com.compomics.util.preferences

Class UtilitiesUserPreferences

java.lang.Object

com.compomics.util.preferences.UtilitiesUserPreferences

All Implemented Interfaces:

java.io.Serializable

public class UtilitiesUserPreferences
extends java.lang.Object
implements java.io.Serializable

Utilities user preferences will be serialized in the user folder and provide useful information to all compomics software, well as soon as they use it of course.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	USER_PREFERENCES_FILE Location of the user preferences file.

Constructor Summary

Constructors

Constructor and Description
UtilitiesUserPreferences() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addFavoriteDB(java.io.File dbFile) Sets the last used databases.
void	addProteinTreeImportTime(long fileSize, long importTime) Adds a protein tree import time.
void	checkDbFiles() Removes the db files which do not exist anymore.
void	clearProteinTreeImportTimes() Clears the protein tree import times.
java.io.File	getDbFolder() Returns the last used database folder.
java.util.ArrayList<java.lang.String>	getDisplayedTips() Returns the list of displayed tips.
java.util.ArrayList<java.io.File>	getFavoriteDBs() Returns the last used databases.
java.lang.String	getLocalPrideFolder() Returns the local PRIDE folder.
int	getMemoryPreference() Returns the preferred upper memory limit in MB.
java.awt.Color	getPeptideSelected() Returns the color for a selected peptide.
java.lang.String	getPeptideShakerPath() Returns the path to the PeptideShaker installation.
java.io.File	getProteinTreeFolder() Returns the protein tree folder.
java.util.HashMap<java.lang.Long,java.util.ArrayList<java.lang.Long>>	getProteinTreeImportTime() Returns the protein tree import times in a map: file size -> list of import sizes.
java.util.ArrayList<java.lang.String>	getReadTweets() Returns the list of read tweets.
java.lang.String	getRelimsPath() Returns the path to the Relims installation.
java.lang.String	getReporterPath() Returns the path to the Reporter installation.
java.lang.String	getSearchGuiPath() Returns the path to the SearchGUI installation.
java.awt.Color	getSparklineColor() Getter for the sparkline color.
java.awt.Color	getSparklineColorNonValidated() Getter for the non-validated sparkline color.
java.awt.Color	getSparklineColorNotFound() Returns the color for a not found sparkline bar chart plots.
java.awt.Color	getSparklineColorPossible() Returns the color for a possible sparkline bar chart plots.
java.awt.Color	getSpectrumAnnotatedPeakColor() Returns the color to use for the annotated peaks.
java.lang.Float	getSpectrumAnnotatedPeakWidth() Returns the width of the annotated peaks.
java.awt.Color	getSpectrumBackgroundPeakColor() Returns the color to use for the background peaks.
java.lang.Float	getSpectrumBackgroundPeakWidth() Returns the width of the background peaks.
static UtilitiesUserPreferences	loadUserPreferences() Loads the user preferences.
static void	saveUserPreferences(UtilitiesUserPreferences userPreferences) Convenience method saving the user preferences.
void	setDbFolder(java.io.File dbFolder) Sets the last used database folder.
void	setDisplayedTips(java.util.ArrayList<java.lang.String> displayedTips) Set the list of displayed tips.
void	setLocalPrideFolder(java.lang.String localPrideFolder) Set the local PRIDE folder.
void	setMemoryPreference(int memoryPreference) Sets the preferred upper memory limit.
void	setPeptideShakerPath(java.lang.String peptideShakerPath) Set the path to the PeptideShaker installation.
void	setProteinTreeFolder(java.io.File proteinTreeFolder) Sets the protein tree folder.
void	setReadTweets(java.util.ArrayList<java.lang.String> readTweets) Set the list of read tweets.
void	setRelimsPath(java.lang.String relimsPath) Set the path to the Relims installation.
void	setReporterPath(java.lang.String reporterPath) Set the path to the PeptideShaker installation.
void	setSearchGuiPath(java.lang.String searchGuiPath) Set the path to the SearchGUI installation.
void	setSparklineColor(java.awt.Color sparklineColorValidated) Setter for the sparkline color.
void	setSparklineColorNonValidated(java.awt.Color sparklineColorNonValidated) Setter for the non-validated sparkline color.
void	setSparklineColorPossible(java.awt.Color sparklineColorPossible) Setter for the possible sparkline color.
void	setSpectrumAnnotatedPeakColor(java.awt.Color spectrumAnnotatedPeakColor) Set the color to use for the annotated peaks.
void	setSpectrumAnnotatedPeakWidth(float spectrumAnnotatedPeakWidth) Set the width of the annotated peaks.
void	setSpectrumBackgroundPeakColor(java.awt.Color spectrumBackgroundPeakColor) Set the color to use for the background peaks.
void	setSpectrumBackgroundPeakWidth(float spectrumBackgroundPeakWidth) Set the width of the background peaks.

Methods inherited from class java.lang.Object

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

Field Detail

USER_PREFERENCES_FILE

public static final java.lang.String USER_PREFERENCES_FILE

Location of the user preferences file.

Constructor Detail

UtilitiesUserPreferences

public UtilitiesUserPreferences()

Constructor.

Method Detail

getSparklineColor

public java.awt.Color getSparklineColor()

Getter for the sparkline color.

Returns:

the sparkline color

setSparklineColor

public void setSparklineColor(java.awt.Color sparklineColorValidated)

Setter for the sparkline color.

Parameters:

sparklineColorValidated - the sparkline color

getSparklineColorNonValidated

public java.awt.Color getSparklineColorNonValidated()

Getter for the non-validated sparkline color.

Returns:

the non-validated sparkline color

getPeptideSelected

public java.awt.Color getPeptideSelected()

Returns the color for a selected peptide.

Returns:

the color for a selected peptide

getSparklineColorNotFound

public java.awt.Color getSparklineColorNotFound()

Returns the color for a not found sparkline bar chart plots.

Returns:

the color for a not found sparkline bar chart plots

setSparklineColorNonValidated

public void setSparklineColorNonValidated(java.awt.Color sparklineColorNonValidated)

Setter for the non-validated sparkline color.

Parameters:

sparklineColorNonValidated - the non-validated sparkline color

getSparklineColorPossible

public java.awt.Color getSparklineColorPossible()

Returns the color for a possible sparkline bar chart plots.

Returns:

the color for a possible sparkline bar chart plots

setSparklineColorPossible

public void setSparklineColorPossible(java.awt.Color sparklineColorPossible)

Setter for the possible sparkline color.

Parameters:

sparklineColorPossible - the possible sparkline color

getMemoryPreference

public int getMemoryPreference()

Returns the preferred upper memory limit in MB.

Returns:

the preferred upper memory limit

setMemoryPreference

public void setMemoryPreference(int memoryPreference)

Sets the preferred upper memory limit.

Parameters:

memoryPreference - the preferred upper memory limit

getSpectrumAnnotatedPeakColor

public java.awt.Color getSpectrumAnnotatedPeakColor()

Returns the color to use for the annotated peaks.

Returns:

the spectrumAnnotatedPeakColor

setSpectrumAnnotatedPeakColor

public void setSpectrumAnnotatedPeakColor(java.awt.Color spectrumAnnotatedPeakColor)

Set the color to use for the annotated peaks.

Parameters:

spectrumAnnotatedPeakColor - the spectrumAnnotatedPeakColor to set

getSpectrumBackgroundPeakColor

public java.awt.Color getSpectrumBackgroundPeakColor()

Returns the color to use for the background peaks.

Returns:

the spectrumBackgroundPeakColor

setSpectrumBackgroundPeakColor

public void setSpectrumBackgroundPeakColor(java.awt.Color spectrumBackgroundPeakColor)

Set the color to use for the background peaks.

Parameters:

spectrumBackgroundPeakColor - the spectrumBackgroundPeakColor to set

getSpectrumAnnotatedPeakWidth

public java.lang.Float getSpectrumAnnotatedPeakWidth()

Returns the width of the annotated peaks.

Returns:

the spectrumAnnotatedPeakWidth

setSpectrumAnnotatedPeakWidth

public void setSpectrumAnnotatedPeakWidth(float spectrumAnnotatedPeakWidth)

Set the width of the annotated peaks.

Parameters:

spectrumAnnotatedPeakWidth - the spectrumAnnotatedPeakWidth to set

getSpectrumBackgroundPeakWidth

public java.lang.Float getSpectrumBackgroundPeakWidth()

Returns the width of the background peaks.

Returns:

the spectrumBackgroundPeakWidth

setSpectrumBackgroundPeakWidth

public void setSpectrumBackgroundPeakWidth(float spectrumBackgroundPeakWidth)

Set the width of the background peaks.

Parameters:

spectrumBackgroundPeakWidth - the spectrumBackgroundPeakWidth to set

getSearchGuiPath

public java.lang.String getSearchGuiPath()

Returns the path to the SearchGUI installation.

Returns:

the path to the SearchGUI installation

setSearchGuiPath

public void setSearchGuiPath(java.lang.String searchGuiPath)

Set the path to the SearchGUI installation.

Parameters:

searchGuiPath - the path to the SearchGUI installation

getRelimsPath

public java.lang.String getRelimsPath()

Returns the path to the Relims installation.

Returns:

the path to the Relims installation

setRelimsPath

public void setRelimsPath(java.lang.String relimsPath)

Set the path to the Relims installation.

Parameters:

relimsPath - the path to the * installation

getPeptideShakerPath

public java.lang.String getPeptideShakerPath()

Returns the path to the PeptideShaker installation.

Returns:

the path to the PeptideShaker installation

setPeptideShakerPath

public void setPeptideShakerPath(java.lang.String peptideShakerPath)

Set the path to the PeptideShaker installation.

Parameters:

peptideShakerPath - the path to the PeptideShaker installation

getReporterPath

public java.lang.String getReporterPath()

Returns the path to the Reporter installation.

Returns:

the path to the Reporter installation

setReporterPath

public void setReporterPath(java.lang.String reporterPath)

Set the path to the PeptideShaker installation.

Parameters:

reporterPath - the path to the PeptideShaker installation

saveUserPreferences

public static void saveUserPreferences(UtilitiesUserPreferences userPreferences)

Convenience method saving the user preferences.

Parameters:

userPreferences -

loadUserPreferences

public static UtilitiesUserPreferences loadUserPreferences()

Loads the user preferences. If an error is encountered, preferences are set back to default.

Returns:

returns the utilities user preferences

getLocalPrideFolder

public java.lang.String getLocalPrideFolder()

Returns the local PRIDE folder.

Returns:

the localPrideFolder

setLocalPrideFolder

public void setLocalPrideFolder(java.lang.String localPrideFolder)

Set the local PRIDE folder.

Parameters:

localPrideFolder - the localPrideFolder to set

getDbFolder

public java.io.File getDbFolder()

Returns the last used database folder. Null if not set.

Returns:

the last used database folder

setDbFolder

public void setDbFolder(java.io.File dbFolder)

Sets the last used database folder.

Parameters:

dbFolder - the last used database folder

getFavoriteDBs

public java.util.ArrayList<java.io.File> getFavoriteDBs()

Returns the last used databases. The most recent ones first.

Returns:

the last used databases.

checkDbFiles

public void checkDbFiles()

Removes the db files which do not exist anymore.

addFavoriteDB

public void addFavoriteDB(java.io.File dbFile)

Sets the last used databases.

Parameters:

dbFile - the last used databases.

getProteinTreeFolder

public java.io.File getProteinTreeFolder()

Returns the protein tree folder.

Returns:

the protein tree folder

setProteinTreeFolder

public void setProteinTreeFolder(java.io.File proteinTreeFolder)

Sets the protein tree folder.

Parameters:

proteinTreeFolder - the protein tree folder

getProteinTreeImportTime

public java.util.HashMap<java.lang.Long,java.util.ArrayList<java.lang.Long>> getProteinTreeImportTime()

Returns the protein tree import times in a map: file size -> list of import sizes.

Returns:

the protein tree import times

addProteinTreeImportTime

public void addProteinTreeImportTime(long fileSize,
                            long importTime)

Adds a protein tree import time.

Parameters:

fileSize - the size of the FASTA file

importTime - the import time

clearProteinTreeImportTimes

public void clearProteinTreeImportTimes()

Clears the protein tree import times.

getReadTweets

public java.util.ArrayList<java.lang.String> getReadTweets()

Returns the list of read tweets.

Returns:

the list of read tweets

setReadTweets

public void setReadTweets(java.util.ArrayList<java.lang.String> readTweets)

Set the list of read tweets.

Parameters:

readTweets - the readTweets to set

getDisplayedTips

public java.util.ArrayList<java.lang.String> getDisplayedTips()

Returns the list of displayed tips.

Returns:

the displayed tips

setDisplayedTips

public void setDisplayedTips(java.util.ArrayList<java.lang.String> displayedTips)

Set the list of displayed tips.

Parameters:

displayedTips - the displayedTips to set