Package eu.isas.peptideshaker.utils

Class DisplayFeaturesGenerator

java.lang.Object
eu.isas.peptideshaker.utils.DisplayFeaturesGenerator
public class DisplayFeaturesGenerator extends Object
This class creates the display features needed for the GUI.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    DisplayFeaturesGenerator​(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, DisplayParameters displayParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
    Constructor

  • Method Summary

    Modifier and Type
    Method
    Description
    String
    addGoLink​(String goAccession)
    Returns the GO accession number as a web link to the given GO term at QuickGO.
    String
    getDatabaseLink​(String proteinAccession)
    Transforms the protein accession number into an HTML link to the corresponding database.
    String
    getDatabaseLink​(String proteinAccession, boolean includeHtmlTags, boolean underlineLink)
    Transforms the protein accession number into an HTML link to the corresponding database.
    String
    getDatabaseLinks​(String[] proteinAccessions)
    Transforms the protein accession number into an HTML link to the corresponding database.
    String
    getDatabaseLinks​(String[] proteinAccessions, boolean underlineLink)
    Transforms the protein accession number into an HTML link to the corresponding database.
    static String[]
    getDisplayedModifications​(String[] modificationArray, HashSet<String> displayedModifications)
    Returns an array containing only the modifications to display.
    static String[]
    getFilteredAmbiguousModificationsRepresentativeSites​(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, HashSet<String> displayedModifications, int peptideLength)
    Exports the ambiguously localized modification representative sites in a map: site > mapped modifications.
    static String[]
    getFilteredAmbiguousModificationsSecondarySites​(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, HashSet<String> displayedModifications, int peptideLength)
    Exports the ambiguously localized modification secondary sites in a map: site > mapped modifications.
    static String[]
    getFilteredConfidentModificationsSites​(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, HashSet<String> displayedModifications, int peptideLength)
    Exports the confidently localized modification sites in a map: site > mapped modifications.
    String
    getGoAccessionLink​(String goAccession)
    Returns the GO accession number as a web link to the given GO term at QuickGO.
    String
    getNcbiAccessionLink​(String proteinAccession)
    Returns the protein accession number as a web link to the given protein at https://www.ncbi.nlm.nih.gov/protein.
    String
    getNextProtAccessionLink​(String proteinAccession)
    Returns the protein accession number as a web link to the given protein at https://www.nextprot.org.
    String
    getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.biology.proteins.Peptide peptide)
    Returns a string with the HTML tooltip for the peptide indicating the modification details.
    String
    getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores)
    Returns a string with the HTML tooltip for the peptide indicating the modification details.
    String
    getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch)
    Returns a string with the HTML tooltip for the peptide indicating the modification details.
    String
    getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch)
    Returns a string with the HTML tooltip for the peptide indicating the modification details.
    static String
    getPrideAccessionLink​(String projectAccession)
    Returns the project accession number as a web link to the given project in PRIDE.
    static String
    getPrideAssayArchiveLink​(String projectAccession, String assayAccession)
    Returns the assay accession number as a web link to the given assay in the PRIDE archive.
    static String
    getPrideProjectArchiveLink​(String projectAccession)
    Returns the project accession number as a web link to the given project in the PRIDE archive.
    HashMap<Integer,​ArrayList<ResidueAnnotation>>
    getResidueAnnotation​(long proteinMatchKey, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.identification.Identification identification, boolean allPeptides, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, boolean enzymatic)
    Returns the residue annotation for a given protein in a map for enzymatic or not enzymatic peptides only.
    String
    getSrsAccessionLink​(String proteinAccession, String database)
    Returns the protein accession number as a web link to the given protein at https://srs.ebi.ac.uk.
    String
    getTaggedPeptideSequence​(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
    Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on the provided modification localization scores.
    String
    getTaggedPeptideSequence​(com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
    Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on PeptideShaker site inference results for the given peptide match.
    String
    getTaggedPeptideSequence​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
    Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on PeptideShaker site inference results for the best assumption of the given spectrum match.
    String
    getTagModificationTooltipAsHtml​(com.compomics.util.experiment.identification.amino_acid_tags.Tag tag)
    Returns a string with the HTML tooltip for the tag indicating the modification details.
    String
    getUniProtAccessionLink​(String proteinAccession)
    Returns the protein accession number as a web link to the given protein at https://www.uniprot.org/uniprot.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • DisplayFeaturesGenerator

      public DisplayFeaturesGenerator​(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, DisplayParameters displayParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
      Constructor
      Parameters:
      identificationParameters - the identification parameters
      displayParameters - the display parameters
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider

  • Method Details

    • getDatabaseLink

      public String getDatabaseLink​(String proteinAccession)
      Transforms the protein accession number into an HTML link to the corresponding database. Note that this is a complete HTML with HTML and a href tags, where the main use is to include it in the protein tables.
      Parameters:
      proteinAccession - the protein to get the database link for
      Returns:
      the transformed accession number

    • getDatabaseLink

      public String getDatabaseLink​(String proteinAccession, boolean includeHtmlTags, boolean underlineLink)
      Transforms the protein accession number into an HTML link to the corresponding database.
      Parameters:
      proteinAccession - the protein to get the database link for
      includeHtmlTags - if true, the starting and ending HTML tags are included
      underlineLink - if true, the link is underlined
      Returns:
      the transformed accession number

    • getDatabaseLinks

      public String getDatabaseLinks​(String[] proteinAccessions)
      Transforms the protein accession number into an HTML link to the corresponding database. Note that this is a complete HTML with HTML and a href tags, where the main use is to include it in the protein tables.
      Parameters:
      proteinAccessions - the list of the accessions of proteins to get the database links for
      Returns:
      the transformed accession number

    • getDatabaseLinks

      public String getDatabaseLinks​(String[] proteinAccessions, boolean underlineLink)
      Transforms the protein accession number into an HTML link to the corresponding database. Note that this is a complete HTML with HTML and a href tags, where the main use is to include it in the protein tables.
      Parameters:
      proteinAccessions - the list of the accessions of proteins to get the database links for
      underlineLink - if true, the link is underlined
      Returns:
      the transformed accession number

    • getSrsAccessionLink

      public String getSrsAccessionLink​(String proteinAccession, String database)
      Returns the protein accession number as a web link to the given protein at https://srs.ebi.ac.uk.
      Parameters:
      proteinAccession - the protein accession number
      database - the protein database
      Returns:
      the protein accession web link

    • getUniProtAccessionLink

      public String getUniProtAccessionLink​(String proteinAccession)
      Returns the protein accession number as a web link to the given protein at https://www.uniprot.org/uniprot.
      Parameters:
      proteinAccession - the protein accession number
      Returns:
      the protein accession web link

    • getNextProtAccessionLink

      public String getNextProtAccessionLink​(String proteinAccession)
      Returns the protein accession number as a web link to the given protein at https://www.nextprot.org.
      Parameters:
      proteinAccession - the protein accession number
      Returns:
      the protein accession web link

    • getNcbiAccessionLink

      public String getNcbiAccessionLink​(String proteinAccession)
      Returns the protein accession number as a web link to the given protein at https://www.ncbi.nlm.nih.gov/protein.
      Parameters:
      proteinAccession - the protein accession number
      Returns:
      the protein accession web link

    • getPrideAccessionLink

      public static String getPrideAccessionLink​(String projectAccession)
      Returns the project accession number as a web link to the given project in PRIDE.
      Parameters:
      projectAccession - the project accession number
      Returns:
      the project accession web link

    • getPrideProjectArchiveLink

      public static String getPrideProjectArchiveLink​(String projectAccession)
      Returns the project accession number as a web link to the given project in the PRIDE archive.
      Parameters:
      projectAccession - the project accession number
      Returns:
      the project accession web link

    • getPrideAssayArchiveLink

      public static String getPrideAssayArchiveLink​(String projectAccession, String assayAccession)
      Returns the assay accession number as a web link to the given assay in the PRIDE archive.
      Parameters:
      projectAccession - the project accession number
      assayAccession - the assay accession number
      Returns:
      the project accession web link

    • getPeptideModificationTooltipAsHtml

      public String getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch)
      Returns a string with the HTML tooltip for the peptide indicating the modification details.
      Parameters:
      spectrumMatch - the spectrum match
      Returns:
      a string with the HTML tooltip for the peptide

    • getPeptideModificationTooltipAsHtml

      public String getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch)
      Returns a string with the HTML tooltip for the peptide indicating the modification details.
      Parameters:
      peptideMatch - the peptide match
      Returns:
      a string with the HTML tooltip for the peptide

    • getPeptideModificationTooltipAsHtml

      public String getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores)
      Returns a string with the HTML tooltip for the peptide indicating the modification details.
      Parameters:
      peptide - the peptide
      modificationScores - the modification scores
      Returns:
      a string with the HTML tooltip for the peptide

    • getDisplayedModifications

      public static String[] getDisplayedModifications​(String[] modificationArray, HashSet<String> displayedModifications)
      Returns an array containing only the modifications to display.
      Parameters:
      modificationArray - the original array
      displayedModifications - the displayed modifications
      Returns:
      an array containing only the modifications to display

    • getPeptideModificationTooltipAsHtml

      public String getPeptideModificationTooltipAsHtml​(com.compomics.util.experiment.biology.proteins.Peptide peptide)
      Returns a string with the HTML tooltip for the peptide indicating the modification details.
      Parameters:
      peptide - the peptide
      Returns:
      a string with the HTML tooltip for the peptide

    • getTagModificationTooltipAsHtml

      public String getTagModificationTooltipAsHtml​(com.compomics.util.experiment.identification.amino_acid_tags.Tag tag)
      Returns a string with the HTML tooltip for the tag indicating the modification details. Null if no modifications.
      Parameters:
      tag - the tag
      Returns:
      a string with the HTML tooltip for the tag

    • getTaggedPeptideSequence

      public String getTaggedPeptideSequence​(com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
      Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on PeptideShaker site inference results for the given peptide match.
      Parameters:
      peptideMatch - the peptide match of interest
      useHtmlColorCoding - if true, color coded HTML is used, otherwise modification tags, e.g, <mox>, are used
      includeHtmlStartEndTags - if true, HTML start and end tags are added
      useShortName - if true the short names are used in the tags
      Returns:
      the tagged peptide sequence

    • getTaggedPeptideSequence

      public String getTaggedPeptideSequence​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
      Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on PeptideShaker site inference results for the best assumption of the given spectrum match.
      Parameters:
      spectrumMatch - the spectrum match of interest
      useHtmlColorCoding - if true, color coded HTML is used, otherwise modification tags, e.g, <mox>, are used
      includeHtmlStartEndTags - if true, HTML start and end tags are added
      useShortName - if true the short names are used in the tags
      Returns:
      the tagged peptide sequence

    • getTaggedPeptideSequence

      public String getTaggedPeptideSequence​(com.compomics.util.experiment.biology.proteins.Peptide peptide, com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName)
      Returns the peptide with modification sites tagged (color coded or with modification tags, e.g, <mox>) in the sequence based on the provided modification localization scores.
      Parameters:
      peptide - the spectrum match of interest
      modificationScores - the modification localization scores
      useHtmlColorCoding - if true, color coded HTML is used, otherwise modification tags, e.g, <mox>, are used
      includeHtmlStartEndTags - if true, HTML start and end tags are added
      useShortName - if true the short names are used in the tags
      Returns:
      the tagged peptide sequence

    • getFilteredConfidentModificationsSites

      public static String[] getFilteredConfidentModificationsSites​(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, HashSet<String> displayedModifications, int peptideLength)
      Exports the confidently localized modification sites in a map: site > mapped modifications.
      Parameters:
      modificationScores - the PeptideShaker modification scores
      displayedModifications - list of modifications to display
      peptideLength - the length of the peptide
      Returns:
      a map of filtered modifications based on the user display preferences

    • getFilteredAmbiguousModificationsRepresentativeSites

      public static String[] getFilteredAmbiguousModificationsRepresentativeSites​(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, HashSet<String> displayedModifications, int peptideLength)
      Exports the ambiguously localized modification representative sites in a map: site > mapped modifications.
      Parameters:
      modificationScores - the PeptideShaker modification scores
      displayedModifications - list of modifications to display
      peptideLength - the length of the peptide
      Returns:
      a map of filtered modifications based on the user display preferences

    • getFilteredAmbiguousModificationsSecondarySites

      public static String[] getFilteredAmbiguousModificationsSecondarySites​(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores modificationScores, HashSet<String> displayedModifications, int peptideLength)
      Exports the ambiguously localized modification secondary sites in a map: site > mapped modifications.
      Parameters:
      modificationScores - the PeptideShaker modification scores
      displayedModifications - list of modifications to display
      peptideLength - the length of the peptide
      Returns:
      a map of filtered modifications based on the user display preferences

    • addGoLink

      public String addGoLink​(String goAccession)
      Returns the GO accession number as a web link to the given GO term at QuickGO.
      Parameters:
      goAccession - the GO accession number
      Returns:
      the GO accession number as a web link to the given GO term at QuickGO

    • getGoAccessionLink

      public String getGoAccessionLink​(String goAccession)
      Returns the GO accession number as a web link to the given GO term at QuickGO.
      Parameters:
      goAccession - the GO accession number
      Returns:
      the GO accession web link

    • getResidueAnnotation

      public HashMap<Integer,​ArrayList<ResidueAnnotation>> getResidueAnnotation​(long proteinMatchKey, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.identification.Identification identification, boolean allPeptides, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, boolean enzymatic)
      Returns the residue annotation for a given protein in a map for enzymatic or not enzymatic peptides only. Residue number > annotations. 0 is the first amino acid.
      Parameters:
      proteinMatchKey - the key of the match of interest
      sequenceMatchingPreferences - The sequence matching preferences
      identificationFeaturesGenerator - the identification feature generator
      metrics - the metrics
      identification - the identification
      allPeptides - if true, all peptides are considered
      searchParameters - the search parameters
      enzymatic - whether enzymatic only or not enzymatic only peptides should be considered
      Returns:
      the residue annotation for a given protein