java.lang.Object

java.lang.Enum<PsProteinFeature>

eu.isas.peptideshaker.export.exportfeatures.PsProteinFeature

All Implemented Interfaces:: com.compomics.util.io.export.ExportFeature, Serializable, Comparable<PsProteinFeature>, java.lang.constant.Constable

public enum PsProteinFeature
extends Enum<PsProteinFeature>
implements com.compomics.util.io.export.ExportFeature

This class lists the protein identification features.

Author:: Marc Vaudel, Harald Barsnes

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants
Enum Constant	Description
`accession`
`all_coverage`
`ambiguous_modification_sites`
`ambiguous_modification_sites_number`
`ambiguous_phosphosites`
`ambiguous_phosphosites_number`
`averagePrecursorIntensty`
`chromosome`
`confidence`
`confident_coverage`
`confident_modification_sites`
`confident_modification_sites_number`
`confident_phosphosites`
`confident_phosphosites_number`
`coverage`
`decoy`
`descriptions`
`ensembl_gene_id`
`fractionMaxMwPeptideRange`
`fractionMaxMwSpectraRange`
`fractionMinMwPeptideRange`
`fractionMinMwSpectraRange`
`gene_name`
`go_accession`
`go_description`
`hidden`
`mw`
`non_enzymatic`
`other_proteins`
`peptides`
`peptidesPerFraction`
`pi`
`possible_coverage`
`protein_description`
`protein_group`
`proteinLength`
`psms`
`raw_score`
`score`
`spectraPerFraction`
`spectrum_counting`
`spectrum_counting_empai`
`spectrum_counting_empai_fmol`
`spectrum_counting_empai_percent`
`spectrum_counting_empai_ppm`
`spectrum_counting_nsaf`
`spectrum_counting_nsaf_fmol`
`spectrum_counting_nsaf_percent`
`spectrum_counting_nsaf_ppm`
`starred`
`taxonomy`
`unique_peptides`
`unique_validated_peptides`
`validated`
`validated_peptides`
`validated_psms`

Field Summary

Fields
Modifier and Type	Field	Description
`String`	`description`	The description of the feature.
`boolean`	`perFraction`	Indicates whether a feature is to be exported per fraction.
`String`	`title`	The title of the feature which will be used for column heading.
`static String`	`type`	The type of export feature.

Fields inherited from interface com.compomics.util.io.export.ExportFeature

serialVersionUID

Method Summary

Modifier and Type	Method	Description
`String`	`getDescription()`
`ArrayList<com.compomics.util.io.export.ExportFeature>`	`getExportFeatures(boolean includeSubFeatures)`
`String`	`getFeatureFamily()`
`String`	`getTitle()`
`boolean`	`isAdvanced()`
`boolean`	`isPerFraction()`	Returns true if the feature is to be exported per fraction.
`static PsProteinFeature`	`valueOf(String name)`	Returns the enum constant of this type with the specified name.
`static PsProteinFeature[]`	`values()`	Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details
- starred
  
  public static final PsProteinFeature starred
- pi
  
  public static final PsProteinFeature pi
- accession
  
  public static final PsProteinFeature accession
- protein_description
  
  public static final PsProteinFeature protein_description
- protein_group
  
  public static final PsProteinFeature protein_group
- descriptions
  
  public static final PsProteinFeature descriptions
- other_proteins
  
  public static final PsProteinFeature other_proteins
- chromosome
  
  public static final PsProteinFeature chromosome
- ensembl_gene_id
  
  public static final PsProteinFeature ensembl_gene_id
- gene_name
  
  public static final PsProteinFeature gene_name
- taxonomy
  
  public static final PsProteinFeature taxonomy
- go_accession
  
  public static final PsProteinFeature go_accession
- go_description
  
  public static final PsProteinFeature go_description
- coverage
  
  public static final PsProteinFeature coverage
- confident_coverage
  
  public static final PsProteinFeature confident_coverage
- all_coverage
  
  public static final PsProteinFeature all_coverage
- possible_coverage
  
  public static final PsProteinFeature possible_coverage
- peptides
  
  public static final PsProteinFeature peptides
- validated_peptides
  
  public static final PsProteinFeature validated_peptides
- unique_peptides
  
  public static final PsProteinFeature unique_peptides
- unique_validated_peptides
  
  public static final PsProteinFeature unique_validated_peptides
- non_enzymatic
  
  public static final PsProteinFeature non_enzymatic
- psms
  
  public static final PsProteinFeature psms
- validated_psms
  
  public static final PsProteinFeature validated_psms
- confident_modification_sites
  
  public static final PsProteinFeature confident_modification_sites
- confident_modification_sites_number
  
  public static final PsProteinFeature confident_modification_sites_number
- ambiguous_modification_sites
  
  public static final PsProteinFeature ambiguous_modification_sites
- ambiguous_modification_sites_number
  
  public static final PsProteinFeature ambiguous_modification_sites_number
- confident_phosphosites
  
  public static final PsProteinFeature confident_phosphosites
- confident_phosphosites_number
  
  public static final PsProteinFeature confident_phosphosites_number
- ambiguous_phosphosites
  
  public static final PsProteinFeature ambiguous_phosphosites
- ambiguous_phosphosites_number
  
  public static final PsProteinFeature ambiguous_phosphosites_number
- spectrum_counting
  
  public static final PsProteinFeature spectrum_counting
- spectrum_counting_nsaf
  
  public static final PsProteinFeature spectrum_counting_nsaf
- spectrum_counting_empai
  
  public static final PsProteinFeature spectrum_counting_empai
- spectrum_counting_nsaf_percent
  
  public static final PsProteinFeature spectrum_counting_nsaf_percent
- spectrum_counting_empai_percent
  
  public static final PsProteinFeature spectrum_counting_empai_percent
- spectrum_counting_nsaf_ppm
  
  public static final PsProteinFeature spectrum_counting_nsaf_ppm
- spectrum_counting_empai_ppm
  
  public static final PsProteinFeature spectrum_counting_empai_ppm
- spectrum_counting_nsaf_fmol
  
  public static final PsProteinFeature spectrum_counting_nsaf_fmol
- spectrum_counting_empai_fmol
  
  public static final PsProteinFeature spectrum_counting_empai_fmol
- mw
  
  public static final PsProteinFeature mw
- proteinLength
  
  public static final PsProteinFeature proteinLength
- peptidesPerFraction
  
  public static final PsProteinFeature peptidesPerFraction
- spectraPerFraction
  
  public static final PsProteinFeature spectraPerFraction
- averagePrecursorIntensty
  
  public static final PsProteinFeature averagePrecursorIntensty
- fractionMinMwPeptideRange
  
  public static final PsProteinFeature fractionMinMwPeptideRange
- fractionMaxMwPeptideRange
  
  public static final PsProteinFeature fractionMaxMwPeptideRange
- fractionMinMwSpectraRange
  
  public static final PsProteinFeature fractionMinMwSpectraRange
- fractionMaxMwSpectraRange
  
  public static final PsProteinFeature fractionMaxMwSpectraRange
- score
  
  public static final PsProteinFeature score
- raw_score
  
  public static final PsProteinFeature raw_score
- confidence
  
  public static final PsProteinFeature confidence
- validated
  
  public static final PsProteinFeature validated
- decoy
  
  public static final PsProteinFeature decoy
- 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:
  
  Constant Field Values
- 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<com.compomics.util.io.export.ExportFeature> getExportFeatures(boolean includeSubFeatures)
  
  Specified by:
  
  getExportFeatures in interface com.compomics.util.io.export.ExportFeature
- getTitle
  
  public String getTitle()
  
  Specified by:
  
  getTitle in interface com.compomics.util.io.export.ExportFeature
- getDescription
  
  public String getDescription()
  
  Specified by:
  
  getDescription in interface com.compomics.util.io.export.ExportFeature
- getFeatureFamily
  
  public String getFeatureFamily()
  
  Specified by:
  
  getFeatureFamily in interface com.compomics.util.io.export.ExportFeature
- isAdvanced
  
  public boolean isAdvanced()
  
  Specified by:
  
  isAdvanced in interface com.compomics.util.io.export.ExportFeature
- 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

Enum PsProteinFeature

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum Constant Summary

Field Summary

Fields inherited from interface com.compomics.util.io.export.ExportFeature

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Details

Field Details

Method Details