Class IonFactory
java.lang.Object
com.compomics.util.experiment.biology.ions.IonFactory
public class IonFactory extends Object
This factory generates the expected ions from a peptide.
- Author:
- Marc Vaudel, Harald Barsnes
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Method Summary
Modifier and Type Method Description static HashSet<String>
getDefaultNeutralLosses()
Returns the default neutral losses.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(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(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a tag.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.static HashSet<String>
getNeutralLosses(ModificationParameters modificationParameters)
Returns a list containing the default neutral losses and the losses found in the given modifications.NeutralLossCombination[]
getNeutralLossesCombinations(HashSet<String> possibleNeutralLosses)
Returns the possible neutral losses combinations as array of arrays of neutral losses.static HashSet<Integer>
getReporterIons(ModificationParameters modificationParameters)
Returns the reporter ions to annotate with the given PTM settings.
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Method Details
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getInstance
Static method which returns the instance of the factory.- Returns:
- the instance of the factory
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getDefaultNeutralLosses
Returns the default neutral losses.- Returns:
- the default neutral losses
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getNeutralLosses
Returns a list containing the default neutral losses and the losses found in the given modifications. Note: modifications must be loaded in the modification factory.- Parameters:
modificationParameters
- the modification parameters- Returns:
- the neutral losses expected in the dataset
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getReporterIons
Returns the reporter ions to annotate with the given PTM settings.- Parameters:
modificationParameters
- the PTMs to annotate- Returns:
- a hashset of the subtype indexes of the reporter ions to annotate
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getFragmentIons
public 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. /!\ this method will work only if the modifications found in the peptide are in the ModificationFactory.- Parameters:
peptide
- The considered peptidemodificationParameters
- the modification parameters the modification parameterssequenceProvider
- a protein sequence providermodificationsSequenceMatchingParameters
- the sequence matching parameters to use for modifications- Returns:
- the expected fragment ions
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getFragmentIons
public 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. /!\ this method will work only if the modifications found in the peptide are in the ModificationFactory.- Parameters:
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 modifications- Returns:
- the expected fragment ions
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getFragmentIons
public HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)This method returns the theoretic ions expected from a tag. /!\ this method will work only if the PTMs found in the tag are in the PTMFactory.- Parameters:
tag
- the considered tagmodificationParameters
- the modification parameters the modification parametersmodificationsSequenceMatchingParameters
- the sequence matching parameters to use for modifications- Returns:
- the expected fragment ions
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getNeutralLossesCombinations
public NeutralLossCombination[] getNeutralLossesCombinations(HashSet<String> possibleNeutralLosses)Returns the possible neutral losses combinations as array of arrays of neutral losses.- Parameters:
possibleNeutralLosses
- the possible neutral losses to include- Returns:
- the possible neutral losses combinations
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getLossesMass
Convenience summing the masses of various neutral losses.- Parameters:
neutralLosses
- list of neutral losses- Returns:
- the sum of the masses
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