Package eu.isas.peptideshaker.utils

Class StarHider

java.lang.Object
eu.isas.peptideshaker.utils.StarHider
public class StarHider extends Object
This class provides information whether a hit should be hidden or starred.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    StarHider(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.gui.filtering.FilterParameters filterParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog, int nThreads, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    hidePeptide(long matchKey)
    Hides a peptide match.
    void
    hideProtein(long matchKey)
    Hides a protein match.
    void
    hidePsm(long matchKey)
    Hides a PSM match.
    boolean
    isPeptideHidden(long matchKey)
    Tests whether a peptide match should be hidden according to the implemented filters.
    boolean
    isPeptideStarred(long matchKey)
    Tests whether a peptide match should be starred according to the implemented filters.
    boolean
    isProteinHidden(long matchKey)
    Tests whether a protein match should be hidden according to the implemented filters.
    boolean
    isProteinStarred(long matchKey)
    Tests whether a protein match should be starred according to the implemented filters.
    boolean
    isPsmHidden(long matchKey)
    Tests whether a PSM match should be hidden according to the implemented filters.
    boolean
    isPsmStarred(long matchKey)
    Tests whether a PSM match should be starred according to the implemented filters.
    void
    starHide()
    Updates the star/hide status of all identification items.
    void
    starPeptide(long matchKey)
    Stars a peptide match.
    void
    starProtein(long matchKey)
    Stars a protein match.
    void
    starPsm(long matchKey)
    Stars a PSM match.
    void
    unHidePeptide(long matchKey)
    Unhides a peptide match.
    void
    unHideProtein(long matchKey)
    Unhides a protein match.
    void
    unHidePsm(long matchKey)
    Unhides a psm match.
    void
    unStarPeptide(long matchKey)
    Unstars a peptide match.
    void
    unStarProtein(long matchKey)
    Unstars a protein match.
    void
    unStarPsm(long matchKey)
    Unstars a PSM match.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • StarHider

      public StarHider(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.gui.filtering.FilterParameters filterParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog, int nThreads, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
      Constructor.
      Parameters:
      identification - The identification.
      filterParameters - The filter parameters.
      sequenceProvider - The sequence provider.
      proteinDetailsProvider - The protein details provider.
      spectrumProvider - The spectrum provider.
      geneMaps - The gene maps.
      identificationFeaturesGenerator - The identification features generator.
      identificationParameters - The identification parameters.
      metrics - The metrics.
      progressDialog - The progress dialog.
      nThreads - The number of threads.
      exceptionHandler - The exception handler.

  • Method Details

    • starHide

      public void starHide()
      Updates the star/hide status of all identification items.

    • starProtein

      public void starProtein(long matchKey)
      Stars a protein match.
      Parameters:
      matchKey - the key of the match

    • unStarProtein

      public void unStarProtein(long matchKey)
      Unstars a protein match.
      Parameters:
      matchKey - the key of the match

    • hideProtein

      public void hideProtein(long matchKey)
      Hides a protein match.
      Parameters:
      matchKey - the key of the match

    • unHideProtein

      public void unHideProtein(long matchKey)
      Unhides a protein match.
      Parameters:
      matchKey - the key of the match

    • starPeptide

      public void starPeptide(long matchKey)
      Stars a peptide match.
      Parameters:
      matchKey - the key of the match

    • unStarPeptide

      public void unStarPeptide(long matchKey)
      Unstars a peptide match.
      Parameters:
      matchKey - the key of the match

    • hidePeptide

      public void hidePeptide(long matchKey)
      Hides a peptide match.
      Parameters:
      matchKey - the key of the match

    • unHidePeptide

      public void unHidePeptide(long matchKey)
      Unhides a peptide match.
      Parameters:
      matchKey - the key of the match

    • starPsm

      public void starPsm(long matchKey)
      Stars a PSM match.
      Parameters:
      matchKey - the key of the match

    • unStarPsm

      public void unStarPsm(long matchKey)
      Unstars a PSM match.
      Parameters:
      matchKey - the key of the match

    • hidePsm

      public void hidePsm(long matchKey)
      Hides a PSM match.
      Parameters:
      matchKey - the key of the match

    • unHidePsm

      public void unHidePsm(long matchKey)
      Unhides a psm match.
      Parameters:
      matchKey - the key of the match

    • isProteinHidden

      public boolean isProteinHidden(long matchKey)
      Tests whether a protein match should be hidden according to the implemented filters.
      Parameters:
      matchKey - the key of the match
      Returns:
      a boolean indicating whether a protein match should be hidden according to the implemented filters

    • isPeptideHidden

      public boolean isPeptideHidden(long matchKey)
      Tests whether a peptide match should be hidden according to the implemented filters.
      Parameters:
      matchKey - the key of the match
      Returns:
      a boolean indicating whether a protein match should be hidden according to the implemented filters

    • isPsmHidden

      public boolean isPsmHidden(long matchKey)
      Tests whether a PSM match should be hidden according to the implemented filters.
      Parameters:
      matchKey - the key of the match
      Returns:
      a boolean indicating whether a protein match should be hidden according to the implemented filters

    • isProteinStarred

      public boolean isProteinStarred(long matchKey)
      Tests whether a protein match should be starred according to the implemented filters.
      Parameters:
      matchKey - the key of the match
      Returns:
      a boolean indicating whether a protein match should be hidden according to the implemented filters

    • isPeptideStarred

      public boolean isPeptideStarred(long matchKey)
      Tests whether a peptide match should be starred according to the implemented filters.
      Parameters:
      matchKey - the key of the match
      Returns:
      a boolean indicating whether a protein match should be hidden according to the implemented filters

    • isPsmStarred

      public boolean isPsmStarred(long matchKey)
      Tests whether a PSM match should be starred according to the implemented filters.
      Parameters:
      matchKey - the key of the match
      Returns:
      a boolean indicating whether a protein match should be hidden according to the implemented filters