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 and 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 and 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.identification.matches.PeptideMatch peptideMatch) 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.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.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.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.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 Detail

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 Detail

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