Package | Description |
---|---|
uk.ac.ebi.pride.utilities.data.controller.impl.Transformer | |
uk.ac.ebi.pride.utilities.data.core |
Modifier and Type | Method and Description |
---|---|
static Map<String,IdentifiableParamGroup> |
MzIdentMLTransformer.transformToFragmentationTable(uk.ac.ebi.jmzidml.model.mzidml.FragmentationTable oldFragmentationTable) |
Modifier and Type | Method and Description |
---|---|
static void |
MzIdentMLTransformer.setFragmentationTable(Map<String,IdentifiableParamGroup> fragTable) |
Modifier and Type | Class and Description |
---|---|
class |
AbundanceAssay
Abundance Assay is the Class to storage the abundance variables for each Protein.
|
class |
Assay
Assay In the mzTab experiment with the corresponding Reagent and sample
|
class |
Chromatogram
Chromatogram object.
|
class |
Contact
This class is just to organize the code, the ConstantRole class have to kind of instance,
one of then is Organization and the Other one if the person both objects extend the IdentifiableParamGroup
in order to organize the code we create a new abstract class named AbstractContact to separate the Contacts types
from the IdentifiableParamGroup.
|
class |
DBSequence
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
|
class |
ExperimentMetaData
General descriptions shared or used for the whole file.
|
class |
ExperimentProtocol
Protocol used to generate the dataset, added by PRIDE XML 2.0.
|
class |
IdentificationMetaData
This class is used to manage and store the information of the metadata for protein and spectrum
identifications.
|
class |
Modification
A molecule modification specification.
|
class |
MzGraph
Abstract object can be extended by both Spectrum and Chromatogram.
|
class |
MzGraphMetaData
This class storage the information related with metadata at the spectrum level.
|
class |
Organization
Organizations are entities like companies, universities, government agencies.
|
class |
PeptideEvidence
PeptideEvidence links a specific Peptide Element to a specific position in a DBSequence.
|
class |
PeptideSequence
One (poly)peptide (a sequence with modifications).
|
class |
Person
A person's name and contact details.
|
class |
Protein
Abstract class for both GelFreeIdentification and TwoDimIdentification
|
class |
ProteinGroup
A set of logically related results from a protein detection, for example to represent conflicting assignments of
peptides to proteins
|
class |
Protocol
The collection of protocols which include the parameters and settings of the performed analyses.
|
class |
QuantScore
The QuantScore is the List of StudyVariable Scores and the Abundance by Assays.
|
class |
Reference
Reference is added by PRIDE XML 2.0., also a generic reference for mzIdentML References.
|
class |
Sample
Description of the sample used to generate the Dataset.
|
class |
Software
Software details.
|
class |
SourceFile
Description of source file, including identification file, location and type.
|
class |
Spectrum
A peak list including the underlying acquisitions.
|
class |
SpectrumIdentification
PSM Spectrum identification match.
|
class |
SpectrumIdentificationList
Represents the set of all search results from SpectrumIdentification.
|
class |
SpectrumIdentificationProtocol
The parameters and settings of a SpectrumIdentification analysis.
|
class |
StudyVariable
Study variable is use for Quantitation on mzTab files.
|
Modifier and Type | Method and Description |
---|---|
IdentifiableParamGroup |
PeptideEvidence.getTranslationTable() |
Modifier and Type | Method and Description |
---|---|
List<IdentifiableParamGroup> |
SpectrumIdentificationList.getFragmentationTable() |
Map<IdentifiableParamGroup,List<Integer>> |
IonType.getMeasures() |
List<IdentifiableParamGroup> |
DataBaseTranslation.getTranslationTables() |
Modifier and Type | Method and Description |
---|---|
void |
PeptideEvidence.setTranslationTable(IdentifiableParamGroup translationTable) |
Modifier and Type | Method and Description |
---|---|
void |
SpectrumIdentificationList.setFragmentationTable(List<IdentifiableParamGroup> fragmentationTable) |
void |
IonType.setMeasures(Map<IdentifiableParamGroup,List<Integer>> measures) |
void |
DataBaseTranslation.setTranslationTables(List<IdentifiableParamGroup> translationTables) |
Constructor and Description |
---|
DataBaseTranslation(List<Integer> allowedFrames,
List<IdentifiableParamGroup> translationTables) |
SpectrumIdentificationList(Comparable id,
String name,
int numSequenceSearched,
List<IdentifiableParamGroup> fragmentationTable,
List<Peptide> spectrumIdentificationList) |
SpectrumIdentificationList(ParamGroup params,
Comparable id,
String name,
int numSequenceSearched,
List<IdentifiableParamGroup> fragmentationTable,
List<Peptide> spectrumIdentificationList) |
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