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 and 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 and Description
HashMap<Integer,HashMap<String,ArrayList<TagAssumption>>>	SpectrumMatch.getTagAssumptionsMap(int keySize, SequenceMatchingPreferences sequenceMatchingPreferences) Returns a map containing the tag assumptions of this spectrum assumptions indexed by the beginning of the longest amino acid sequence.

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

Modifier and Type	Method and Description
void	SpectrumMatch.setBestTagAssumption(TagAssumption bestTagAsssumption) Setter for the best tag assumption.

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 and Description
TagAssumption	TagAssumption.reverse(boolean yIon) Retunrs 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 and 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.