Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
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com.compomics.util.pride |
Objects related to mapping to PRIDE.
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com.compomics.util.pride.prideobjects |
Objects related to mapping experiment annotation to PRIDE.
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Modifier and Type | Method and Description |
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CvTerm |
PTM.getCvTerm()
Returns the CV term associated with this PTM.
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static CvTerm |
EnzymeFactory.getEnzymeCvTerm(Enzyme enzyme)
Tries to convert the given enzyme to a CvTerm for use in mzIdentML etc.
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abstract CvTerm |
Ion.getPrideCvTerm()
Returns the pride cv term adapted to the fragment ion.
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Modifier and Type | Method and Description |
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void |
PTM.setCvTerm(CvTerm cvTerm)
Set the CV term associated with this PTM.
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Constructor and Description |
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PTM(int type,
String name,
String shortName,
AtomChain atomChainAdded,
AtomChain atomChainRemoved,
AminoAcidPattern aminoAcidPattern,
CvTerm cvTerm)
Constructor for a reference modification.
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Modifier and Type | Method and Description |
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CvTerm |
TagFragmentIon.getPrideCvTerm() |
CvTerm |
ReporterIon.getPrideCvTerm() |
CvTerm |
RelatedIon.getPrideCvTerm() |
CvTerm |
PrecursorIon.getPrideCvTerm() |
CvTerm |
PeptideFragmentIon.getPrideCvTerm() |
CvTerm |
ImmoniumIon.getPrideCvTerm() |
CvTerm |
Glycan.getPrideCvTerm() |
CvTerm |
ElementaryIon.getPrideCvTerm() |
Modifier and Type | Method and Description |
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CvTerm |
IonMatch.getChargePrideCvTerm()
Returns the pride CV term for the ion match charge.
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CvTerm |
IonMatch.getIntensityPrideCvTerm()
Returns the pride CV term for the ion match intensity.
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CvTerm |
IonMatch.getIonMassErrorPrideCvTerm(int minIsotope,
int maxIsotope)
Returns the pride CV term for the ion match error.
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CvTerm |
IonMatch.getMZPrideCvTerm()
Returns the pride CV term for the ion match m/z.
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Modifier and Type | Method and Description |
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CvTerm |
PtmToPrideMap.getCVTerm(String ptmName)
Returns the CV term corresponding to the given PTM name.
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static CvTerm |
PtmToPrideMap.getDefaultCVTerm(String ptmName)
Deprecated.
use the getCvTerm method for the PTM instead
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Modifier and Type | Method and Description |
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void |
PtmToPrideMap.putCVTerm(String modName,
CvTerm cvTerm)
Puts a new mapping in the map.
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Modifier and Type | Method and Description |
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CvTerm |
Instrument.getDetector()
Returns the instrument detector.
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CvTerm |
Instrument.getSource()
Returns the instrument source.
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Modifier and Type | Method and Description |
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ArrayList<CvTerm> |
Sample.getCvTerms()
Returns the CV terms.
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ArrayList<CvTerm> |
Protocol.getCvTerms()
Returns the CV terms.
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ArrayList<CvTerm> |
Instrument.getCvTerms()
Returns the CV terms.
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Modifier and Type | Method and Description |
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void |
Instrument.setDetector(CvTerm detector)
Set the instrument detector.
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void |
Instrument.setSource(CvTerm source)
Set the instrument source.
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Modifier and Type | Method and Description |
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void |
Sample.setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms.
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void |
Protocol.setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms.
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void |
Instrument.setCvTerms(ArrayList<CvTerm> cvTerms)
Set the CV terms.
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Constructor and Description |
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Instrument(String name,
CvTerm source,
CvTerm detector,
ArrayList<CvTerm> cvTerms)
Create a new Instrument object.
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Constructor and Description |
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Instrument(String name,
CvTerm source,
CvTerm detector,
ArrayList<CvTerm> cvTerms)
Create a new Instrument object.
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Protocol(String name,
ArrayList<CvTerm> cvTerms)
Create a new Protocol object.
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Sample(String name,
ArrayList<CvTerm> cvTerms)
Create a new Sample object.
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