public class UtilitiesUserPreferences extends Object implements Serializable
Constructor and Description |
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UtilitiesUserPreferences()
Constructor.
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Modifier and Type | Method and Description |
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void |
addFavoriteDB(File dbFile)
Sets the last used databases.
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void |
addProteinTreeImportTime(long fileSize,
long importTime)
Adds a protein tree import time.
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void |
checkDbFiles()
Removes the db files which do not exist anymore.
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void |
clearProteinTreeImportTimes()
Clears the protein tree import times.
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File |
getDbFolder()
Returns the last used database folder.
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ArrayList<String> |
getDisplayedTips()
Returns the list of displayed tips.
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ArrayList<File> |
getFavoriteDBs()
Returns the last used databases.
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LastSelectedFolder |
getLastSelectedFolder()
Returns the last selected folder.
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String |
getLocalPrideFolder()
Returns the local PRIDE folder.
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int |
getMemoryPreference()
Returns the preferred upper memory limit in MB.
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Color |
getPeptideSelected()
Returns the color for a selected peptide.
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String |
getPeptideShakerPath()
Returns the path to the PeptideShaker installation.
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File |
getProteinTreeFolder()
Returns the protein tree folder.
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HashMap<Long,ArrayList<Long>> |
getProteinTreeImportTime()
Returns the protein tree import times in a map: file size > list of
import sizes.
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ArrayList<String> |
getReadTweets()
Returns the list of read tweets.
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String |
getRelimsPath()
Returns the path to the Relims installation.
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String |
getReporterPath()
Returns the path to the Reporter installation.
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String |
getSearchGuiPath()
Returns the path to the SearchGUI installation.
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Color |
getSparklineColor()
Getter for the sparkline color.
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Color |
getSparklineColorDoubtful()
Returns the color for a doubtful sparkline bar chart plots.
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Color |
getSparklineColorFalsePositives()
Returns the color for false positives in sparkline bar chart plots.
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Color |
getSparklineColorNonValidated()
Getter for the non-validated sparkline color.
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Color |
getSparklineColorNotFound()
Returns the color for a not found sparkline bar chart plots.
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Color |
getSparklineColorPossible()
Returns the color for a possible sparkline bar chart plots.
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Color |
getSpectrumAnnotatedMirroredPeakColor()
Returns the color to use for the annotated mirrored peaks.
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Color |
getSpectrumAnnotatedPeakColor()
Returns the color to use for the annotated peaks.
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Float |
getSpectrumAnnotatedPeakWidth()
Returns the width of the annotated peaks.
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Color |
getSpectrumBackgroundPeakColor()
Returns the color to use for the background peaks.
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Float |
getSpectrumBackgroundPeakWidth()
Returns the width of the background peaks.
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static String |
getUserPreferencesFile()
Returns the user preferences file to be used.
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static String |
getUserPreferencesFolder()
Returns the user preferences file to be used.
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Boolean |
isAutoUpdate()
Indicates whether the tools should use the auto update function.
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Boolean |
isNotifyStart()
Indicates whether the tools should notify their start.
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static UtilitiesUserPreferences |
loadUserPreferences()
Loads the user preferences.
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static void |
saveUserPreferences(UtilitiesUserPreferences userPreferences)
Convenience method saving the user preferences.
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void |
setAutoUpdate(Boolean autoUpdate)
Sets whether the tools should use the auto update function.
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void |
setDbFolder(File dbFolder)
Sets the last used database folder.
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void |
setDisplayedTips(ArrayList<String> displayedTips)
Set the list of displayed tips.
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void |
setLastSelectedFolder(LastSelectedFolder lastSelectedFolder)
Sets the last selected folder.
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void |
setLocalPrideFolder(String localPrideFolder)
Set the local PRIDE folder.
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void |
setMemoryPreference(int memoryPreference)
Sets the preferred upper memory limit.
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void |
setNotifyStart(Boolean notifyStart)
Sets whether the tools should notify their start.
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void |
setPeptideShakerPath(String peptideShakerPath)
Set the path to the PeptideShaker installation.
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void |
setProteinTreeFolder(File proteinTreeFolder)
Sets the protein tree folder.
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void |
setReadTweets(ArrayList<String> readTweets)
Set the list of read tweets.
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void |
setRelimsPath(String relimsPath)
Set the path to the Relims installation.
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void |
setReporterPath(String reporterPath)
Set the path to the PeptideShaker installation.
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void |
setSearchGuiPath(String searchGuiPath)
Set the path to the SearchGUI installation.
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void |
setSparklineColor(Color sparklineColorValidated)
Setter for the sparkline color.
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void |
setSparklineColorDoubtful(Color sparklineColorDoubtful)
Setter for the doubtful sparkline color.
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void |
setSparklineColorFalsePositives(Color sparklineColorFalsePositive)
Setter for the false positives sparkline color.
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void |
setSparklineColorNonValidated(Color sparklineColorNonValidated)
Setter for the non-validated sparkline color.
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void |
setSparklineColorPossible(Color sparklineColorPossible)
Setter for the possible sparkline color.
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void |
setSpectrumAnnotatedMirroredPeakColor(Color spectrumAnnotatedMirroredPeakColor)
Set the color to use for the annotated mirrored peaks.
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void |
setSpectrumAnnotatedPeakColor(Color spectrumAnnotatedPeakColor)
Set the color to use for the annotated peaks.
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void |
setSpectrumAnnotatedPeakWidth(float spectrumAnnotatedPeakWidth)
Set the width of the annotated peaks.
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void |
setSpectrumBackgroundPeakColor(Color spectrumBackgroundPeakColor)
Set the color to use for the background peaks.
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void |
setSpectrumBackgroundPeakWidth(float spectrumBackgroundPeakWidth)
Set the width of the background peaks.
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static void |
setUserPreferencesFolder(String userPreferencesFolder)
Sets the user preferences file to be used.
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public Color getSparklineColor()
public void setSparklineColor(Color sparklineColorValidated)
sparklineColorValidated
- the sparkline colorpublic Color getSparklineColorNonValidated()
public Color getPeptideSelected()
public Color getSparklineColorNotFound()
public void setSparklineColorNonValidated(Color sparklineColorNonValidated)
sparklineColorNonValidated
- the non-validated sparkline colorpublic Color getSparklineColorPossible()
public void setSparklineColorPossible(Color sparklineColorPossible)
sparklineColorPossible
- the possible sparkline colorpublic Color getSparklineColorDoubtful()
public void setSparklineColorDoubtful(Color sparklineColorDoubtful)
sparklineColorDoubtful
- the doubtful sparkline colorpublic Color getSparklineColorFalsePositives()
public void setSparklineColorFalsePositives(Color sparklineColorFalsePositive)
sparklineColorFalsePositive
- the false positives sparkline colorpublic int getMemoryPreference()
public void setMemoryPreference(int memoryPreference)
memoryPreference
- the preferred upper memory limitpublic Color getSpectrumAnnotatedPeakColor()
public void setSpectrumAnnotatedPeakColor(Color spectrumAnnotatedPeakColor)
spectrumAnnotatedPeakColor
- the spectrumAnnotatedPeakColor to setpublic Color getSpectrumAnnotatedMirroredPeakColor()
public void setSpectrumAnnotatedMirroredPeakColor(Color spectrumAnnotatedMirroredPeakColor)
spectrumAnnotatedMirroredPeakColor
- the
spectrumAnnotatedMirroredPeakColor to setpublic Color getSpectrumBackgroundPeakColor()
public void setSpectrumBackgroundPeakColor(Color spectrumBackgroundPeakColor)
spectrumBackgroundPeakColor
- the spectrumBackgroundPeakColor to setpublic Float getSpectrumAnnotatedPeakWidth()
public void setSpectrumAnnotatedPeakWidth(float spectrumAnnotatedPeakWidth)
spectrumAnnotatedPeakWidth
- the spectrumAnnotatedPeakWidth to setpublic Float getSpectrumBackgroundPeakWidth()
public void setSpectrumBackgroundPeakWidth(float spectrumBackgroundPeakWidth)
spectrumBackgroundPeakWidth
- the spectrumBackgroundPeakWidth to setpublic String getSearchGuiPath()
public void setSearchGuiPath(String searchGuiPath)
searchGuiPath
- the path to the SearchGUI installationpublic String getRelimsPath()
public void setRelimsPath(String relimsPath)
relimsPath
- the path to the * installationpublic String getPeptideShakerPath()
public void setPeptideShakerPath(String peptideShakerPath)
peptideShakerPath
- the path to the PeptideShaker installationpublic String getReporterPath()
public void setReporterPath(String reporterPath)
reporterPath
- the path to the PeptideShaker installationpublic static void saveUserPreferences(UtilitiesUserPreferences userPreferences)
userPreferences
- public static UtilitiesUserPreferences loadUserPreferences()
public String getLocalPrideFolder()
public void setLocalPrideFolder(String localPrideFolder)
localPrideFolder
- the localPrideFolder to setpublic File getDbFolder()
public void setDbFolder(File dbFolder)
dbFolder
- the last used database folderpublic ArrayList<File> getFavoriteDBs()
public void checkDbFiles()
public void addFavoriteDB(File dbFile)
dbFile
- the last used databases.public File getProteinTreeFolder()
public void setProteinTreeFolder(File proteinTreeFolder)
proteinTreeFolder
- the protein tree folderpublic HashMap<Long,ArrayList<Long>> getProteinTreeImportTime()
public void addProteinTreeImportTime(long fileSize, long importTime)
fileSize
- the size of the FASTA fileimportTime
- the import timepublic void clearProteinTreeImportTimes()
public ArrayList<String> getReadTweets()
public void setReadTweets(ArrayList<String> readTweets)
readTweets
- the readTweets to setpublic ArrayList<String> getDisplayedTips()
public void setDisplayedTips(ArrayList<String> displayedTips)
displayedTips
- the displayedTips to setpublic static String getUserPreferencesFile()
public static String getUserPreferencesFolder()
public static void setUserPreferencesFolder(String userPreferencesFolder)
userPreferencesFolder
- the user preferences file to be usedpublic Boolean isAutoUpdate()
public void setAutoUpdate(Boolean autoUpdate)
autoUpdate
- whether the tools should use the auto update functionpublic Boolean isNotifyStart()
public void setNotifyStart(Boolean notifyStart)
notifyStart
- whether the tools should notify their startpublic LastSelectedFolder getLastSelectedFolder()
public void setLastSelectedFolder(LastSelectedFolder lastSelectedFolder)
lastSelectedFolder
- the last selected folderCopyright © 2014. All rights reserved.