Uses of Class
com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption

Packages that use TagAssumption

Package	Description
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.

Uses of TagAssumption in com.compomics.util.experiment.identification.matches

Methods in com.compomics.util.experiment.identification.matches that return TagAssumption

Modifier and Type	Method	Description
TagAssumption	SpectrumMatch.getBestTagAssumption()	Getter for the best tag assumption.

Methods in com.compomics.util.experiment.identification.matches that return types with arguments of type TagAssumption

Modifier and Type	Method	Description
java.util.stream.Stream<TagAssumption>	SpectrumMatch.getAllTagAssumptions()	Returns a stream of all tag assumptions
TreeMap<Double,ArrayList<TagAssumption>>	SpectrumMatch.getAllTagAssumptions(int advocateId)	Returns all tag assumptions for the specified search engine indexed by their score.
HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>>	SpectrumMatch.getTagAssumptionsMap()	Returns the tag assumptions map: advocate id > score > list of assumptions.

Methods in com.compomics.util.experiment.identification.matches with parameters of type TagAssumption

Modifier and Type	Method	Description
void	SpectrumMatch.addTagAssumption(int advocateId, TagAssumption tagAssumption)	Add a hit.
void	SpectrumMatch.removeTagAssumption(TagAssumption tagAssumption)	Removes an assumption from the mapping.
void	SpectrumMatch.setBestTagAssumption(TagAssumption bestTagAssumption)	Setter for the best tag assumption.

Method parameters in com.compomics.util.experiment.identification.matches with type arguments of type TagAssumption

Modifier and Type	Method	Description
void	SpectrumMatch.setTagAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> tagAssumptionsMap)	Sets the tag assumption map.

Uses of TagAssumption in com.compomics.util.experiment.identification.spectrum_assumptions

Methods in com.compomics.util.experiment.identification.spectrum_assumptions that return TagAssumption

Modifier and Type	Method	Description
TagAssumption	TagAssumption.reverse(boolean yIon)	Returns a new TagAssumption instance where the tag is a reversed version of this tag.

Methods in com.compomics.util.experiment.identification.spectrum_assumptions that return types with arguments of type TagAssumption

Modifier and Type	Method	Description
ArrayList<TagAssumption>	TagAssumption.getPossibleTags(boolean forwardIon, int minCharge, int maxCharge, int maxIsotope)	Computes the possible tag assumptions which can be obtained from this one by accounting for other charges and isotopes.