Class NeutralLossesMap
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap
- All Implemented Interfaces:
Serializable
public class NeutralLossesMap extends ExperimentObject
This class contains the informations relative to the accounting of neutral
losses
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description NeutralLossesMap()
Constructor. -
Method Summary
Modifier and Type Method Description void
addNeutralLoss(NeutralLoss neutralLoss, int bStart, int yStart)
Adds a new neutral loss to the map.void
addNeutralLoss(String neutralLossName, int bStart, int yStart)
Adds a new neutral loss to the map.void
clearNeutralLosses()
Clears the mapping.NeutralLossesMap
clone()
boolean
containsLoss(String neutralLossName)
Returns a boolean indicating whether a loss is implemented in the mapping.ArrayList<String>
getAccountedNeutralLosses()
Returns an arraylist of the names of the implemented neutral losses.Integer
getForwardStart(String neutralLossName)
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).int
getRewindStart(String neutralLossName)
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).boolean
isEmpty()
Returns a boolean indicating if the mapping is empty.void
makeSequenceIndependant()
Makes the neutral losses sequence independent.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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NeutralLossesMap
public NeutralLossesMap()Constructor.
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Method Details
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addNeutralLoss
Adds a new neutral loss to the map.- Parameters:
neutralLoss
- the new neutral lossbStart
- the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)yStart
- the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)
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addNeutralLoss
Adds a new neutral loss to the map.- Parameters:
neutralLossName
- the new neutral loss namebStart
- the amino acid position where the neutral loss should start being accounted starting from the N-terminus (first is 1)yStart
- the amino acid position where the neutral loss should start being accounted starting from the C-terminus (first is 1)
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clearNeutralLosses
public void clearNeutralLosses()Clears the mapping. -
makeSequenceIndependant
public void makeSequenceIndependant()Makes the neutral losses sequence independent. -
isEmpty
public boolean isEmpty()Returns a boolean indicating if the mapping is empty.- Returns:
- a boolean indicating if the mapping is empty
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getAccountedNeutralLosses
Returns an arraylist of the names of the implemented neutral losses.- Returns:
- an arraylist of the names of the implemented neutral losses
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getForwardStart
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).- Parameters:
neutralLossName
- the name of the neutral loss of interest- Returns:
- the first amino acid where to account for the neutral loss
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getRewindStart
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1).- Parameters:
neutralLossName
- the name of the neutral loss of interest- Returns:
- the first amino acid where to account for the neutral loss
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containsLoss
Returns a boolean indicating whether a loss is implemented in the mapping.- Parameters:
neutralLossName
- the name of the neutral loss of interest- Returns:
- a boolean indicating whether a loss is implemented in the mapping
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clone
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