public class DigestionParameters extends ExperimentObject
Modifier and Type | Class and Description |
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static class |
DigestionParameters.CleavageParameter
Enum for the different types of digestion.
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static class |
DigestionParameters.Specificity
Enum for the different types of enzyme specificity.
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NO_KEY
Constructor and Description |
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DigestionParameters()
Constructor for empty parameters.
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Modifier and Type | Method and Description |
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void |
addEnzyme(Enzyme enzyme)
Adds an enzyme.
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void |
clear()
Clears the parameters.
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void |
clearEnzymes()
Clears the enzymes set including specificity and missed cleavages.
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static DigestionParameters |
clone(DigestionParameters digestionParameters)
Clones the given parameters.
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DigestionParameters.CleavageParameter |
getCleavageParameter()
Returns the cleavage parameters.
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static DigestionParameters |
getDefaultParameters()
Returns default digestion parameters.
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ArrayList<Enzyme> |
getEnzymes()
Returns the enzymes used for digestion in a list.
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String |
getMyriMatchFormat()
Get the MyriMatch enzyme format.
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Integer |
getnMissedCleavages(String enzymeName)
Returns the number of allowed missed cleavages for the given enzyme.
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String |
getShortDescription()
Returns a short description of the parameters.
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DigestionParameters.Specificity |
getSpecificity(String enzymeName)
Returns the expected specificity of the given enzyme.
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String |
getXTandemFormat()
Get the X!Tandem enzyme format.
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boolean |
hasEnzymes()
Returns a boolean indicating whether enzyme settings were set.
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boolean |
isSameAs(DigestionParameters otherDigestionParameters)
Returns a boolean indicating whether these digestion parameters are the
same as the given other parameters.
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void |
setCleavageParameter(DigestionParameters.CleavageParameter cleavageParameter)
Sets the cleavage parameters.
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void |
setEnzymes(ArrayList<Enzyme> enzymes)
Sets the enzymes used for digestion.
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void |
setnMissedCleavages(String enzymeName,
int enzymeMissedCleavages)
Sets the number of allowed missed cleavages.
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void |
setSpecificity(String enzymeName,
DigestionParameters.Specificity enzymeSpecificity)
Sets the expected specificity of the enzyme.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public DigestionParameters()
public static DigestionParameters clone(DigestionParameters digestionParameters)
digestionParameters
- the parameters to clonepublic static DigestionParameters getDefaultParameters()
public boolean hasEnzymes()
public ArrayList<Enzyme> getEnzymes()
public void setEnzymes(ArrayList<Enzyme> enzymes)
enzymes
- the enzymes used for digestion in a listpublic void addEnzyme(Enzyme enzyme)
enzyme
- an enzyme used for digestion.public void clear()
public void clearEnzymes()
public Integer getnMissedCleavages(String enzymeName)
enzymeName
- the name of the enzymepublic void setnMissedCleavages(String enzymeName, int enzymeMissedCleavages)
enzymeName
- the name of the enzymeenzymeMissedCleavages
- the number of allowed missed cleavagespublic DigestionParameters.Specificity getSpecificity(String enzymeName)
enzymeName
- the name of the enzymepublic void setSpecificity(String enzymeName, DigestionParameters.Specificity enzymeSpecificity)
enzymeName
- the name of the enzymeenzymeSpecificity
- the expected specificity of the enzymepublic DigestionParameters.CleavageParameter getCleavageParameter()
public void setCleavageParameter(DigestionParameters.CleavageParameter cleavageParameter)
cleavageParameter
- the cleavage parameterspublic String getShortDescription()
public boolean isSameAs(DigestionParameters otherDigestionParameters)
otherDigestionParameters
- the other digestion parameterspublic String getXTandemFormat()
public String getMyriMatchFormat()
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