Package eu.isas.peptideshaker.preferences

Class DisplayParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
eu.isas.peptideshaker.preferences.DisplayParameters
All Implemented Interfaces:
Serializable
public class DisplayParameters
extends com.compomics.util.experiment.personalization.ExperimentObject
This class contains the display preferences for the current project.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form

  • Field Summary

    Fields 
    Modifier and Type Field Description
    static String LOADING_MESSAGE
    The text displayed in the cell of a table in case the data is not loaded.

    Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

    NO_KEY

  • Constructor Summary

    Constructors 
    Constructor Description
    DisplayParameters()
    Constructor.

  • Method Summary

    Modifier and Type Method Description
    HashSet<String> getDisplayedModifications()
    Returns a list containing the names of the PTMs to display.
    int getnAASurroundingPeptides()
    Returns the number of amino acids surrounding a peptide sequence (1 by default).
    boolean isDisplayedPTM​(String ptmName)
    Indicates whether a PTM shall be displayed on the interface.
    void setDefaultSelection​(ArrayList<String> modifications)
    Set the list of visible modifications.
    void setDisplayedModification​(String ptmName, boolean displayed)
    Sets whether a PTM shall be displayed on the sequences or not.
    void setIntensityIonTable​(boolean intensityIonTable)
    Set if the intensity or m/z ion table should be shown.
    void setnAASurroundingPeptides​(int nAASurroundingPeptides)
    Sets the number of amino acids surrounding a peptide sequence.
    void setShowBars​(boolean showBars)
    Set if the bars in the bubble plot are to be shown or not.
    boolean showBars()
    If true, bars are shown in the bubble plot highlighting the ions.
    boolean showHiddenProteins()
    Returns whether hidden proteins should be displayed.
    void showHiddenProteins​(boolean showHiddenProteins)
    Sets whether hidden proteins should be displayed.
    boolean showScores()
    Returns whether scores should be displayed.
    void showScores​(boolean showScores)
    Sets whether scores should be displayed.
    boolean showValidatedProteinsOnly()
    Returns whether only the validated proteins should be displayed.
    void showValidatedProteinsOnly​(boolean showValidatedProteinsOnly)
    Sets whether only the validated proteins should be displayed.
    boolean useIntensityIonTable()
    If true, the ion table is shown as an intensity version, false displays the standard Mascot version.

    Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

    addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

  • Method Details

    • showHiddenProteins

      public void showHiddenProteins​(boolean showHiddenProteins)
      Sets whether hidden proteins should be displayed.
      Parameters:
      showHiddenProteins - a boolean indicating whether hidden proteins should be displayed

    • showHiddenProteins

      public boolean showHiddenProteins()
      Returns whether hidden proteins should be displayed.
      Returns:
      true if the hidden proteins should be displayed

    • showScores

      public void showScores​(boolean showScores)
      Sets whether scores should be displayed.
      Parameters:
      showScores - a boolean indicating whether scores should be displayed

    • showScores

      public boolean showScores()
      Returns whether scores should be displayed.
      Returns:
      true if the scores are to be displayed

    • showValidatedProteinsOnly

      public void showValidatedProteinsOnly​(boolean showValidatedProteinsOnly)
      Sets whether only the validated proteins should be displayed.
      Parameters:
      showValidatedProteinsOnly - a boolean indicating whether only the validated proteins should be displayed

    • showValidatedProteinsOnly

      public boolean showValidatedProteinsOnly()
      Returns whether only the validated proteins should be displayed.
      Returns:
      true if only the validated proteins are to be displayed

    • getnAASurroundingPeptides

      public int getnAASurroundingPeptides()
      Returns the number of amino acids surrounding a peptide sequence (1 by default).
      Returns:
      the number of amino acids surrounding a peptide sequence

    • setnAASurroundingPeptides

      public void setnAASurroundingPeptides​(int nAASurroundingPeptides)
      Sets the number of amino acids surrounding a peptide sequence.
      Parameters:
      nAASurroundingPeptides - the number of amino acids surrounding a peptide sequence

    • setDisplayedModification

      public void setDisplayedModification​(String ptmName, boolean displayed)
      Sets whether a PTM shall be displayed on the sequences or not.
      Parameters:
      ptmName - the name of the PTM
      displayed - a boolean indicating whether the PTM shall be displayed

    • isDisplayedPTM

      public boolean isDisplayedPTM​(String ptmName)
      Indicates whether a PTM shall be displayed on the interface.
      Parameters:
      ptmName - the name of the PTM
      Returns:
      a boolean indicating whether the PTM shall be displayed

    • setDefaultSelection

      public void setDefaultSelection​(ArrayList<String> modifications)
      Set the list of visible modifications.
      Parameters:
      modifications - the modifications to display

    • getDisplayedModifications

      public HashSet<String> getDisplayedModifications()
      Returns a list containing the names of the PTMs to display.
      Returns:
      a list containing the names of the PTMs to display

    • showBars

      public boolean showBars()
      If true, bars are shown in the bubble plot highlighting the ions.
      Returns:
      true if bars are to be shown in the bubble plot

    • setShowBars

      public void setShowBars​(boolean showBars)
      Set if the bars in the bubble plot are to be shown or not.
      Parameters:
      showBars - if the bars in the bubble plot are to be shown

    • useIntensityIonTable

      public boolean useIntensityIonTable()
      If true, the ion table is shown as an intensity version, false displays the standard Mascot version.
      Returns:
      if true, the ion table is shown as an intensity version, false displays the standard Mascot version

    • setIntensityIonTable

      public void setIntensityIonTable​(boolean intensityIonTable)
      Set if the intensity or m/z ion table should be shown.
      Parameters:
      intensityIonTable - if the intensity or m/z ion table should be shown