Class SequenceMatchingParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
- All Implemented Interfaces:
Serializable
public class SequenceMatchingParameters extends ExperimentObject
The sequence matching options.
- 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
SequenceMatchingParameters.MatchingType
The different types of amino acid matching. -
Field Summary
Fields Modifier and Type Field Description static SequenceMatchingParameters
DEFAULT_STRING_MATCHING
Default string matching. -
Constructor Summary
Constructors Constructor Description SequenceMatchingParameters()
Constructor for empty preferences. -
Method Summary
Modifier and Type Method Description static SequenceMatchingParameters
getDefaultSequenceMatching()
Returns default preferences from amino acid matching.double
getLimitX()
Returns the maximal share of X's a match can contain, range [0.0-1.0].int
getMaxPtmsPerTagPeptide()
Returns the maximum number of PTMs to consider when mapping tags to protein sequences.int
getMinAminoAcidScore()
Returns the minimum amino acid score.int
getMinTagLength()
Returns the minimum tag length.SequenceMatchingParameters.MatchingType
getSequenceMatchingType()
Returns the sequence matching type.String
getShortDescription()
Returns a short description of the parameters.static SequenceMatchingParameters
getStringMatching()
Returns preferences for simple string matching.boolean
isEnzymaticTagsOnly()
Returns true if tags should only be mapped to enzymatic peptides.boolean
isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another sequence matching preferences is the same as this one.void
setEnzymaticTagsOnly(boolean enzymaticTagsOnly)
Sets whether tags should only be mapped to enzymatic peptides.void
setLimitX(double limitX)
Sets the maximal share of X's a match can contain, range [0.0-1.0].void
setMaxPtmsPerTagPeptide(int numberOfPtmsPerTagPeptide)
Sets the maximum number of PTMs to consider when mapping tags to protein sequences.void
setMinAminoAcidScore(int minAminoAcidScore)
Set the minimum amino acid score.void
setMinTagLength(int minTagLength)
Set the minimum tag length.void
setSequenceMatchingType(SequenceMatchingParameters.MatchingType sequenceMatchingType)
Sets the sequence matching type.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Field Details
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DEFAULT_STRING_MATCHING
Default string matching.
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Constructor Details
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SequenceMatchingParameters
public SequenceMatchingParameters()Constructor for empty preferences.
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Method Details
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getStringMatching
Returns preferences for simple string matching.- Returns:
- preferences for simple string matching
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getDefaultSequenceMatching
Returns default preferences from amino acid matching.- Returns:
- default preferences from amino acid matching
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getSequenceMatchingType
Returns the sequence matching type.- Returns:
- the sequence matching type
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setSequenceMatchingType
Sets the sequence matching type.- Parameters:
sequenceMatchingType
- the sequence matching type
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getLimitX
public double getLimitX()Returns the maximal share of X's a match can contain, range [0.0-1.0]. Null if not set.- Returns:
- the maximal share of X's a match can contain
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setLimitX
public void setLimitX(double limitX)Sets the maximal share of X's a match can contain, range [0.0-1.0].- Parameters:
limitX
- the maximal share of X's a match can contain
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isSameAs
Indicates whether another sequence matching preferences is the same as this one.- Parameters:
sequenceMatchingPreferences
- the other sequence matching preferences- Returns:
- whether another sequence matching 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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isEnzymaticTagsOnly
public boolean isEnzymaticTagsOnly()Returns true if tags should only be mapped to enzymatic peptides.- Returns:
- true if tags should only be mapped to enzymatic peptides
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setEnzymaticTagsOnly
public void setEnzymaticTagsOnly(boolean enzymaticTagsOnly)Sets whether tags should only be mapped to enzymatic peptides.- Parameters:
enzymaticTagsOnly
- the enzymaticTagsOnly to set
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getMaxPtmsPerTagPeptide
public int getMaxPtmsPerTagPeptide()Returns the maximum number of PTMs to consider when mapping tags to protein sequences.- Returns:
- the maximum number of PTMs to consider when mapping tags to protein sequences
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setMaxPtmsPerTagPeptide
public void setMaxPtmsPerTagPeptide(int numberOfPtmsPerTagPeptide)Sets the maximum number of PTMs to consider when mapping tags to protein sequences.- Parameters:
numberOfPtmsPerTagPeptide
- the maxPtmsPerTagPeptide to set
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getMinAminoAcidScore
public int getMinAminoAcidScore()Returns the minimum amino acid score.- Returns:
- the minAminoAcidScore
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setMinAminoAcidScore
public void setMinAminoAcidScore(int minAminoAcidScore)Set the minimum amino acid score.- Parameters:
minAminoAcidScore
- the minAminoAcidScore to set
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getMinTagLength
public int getMinTagLength()Returns the minimum tag length.- Returns:
- the minTagLength
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setMinTagLength
public void setMinTagLength(int minTagLength)Set the minimum tag length.- Parameters:
minTagLength
- the minTagLength to set
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