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

  • Constructor Details

    • PrideWebService

      public PrideWebService()
      Empty default constructor

  • Method Details

    • getProjectSummaryList

      public static uk.ac.ebi.pride.archive.web.service.model.project.ProjectSummaryList getProjectSummaryList(String query, PrideFilter... filters) throws IOException
      Returns a ProjectSummaryList for the given query and filters.
      Parameters:
      query - the criteria for a search
      filters - 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

    • getProjectCount

      public static int getProjectCount(String query, PrideFilter... filters) throws IOException
      Returns a project count for the given criteria and filters.
      Parameters:
      query - the criteria for the search
      filters - 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

    • getProjectDetail

      public static uk.ac.ebi.pride.archive.web.service.model.project.ProjectDetail getProjectDetail(String projectAccession) throws IOException
      Returns 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

    • getAssayDetails

      public static uk.ac.ebi.pride.archive.web.service.model.assay.AssayDetailList getAssayDetails(String projectAccession) throws IOException
      Returns 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

    • getAssayCount

      public static int getAssayCount(String projectAccession) throws IOException
      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

    • getAssayDetail

      public static uk.ac.ebi.pride.archive.web.service.model.assay.AssayDetail getAssayDetail(String assayAccession) throws IOException
      Returns 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

    • getProjectFileDetails

      public static uk.ac.ebi.pride.archive.web.service.model.file.FileDetailList getProjectFileDetails(String projectAccession) throws IOException
      Returns 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

    • getProjectFileCount

      public static int getProjectFileCount(String projectAccession) throws IOException
      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

    • getAssayFileDetails

      public static uk.ac.ebi.pride.archive.web.service.model.file.FileDetailList getAssayFileDetails(String assayAccession) throws IOException
      Returns 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

    • getAssayFileCount

      public static int getAssayFileCount(String assayAccession) throws IOException
      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

    • getProteinIdentificationByProject

      public static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList getProteinIdentificationByProject(String projectAccession) throws IOException
      Returns 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

    • getProteinIdentificationCountByProject

      public static int getProteinIdentificationCountByProject(String projectAccession) throws IOException
      Returns 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

    • getProteinIdentificationsByProjectAndProtein

      public static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList getProteinIdentificationsByProjectAndProtein(String projectAccession, String proteinAccesion) throws IOException
      Returns a list of protein details for a given project and a given protein accession.
      Parameters:
      projectAccession - the project accession
      proteinAccesion - 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

    • getProteinIdentificationsCountByProjectAndProtein

      public static int getProteinIdentificationsCountByProjectAndProtein(String projectAccession, String proteinAccession) throws IOException
      Returns a count of protein details for a given project and a given protein accession.
      Parameters:
      projectAccession - the project accession
      proteinAccession - 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

    • getProteinIdentificationByAssay

      public static uk.ac.ebi.pride.archive.web.service.model.protein.ProteinDetailList getProteinIdentificationByAssay(String assayAccession) throws IOException
      Returns 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

      public static int getProteinIdentificationCountByAssay(String assayAccession) throws IOException
      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 IOException
      Returns 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

    • getPSMCountByProject

      public static int getPSMCountByProject(String projectAccession) throws IOException
      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 IOException
      Returns a list of PSM details for a given project and a given peptide sequence.
      Parameters:
      projectAccession - the project accession
      sequence - 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 IOException
      Returns a count of PSM details for a given project and a given peptide sequence.
      Parameters:
      projectAccession - the project accession
      sequence - 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 IOException
      Returns 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

      public static int getPSMCountByAssay(String assayAccession) throws IOException
      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 IOException
      Returns a list of PSM details for a given assay and a given peptide sequence.
      Parameters:
      assayAccession - the project accession
      sequence - 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 IOException
      Returns a count of PSM details for a given assay and a given peptide sequence.
      Parameters:
      assayAccession - the project accession
      sequence - 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