Package com.compomics.util.pride
Class PrideWebService
java.lang.Object
com.compomics.util.pride.PrideWebService
public class PrideWebService extends Object
A java representation of the PRIDE web service.
- Author:
- Kenneth Verheggen
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Constructor Summary
Constructors Constructor Description PrideWebService()
Empty default constructor -
Method Summary
Modifier and Type Method Description static int
getAssayCount(String projectAccession)
Returns the assay count for a given project.static uk.ac.ebi.pride.archive.web.service.model.assay.AssayDetail
getAssayDetail(String assayAccession)
Returns the assay details for a given assay.static uk.ac.ebi.pride.archive.web.service.model.assay.AssayDetailList
getAssayDetails(String projectAccession)
Returns the assay details for a given project.static int
getAssayFileCount(String assayAccession)
Returns a count of file details for a given assay.static uk.ac.ebi.pride.archive.web.service.model.file.FileDetailList
getAssayFileDetails(String assayAccession)
Returns a list of file details for a given assay.static int
getProjectCount(String query, PrideFilter... filters)
Returns a project count for the given criteria and filters.static uk.ac.ebi.pride.archive.web.service.model.project.ProjectDetail
getProjectDetail(String projectAccession)
Returns the project details for a given accession.static int
getProjectFileCount(String projectAccession)
Returns a count of file details for a given project.static uk.ac.ebi.pride.archive.web.service.model.file.FileDetailList
getProjectFileDetails(String projectAccession)
Returns a list of file details for a given project.static uk.ac.ebi.pride.archive.web.service.model.project.ProjectSummaryList
getProjectSummaryList(String query, PrideFilter... filters)
Returns a ProjectSummaryList for the given query and filters.static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList
getProteinIdentificationByAssay(String assayAccession)
Returns a list of protein details for a given assay.static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList
getProteinIdentificationByProject(String projectAccession)
Returns a list of protein details for a given project.static int
getProteinIdentificationCountByAssay(String assayAccession)
Returns a count of protein details for a given assay.static int
getProteinIdentificationCountByProject(String projectAccession)
Returns a count of protein details for a given project.static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList
getProteinIdentificationsByProjectAndProtein(String projectAccession, String proteinAccesion)
Returns a list of protein details for a given project and a given protein accession.static int
getProteinIdentificationsCountByProjectAndProtein(String projectAccession, String proteinAccession)
Returns a count of protein details for a given project and a given protein accession.static int
getPSMCountByAssay(String assayAccession)
Returns a count of PSM details for a given assay.static int
getPSMCountByAssayAndSequence(String assayAccession, String sequence)
Returns a count of PSM details for a given assay and a given peptide sequence.static int
getPSMCountByProject(String projectAccession)
Returns a count of PSM details for a given project.static int
getPSMCountByProjectAndSequence(String projectAccession, String sequence)
Returns a count of PSM details for a given project and a given peptide sequence.static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList
getPSMsByAssay(String assayAccession)
Returns a list of PSM details for a given assay.static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList
getPSMsByAssayAndSequence(String assayAccession, String sequence)
Returns a list of PSM details for a given assay and a given peptide sequence.static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList
getPSMsByProject(String projectAccession)
Returns a list of PSM details for a given project.static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList
getPSMsByProjectAndSequence(String projectAccession, String sequence)
Returns a list of PSM details for a given project and a given peptide sequence.
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Constructor Details
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PrideWebService
public PrideWebService()Empty default constructor
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Method Details
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getProjectSummaryList
public static uk.ac.ebi.pride.archive.web.service.model.project.ProjectSummaryList getProjectSummaryList(String query, PrideFilter... filters) throws IOExceptionReturns a ProjectSummaryList for the given query and filters.- Parameters:
query
- the criteria for a searchfilters
- the filters for a search- Returns:
- a ProjectSummaryList for the given query and filters
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProjectCount
Returns a project count for the given criteria and filters.- Parameters:
query
- the criteria for the searchfilters
- the filters for the search- Returns:
- a project count for the given criteria and filters
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProjectDetail
public static uk.ac.ebi.pride.archive.web.service.model.project.ProjectDetail getProjectDetail(String projectAccession) throws IOExceptionReturns the project details for a given accession.- Parameters:
projectAccession
- the project accession- Returns:
- the project details for a given accession
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getAssayDetails
public static uk.ac.ebi.pride.archive.web.service.model.assay.AssayDetailList getAssayDetails(String projectAccession) throws IOExceptionReturns the assay details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- the assay details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getAssayCount
Returns the assay count for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- the assay count for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getAssayDetail
public static uk.ac.ebi.pride.archive.web.service.model.assay.AssayDetail getAssayDetail(String assayAccession) throws IOExceptionReturns the assay details for a given assay.- Parameters:
assayAccession
- the project assayAccession- Returns:
- the assay details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProjectFileDetails
public static uk.ac.ebi.pride.archive.web.service.model.file.FileDetailList getProjectFileDetails(String projectAccession) throws IOExceptionReturns a list of file details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- a list of file details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProjectFileCount
Returns a count of file details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- a count of file details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getAssayFileDetails
public static uk.ac.ebi.pride.archive.web.service.model.file.FileDetailList getAssayFileDetails(String assayAccession) throws IOExceptionReturns a list of file details for a given assay.- Parameters:
assayAccession
- the assay accession- Returns:
- a list of file details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getAssayFileCount
Returns a count of file details for a given assay.- Parameters:
assayAccession
- the assay accession- Returns:
- a count of file details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProteinIdentificationByProject
public static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList getProteinIdentificationByProject(String projectAccession) throws IOExceptionReturns a list of protein details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- a list of protein details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProteinIdentificationCountByProject
public static int getProteinIdentificationCountByProject(String projectAccession) throws IOExceptionReturns a count of protein details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- a count of protein details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProteinIdentificationsByProjectAndProtein
public static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList getProteinIdentificationsByProjectAndProtein(String projectAccession, String proteinAccesion) throws IOExceptionReturns a list of protein details for a given project and a given protein accession.- Parameters:
projectAccession
- the project accessionproteinAccesion
- the protein accession- Returns:
- a list of protein details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProteinIdentificationsCountByProjectAndProtein
public static int getProteinIdentificationsCountByProjectAndProtein(String projectAccession, String proteinAccession) throws IOExceptionReturns a count of protein details for a given project and a given protein accession.- Parameters:
projectAccession
- the project accessionproteinAccession
- the protein accession- Returns:
- a count of protein details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getProteinIdentificationByAssay
public static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList getProteinIdentificationByAssay(String assayAccession) throws IOExceptionReturns a list of protein details for a given assay.- Parameters:
assayAccession
- the assay accession- Returns:
- a list of protein details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getProteinIdentificationCountByAssay
Returns a count of protein details for a given assay.- Parameters:
assayAccession
- the assay accession- Returns:
- a count of protein details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMsByProject
public static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList getPSMsByProject(String projectAccession) throws IOExceptionReturns a list of PSM details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- a list of protein details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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getPSMCountByProject
Returns a count of PSM details for a given project.- Parameters:
projectAccession
- the project accession- Returns:
- a count of PSM details for a given project
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMsByProjectAndSequence
public static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList getPSMsByProjectAndSequence(String projectAccession, String sequence) throws IOExceptionReturns a list of PSM details for a given project and a given peptide sequence.- Parameters:
projectAccession
- the project accessionsequence
- the peptide sequence- Returns:
- a list of PSM details for a given project and a given peptide sequence
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMCountByProjectAndSequence
public static int getPSMCountByProjectAndSequence(String projectAccession, String sequence) throws IOExceptionReturns a count of PSM details for a given project and a given peptide sequence.- Parameters:
projectAccession
- the project accessionsequence
- the peptide sequence- Returns:
- a count of PSM details for a given project and a given peptide sequence
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMsByAssay
public static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList getPSMsByAssay(String assayAccession) throws IOExceptionReturns a list of PSM details for a given assay.- Parameters:
assayAccession
- the project accession- Returns:
- a list of PSM details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMCountByAssay
Returns a count of PSM details for a given assay.- Parameters:
assayAccession
- the project accession- Returns:
- a count of PSM details for a given assay
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMsByAssayAndSequence
public static uk.ac.ebi.pride.archive.web.service.model.peptide.PsmDetailList getPSMsByAssayAndSequence(String assayAccession, String sequence) throws IOExceptionReturns a list of PSM details for a given assay and a given peptide sequence.- Parameters:
assayAccession
- the project accessionsequence
- the peptide sequence- Returns:
- a list of PSM details for a given assay and a given peptide sequence
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
-
getPSMCountByAssayAndSequence
public static int getPSMCountByAssayAndSequence(String assayAccession, String sequence) throws IOExceptionReturns a count of PSM details for a given assay and a given peptide sequence.- Parameters:
assayAccession
- the project accessionsequence
- the peptide sequence- Returns:
- a count of PSM details for a given assay and a given peptide sequence
- Throws:
IOException
- thrown if the webservice is down or the json response was invalid
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