net.maizegenetics.tassel.TASSELGUI.kt Maven / Gradle / Ivy
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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
package net.maizegenetics.tassel
import javafx.application.Application
import javafx.application.Platform
import javafx.event.ActionEvent
import javafx.event.EventHandler
import javafx.geometry.Orientation
import javafx.scene.Scene
import javafx.scene.control.*
import javafx.scene.image.ImageView
import javafx.scene.input.KeyCombination
import javafx.scene.layout.*
import javafx.scene.paint.Paint
import javafx.stage.Stage
import javafx.stage.WindowEvent
import net.maizegenetics.analysis.data.FileLoadPlugin
import net.maizegenetics.analysis.data.GenotypeSummaryPlugin
import net.maizegenetics.dna.factor.FeatureTable
import net.maizegenetics.gui.*
import net.maizegenetics.plugindef.AbstractPlugin
import net.maizegenetics.plugindef.Datum
import net.maizegenetics.plugindef.Plugin
import net.maizegenetics.util.TableReport
import org.apache.logging.log4j.LogManager
import java.util.*
/**
* @author Terry Casstevens
* Created November 01, 2018
*/
private val myLogger = LogManager.getLogger(TASSELGUI::class.java)
private val EMPTY_NODE = StackPane().also {
it.background = Background(BackgroundFill(Paint.valueOf("grey"), null, null))
it.children += ImageView("/images/Tassel_Logo.png")
}
class TASSELGUI : Application() {
lateinit var primaryStage: Stage
private val myDataTree = DataTree()
private val myInfo = InfoViewer()
private val myMenuItemHash = HashMap()
private val myMainPane = BorderPane()
private val myProgressViewer = ProgressViewer()
private val myMainControls = MainControls()
private val myMainView = StackPane()
override fun start(stage: Stage) {
instance = this
primaryStage = stage
stage.onCloseRequest = EventHandler { stop() }
val left = SplitPane()
left.orientation = Orientation.VERTICAL
left.setDividerPositions(0.6)
left.items += myDataTree.view
left.items += myInfo.view
left.prefWidth = 300.0
val spacer = Region()
spacer.styleClass.add("menu-bar")
HBox.setHgrow(spacer, Priority.SOMETIMES)
myMainPane.top = HBox(leftMenuBar(), spacer, rightMenuBar())
updatePluginsWithGlobalConfigParameters()
myMainPane.center = myMainView
myMainView.children += EMPTY_NODE
myMainPane.left = left
val bottomSpacer = Region()
HBox.setHgrow(bottomSpacer, Priority.ALWAYS)
val bottom = HBox(myProgressViewer.view, bottomSpacer, myMainControls.view)
myMainPane.bottom = bottom
stage.title = "TASSEL 6"
val scene = Scene(myMainPane, 1000.0, 750.0)
scene.stylesheets += "/javafx/AppStyle.css"
stage.scene = scene
stage.show()
}
private fun leftMenuBar(): MenuBar {
val result = MenuBar()
result.menus += fileMenu()
result.menus += dataMenu()
return result
}
private fun rightMenuBar(): MenuBar {
return MenuBar(helpMenu())
}
private fun fileMenu(): Menu {
val result = Menu("File")
val autoGuessPlugin = FileLoadPlugin(true, true)
result.items += createMenuItem(autoGuessPlugin, name = "Open", action = EventHandler {
myProgressViewer.showProgress(autoGuessPlugin)
Thread { autoGuessPlugin.processData(null) }.start()
})
result.items += createMenuItem(FileLoadPlugin(true))
result.items += MenuItem("Delete", ImageView("/images/trash.gif")).also {
it.onAction = EventHandler { myDataTree.deleteSelectedNodes() }
}
result.items += createMenuItem(PreferencesDialog(true))
result.items += SeparatorMenuItem()
val exit = MenuItem("Exit")
exit.onAction = EventHandler { stop() }
result.items += exit
return result
}
private fun dataMenu(): Menu {
val result = Menu("Data")
result.items += createMenuItem(GenotypeSummaryPlugin(true))
return result
}
private fun helpMenu(): Menu {
val result = Menu("Help")
result.items += createMenuItem(TasselLogging.instance)
return result
}
private fun createMenuItem(plugin: Plugin, mnemonic: String? = null, name: String? = null, action: EventHandler? = null): MenuItem {
val menuItem = MenuItem(name ?: plugin.buttonName)
try {
menuItem.graphic = ImageView(plugin.icon())
} catch (e: Exception) {
myLogger.warn("Problem loading icon: ${plugin.icon()} for plugin: ${plugin.javaClass}")
}
if (mnemonic != null) {
menuItem.accelerator = KeyCombination.keyCombination(mnemonic)
}
if (action == null) {
menuItem.onAction = EventHandler {
myProgressViewer.showProgress(plugin)
Thread(Runnable { plugin.performFunction(myDataTree.selectedData()) }).start()
}
} else {
menuItem.onAction = action
}
plugin.addListener(myDataTree)
myMenuItemHash[menuItem] = plugin
return menuItem
}
fun updatePluginsWithGlobalConfigParameters() {
myMenuItemHash.values.forEach { (it as AbstractPlugin).setConfigParameters() }
}
fun changeView(datum: Datum) = Platform.runLater {
myProgressViewer.showSelected(datum)
myInfo.show(datum)
myMainControls.clear()
myMainView.children.clear()
when (val data = datum.data) {
is TableReport -> myMainView.children += TableReportViewer.instance(data).view
is FeatureTable -> {
val viewer = FactorTableViewer.instance(data, myMainView.widthProperty())
myMainView.children += viewer.view
myMainControls.add(viewer.controls)
}
else -> myMainView.children += EMPTY_NODE
}
}
override fun stop() {
Platform.exit()
}
companion object {
@JvmStatic
lateinit var instance: TASSELGUI
}
}