public class MsgfParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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MsgfParameters()
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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int |
getFragmentationType()
Return the fragmentation ID.
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int |
getInstrumentID()
Return the instrument ID.
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Integer |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
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Integer |
getMinPeptideLength()
Sets the minimal peptide length allowed.
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Integer |
getNumberOfPtmsPerPeptide()
Returns the maximum number of PTMs per peptide.
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Integer |
getNumberOfSpectrumMatches()
Returns the maximum number of spectrum matches.
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Integer |
getNumberTolerableTermini()
Returns the number of tolerable termini.
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int |
getProtocol()
Returns the protocol ID.
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boolean |
isAdditionalOutput()
Returns if additional output is to be included.
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boolean |
searchDecoyDatabase()
Returns whether MS-GF+ is to create and search a decoy database.
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void |
setAdditionalOutput(boolean additionalOutput)
Set if additional output is to be included.
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void |
setFragmentationType(int fragmentationType)
Set the fragmentation ID.
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void |
setInstrumentID(int instrumentID)
Set the instrument ID.
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void |
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.
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void |
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.
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void |
setNumberOfPtmsPerPeptide(Integer numberOfPtmsPerPeptide)
Set the maximum number of PTMs per peptide.
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void |
setNumberOfSpectrumMarches(Integer numberOfSpectrumMarches)
Set the maximum number of spectrum matches.
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void |
setNumberTolerableTermini(Integer numberTolerableTermini)
Set the number of tolerable termini.
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void |
setProtocol(int protocol)
Set the protocol ID.
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void |
setSearchDecoyDatabase(boolean searchDecoyDatabase)
Set whether MS-GF+ is to create and search a decoy database.
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String |
toString(boolean html)
Returns the parameters as a string.
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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 formattingpublic boolean searchDecoyDatabase()
public void setSearchDecoyDatabase(boolean searchDecoyDatabase)
searchDecoyDatabase
- the searchDecoyDatabase to setpublic 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 int getInstrumentID()
public void setInstrumentID(int instrumentID)
instrumentID
- the instrumentID to setpublic int getFragmentationType()
public void setFragmentationType(int fragmentationType)
fragmentationType
- the fragmentationType to setpublic int getProtocol()
public void setProtocol(int protocol)
protocol
- the protocol to setpublic Integer getNumberOfSpectrumMatches()
public void setNumberOfSpectrumMarches(Integer numberOfSpectrumMarches)
numberOfSpectrumMarches
- the numberOfSpectrumMarches to setpublic boolean isAdditionalOutput()
public void setAdditionalOutput(boolean additionalOutput)
additionalOutput
- the additionalOutput to setpublic Integer getNumberTolerableTermini()
public void setNumberTolerableTermini(Integer numberTolerableTermini)
numberTolerableTermini
- the numberTolerableTermini to setpublic Integer getNumberOfPtmsPerPeptide()
public void setNumberOfPtmsPerPeptide(Integer numberOfPtmsPerPeptide)
numberOfPtmsPerPeptide
- the numberOfPtmsPerPeptide to setCopyright © 2016. All rights reserved.