Package eu.isas.searchgui.gui

Class SearchGUI

java.lang.Object
java.awt.Component
java.awt.Container
java.awt.Window
java.awt.Frame
javax.swing.JFrame
eu.isas.searchgui.gui.SearchGUI
All Implemented Interfaces:
com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent, ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants
public class SearchGUI extends JFrame implements com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent
The main frame of SearchGUI.
Author:
Harald Barsnes, Marc Vaudel
See Also:

  • Field Details

    • TITLED_BORDER_HORIZONTAL_PADDING

      public static String TITLED_BORDER_HORIZONTAL_PADDING
      The horizontal padding used before and after the text in the titled borders. (Needed to make it look as good in Java 7 as it did in Java 6...)

    • MODIFICATION_SEPARATOR

      public static final String MODIFICATION_SEPARATOR
      Reference for the separation of modifications.
      See Also:

    • MODIFICATION_USE_SEPARATOR

      public static final String MODIFICATION_USE_SEPARATOR
      Reference for the separation of modification and its frequency.
      See Also:

    • msAmandaErrorMessage

      public static String msAmandaErrorMessage
      The error message shown if there is an issue with the MS Amanda installation.

  • Constructor Details

    • SearchGUI

      public SearchGUI(ArrayList<File> spectrumFiles, File fastaFile, ArrayList<File> rawFiles, File identificationParametersFile, File outputFolder, File configFolder, String species, String speciesType, String projectName)
      Creates a SearchGUI dialog.
      Parameters:
      spectrumFiles - the spectrum files (can be null)
      fastaFile - the FASTA file
      rawFiles - the raw files (can be null)
      identificationParametersFile - the identification settings file (can be null)
      outputFolder - the output folder (can be null)
      configFolder - the config folder (can be null)
      species - the species (can be null)
      speciesType - the species type (can be null)
      projectName - the PeptideShaker project name

  • Method Details

    • editPathParameters

      public void editPathParameters()
      Opens a dialog allowing the setting of paths.

    • getOutputFolder

      public File getOutputFolder()
      Returns the output folder.
      Returns:
      the output folder

    • getMgfFiles

      public ArrayList<File> getMgfFiles()
      Returns the spectra files selected.
      Returns:
      the spectra file selected

    • validateSearchEngines

      public boolean validateSearchEngines(boolean showMessage)
      Validate that the search engines work.
      Parameters:
      showMessage - show massage to the user
      Returns:
      true, if both search engines seem to work

    • validateParametersInput

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

    • verifySpectrumFileNames

      public boolean verifySpectrumFileNames()
      Verifies that all spectrum files have different names and displays a warning with the first conflict encountered.
      Returns:
      true if all spectrum files have different names, false otherwise

    • settingsDisplayed

      public boolean settingsDisplayed()
      Returns true if the settings have been displayed.
      Returns:
      true if the settings have has been displayed

    • setParametersDisplayed

      public void setParametersDisplayed(boolean settingsDisplayed)
      Set if the settings have been displayed.
      Parameters:
      settingsDisplayed - boolean indicating whether the settings have been displayed

    • main

      public static void main(String[] args)
      The main method used to start SearchGUI.
      Parameters:
      args - the command line arguments

    • getLastSelectedFolder

      public com.compomics.util.io.file.LastSelectedFolder getLastSelectedFolder()
      Returns the last selected folder.
      Returns:
      the last selected folder

    • setLastSelectedFolder

      public void setLastSelectedFolder(com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder)
      Set the last selected folder.
      Parameters:
      lastSelectedFolder - the folder to set

    • startSearch

      public void startSearch()
      This method is called whenever the 'Search' button is pressed. It starts the search.

    • getSearchHandler

      public SearchHandler getSearchHandler()
      Returns a reference to the SearchGUI command line interface.
      Returns:
      a reference to the SearchGUI command line interface

    • enableSearchEngines

      public void enableSearchEngines(boolean enableOmssa, boolean enbleXTandem, boolean enableMsgf, boolean enableMsAmanda, boolean enableMyriMatch, boolean enableComet, boolean enableTide, boolean enableAndromeda, boolean enableMetaMorpheus, boolean enableSage, boolean enableNovor, boolean enableDirecTag)
      Enable or disable the search engines.
      Parameters:
      enableOmssa - enable OMSSA?
      enbleXTandem - enable X!Tandem?
      enableMsgf - enable MS-GF+?
      enableMsAmanda - enable MS Amanda
      enableMyriMatch - enable MyriMatch
      enableComet - enable Comet
      enableTide - enable Tide
      enableAndromeda - enable Andromeda
      enableMetaMorpheus - enable MetaMorpheus
      enableSage - enable Sage
      enableNovor - enable Novor
      enableDirecTag - enable DirecTag

    • getIdentificationParameters

      public com.compomics.util.parameters.identification.IdentificationParameters getIdentificationParameters()
      Returns the identification parameters.
      Returns:
      the identification parameters

    • setIdentificationParameters

      public void setIdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
      Sets the search parameters.
      Parameters:
      identificationParameters - the identification parameters

    • getJarFilePath

      public String getJarFilePath()
      Returns the path to the jar file.
      Returns:
      the path to the jar file

    • getConfigFolder

      public File getConfigFolder()
      Returns the folder where the configuration files are stored.
      Returns:
      the folder where the configuration files are stored

    • setConfigFolder

      public void setConfigFolder(File configFolder)
      Set the config folder.
      Parameters:
      configFolder - the config folder to set

    • setPathConfiguration

      public void setPathConfiguration() throws IOException
      Sets the path configuration.
      Throws:
      IOException - exception thrown whenever an error occurs while reading or writing the paths configuration file

    • restart

      public void restart()
      Specified by:
      restart in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent

    • getUtilitiesUserParameters

      public com.compomics.util.parameters.UtilitiesUserParameters getUtilitiesUserParameters()
      Specified by:
      getUtilitiesUserParameters in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent

    • validateSearchEngineInstallation

      public static boolean validateSearchEngineInstallation(com.compomics.util.experiment.identification.Advocate advocate, File searchEngineLocation, boolean feedBackInDialog)
      Tries to validate the search engine installation by running the executable.
      Parameters:
      advocate - the search engine advocate
      searchEngineLocation - the folder where the search engine is installed
      feedBackInDialog - shows feedback in dialog, otherwise the feedbackDialog will be used
      Returns:
      true if the search engine seems to be correctly installed, false otherwise

    • getTips

      public ArrayList<String> getTips()
      Returns the tips of the day.
      Returns:
      the tips of the day in an ArrayList

    • checkForNewVersion

      public boolean checkForNewVersion()
      Check for new version.
      Returns:
      true if a new version is to be downloaded

    • editProteoWizardInstallation

      public boolean editProteoWizardInstallation()
      Opens a dialog allowing the edition of the ProteoWizard installation folder.
      Returns:
      true of the installation is now set