Uses of Class
com.compomics.util.experiment.identification.amino_acid_tags.Tag

Packages that use Tag

Package	Description
com.compomics.cli.peptide_mapper	Command line for PeptideMapper.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.identification.amino_acid_tags	Amino Acid Tag classes.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of Tag in com.compomics.cli.peptide_mapper

Methods in com.compomics.cli.peptide_mapper with parameters of type Tag

Modifier and Type	Method	Description
static String	PeptideMapperCLI.tagToString(Tag tag)

Uses of Tag in com.compomics.util.experiment.biology.ions

Methods in com.compomics.util.experiment.biology.ions with parameters of type Tag

Modifier and Type	Method	Description
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a tag.

Uses of Tag in com.compomics.util.experiment.identification.amino_acid_tags

Methods in com.compomics.util.experiment.identification.amino_acid_tags that return Tag

Modifier and Type	Method	Description
Tag	Tag.reverse(boolean yIon)	Returns a new tag instance which is a reversed version of the current tag.

Methods in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type Tag

Modifier and Type	Method	Description
static String	Tag.getTaggedModifiedSequence(ModificationParameters modificationParameters, Tag tag, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean includeTerminalGaps, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.
static String	Tag.getTagModificationsAsString(Tag tag)	Returns the tag modifications as a string.
boolean	Tag.isSameAs(Tag anotherTag, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether this tag is the same as another tag.
boolean	Tag.isSameSequenceAndModificationStatusAs(Tag anotherTag, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether this tag is the same as another tag without accounting for modification localization.

Constructors in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type Tag

Modifier	Constructor	Description
	Tag(Tag tag)	Creates a new tag instance based on the given one.

Uses of Tag in com.compomics.util.experiment.identification.protein_inference

Methods in com.compomics.util.experiment.identification.protein_inference with parameters of type Tag

Modifier and Type	Method	Description
ArrayList<PeptideProteinMapping>	FastaMapper.getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)	Returns the protein mappings for the given peptide sequence.

Uses of Tag in com.compomics.util.experiment.identification.protein_inference.fm_index

Methods in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type Tag

Modifier and Type	Method	Description
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithoutVariants(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences, int indexPart)	Mapping tags against proteome without variants.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariants(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences, int indexPart)	Mapping tags against proteome with variants.

Uses of Tag in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators that return Tag

Modifier and Type	Method	Description
Tag	TagSpectrumAnnotator.getTag()	Returns the tag to annotate.

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type Tag

Modifier and Type	Method	Description
static NeutralLossesMap	TagSpectrumAnnotator.getDefaultLosses(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given tag.
IonMatch[]	TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag)	Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
IonMatch[]	TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a list of IonMatches.
void	TagSpectrumAnnotator.setTag(Tag newTag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, int precursorCharge)	Sets a new tag to match.

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

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

Modifier and Type	Method	Description
Tag	TagAssumption.getTag()	Returns the tag of this assumption.

Methods in com.compomics.util.experiment.identification.spectrum_assumptions with parameters of type Tag

Modifier and Type	Method	Description
void	TagAssumption.setTag(Tag tag)

Constructors in com.compomics.util.experiment.identification.spectrum_assumptions with parameters of type Tag

Modifier	Constructor	Description
	TagAssumption(int advocate, int rank, Tag tag, int identificationCharge, double rawScore, double score)	Constructor.Note: if PsmScores.scoreRoundingDecimal is not null the scored will be floored accordingly.

Uses of Tag in com.compomics.util.experiment.identification.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type Tag

Modifier and Type	Method	Description
static HashSet<String>	ModificationUtils.getAllModifications(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters sequenceMatchingParameters)	Returns a set of the names of all modifications found on a tag.

Uses of Tag in com.compomics.util.gui.spectrum

Methods in com.compomics.util.gui.spectrum with parameters of type Tag

Modifier and Type	Method	Description
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored)	Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showReverseTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored)	Add reference areas annotating the de novo tags.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Tag tag, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.