public class OmssaParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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OmssaParameters()
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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Integer |
getHitListLength()
Returns the length of the hit list for OMSSA.
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Double |
getMaxEValue()
Returns the maximal e-value searched for.
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Integer |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
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Charge |
getMinimalChargeForMultipleChargedFragments()
Returns the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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Integer |
getMinPeptideLength()
Sets the minimal peptide length allowed.
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static String[] |
getOmssaOutputTypes()
Returns the output types available.
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String |
getSelectedOutput()
Returns the selected output type, omx or csv.
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Boolean |
isEstimateCharge()
Indicates whether the precursor charge shall be estimated for OMSSA.
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Boolean |
isRemovePrecursor()
Indicates whether the precursor shall be removed for OMSSA.
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Boolean |
isScalePrecursor()
Indicates whether the precursor shall be scaled for OMSSA.
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void |
setEstimateCharge(Boolean estimateCharge)
Sets whether the precursor charge shall be estimated for OMSSA.
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void |
setHitListLength(Integer hitListLength)
Sets the length of the hit list for OMSSA.
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void |
setMaxEValue(Double maxEValue)
Sets the maximal e-value searched for.
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void |
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.
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void |
setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
Sets the minimal precursor charge to account for multiply charged
fragments in OMSSA.
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void |
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.
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void |
setRemovePrecursor(Boolean removePrecursor)
Sets whether the precursor shall be removed for OMSSA.
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void |
setScalePrecursor(Boolean scalePrecursor)
Sets whether the precursor shall be scaled for OMSSA.
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void |
setSelectedOutput(String selectedOutput)
Sets the output type, omx or csv.
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String |
toString(boolean html)
Returns the parameters as a string.
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public Double getMaxEValue()
public void setMaxEValue(Double maxEValue)
maxEValue
- the maximal e-value searched forpublic Integer getHitListLength()
public void setHitListLength(Integer hitListLength)
hitListLength
- the length of the hit list for OMSSApublic Charge getMinimalChargeForMultipleChargedFragments()
public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)
minimalChargeForMultipleChargedFragments
- the minimal precursor
charge to account for multiply charged fragments in OMSSApublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic Integer getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic Boolean isEstimateCharge()
public void setEstimateCharge(Boolean estimateCharge)
estimateCharge
- a boolean indicating whether the precursor charge
shall be estimated for OMSSApublic Boolean isRemovePrecursor()
public void setRemovePrecursor(Boolean removePrecursor)
removePrecursor
- a boolean indicating whether the precursor shall
be removed for OMSSApublic Boolean isScalePrecursor()
public void setScalePrecursor(Boolean scalePrecursor)
scalePrecursor
- a boolean indicating whether the precursor shall be
scaled for OMSSApublic String getSelectedOutput()
public void setSelectedOutput(String selectedOutput)
selectedOutput
- the output typepublic static String[] getOmssaOutputTypes()
public Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingCopyright © 2014. All Rights Reserved.