Package com.compomics.util.parameters

Class UtilitiesUserParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.UtilitiesUserParameters
All Implemented Interfaces:
Serializable
public class UtilitiesUserParameters extends ExperimentObject
Utilities user parameters can be used to store user parameters.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • UtilitiesUserParameters

      public UtilitiesUserParameters()
      Constructor.

  • Method Details

    • getSparklineColor

      public Color getSparklineColor()
      Getter for the sparkline color.
      Returns:
      the sparkline color

    • setSparklineColor

      public void setSparklineColor(Color sparklineColorValidated)
      Setter for the sparkline color.
      Parameters:
      sparklineColorValidated - the sparkline color

    • getSparklineColorNonValidated

      public Color getSparklineColorNonValidated()
      Getter for the non-validated sparkline color.
      Returns:
      the non-validated sparkline color

    • getPeptideSelected

      public Color getPeptideSelected()
      Returns the color for a selected peptide.
      Returns:
      the color for a selected peptide

    • getSparklineColorNotFound

      public Color getSparklineColorNotFound()
      Returns the color for a not found sparkline bar chart plots.
      Returns:
      the color for a not found sparkline bar chart plots

    • setSparklineColorNotFound

      public void setSparklineColorNotFound(Color sparklineColorNotFound)
      Setter for the not found sparkline color.
      Parameters:
      sparklineColorNotFound - the not found sparkline color

    • setSparklineColorNonValidated

      public void setSparklineColorNonValidated(Color sparklineColorNonValidated)
      Setter for the non-validated sparkline color.
      Parameters:
      sparklineColorNonValidated - the non-validated sparkline color

    • getSparklineColorPossible

      public 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(Color sparklineColorPossible)
      Setter for the possible sparkline color.
      Parameters:
      sparklineColorPossible - the possible sparkline color

    • getSparklineColorDoubtful

      public Color getSparklineColorDoubtful()
      Returns the color for a doubtful sparkline bar chart plots.
      Returns:
      the color for a doubtful sparkline bar chart plots

    • setSparklineColorDoubtful

      public void setSparklineColorDoubtful(Color sparklineColorDoubtful)
      Setter for the doubtful sparkline color.
      Parameters:
      sparklineColorDoubtful - the doubtful sparkline color

    • getSparklineColorFalsePositives

      public Color getSparklineColorFalsePositives()
      Returns the color for false positives in sparkline bar chart plots.
      Returns:
      the color for a false positives in sparkline bar chart plots

    • setSparklineColorFalsePositives

      public void setSparklineColorFalsePositives(Color sparklineColorFalsePositive)
      Setter for the false positives sparkline color.
      Parameters:
      sparklineColorFalsePositive - the false positives sparkline color

    • getMemoryParameter

      public Integer getMemoryParameter()
      Returns the upper memory limit in MB.
      Returns:
      the upper memory limit

    • setMemoryParameter

      public void setMemoryParameter(int memoryParameter)
      Sets the upper memory limit.
      Parameters:
      memoryParameter - the preferred upper memory limit

    • getJavaHome

      public String getJavaHome()
      Returns the Java Home folder.
      Returns:
      the Java Home folder

    • setJavaHome

      public void setJavaHome(String javaHome)
      Set the Java Home folder.
      Parameters:
      javaHome - the new Java Home

    • getSpectrumAnnotatedPeakColor

      public Color getSpectrumAnnotatedPeakColor()
      Returns the color to use for the annotated peaks.
      Returns:
      the spectrumAnnotatedPeakColor

    • setSpectrumAnnotatedPeakColor

      public void setSpectrumAnnotatedPeakColor(Color spectrumAnnotatedPeakColor)
      Set the color to use for the annotated peaks.
      Parameters:
      spectrumAnnotatedPeakColor - the spectrumAnnotatedPeakColor to set

    • getSpectrumAnnotatedMirroredPeakColor

      public Color getSpectrumAnnotatedMirroredPeakColor()
      Returns the color to use for the annotated mirrored peaks.
      Returns:
      the spectrumAnnotatedMirroredPeakColor

    • setSpectrumAnnotatedMirroredPeakColor

      public void setSpectrumAnnotatedMirroredPeakColor(Color spectrumAnnotatedMirroredPeakColor)
      Set the color to use for the annotated mirrored peaks.
      Parameters:
      spectrumAnnotatedMirroredPeakColor - the spectrumAnnotatedMirroredPeakColor to set

    • getSpectrumBackgroundPeakColor

      public Color getSpectrumBackgroundPeakColor()
      Returns the color to use for the background peaks.
      Returns:
      the spectrumBackgroundPeakColor

    • setSpectrumBackgroundPeakColor

      public void setSpectrumBackgroundPeakColor(Color spectrumBackgroundPeakColor)
      Set the color to use for the background peaks.
      Parameters:
      spectrumBackgroundPeakColor - the spectrumBackgroundPeakColor to set

    • getSpectrumAnnotatedPeakWidth

      public 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 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 String getSearchGuiPath()
      Returns the path to the SearchGUI installation.
      Returns:
      the path to the SearchGUI installation

    • setSearchGuiPath

      public void setSearchGuiPath(String searchGuiPath)
      Set the path to the SearchGUI installation.
      Parameters:
      searchGuiPath - the path to the SearchGUI installation

    • getDeNovoGuiPath

      public String getDeNovoGuiPath()
      Returns the path to the DeNovoGUI installation.
      Returns:
      the path to the DeNovoGUI installation

    • setDeNovoGuiPath

      public void setDeNovoGuiPath(String deNovoGuiPath)
      Set the path to the DeNovoGUI installation.
      Parameters:
      deNovoGuiPath - the path to the DeNovoGUI installation

    • getProteoWizardPath

      public String getProteoWizardPath()
      Returns the path to ProteoWizard.
      Returns:
      the path to ProteoWizard

    • setProteoWizardPath

      public void setProteoWizardPath(String proteoWizardPath)
      Set the path to ProteoWizard.
      Parameters:
      proteoWizardPath - the path to ProteoWizard

    • getRelimsPath

      public String getRelimsPath()
      Returns the path to the Relims installation.
      Returns:
      the path to the Relims installation

    • setRelimsPath

      public void setRelimsPath(String relimsPath)
      Set the path to the Relims installation.
      Parameters:
      relimsPath - the path to the * installation

    • getPeptideShakerPath

      public String getPeptideShakerPath()
      Returns the path to the PeptideShaker installation.
      Returns:
      the path to the PeptideShaker installation

    • setPeptideShakerPath

      public void setPeptideShakerPath(String peptideShakerPath)
      Set the path to the PeptideShaker installation.
      Parameters:
      peptideShakerPath - the path to the PeptideShaker installation

    • getReporterPath

      public String getReporterPath()
      Returns the path to the Reporter installation.
      Returns:
      the path to the Reporter installation

    • setReporterPath

      public void setReporterPath(String reporterPath)
      Set the path to the PeptideShaker installation.
      Parameters:
      reporterPath - the path to the PeptideShaker installation

    • saveUserParameters

      public static void saveUserParameters(UtilitiesUserParameters userParameters)
      Convenience method saving the user parameters. Exceptions are ignored silently and written to the stack trace.
      Parameters:
      userParameters - the user preferences

    • loadUserParameters

      public static UtilitiesUserParameters loadUserParameters()
      Loads the user parameters. If an error is encountered, parameters are set back to default.
      Returns:
      returns the utilities user preferences

    • getLocalPrideFolder

      public String getLocalPrideFolder()
      Returns the local PRIDE folder.
      Returns:
      the localPrideFolder

    • setLocalPrideFolder

      public void setLocalPrideFolder(String localPrideFolder)
      Set the local PRIDE folder.
      Parameters:
      localPrideFolder - the localPrideFolder to set

    • getDbFolder

      public File getDbFolder()
      Returns the last used database folder. Null if not set.
      Returns:
      the last used database folder

    • setDbFolder

      public void setDbFolder(File dbFolder)
      Sets the last used database folder.
      Parameters:
      dbFolder - the last used database folder

    • getSpectrumFolder

      public File getSpectrumFolder()
      Returns the last used spectrum folder. Null if not set.
      Returns:
      the last used spectrum folder

    • setSpectrumFolder

      public void setSpectrumFolder(File spectrumFolder)
      Sets the last used spectrum folder.
      Parameters:
      spectrumFolder - the last used spectrum folder

    • getOutputFolder

      public File getOutputFolder()
      Returns the last used output folder. Null if not set.
      Returns:
      the last used output folder

    • setOutputFolder

      public void setOutputFolder(File outputFolder)
      Sets the last used output folder.
      Parameters:
      outputFolder - the last used output folder

    • getReadTweets

      public ArrayList<String> getReadTweets()
      Returns the list of read tweets.
      Returns:
      the list of read tweets

    • setReadTweets

      public void setReadTweets(ArrayList<String> readTweets)
      Set the list of read tweets.
      Parameters:
      readTweets - the readTweets to set

    • getDisplayedTips

      public ArrayList<String> getDisplayedTips()
      Returns the list of displayed tips.
      Returns:
      the displayed tips

    • setDisplayedTips

      public void setDisplayedTips(ArrayList<String> displayedTips)
      Set the list of displayed tips.
      Parameters:
      displayedTips - the displayedTips to set

    • getUserParametersFile

      public static String getUserParametersFile()
      Returns the user preferences file to be used.
      Returns:
      the user preferences file

    • getUserParametersFolder

      public static String getUserParametersFolder()
      Returns the user preferences file to be used.
      Returns:
      the user preferences file

    • setUserParametersFolder

      public static void setUserParametersFolder(String userParametersFolder)
      Sets the user preferences file to be used.
      Parameters:
      userParametersFolder - the user preferences file to be used

    • isAutoUpdate

      public boolean isAutoUpdate()
      Indicates whether the tools should use the auto update function.
      Returns:
      whether the tools should use the auto update function

    • setAutoUpdate

      public void setAutoUpdate(Boolean autoUpdate)
      Sets whether the tools should use the auto update function.
      Parameters:
      autoUpdate - whether the tools should use the auto update function

    • getLastSelectedFolder

      public LastSelectedFolder getLastSelectedFolder()
      Returns the last selected folder.
      Returns:
      the last selected folder

    • setLastSelectedFolder

      public void setLastSelectedFolder(LastSelectedFolder lastSelectedFolder)
      Sets the last selected folder.
      Parameters:
      lastSelectedFolder - the last selected folder

    • getSortPsmsOnRt

      public boolean getSortPsmsOnRt()
      Returns true if the PSMs are sorted on retention time, false sorts on PSM score.
      Returns:
      the sortPsmsOnRt

    • setSortPsmsOnRt

      public void setSortPsmsOnRt(Boolean sortPsmsOnRt)
      Set if the PSMs are sorted on retention time, false sorts on PSM score.
      Parameters:
      sortPsmsOnRt - the sortPsmsOnRt to set

    • checkPeakPicking

      public boolean checkPeakPicking()
      Returns if the spectra should be checked for peak picking or not.
      Returns:
      true if the spectra should be checked for peak picking

    • setCheckPeakPicking

      public void setCheckPeakPicking(boolean checkPeakPicking)
      Set if the spectra should be checked for peak picking or not.
      Parameters:
      checkPeakPicking - the checkPeakPicking to set

    • checkDuplicateTitles

      public boolean checkDuplicateTitles()
      Returns if the spectra should be checked for duplicate titles or not.
      Returns:
      true if the spectra should be checked for duplicate titles

    • setCheckDuplicateTitles

      public void setCheckDuplicateTitles(boolean checkDuplicateTitles)
      Set if the spectra should be checked for duplicate titles or not.
      Parameters:
      checkDuplicateTitles - the checkDuplicateTitles to set

    • checkMgfSize

      public boolean checkMgfSize()
      Returns if the mgf should be checked for size.
      Returns:
      true if the mgf should be checked for size

    • setCheckMgfSize

      public void setCheckMgfSize(boolean checkMgfSize)
      Set if the mgf should be checked for size.
      Parameters:
      checkMgfSize - the mgf should be checked for size

    • getMgfMaxSize

      public double getMgfMaxSize()
      Returns the max mgf file size before splitting.
      Returns:
      the mgfMaxSize

    • setMgfMaxSize

      public void setMgfMaxSize(double mgfMaxSize)
      Set the max mgf file size before splitting.
      Parameters:
      mgfMaxSize - the mgfMaxSize to set

    • getMgfNSpectra

      public int getMgfNSpectra()
      Get the max number of spectra in an mgf file.
      Returns:
      the mgfNSpectra

    • setMgfNSpectra

      public void setMgfNSpectra(int mgfNSpectra)
      Set the max number of spectra in an mgf file.
      Parameters:
      mgfNSpectra - the mgfNSpectra to set

    • getRefMass

      public double getRefMass()
      Returns the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
      Returns:
      the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton

    • setRefMass

      public void setRefMass(double refMass)
      Sets the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
      Parameters:
      refMass - the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton

    • setSearchGuiOutputParameters

      public void setSearchGuiOutputParameters(OutputParameters outputOption)
      Sets how SearchGUI output files should be organized.
      Parameters:
      outputOption - the SearchGUI output option

    • getSearchGuiOutputParameters

      public OutputParameters getSearchGuiOutputParameters()
      Returns the selected SearchGUI output option.
      Returns:
      the selected SearchGUI output option

    • isGzip

      public boolean isGzip()
      Indicates whether identification files should be gzipped.
      Returns:
      A boolean indicating whether identification files should be gzipped.

    • setGzip

      public void setGzip(boolean gzip)
      Sets whether identification files should be gzipped.
      Parameters:
      gzip - A boolean indicating whether identification files should be gzipped.

    • outputData

      public boolean outputData()
      Indicates whether data should be copied along with the identification files in the SearchGUI output.
      Returns:
      a boolean indicating whether data should be copied along with the identification files in the SearchGUI output

    • setOutputData

      public void setOutputData(boolean outputData)
      Sets whether data should be copied along with the identification files in the SearchGUI output.
      Parameters:
      outputData - whether data should be copied along with the identification files in the SearchGUI output

    • isIncludeDateInOutputName

      public boolean isIncludeDateInOutputName()
      Indicates whether the date should be included in the SearchGUI output name.
      Returns:
      a boolean indicating whether the date should be included in the SearchGUI output name

    • setIncludeDateInOutputName

      public void setIncludeDateInOutputName(boolean includeDateInOutputName)
      Sets whether the date should be included in the SearchGUI output name.
      Parameters:
      includeDateInOutputName - whether the date should be included in the SearchGUI output name

    • renameXTandemFile

      public boolean renameXTandemFile()
      Returns true if the X! Tandem file should be renamed.
      Returns:
      true if the X! Tandem file should be renamed

    • setRenameXTandemFile

      public void setRenameXTandemFile(boolean renameXTandemFile)
      Set if the X! Tandem file should be renamed.
      Parameters:
      renameXTandemFile - rename file?

    • isCheckSpectrumCharges

      public boolean isCheckSpectrumCharges()
      Returns whether the spectra are to be checked for missing charges.
      Returns:
      true, if the spectra are to be checked for missing charges

    • setCheckSpectrumCharges

      public void setCheckSpectrumCharges(boolean checkSpectrumCharges)
      Set if the spectra are to be checked for missing charges.
      Parameters:
      checkSpectrumCharges - the checkSpectrumCharges to set

    • getMinSpectrumChargeRange

      public int getMinSpectrumChargeRange()
      Returns the minimum charge added when the charge is missing for a given spectrum.
      Returns:
      the minimum charge added when the charge is missing for a given spectrum

    • setMinSpectrumChargeRange

      public void setMinSpectrumChargeRange(int minSpectrumChargeRange)
      Set the minimum charge added when the charge is missing for a given spectrum.
      Parameters:
      minSpectrumChargeRange - the minSpectrumChargeRange to set

    • getMaxSpectrumChargeRange

      public int getMaxSpectrumChargeRange()
      Returns the maximum charge added when the charge is missing for a given spectrum.
      Returns:
      the maximum charge added when the charge is missing for a given spectrum

    • setMaxSpectrumChargeRange

      public void setMaxSpectrumChargeRange(int maxSpectrumChargeRange)
      Set the maximum charge added when the charge is missing for a given spectrum.
      Parameters:
      maxSpectrumChargeRange - the maxSpectrumChargeRange to set

    • getDbSummaryFolder

      public File getDbSummaryFolder()
      Returns the folder where FASTA files summary statistics are stored.
      Returns:
      the folder where FASTA files summary statistics are stored