Class MsgfParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.MsgfParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class MsgfParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The MS-GF+ specific parameters.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description MsgfParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.Advocate
getAlgorithm()
Returns the identification algorithm.int
getFragmentationType()
Return the fragmentation ID.int
getInstrumentID()
Return the instrument ID.Integer
getMaxPeptideLength()
Returns the maximal peptide length allowed.Integer
getMinPeptideLength()
Sets the minimal peptide length allowed.Integer
getNumberOfModificationsPerPeptide()
Returns the maximum number of modifications per peptide.Integer
getNumberOfSpectrumMatches()
Returns the maximum number of spectrum matches.Integer
getNumberOfTasks()
Returns the number of tasks, null if not set.Integer
getNumberTolerableTermini()
Returns the number of tolerable termini.int
getProtocol()
Returns the protocol ID.boolean
isAdditionalOutput()
Returns if additional output is to be included.boolean
searchDecoyDatabase()
Returns whether MS-GF+ is to create and search a decoy database.void
setAdditionalOutput(boolean additionalOutput)
Set if additional output is to be included.void
setFragmentationType(int fragmentationType)
Set the fragmentation ID.void
setInstrumentID(int instrumentID)
Set the instrument ID.void
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.void
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.void
setNumberOfModificationsPerPeptide(Integer numberOfModificationsPerPeptide)
Set the maximum number of modifications per peptide.void
setNumberOfSpectrumMarches(Integer numberOfSpectrumMarches)
Set the maximum number of spectrum matches.void
setNumberOfTasks(Integer numberOfTasks)
Set the number of tasks.void
setNumberTolerableTermini(Integer numberTolerableTermini)
Set the number of tolerable termini.void
setProtocol(int protocol)
Set the protocol ID.void
setSearchDecoyDatabase(boolean searchDecoyDatabase)
Set whether MS-GF+ is to create and search a decoy database.String
toString(boolean html)
Returns the parameters as a string.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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MsgfParameters
public MsgfParameters()Constructor.
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Method Details
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getAlgorithm
Description copied from interface:IdentificationAlgorithmParameter
Returns the identification algorithm.- Specified by:
getAlgorithm
in interfaceIdentificationAlgorithmParameter
- Returns:
- the identification algorithm
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equals
Description copied from interface:IdentificationAlgorithmParameter
Indicates whether another identificationAlgorithmParameter has the same parameters.- Specified by:
equals
in interfaceIdentificationAlgorithmParameter
- Parameters:
identificationAlgorithmParameter
- the other identificationAlgorithmParameter- Returns:
- true if the algorithm and parameters are the same
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toString
Description copied from interface:IdentificationAlgorithmParameter
Returns the parameters as a string.- Specified by:
toString
in interfaceIdentificationAlgorithmParameter
- Parameters:
html
- use HTML formatting- Returns:
- the parameters as a string
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searchDecoyDatabase
public boolean searchDecoyDatabase()Returns whether MS-GF+ is to create and search a decoy database.- Returns:
- whether MS-GF+ is to create and search a decoy database
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setSearchDecoyDatabase
public void setSearchDecoyDatabase(boolean searchDecoyDatabase)Set whether MS-GF+ is to create and search a decoy database.- Parameters:
searchDecoyDatabase
- the searchDecoyDatabase to set
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getMaxPeptideLength
Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
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setMaxPeptideLength
Sets the maximal peptide length allowed.- Parameters:
maxPeptideLength
- the maximal peptide length allowed
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getMinPeptideLength
Sets the minimal peptide length allowed.- Returns:
- the minimal peptide length allowed
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setMinPeptideLength
Sets the minimal peptide length allowed.- Parameters:
minPeptideLength
- the minimal peptide length allowed
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getInstrumentID
public int getInstrumentID()Return the instrument ID.- Returns:
- the instrumentID
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setInstrumentID
public void setInstrumentID(int instrumentID)Set the instrument ID.- Parameters:
instrumentID
- the instrumentID to set
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getFragmentationType
public int getFragmentationType()Return the fragmentation ID.- Returns:
- the fragmentationType
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setFragmentationType
public void setFragmentationType(int fragmentationType)Set the fragmentation ID.- Parameters:
fragmentationType
- the fragmentationType to set
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getProtocol
public int getProtocol()Returns the protocol ID.- Returns:
- the protocol
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setProtocol
public void setProtocol(int protocol)Set the protocol ID.- Parameters:
protocol
- the protocol to set
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getNumberOfSpectrumMatches
Returns the maximum number of spectrum matches.- Returns:
- the numberOfSpectrumMarches
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setNumberOfSpectrumMarches
Set the maximum number of spectrum matches.- Parameters:
numberOfSpectrumMarches
- the numberOfSpectrumMarches to set
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isAdditionalOutput
public boolean isAdditionalOutput()Returns if additional output is to be included.- Returns:
- the additionalOutput
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setAdditionalOutput
public void setAdditionalOutput(boolean additionalOutput)Set if additional output is to be included.- Parameters:
additionalOutput
- the additionalOutput to set
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getNumberTolerableTermini
Returns the number of tolerable termini.- Returns:
- the numberTolerableTermini
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setNumberTolerableTermini
Set the number of tolerable termini.- Parameters:
numberTolerableTermini
- the numberTolerableTermini to set
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getNumberOfModificationsPerPeptide
Returns the maximum number of modifications per peptide.- Returns:
- the maximum number of modifications per peptide
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setNumberOfModificationsPerPeptide
Set the maximum number of modifications per peptide.- Parameters:
numberOfModificationsPerPeptide
- the maximum number of modifications per peptide
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getNumberOfTasks
Returns the number of tasks, null if not set.- Returns:
- the number of tasks
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setNumberOfTasks
Set the number of tasks. Set to null to leave the choice to MS-GF+.- Parameters:
numberOfTasks
- the number of tasks
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