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 and 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 and Description
DisplayParameters() Constructor.

Method Summary

Modifier and Type	Method and 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 Detail

LOADING_MESSAGE

public static final String LOADING_MESSAGE

The text displayed in the cell of a table in case the data is not loaded.

See Also:

Constant Field Values

Constructor Detail

DisplayParameters

public DisplayParameters()

Constructor.

Method Detail

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