public class SequenceMatchingParameters extends ExperimentObject
Modifier and Type | Class and Description |
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static class |
SequenceMatchingParameters.MatchingType
The different types of amino acid matching.
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Modifier and Type | Field and Description |
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static SequenceMatchingParameters |
DEFAULT_STRING_MATCHING
Default string matching.
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NO_KEY
Constructor and Description |
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SequenceMatchingParameters()
Constructor for empty preferences.
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Modifier and Type | Method and Description |
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static SequenceMatchingParameters |
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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int |
getMaxPtmsPerTagPeptide()
Returns the maximum number of PTMs to consider when mapping tags to
protein sequences.
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int |
getMinAminoAcidScore()
Returns the minimum amino acid score.
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int |
getMinTagLength()
Returns the minimum tag length.
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SequenceMatchingParameters.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 SequenceMatchingParameters |
getStringMatching()
Returns preferences for simple string matching.
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boolean |
isEnzymaticTagsOnly()
Returns true if tags should only be mapped to enzymatic peptides.
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boolean |
isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another sequence matching preferences is the same as
this one.
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void |
setEnzymaticTagsOnly(boolean enzymaticTagsOnly)
Sets whether tags should only be mapped to enzymatic peptides.
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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 |
setMaxPtmsPerTagPeptide(int numberOfPtmsPerTagPeptide)
Sets the maximum number of PTMs to consider when mapping tags to protein
sequences.
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void |
setMinAminoAcidScore(int minAminoAcidScore)
Set the minimum amino acid score.
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void |
setMinTagLength(int minTagLength)
Set the minimum tag length.
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void |
setSequenceMatchingType(SequenceMatchingParameters.MatchingType sequenceMatchingType)
Sets the sequence matching type.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final SequenceMatchingParameters DEFAULT_STRING_MATCHING
public SequenceMatchingParameters()
public static SequenceMatchingParameters getStringMatching()
public static SequenceMatchingParameters getDefaultSequenceMatching()
public SequenceMatchingParameters.MatchingType getSequenceMatchingType()
public void setSequenceMatchingType(SequenceMatchingParameters.MatchingType sequenceMatchingType)
sequenceMatchingType
- the sequence matching typepublic double getLimitX()
public void setLimitX(double limitX)
limitX
- the maximal share of X's a match can containpublic boolean isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)
sequenceMatchingPreferences
- the other sequence matching
preferencespublic String getShortDescription()
public boolean isEnzymaticTagsOnly()
public void setEnzymaticTagsOnly(boolean enzymaticTagsOnly)
enzymaticTagsOnly
- the enzymaticTagsOnly to setpublic int getMaxPtmsPerTagPeptide()
public void setMaxPtmsPerTagPeptide(int numberOfPtmsPerTagPeptide)
numberOfPtmsPerTagPeptide
- the maxPtmsPerTagPeptide to setpublic int getMinAminoAcidScore()
public void setMinAminoAcidScore(int minAminoAcidScore)
minAminoAcidScore
- the minAminoAcidScore to setpublic int getMinTagLength()
public void setMinTagLength(int minTagLength)
minTagLength
- the minTagLength to setCopyright © 2021. All rights reserved.