public class IonFactory extends Object
Modifier and Type | Method and Description |
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static HashSet<String> |
getDefaultNeutralLosses()
Returns the default neutral losses.
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HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns all the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Peptide peptide,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a peptide.
|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
getFragmentIons(Tag tag,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a tag.
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static IonFactory |
getInstance()
Static method which returns the instance of the factory.
|
static double |
getLossesMass(NeutralLoss[] neutralLosses)
Convenience summing the masses of various neutral losses.
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static HashSet<String> |
getNeutralLosses(ModificationParameters modificationParameters)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
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NeutralLossCombination[] |
getNeutralLossesCombinations(HashSet<String> possibleNeutralLosses)
Returns the possible neutral losses combinations as array of arrays of
neutral losses.
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static HashSet<Integer> |
getReporterIons(ModificationParameters modificationParameters)
Returns the reporter ions to annotate with the given PTM settings.
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public static IonFactory getInstance()
public static HashSet<String> getDefaultNeutralLosses()
public static HashSet<String> getNeutralLosses(ModificationParameters modificationParameters)
modificationParameters
- the modification parameterspublic static HashSet<Integer> getReporterIons(ModificationParameters modificationParameters)
modificationParameters
- the PTMs to annotatepublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
peptide
- The considered peptidemodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Peptide peptide, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)
peptide
- the considered peptidespecificAnnotationSettings
- if provided, only the ions detectable
using these settings will be selectedmodificationParameters
- the modification parameters the
modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)
tag
- the considered tagmodificationParameters
- the modification parameters the
modification parametersmodificationsSequenceMatchingParameters
- the sequence matching
parameters to use for modificationspublic NeutralLossCombination[] getNeutralLossesCombinations(HashSet<String> possibleNeutralLosses)
possibleNeutralLosses
- the possible neutral losses to includepublic static double getLossesMass(NeutralLoss[] neutralLosses)
neutralLosses
- list of neutral lossesCopyright © 2021. All rights reserved.