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