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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Boolean |
checkDuplicateTitles()
Returns if the spectra should be checked for duplicate titles or not.
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Boolean |
checkMgfSize()
Returns if the mgf should be checked for size.
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Boolean |
checkPeakPicking()
Returns if the spectra should be checked for peak picking or not.
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void |
clearProteinTreeImportTimes()
Clears the protein tree import times.
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Boolean |
generateProteinTree()
Returns true if the protein tree will be created parallel to the
searches.
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File |
getDbFolder()
Returns the last used database folder.
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String |
getDeNovoGuiPath()
Returns the path to the DeNovoGUI installation.
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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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String |
getJavaHome()
Returns the Java Home folder.
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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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Integer |
getMaxSpectrumChargeRange()
Returns the maximum charge added when the charge is missing for a given
spectrum.
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Integer |
getMemoryPreference()
Returns the preferred upper memory limit in MB.
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double |
getMgfMaxSize()
Returns the max mgf file size before splitting.
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int |
getMgfNSpectra()
Get the max number of spectra in an mgf file.
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Integer |
getMinSpectrumChargeRange()
Returns the minimum charge added when the charge is missing for a given
spectrum.
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SearchGuiOutputOption |
getOutputOption()
Returns the selected SearchGUI output option.
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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 |
getProteinSequencesManagerFolder()
returns the folder to use in the protein sequences manager.
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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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String |
getProteoWizardPath()
Returns the path to ProteoWizard.
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ArrayList<String> |
getReadTweets()
Returns the list of read tweets.
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Double |
getRefMass()
Returns the reference mass for the conversion of the fragment ion
tolerance from ppm to Dalton.
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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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Boolean |
getSortPsmsOnRt()
Returns true if the PSMs are sorted on retention time, false sorts on PSM
score.
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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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String |
getTargetDecoyFileNameTag()
Returns the target-decoy file name tag.
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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 |
isCheckSpectrumCharges()
Returns whether the spectra are to be checked for missing charges.
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Boolean |
isIncludeDateInOutputName()
Indicates whether the date should be included in the SearchGUI output
name.
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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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Boolean |
outputData()
Indicates whether data should be copied along with the identification
files in the SearchGUI output.
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Boolean |
renameXTandemFile()
Returns true if the X! Tandem file should be renamed.
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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 |
setCheckDuplicateTitles(boolean checkDuplicateTitles)
Set if the spectra should be checked for duplicate titles or not.
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void |
setCheckMgfSize(boolean checkMgfSize)
Set if the mgf should be checked for size.
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void |
setCheckPeakPicking(boolean checkPeakPicking)
Set if the spectra should be checked for peak picking or not.
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void |
setCheckSpectrumCharges(Boolean checkSpectrumCharges)
Set if the spectra are to be checked for missing charges.
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void |
setDbFolder(File dbFolder)
Sets the last used database folder.
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void |
setDeNovoGuiPath(String deNovoGuiPath)
Set the path to the DeNovoGUI installation.
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void |
setDisplayedTips(ArrayList<String> displayedTips)
Set the list of displayed tips.
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void |
setGenerateProteinTree(Boolean generateProteinTree)
Set if the the protein tree will be created parallel to the searches.
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void |
setIncludeDateInOutputName(Boolean includeDateInOutputName)
Sets whether the date should be included in the SearchGUI output name.
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void |
setJavaHome(String javaHome)
Set the Java Home folder.
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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 |
setMaxSpectrumChargeRange(Integer maxSpectrumChargeRange)
Set the maximum charge added when the charge is missing for a given
spectrum.
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void |
setMemoryPreference(int memoryPreference)
Sets the preferred upper memory limit.
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void |
setMgfMaxSize(double mgfMaxSize)
Set the max mgf file size before splitting.
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void |
setMgfNSpectra(int mgfNSpectra)
Set the max number of spectra in an mgf file.
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void |
setMinSpectrumChargeRange(Integer minSpectrumChargeRange)
Set the minimum charge added when the charge is missing for a given
spectrum.
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void |
setNotifyStart(Boolean notifyStart)
Sets whether the tools should notify their start.
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void |
setOutputData(Boolean outputData)
Sets whether data should be copied along with the identification files in
the SearchGUI output.
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void |
setOutputOption(SearchGuiOutputOption outputOption)
Sets how SearchGUI output files should be organized.
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void |
setPeptideShakerPath(String peptideShakerPath)
Set the path to the PeptideShaker installation.
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void |
setProteinSequencesManagerFolder(File proteinSequencesManagerFolder)
Sets the folder to use in the protein sequences manager.
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void |
setProteinTreeFolder(File proteinTreeFolder)
Sets the protein tree folder.
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void |
setProteoWizardPath(String proteoWizardPath)
Set the path to ProteoWizard.
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void |
setReadTweets(ArrayList<String> readTweets)
Set the list of read tweets.
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void |
setRefMass(Double refMass)
Sets the reference mass for the conversion of the fragment ion tolerance
from ppm to Dalton.
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void |
setRelimsPath(String relimsPath)
Set the path to the Relims installation.
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void |
setRenameXTandemFile(Boolean renameXTandemFile)
Set if the X! Tandem file should be renamed.
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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 |
setSortPsmsOnRt(Boolean sortPsmsOnRt)
Set if the PSMs are sorted on retention time, false sorts on PSM score.
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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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void |
setTargetDecoyFileNameTag(String targetDecoyFileNameTag)
Set the target-decoy file name tag.
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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 Integer getMemoryPreference()
public void setMemoryPreference(int memoryPreference)
memoryPreference
- the preferred upper memory limitpublic String getJavaHome()
public void setJavaHome(String javaHome)
javaHome
- the new Java Homepublic 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 getDeNovoGuiPath()
public void setDeNovoGuiPath(String deNovoGuiPath)
deNovoGuiPath
- the path to the DeNovoGUI installationpublic String getProteoWizardPath()
public void setProteoWizardPath(String proteoWizardPath)
proteoWizardPath
- the path to ProteoWizardpublic 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
- the user preferencespublic 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 File getProteinSequencesManagerFolder()
public void setProteinSequencesManagerFolder(File proteinSequencesManagerFolder)
proteinSequencesManagerFolder
- the folder to use in the protein
sequences managerpublic 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 folderpublic Boolean getSortPsmsOnRt()
public void setSortPsmsOnRt(Boolean sortPsmsOnRt)
sortPsmsOnRt
- the sortPsmsOnRt to setpublic String getTargetDecoyFileNameTag()
public void setTargetDecoyFileNameTag(String targetDecoyFileNameTag)
targetDecoyFileNameTag
- the targetDecoyFileNameTag to setpublic Boolean checkPeakPicking()
public void setCheckPeakPicking(boolean checkPeakPicking)
checkPeakPicking
- the checkPeakPicking to setpublic Boolean checkDuplicateTitles()
public void setCheckDuplicateTitles(boolean checkDuplicateTitles)
checkDuplicateTitles
- the checkDuplicateTitles to setpublic Boolean checkMgfSize()
public void setCheckMgfSize(boolean checkMgfSize)
checkMgfSize
- the mgf should be checked for sizepublic double getMgfMaxSize()
public void setMgfMaxSize(double mgfMaxSize)
mgfMaxSize
- the mgfMaxSize to setpublic int getMgfNSpectra()
public void setMgfNSpectra(int mgfNSpectra)
mgfNSpectra
- the mgfNSpectra to setpublic Double getRefMass()
public void setRefMass(Double refMass)
refMass
- the reference mass for the conversion of the fragment ion
tolerance from ppm to Daltonpublic Boolean generateProteinTree()
public void setGenerateProteinTree(Boolean generateProteinTree)
generateProteinTree
- create protein tree?public void setOutputOption(SearchGuiOutputOption outputOption)
outputOption
- the SearchGUI output optionpublic SearchGuiOutputOption getOutputOption()
public Boolean outputData()
public void setOutputData(Boolean outputData)
outputData
- whether data should be copied along with the
identification files in the SearchGUI outputpublic Boolean isIncludeDateInOutputName()
public void setIncludeDateInOutputName(Boolean includeDateInOutputName)
includeDateInOutputName
- whether the date should be included in the
SearchGUI output namepublic Boolean renameXTandemFile()
public void setRenameXTandemFile(Boolean renameXTandemFile)
renameXTandemFile
- rename file?public Boolean isCheckSpectrumCharges()
public void setCheckSpectrumCharges(Boolean checkSpectrumCharges)
checkSpectrumCharges
- the checkSpectrumCharges to setpublic Integer getMinSpectrumChargeRange()
public void setMinSpectrumChargeRange(Integer minSpectrumChargeRange)
minSpectrumChargeRange
- the minSpectrumChargeRange to setpublic Integer getMaxSpectrumChargeRange()
public void setMaxSpectrumChargeRange(Integer maxSpectrumChargeRange)
maxSpectrumChargeRange
- the maxSpectrumChargeRange to setCopyright © 2016. All rights reserved.