Package com.compomics.util.io.export.features.peptideshaker

Enum PsProteinFeature

java.lang.Object
java.lang.Enum<PsProteinFeature>
com.compomics.util.io.export.features.peptideshaker.PsProteinFeature
All Implemented Interfaces:
ExportFeature, Serializable, Comparable<PsProteinFeature>, java.lang.constant.Constable
public enum PsProteinFeature extends Enum<PsProteinFeature> implements ExportFeature
This class lists the protein identification features.
Author:
Marc Vaudel, Harald Barsnes

  • Enum Constant Details

    • starred

      @SerializedName("PsProteinFeature.starred") public static final PsProteinFeature starred

    • pi

      @SerializedName("PsProteinFeature.pi") public static final PsProteinFeature pi

    • accession

      @SerializedName("PsProteinFeature.accession") public static final PsProteinFeature accession

    • protein_description

      @SerializedName("PsProteinFeature.protein_description") public static final PsProteinFeature protein_description

    • protein_group

      @SerializedName("PsProteinFeature.protein_group") public static final PsProteinFeature protein_group

    • descriptions

      @SerializedName("PsProteinFeature.descriptions") public static final PsProteinFeature descriptions

    • other_proteins

      @SerializedName("PsProteinFeature.other_proteins") public static final PsProteinFeature other_proteins

    • chromosome

      @SerializedName("PsProteinFeature.chromosome") public static final PsProteinFeature chromosome

    • ensembl_gene_id

      @SerializedName("PsProteinFeature.ensembl_gene_id") public static final PsProteinFeature ensembl_gene_id

    • gene_name

      @SerializedName("PsProteinFeature.gene_name") public static final PsProteinFeature gene_name

    • taxonomy

      @SerializedName("PsProteinFeature.taxonomy") public static final PsProteinFeature taxonomy

    • organism_identifier

      @SerializedName("PsProteinFeature.organism_identifier") public static final PsProteinFeature organism_identifier

    • go_accession

      @SerializedName("PsProteinFeature.go_accession") public static final PsProteinFeature go_accession

    • go_description

      @SerializedName("PsProteinFeature.go_description") public static final PsProteinFeature go_description

    • coverage

      @SerializedName("PsProteinFeature.coverage") public static final PsProteinFeature coverage

    • confident_coverage

      @SerializedName("PsProteinFeature.confident_coverage") public static final PsProteinFeature confident_coverage

    • all_coverage

      @SerializedName("PsProteinFeature.all_coverage") public static final PsProteinFeature all_coverage

    • possible_coverage

      @SerializedName("PsProteinFeature.possible_coverage") public static final PsProteinFeature possible_coverage

    • peptides

      @SerializedName("PsProteinFeature.peptides") public static final PsProteinFeature peptides

    • validated_peptides

      @SerializedName("PsProteinFeature.validated_peptides") public static final PsProteinFeature validated_peptides

    • unique_peptides

      @SerializedName("PsProteinFeature.unique_peptides") public static final PsProteinFeature unique_peptides

    • unique_validated_peptides

      @SerializedName("PsProteinFeature.unique_validated_peptides") public static final PsProteinFeature unique_validated_peptides

    • non_enzymatic

      @SerializedName("PsProteinFeature.non_enzymatic") public static final PsProteinFeature non_enzymatic

    • psms

      @SerializedName("PsProteinFeature.psms") public static final PsProteinFeature psms

    • validated_psms

      @SerializedName("PsProteinFeature.validated_psms") public static final PsProteinFeature validated_psms

    • confident_modification_sites

      @SerializedName("PsProteinFeature.confident_modification_sites") public static final PsProteinFeature confident_modification_sites

    • confident_modification_sites_number

      @SerializedName("PsProteinFeature.confident_modification_sites_number") public static final PsProteinFeature confident_modification_sites_number

    • ambiguous_modification_sites

      @SerializedName("PsProteinFeature.ambiguous_modification_sites") public static final PsProteinFeature ambiguous_modification_sites

    • ambiguous_modification_sites_number

      @SerializedName("PsProteinFeature.ambiguous_modification_sites_number") public static final PsProteinFeature ambiguous_modification_sites_number

    • confident_phosphosites

      @SerializedName("PsProteinFeature.confident_phosphosites") public static final PsProteinFeature confident_phosphosites

    • confident_phosphosites_number

      @SerializedName("PsProteinFeature.confident_phosphosites_number") public static final PsProteinFeature confident_phosphosites_number

    • ambiguous_phosphosites

      @SerializedName("PsProteinFeature.ambiguous_phosphosites") public static final PsProteinFeature ambiguous_phosphosites

    • ambiguous_phosphosites_number

      @SerializedName("PsProteinFeature.ambiguous_phosphosites_number") public static final PsProteinFeature ambiguous_phosphosites_number

    • spectrum_counting

      @SerializedName("PsProteinFeature.spectrum_counting") public static final PsProteinFeature spectrum_counting

    • spectrum_counting_nsaf

      @SerializedName("PsProteinFeature.spectrum_counting_nsaf") public static final PsProteinFeature spectrum_counting_nsaf

    • spectrum_counting_empai

      @SerializedName("PsProteinFeature.spectrum_counting_empai") public static final PsProteinFeature spectrum_counting_empai

    • label_free_quantification

      @SerializedName("PsProteinFeature.label_free_quantification") public static final PsProteinFeature label_free_quantification

    • spectrum_counting_nsaf_percent

      @SerializedName("PsProteinFeature.spectrum_counting_nsaf_percent") public static final PsProteinFeature spectrum_counting_nsaf_percent

    • spectrum_counting_empai_percent

      @SerializedName("PsProteinFeature.spectrum_counting_empai_percent") public static final PsProteinFeature spectrum_counting_empai_percent

    • label_free_quantification_percent

      @SerializedName("PsProteinFeature.label_free_quantification_percent") public static final PsProteinFeature label_free_quantification_percent

    • spectrum_counting_nsaf_ppm

      @SerializedName("PsProteinFeature.spectrum_counting_nsaf_ppm") public static final PsProteinFeature spectrum_counting_nsaf_ppm

    • spectrum_counting_empai_ppm

      @SerializedName("PsProteinFeature.spectrum_counting_empai_ppm") public static final PsProteinFeature spectrum_counting_empai_ppm

    • label_free_quantification_ppm

      @SerializedName("PsProteinFeature.label_free_quantification_ppm") public static final PsProteinFeature label_free_quantification_ppm

    • spectrum_counting_nsaf_fmol

      @SerializedName("PsProteinFeature.spectrum_counting_nsaf_fmol") public static final PsProteinFeature spectrum_counting_nsaf_fmol

    • spectrum_counting_empai_fmol

      @SerializedName("PsProteinFeature.spectrum_counting_empai_fmol") public static final PsProteinFeature spectrum_counting_empai_fmol

    • label_free_quantification_fmol

      @SerializedName("PsProteinFeature.label_free_quantification_[fmol]") public static final PsProteinFeature label_free_quantification_fmol

    • mw

      @SerializedName("PsProteinFeature.mw") public static final PsProteinFeature mw

    • proteinLength

      @SerializedName("PsProteinFeature.proteinLength") public static final PsProteinFeature proteinLength

    • peptidesPerFraction

      @SerializedName("PsProteinFeature.peptidesPerFraction") public static final PsProteinFeature peptidesPerFraction

    • spectraPerFraction

      @SerializedName("PsProteinFeature.spectraPerFraction") public static final PsProteinFeature spectraPerFraction

    • averagePrecursorIntensty

      @SerializedName("PsProteinFeature.averagePrecursorIntensty") public static final PsProteinFeature averagePrecursorIntensty

    • fractionMinMwPeptideRange

      @SerializedName("PsProteinFeature.fractionMinMwPeptideRange") public static final PsProteinFeature fractionMinMwPeptideRange

    • fractionMaxMwPeptideRange

      @SerializedName("PsProteinFeature.fractionMaxMwPeptideRange") public static final PsProteinFeature fractionMaxMwPeptideRange

    • fractionMinMwSpectraRange

      @SerializedName("PsProteinFeature.fractionMinMwSpectraRange") public static final PsProteinFeature fractionMinMwSpectraRange

    • fractionMaxMwSpectraRange

      @SerializedName("PsProteinFeature.fractionMaxMwSpectraRange") public static final PsProteinFeature fractionMaxMwSpectraRange

    • score

      @SerializedName("PsProteinFeature.score") public static final PsProteinFeature score

    • raw_score

      @SerializedName("PsProteinFeature.raw_score") public static final PsProteinFeature raw_score

    • confidence

      @SerializedName("PsProteinFeature.confidence") public static final PsProteinFeature confidence

    • validated

      @SerializedName("PsProteinFeature.validated") public static final PsProteinFeature validated

    • decoy

      @SerializedName("PsProteinFeature.decoy") public static final PsProteinFeature decoy

    • hidden

      @SerializedName("PsProteinFeature.hidden") public static final PsProteinFeature hidden

  • Field Details

    • title

      public String title
      The title of the feature which will be used for column heading.

    • description

      public String description
      The description of the feature.

    • type

      public static final String type
      The type of export feature.
      See Also:

    • perFraction

      public final boolean perFraction
      Indicates whether a feature is to be exported per fraction.

  • Method Details

    • values

      public static PsProteinFeature[] values()
      Returns an array containing the constants of this enum type, in the order they are declared.
      Returns:
      an array containing the constants of this enum type, in the order they are declared

    • valueOf

      public static PsProteinFeature valueOf(String name)
      Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum type has no constant with the specified name
      NullPointerException - if the argument is null

    • getExportFeatures

      public ArrayList<ExportFeature> getExportFeatures(boolean includeSubFeatures)
      Description copied from interface: ExportFeature
      Returns a list of all implemented export features.
      Specified by:
      getExportFeatures in interface ExportFeature
      Parameters:
      includeSubFeatures - boolean indicating whether sub features should be included
      Returns:
      a list of all implemented export features

    • getTitle

      public String getTitle()
      Description copied from interface: ExportFeature
      Returns the column title of the feature.
      Specified by:
      getTitle in interface ExportFeature
      Returns:
      the column title of the feature

    • getDescription

      public String getDescription()
      Description copied from interface: ExportFeature
      Returns the description of the feature.
      Specified by:
      getDescription in interface ExportFeature
      Returns:
      the description of the feature

    • getFeatureFamily

      public String getFeatureFamily()
      Description copied from interface: ExportFeature
      Returns the family type of this export feature.
      Specified by:
      getFeatureFamily in interface ExportFeature
      Returns:
      the family type of this export feature

    • isAdvanced

      public boolean isAdvanced()
      Description copied from interface: ExportFeature
      Indicates whether a feature is for advanced user only.
      Specified by:
      isAdvanced in interface ExportFeature
      Returns:
      a boolean indicating whether a feature is for advanced user only

    • isPerFraction

      public boolean isPerFraction()
      Returns true if the feature is to be exported per fraction.
      Returns:
      true if the feature is to be exported per fraction