Package com.compomics.util.gui.parameters.identification.algorithm

Class XTandemParametersDialog

java.lang.Object
java.awt.Component
java.awt.Container
java.awt.Window
java.awt.Dialog
javax.swing.JDialog
com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog
All Implemented Interfaces:
AlgorithmParametersDialog, ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants
public class XTandemParametersDialog extends JDialog implements AlgorithmParametersDialog
Dialog for the X!Tandem specific settings.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • XTandemParametersDialog

      public XTandemParametersDialog()
      Empty default constructor

    • XTandemParametersDialog

      public XTandemParametersDialog(Frame parent, XtandemParameters xtandemParameters, ModificationParameters modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable)
      Creates new form XtandemParametersDialog with a frame as owner.
      Parameters:
      parent - the parent frame
      xtandemParameters - the X!Tandem parameters
      modificationProfile - the modification profile of the search
      fragmentIonMassAccuracyInDa - the fragment ion mass accuracy of the mass spectrometer
      editable - boolean indicating whether the settings can be edited by the user

    • XTandemParametersDialog

      public XTandemParametersDialog(Dialog owner, Frame parent, XtandemParameters xtandemParameters, ModificationParameters modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable)
      Creates new form XtandemParametersDialog with a dialog as owner.
      Parameters:
      owner - the dialog owner
      parent - the parent frame
      xtandemParameters - the X!Tandem parameters
      modificationProfile - the modification profile of the search
      fragmentIonMassAccuracyInDa - the fragment ion mass accuracy of the mass spectrometer
      editable - boolean indicating whether the settings can be edited by the user

  • Method Details

    • isCancelled

      public boolean isCancelled()
      Description copied from interface: AlgorithmParametersDialog
      Indicates whether the user canceled the editing.
      Specified by:
      isCancelled in interface AlgorithmParametersDialog
      Returns:
      true if cancel was pressed

    • getParameters

      public IdentificationAlgorithmParameter getParameters()
      Description copied from interface: AlgorithmParametersDialog
      Returns the parameters as set by the user.
      Specified by:
      getParameters in interface AlgorithmParametersDialog
      Returns:
      the parameters as set by the user

    • getInput

      public XtandemParameters getInput()
      Returns the user selection as X!tandem parameters object.
      Returns:
      the user selection

    • getModificationProfile

      public ModificationParameters getModificationProfile()
      Returns the modification profile corresponding to the input by the user.
      Returns:
      the modification profile corresponding to the input by the user

    • modProfileEdited

      public boolean modProfileEdited()
      Returns true if the user edited the modification profile. Note that it only checks if the user has made changed to the selection, not if the end result is different or not.
      Returns:
      true if the user edited the modification profile

    • validateInput

      public boolean validateInput(boolean showMessage)
      Inspects the parameters validity.
      Parameters:
      showMessage - if true an error messages are shown to the users
      Returns:
      a boolean indicating if the parameters are valid