public class DigestionPreferences extends Object implements Serializable
Modifier and Type | Class and Description |
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static class |
DigestionPreferences.CleavagePreference
Enum for the different types of digestion.
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static class |
DigestionPreferences.Specificity
Enum for the different types of enzyme specificity.
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Constructor and Description |
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DigestionPreferences()
Constructor for empty preferences.
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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 DigestionPreferences |
clone(DigestionPreferences digestionPreferences)
Clones the given preferences.
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DigestionPreferences.CleavagePreference |
getCleavagePreference()
Returns the cleavage preferences.
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static DigestionPreferences |
getDefaultPreferences()
Returns default digestion preferences.
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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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DigestionPreferences.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(DigestionPreferences otherDigestionPreferences)
Returns a boolean indicating whether these digestion preferences are the
same as the given other preferences.
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void |
setCleavagePreference(DigestionPreferences.CleavagePreference cleavagePreference)
Sets the cleavage preferences.
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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,
DigestionPreferences.Specificity enzymeSpecificity)
Sets the expected specificity of the enzyme.
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public DigestionPreferences()
public static DigestionPreferences clone(DigestionPreferences digestionPreferences)
digestionPreferences
- the preferences to clonepublic static DigestionPreferences getDefaultPreferences()
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 DigestionPreferences.Specificity getSpecificity(String enzymeName)
enzymeName
- the name of the enzymepublic void setSpecificity(String enzymeName, DigestionPreferences.Specificity enzymeSpecificity)
enzymeName
- the name of the enzymeenzymeSpecificity
- the expected specificity of the enzymepublic DigestionPreferences.CleavagePreference getCleavagePreference()
public void setCleavagePreference(DigestionPreferences.CleavagePreference cleavagePreference)
cleavagePreference
- the cleavage preferencespublic String getShortDescription()
public boolean isSameAs(DigestionPreferences otherDigestionPreferences)
otherDigestionPreferences
- the other digestion preferencespublic String getXTandemFormat()
public String getMyriMatchFormat()
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