Package eu.isas.reporter.gui

Class NewDialog

java.lang.Object
java.awt.Component
java.awt.Container
java.awt.Window
java.awt.Dialog
javax.swing.JDialog
eu.isas.reporter.gui.NewDialog
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants
public class NewDialog extends JDialog
This panel will be used to load the necessary files and settings to start the analysis.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • NewDialog

      public NewDialog(ReporterGUI reporterGUI, boolean modal)
      Constructor.
      Parameters:
      reporterGUI - the reporter class
      modal - if the dialog is modal or not

    • NewDialog

      public NewDialog(WelcomeDialog welcomeDialog, ReporterGUI reporterGui, boolean modal)
      Constructor.
      Parameters:
      welcomeDialog - the welcome dialog parent frame
      reporterGui - the reporter class
      modal - if the dialog is modal or not

  • Method Details

    • getProjectDetails

      public eu.isas.peptideshaker.preferences.ProjectDetails getProjectDetails()
      Returns the project details.
      Returns:
      the project details

    • getSearchParameters

      public com.compomics.util.parameters.identification.search.SearchParameters getSearchParameters()
      Returns the search parameters.
      Returns:
      the search parameters

    • getIdentification

      public com.compomics.util.experiment.identification.Identification getIdentification()
      Returns the identification displayed.
      Returns:
      the identification displayed

    • getSelectedMethod

      public com.compomics.util.experiment.quantification.reporterion.ReporterMethod getSelectedMethod()
      Returns the selected method.
      Returns:
      the selectedMethod

    • setSelectedMethod

      public void setSelectedMethod(com.compomics.util.experiment.quantification.reporterion.ReporterMethod selectedMethod)
      Set the selected method.
      Parameters:
      selectedMethod - the selectedMethod to set

    • getReagents

      public ArrayList<String> getReagents()
      Returns the reagents.
      Returns:
      the reagents

    • setReagents

      public void setReagents(ArrayList<String> reagents)
      Set the reagents.
      Parameters:
      reagents - the reagents to set

    • getMethodsFile

      public File getMethodsFile()
      Returns the current methods file.
      Returns:
      the methodsFile

    • setMethodsFile

      public void setMethodsFile(File methodsFile)
      Set the current method file.
      Parameters:
      methodsFile - the methodsFile to set

    • getReporterGui

      public ReporterGUI getReporterGui()
      Returns:
      the reporterGui

    • isCancelled

      public boolean isCancelled()
      Indicates whether the user canceled the project creation.
      Returns:
      a boolean indicating whether the user canceled the project creation

    • getPsdbBean

      public eu.isas.peptideshaker.utils.PsdbParent getPsdbBean()
      Returns the psdb parent object providing all information contained in the psdb file
      Returns:
      the psdb parent object providing all information contained in the psdb file

    • getReporterSettings

      public ReporterSettings getReporterSettings()
      Returns the reporter settings.
      Returns:
      the reporter settings

    • getReporterIonQuantification

      public com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification getReporterIonQuantification()
      Returns the reporter ion quantification. Note that this object is only set after the user has pressed "Load".
      Returns:
      the reporter ion quantification containing all quantification parameters

    • updateReagentNames

      public void updateReagentNames()
      Update the reagent names in the sample assignment table.