Package | Description |
---|---|
com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Class and 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.
|
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