public class ReporterIonQuantification extends Quantification
Quantification.QuantificationMethod
methodUsed
Constructor and Description |
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ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
Constructor for the reporter ion quantification.
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Modifier and Type | Method and Description |
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void |
addNormalisationFactor(int sampleIndex,
double normalisationFactor)
Adds a normalisation factor.
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void |
assignSample(int reporterIndex,
Sample sample)
Assign a sample to an ion referenced by its static index.
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ArrayList<Integer> |
getControlSamples()
Returns the indexes of the samples labelled as control.
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static String |
getDefaultReference(String experimentReference,
String sampleReference,
int replicateNumber)
Returns the default reference for an identification.
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double |
getNormalisationFactor(int sampleIndex)
Returns the normalisation factor for the given sample.
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Integer |
getReporterIndex(Sample aSample)
This method returns the ion associated to the given sample.
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ReporterMethod |
getReporterMethod()
returns the reporter method used.
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Sample |
getSample(int reporterIndex)
This method returns the sample associated to the given ion.
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Set<Integer> |
getSampleIndexes()
Returns a set containing the indexes of every sample.
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boolean |
hasNormalisationFactors()
Indicates whether the normalisation factors are set.
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void |
resetNormalisationFactors()
Resets the normalisation factors.
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void |
setControlSamples(ArrayList<Integer> controlSamples)
Sets the indexes of the samples labelled as control.
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void |
setMethod(ReporterMethod reporterMethod)
Sets the reporter method used.
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getMethodUsed, setMethodUsed
addUrParam, getParameterKey, getUrParam
public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
methodUsed
- the method used for this quantificationpublic void assignSample(int reporterIndex, Sample sample)
reporterIndex
- the index of the ionsample
- the samplepublic Sample getSample(int reporterIndex)
reporterIndex
- the static index of the reporter ionpublic Integer getReporterIndex(Sample aSample)
aSample
- the samplepublic ReporterMethod getReporterMethod()
public void setMethod(ReporterMethod reporterMethod)
reporterMethod
- the reporter method usedpublic static String getDefaultReference(String experimentReference, String sampleReference, int replicateNumber)
experimentReference
- the experiment referencesampleReference
- the sample referencereplicateNumber
- the replicate numberpublic ArrayList<Integer> getControlSamples()
public void setControlSamples(ArrayList<Integer> controlSamples)
controlSamples
- the indexes of the samples to label as controlpublic boolean hasNormalisationFactors()
public void resetNormalisationFactors()
public void addNormalisationFactor(int sampleIndex, double normalisationFactor)
sampleIndex
- the index of the samplenormalisationFactor
- the normalisation factorpublic double getNormalisationFactor(int sampleIndex)
sampleIndex
- the index of the sampleCopyright © 2014. All Rights Reserved.