Class NormalizationFactors
java.lang.Object
com.compomics.util.experiment.normalization.NormalizationFactors
public class NormalizationFactors extends Object
Class grouping the normalization factors used to normalize quantification
results.
- Author:
- Marc Vaudel
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Constructor Summary
Constructors Constructor Description NormalizationFactors()
Constructor. -
Method Summary
Modifier and Type Method Description void
addPeptideNormalisationFactor(String sampleName, double normalisationFactor)
Adds a peptide normalization factor.void
addProteinNormalisationFactor(String sampleName, double normalisationFactor)
Adds a protein normalization factor.void
addPsmNormalisationFactor(String sampleName, double normalisationFactor)
Adds a PSM normalization factor.double
getPeptideNormalisationFactor(String sampleName)
Returns the peptide normalization factor for the given sample, 1.0 if not set.double
getProteinNormalisationFactor(String sampleName)
Returns the protein normalization factor for the given sample, 1.0 if not set.double
getPsmNormalisationFactor(String sampleName)
Returns the PSM normalization factor for the given sample, 1.0 if not set.boolean
hasNormalizationFactors()
Indicates whether normalization factors are set.boolean
hasPeptideNormalisationFactors()
Indicates whether the peptide normalization factors are set.boolean
hasProteinNormalisationFactors()
Indicates whether the protein normalization factors are set.boolean
hasPsmNormalisationFactors()
Indicates whether the PSM normalization factors are set.void
resetPeptideNormalisationFactors()
Resets the peptide normalization factors.void
resetProteinNormalisationFactors()
Resets the protein normalization factors.void
resetPsmNormalisationFactors()
Resets the PSM normalization factors.
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Constructor Details
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NormalizationFactors
public NormalizationFactors()Constructor.
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Method Details
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hasNormalizationFactors
public boolean hasNormalizationFactors()Indicates whether normalization factors are set.- Returns:
- a boolean indicating whether the protein normalization factors are set
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hasProteinNormalisationFactors
public boolean hasProteinNormalisationFactors()Indicates whether the protein normalization factors are set.- Returns:
- a boolean indicating whether the protein normalization factors are set
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hasPeptideNormalisationFactors
public boolean hasPeptideNormalisationFactors()Indicates whether the peptide normalization factors are set.- Returns:
- a boolean indicating whether the peptide normalization factors are set
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hasPsmNormalisationFactors
public boolean hasPsmNormalisationFactors()Indicates whether the PSM normalization factors are set.- Returns:
- a boolean indicating whether the PSM normalization factors are set
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resetProteinNormalisationFactors
public void resetProteinNormalisationFactors()Resets the protein normalization factors. -
resetPeptideNormalisationFactors
public void resetPeptideNormalisationFactors()Resets the peptide normalization factors. -
resetPsmNormalisationFactors
public void resetPsmNormalisationFactors()Resets the PSM normalization factors. -
addProteinNormalisationFactor
Adds a protein normalization factor.- Parameters:
sampleName
- the index of the samplenormalisationFactor
- the normalization factor
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addPeptideNormalisationFactor
Adds a peptide normalization factor.- Parameters:
sampleName
- the index of the samplenormalisationFactor
- the normalization factor
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addPsmNormalisationFactor
Adds a PSM normalization factor.- Parameters:
sampleName
- the index of the samplenormalisationFactor
- the normalization factor
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getProteinNormalisationFactor
Returns the protein normalization factor for the given sample, 1.0 if not set.- Parameters:
sampleName
- the index of the sample- Returns:
- the normalization factor
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getPeptideNormalisationFactor
Returns the peptide normalization factor for the given sample, 1.0 if not set.- Parameters:
sampleName
- the index of the sample- Returns:
- the normalization factor
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getPsmNormalisationFactor
Returns the PSM normalization factor for the given sample, 1.0 if not set.- Parameters:
sampleName
- the index of the sample- Returns:
- the normalization factor
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