com.compomics.util.preferences
Class UtilitiesUserPreferences

java.lang.Object
  extended by 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
static java.lang.String USER_PREFERENCES_FILE
          Location of the user preferences file.
 
Constructor Summary
UtilitiesUserPreferences()
          Constructor
 
Method Summary
 java.lang.String getLocalPrideFolder()
          Returns the local PRIDE folder.
 int getMemoryPreference()
          Returns the preferred upper memory limit.
 java.awt.Color getPeptideSelected()
          Returns the color for a selected peptide.
 java.lang.String getPeptideShakerPath()
          Returns the path to the PeptideShaker installation.
 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()
          Convenience method retrieving the user preferences.
static void saveUserPreferences(UtilitiesUserPreferences userPreferences)
          Convenience method saving the user preferences.
 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 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.

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)
                                throws java.io.FileNotFoundException,
                                       java.io.IOException
Convenience method saving the user preferences.

Parameters:
userPreferences -
Throws:
java.io.FileNotFoundException
java.io.IOException

loadUserPreferences

public static UtilitiesUserPreferences loadUserPreferences()
                                                    throws java.io.FileNotFoundException,
                                                           java.io.IOException,
                                                           java.lang.ClassNotFoundException
Convenience method retrieving the user preferences.

Returns:
returns the utilities user preferences
Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.ClassNotFoundException

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


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