Uses of Class
com.compomics.util.experiment.identification.IdentificationMatch
Package | Description |
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com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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Uses of IdentificationMatch in com.compomics.util.experiment.identification.features
Methods in com.compomics.util.experiment.identification.features with parameters of type IdentificationMatch Modifier and Type Method Description String
IdentificationFeaturesGenerator. getAmbiguousModificationSiteNumber(IdentificationMatch identificationMatch)
Returns a summary of the number of modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.String
IdentificationFeaturesGenerator. getAmbiguousModificationSiteNumber(IdentificationMatch match, ArrayList<String> targetedModifications)
Returns a summary of the number of modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.String
IdentificationFeaturesGenerator. getAmbiguousModificationSites(IdentificationMatch identificationMatch, String sequence)
Returns a list of the modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.String
IdentificationFeaturesGenerator. getAmbiguousModificationSites(IdentificationMatch match, String sequence, ArrayList<String> targetedModifications)
Returns a list of the modifications present on the sequence ambiguously assigned to an amino acid grouped by representative site followed by secondary ambiguous sites.String
IdentificationFeaturesGenerator. getConfidentModificationSites(IdentificationMatch identificationMatch, String sequence)
Returns a summary of all modifications present on the sequence confidently assigned to an amino acid.String
IdentificationFeaturesGenerator. getConfidentModificationSites(IdentificationMatch match, String sequence, ArrayList<String> targetedModifications)
Returns a summary of the modifications present on the peptide sequence confidently assigned to an amino acid with focus on given list of modifications.String
IdentificationFeaturesGenerator. getConfidentModificationSitesNumber(IdentificationMatch identificationMatch)
Returns the number of confidently localized variable modifications.String
IdentificationFeaturesGenerator. getConfidentModificationSitesNumber(IdentificationMatch match, ArrayList<String> targetedModifications)
Returns the number of confidently localized variable modifications.String
IdentificationFeaturesGenerator. getModifiedSequence(IdentificationMatch identificationMatch, String sequence)
Returns the match sequence annotated with modifications. -
Uses of IdentificationMatch in com.compomics.util.experiment.identification.matches
Subclasses of IdentificationMatch in com.compomics.util.experiment.identification.matches Modifier and Type Class Description class
PeptideMatch
This class models a peptide match.class
ProteinMatch
This class models a protein match.class
SpectrumMatch
This class models a spectrum match.