Package eu.isas.reporter.settings

Class ReporterIonSelectionSettings

java.lang.Object
eu.isas.reporter.settings.ReporterIonSelectionSettings
All Implemented Interfaces:
Serializable
public class ReporterIonSelectionSettings extends Object implements Serializable
Preferences for the reporter ions selection in spectra.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • ReporterIonSelectionSettings

      public ReporterIonSelectionSettings()
      Constructor. Creates new reporter ion selection settings set to default.

  • Method Details

    • clone

      public ReporterIonSelectionSettings clone()
      Overrides:
      clone in class Object

    • isSameAs

      public boolean isSameAs(ReporterIonSelectionSettings anotherSetting)
      Indicates whether another setting is the same as this one.
      Parameters:
      anotherSetting - another setting
      Returns:
      a boolean indicating whether another setting is the same as this one

    • getReporterIonsMzTolerance

      public double getReporterIonsMzTolerance()
      Returns the tolerance used to match reporter ions.
      Returns:
      the tolerance used to match reporter ions

    • setReporterIonsMzTolerance

      public void setReporterIonsMzTolerance(double ReporterIonsMzTolerance)
      Sets the tolerance used to match reporter ions.
      Parameters:
      ReporterIonsMzTolerance - the tolerance used to match reporter ions

    • isMostAccurate

      public boolean isMostAccurate()
      Returns a boolean indicating whether the most accurate ion should be retained for quantification. The most intense will be used otherwise.
      Returns:
      a boolean indicating whether the most accurate ion should be retained for quantification

    • setMostAccurate

      public void setMostAccurate(boolean mostAccurate)
      Sets whether the most accurate ion should be retained for quantification. The most intense will be used otherwise.
      Parameters:
      mostAccurate - a boolean indicating whether the most accurate ion should be retained for quantification

    • getPrecursorMzTolerance

      public double getPrecursorMzTolerance()
      Returns the precursor m/Z tolerance used to match quantification spectra to identification spectra.
      Returns:
      the precursor m/Z tolerance used to match quantification spectra to identification spectra

    • setPrecursorMzTolerance

      public void setPrecursorMzTolerance(double precursorMzTolerance)
      Sets the precursor m/z tolerance used to match quantification spectra to identification spectra.
      Parameters:
      precursorMzTolerance - the precursor m/z tolerance used to match quantification spectra to identification spectra

    • getPrecursorRTTolerance

      public double getPrecursorRTTolerance()
      Returns the precursor RT tolerance used to match quantification spectra to identification spectra.
      Returns:
      the precursor RT tolerance used to match quantification spectra to identification spectra

    • setPrecursorRTTolerance

      public void setPrecursorRTTolerance(double precursorRTTolerance)
      Sets the precursor RT tolerance used to match quantification spectra to identification spectra.
      Parameters:
      precursorRTTolerance - the precursor RT tolerance used to match quantification spectra to identification spectra

    • getReporterIonsLocation

      public ReporterIonsLocationType getReporterIonsLocation()
      Returns the reporter ions location.
      Returns:
      the reporter ions location

    • setReporterIonsLocation

      public void setReporterIonsLocation(ReporterIonsLocationType reporterIonsLocation)
      Set the reporter ions location.
      Parameters:
      reporterIonsLocation - the reporter ions location

    • isPrecursorMzPpm

      public boolean isPrecursorMzPpm()
      Indicates whether the precursor matching tolerance is in ppm or in m/z
      Returns:
      true if ppm

    • setPrecursorMzPpm

      public void setPrecursorMzPpm(boolean precursorMzPpm)
      Sets whether the precursor matching tolerance is in ppm or in m/z
      Parameters:
      precursorMzPpm - true for ppm