public class SequenceMatchingPreferences extends Object implements Serializable
Modifier and Type | Class and Description |
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static class |
SequenceMatchingPreferences.MatchingType
The different types of amino acid matching.
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Modifier and Type | Field and Description |
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static SequenceMatchingPreferences |
defaultStringMatching
Default string matching.
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Constructor and Description |
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SequenceMatchingPreferences()
Constructor for empty preferences.
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Modifier and Type | Method and Description |
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static SequenceMatchingPreferences |
getDefaultSequenceMatching()
Returns default preferences from amino acid matching.
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Double |
getLimitX()
Returns the maximal share of X's a match can contain, range [0.0-1.0].
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Integer |
getMaxMutationsPerPeptide()
Returns the maximal number of mutations allowed per peptide.
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MutationMatrix |
getMutationMatrix()
Returns the mutation matrix to use.
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SequenceMatchingPreferences.MatchingType |
getSequenceMatchingType()
Returns the sequence matching type.
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String |
getShortDescription()
Returns a short description of the parameters.
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static SequenceMatchingPreferences |
getStringMatching()
Returns preferences for simple string matching.
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boolean |
hasLimitX()
Indicates whether the share of X's should be limited.
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boolean |
hasMutationMatrix()
Indicates whether a mutation matrix shall be used.
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boolean |
isSameAs(SequenceMatchingPreferences proteinInferencePreferences)
Indicates whether another protein inference preferences is the same as
this one.
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void |
setLimitX(Double limitX)
Sets the maximal share of X's a match can contain, range [0.0-1.0].
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void |
setMaxMutationsPerPeptide(Integer maxMutationsPerPeptide)
Sets the maximal number of mutations allowed per peptide.
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void |
setMutationMatrix(MutationMatrix mutationMatrix)
Sets the mutation matrix to use.
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void |
setSequenceMatchingType(SequenceMatchingPreferences.MatchingType sequenceMatchingType)
Sets the sequence matching type.
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public static final SequenceMatchingPreferences defaultStringMatching
public SequenceMatchingPreferences()
public static SequenceMatchingPreferences getStringMatching()
public static SequenceMatchingPreferences getDefaultSequenceMatching()
public SequenceMatchingPreferences.MatchingType getSequenceMatchingType()
public void setSequenceMatchingType(SequenceMatchingPreferences.MatchingType sequenceMatchingType)
sequenceMatchingType
- the sequence matching typepublic Double getLimitX()
public boolean hasLimitX()
public void setLimitX(Double limitX)
limitX
- the maximal share of X's a match can containpublic MutationMatrix getMutationMatrix()
public void setMutationMatrix(MutationMatrix mutationMatrix)
mutationMatrix
- the mutation matrix to usepublic boolean hasMutationMatrix()
public Integer getMaxMutationsPerPeptide()
public void setMaxMutationsPerPeptide(Integer maxMutationsPerPeptide)
maxMutationsPerPeptide
- the maximal number of mutations allowed per
peptidepublic boolean isSameAs(SequenceMatchingPreferences proteinInferencePreferences)
proteinInferencePreferences
- the other protein inference
preferencespublic String getShortDescription()
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