDefaultParameters
Returns default digestion parameters. Trypsin specific with two missed cleavages.- Returns:
- default digestion parameters
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hasEnzymes
public boolean hasEnzymes()Returns a boolean indicating whether enzyme settings were set.- Returns:
- a boolean indicating whether enzyme settings were set
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getEnzymes
Returns the enzymes used for digestion in a list.- Returns:
- the enzymes used for digestion in a list
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setEnzymes
Sets the enzymes used for digestion.- Parameters:
enzymes
- the enzymes used for digestion in a list
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addEnzyme
Adds an enzyme. The specificity of the enzyme is set by default to specific and the number of allowed missed cleavages to 0.- Parameters:
enzyme
- an enzyme used for digestion.
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clear
public void clear()Clears the parameters. -
clearEnzymes
public void clearEnzymes()Clears the enzymes set including specificity and missed cleavages. -
getnMissedCleavages
Returns the number of allowed missed cleavages for the given enzyme. Null if not set.- Parameters:
enzymeName
- the name of the enzyme- Returns:
- the number of allowed missed cleavages
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setnMissedCleavages
Sets the number of allowed missed cleavages.- Parameters:
enzymeName
- the name of the enzymeenzymeMissedCleavages
- the number of allowed missed cleavages
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getSpecificity
Returns the expected specificity of the given enzyme. Null if not set.- Parameters:
enzymeName
- the name of the enzyme- Returns:
- the specificity
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setSpecificity
Sets the expected specificity of the enzyme.- Parameters:
enzymeName
- the name of the enzymeenzymeSpecificity
- the expected specificity of the enzyme
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getCleavageParameter
Returns the cleavage parameters.- Returns:
- the cleavage parameters
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setCleavageParameter
Sets the cleavage parameters.- Parameters:
cleavageParameter
- the cleavage parameters
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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isSameAs
Returns a boolean indicating whether these digestion parameters are the same as the given other parameters.- Parameters:
otherDigestionParameters
- the other digestion parameters- Returns:
- a boolean indicating whether these digestion parameters are the same as the given other parameters
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getXTandemFormat
Get the X!Tandem enzyme format.- Returns:
- the enzyme X!Tandem format as String
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getMyriMatchFormat
Get the MyriMatch enzyme format. In case multiple enzymes are present all possible cleavage sites will be included.- Returns:
- the enzyme MyriMatch format as String
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