Merge pull request #63 from Integrative-Transcriptomics/fileFormats

merge versions

src/main/java/controller/VisualizationController.java

@@ -0,0 +1,336 @@
+package controller;
+
+import Logging.LogClass;
+import javafx.scene.Scene;
+import javafx.scene.control.*;
+import javafx.scene.text.Font;
+import javafx.scene.text.Text;
+import javafx.stage.Stage;
+import org.apache.log4j.Logger;
+import view.MitoBenchWindow;
+import view.menus.VisualizationMenu;
+import view.visualizations.*;
+
+import java.net.MalformedURLException;
+import java.util.HashMap;
+import java.util.List;
+
+public class VisualizationController {
+
+    private final Logger LOG;
+    private MitoBenchWindow mito;
+    private Stage stage;
+    private Scene scene;
+
+    private TableControllerUserBench tableController;
+    private ChartController chartController;
+    private HaplotreeController treeController;
+    private GroupController groupController;
+
+    private BarPlotHaplo barPlotHaplo;
+    private BarPlotHaplo2 barPlotHaplo2;
+    private BarChartGrouping barChartGrouping;
+    private StackedBar stackedBar;
+   // private SunburstChartCreator sunburstChart;
+    private TreeView treeView;
+    private ProfilePlot profilePlot;
+    private PieChartViz pieChartViz;
+    private ColorSchemeStackedBarChart colorScheme;
+
+    private TabPane tabPane;
+    private TabPane statsTabpane;
+    private Menu menuGraphics;
+
+    private HashMap<String, List<String>> treeMap_path_to_root;
+    private int profilePlotID=1;
+    private TreeItem<String> tree_root;
+
+    private LogClass logClass;
+
+
+
+    public VisualizationController(MitoBenchWindow mitoBenchWindow){
+        this.mito = mitoBenchWindow;
+
+        treeController = mitoBenchWindow.getTreeController();
+        this.tableController = mitoBenchWindow.getTableControllerUserBench();
+        chartController = mitoBenchWindow.getChartController();
+        groupController = mitoBenchWindow.getGroupController();
+
+        tabPane = mitoBenchWindow.getTabpane_visualization();
+        treeMap_path_to_root = treeController.getTreeMap_leaf_to_root();
+        tree_root = treeController.deepcopy(treeController.getTree().getTree().getRoot());
+        treeView = treeController.getTree().getTree();
+        statsTabpane = mitoBenchWindow.getTabpane_statistics();
+
+        this.LOG = mitoBenchWindow.getLogClass().getLogger(this.getClass());
+        this.logClass = mitoBenchWindow.getLogClass();
+
+        this.stage = mitoBenchWindow.getPrimaryStage();
+    }
+
+    public void initHaploBarchart(String titlePart) {
+        LOG.info("Visualize data: Haplogroup frequency " + titlePart + " (Barchart)");
+        Text t = new Text();
+        t.setText("Haplogroup occurrences " + titlePart);
+        t.setFont(Font.font(25));
+
+        barPlotHaplo = new BarPlotHaplo(
+                t.getText(),
+                "Counts",
+                stage,
+                tableController,
+                tabPane,
+                logClass
+        );
+        //barPlotHaplo.setStyleSheet(stage);
+        Tab tab = new Tab();
+        tab.setId("tab_haplo_barchart");
+        tab.setText("Haplogroup occurrences");
+        tab.setContent(barPlotHaplo.getBarChart());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+
+    }
+
+    public void initHaploBarchart2(String titlePart) throws MalformedURLException {
+        LOG.info("Visualize data: Haplogroup frequency " + titlePart + " (Barchart)");
+        Text t = new Text();
+        t.setText("Haplogroup occurrences " + titlePart);
+        t.setFont(Font.font(25));
+
+        this.barPlotHaplo2 = new BarPlotHaplo2(
+                t.getText(),
+                "Number of samples",
+                "Occurrences of haplogroups",
+                stage,
+                tableController,
+                tabPane,
+                logClass
+        );
+
+        //barPlotHaplo2.setStyleSheet(stage);
+        Tab tab = new Tab();
+        tab.setId("tab_haplo_barchart");
+        tab.setText("Haplogroup occurrences");
+        tab.setContent(barPlotHaplo2.getBarChart());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+
+    }
+
+    public void initGroupBarChart() throws MalformedURLException {
+        LOG.info("Visualize data: Group frequency (Barchart)");
+
+        Text t = new Text();
+        t.setText("Number of samples per group");
+        t.setFont(Font.font(25));
+
+        barChartGrouping = new BarChartGrouping(t.getText(), "# of Samples", tabPane, logClass);
+        barChartGrouping.setStyleSheet(stage);
+
+        Tab tab = new Tab();
+        tab.setId("tab_group_barchart");
+        tab.setText("Bar Chart Grouping");
+        tab.setContent(barChartGrouping.getBarChart());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+    }
+
+
+    public void initStackedBarchart(VisualizationMenu visualizationMenu) throws MalformedURLException {
+        LOG.info("Visualize data: Haplogroup frequency per group (Stacked Barchart)");
+
+        Text t = new Text();
+        t.setText("Haplogroup frequency per group");
+        t.setFont(Font.font(25));
+
+        this.stackedBar = new StackedBar(t.getText(), tabPane, visualizationMenu, chartController, tableController, this);
+        stackedBar.setStyleSheet(stage);
+        Tab tab = new Tab();
+        tab.setId("tab_stacked_bar_chart");
+        tab.setText("Haplogroup frequency per group");
+        tab.setContent(stackedBar.getSbc());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+
+    }
+
+//    private void initSunburst(){
+//        LOG.info("Visualize data: Sunburst Chart");
+//
+//        sunburstChart = new SunburstChartCreator(stage, tabPane, logClass);
+//        Tab tab = new Tab();
+//        tab.setId("tab_sunburst");
+//        tab.setText("Sunburst Chart");
+//        sunburstChart.getBorderPane().prefHeightProperty().bind(stage.heightProperty());
+//        sunburstChart.getBorderPane().prefWidthProperty().bind(stage.widthProperty());
+//        tab.setContent(sunburstChart.getBorderPane());
+//        tabPane.getTabs().add(tab);
+//        tabPane.getSelectionModel().select(tab);
+//
+//    }
+
+
+    public void initPieChart(String title) throws MalformedURLException {
+        LOG.info("Visualize data: Haplotypes in Group " + title + " (PieChart)");
+
+        Text t = new Text(title);
+        t.setFont(Font.font(25));
+
+        pieChartViz = new PieChartViz(t.getText(), tabPane, logClass);
+        pieChartViz.setStyleSheet(stage);
+        Tab tab = new Tab();
+        tab.setId("tab_piechart");
+        tab.setText("Pie Chart");
+        pieChartViz.getChart().prefHeightProperty().bind(stage.heightProperty());
+        pieChartViz.getChart().prefWidthProperty().bind(stage.widthProperty());
+        tab.setContent(pieChartViz.getChart());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+
+    }
+
+
+    public void initProfilePlot() throws MalformedURLException {
+        LOG.info("Visualize data: Haplotypes per Group (Profile Plot)");
+
+        Text t = new Text();
+        t.setText("Haplogroup profile");
+        t.setFont(Font.font(100));
+
+        profilePlot = new ProfilePlot(t.getText(), "Haplogroup", "Frequency in %", tabPane,
+                logClass, profilePlotID);
+        profilePlot.setStyleSheet(stage);
+
+        Tab tab = new Tab();
+        tab.setId("tab_profilePlot_" + profilePlotID);
+        tab.setText("Profile Plot (pp " + profilePlotID + ")");
+        tab.setContent(profilePlot.getPlot());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+        profilePlotID++;
+
+    }
+
+
+    public void initMap(){
+        LOG.info("Visualize data: Visualize all samples on map");
+
+        GeographicalMapViz geographicalMapViz = new GeographicalMapViz();
+
+        GeographicalMapController mapViewController = new GeographicalMapController(
+                mito,
+                groupController,
+                geographicalMapViz
+        );
+
+        Tab tab = new Tab();
+        tab.setId("tab_map");
+        tab.setText("Map");
+        tab.setContent(geographicalMapViz.getMapBasicPane());
+        tabPane.getTabs().add(tab);
+        tabPane.getSelectionModel().select(tab);
+
+    }
+
+
+    public void clearCharts(){
+        stackedBar = null;
+        barPlotHaplo = null;
+        tabPane.getTabs().clear();
+    }
+
+
+    public Logger getLOG() {
+        return LOG;
+    }
+
+    public MitoBenchWindow getMito() {
+        return mito;
+    }
+
+    public Stage getStage() {
+        return stage;
+    }
+
+    public Scene getScene() {
+        return scene;
+    }
+
+    public TableControllerUserBench getTableController() {
+        return tableController;
+    }
+
+    public ChartController getChartController() {
+        return chartController;
+    }
+
+    public HaplotreeController getTreeController() {
+        return treeController;
+    }
+
+    public GroupController getGroupController() {
+        return groupController;
+    }
+
+    public BarPlotHaplo getBarPlotHaplo() {
+        return barPlotHaplo;
+    }
+
+    public BarPlotHaplo2 getBarPlotHaplo2() {
+        return barPlotHaplo2;
+    }
+
+    public BarChartGrouping getBarChartGrouping() {
+        return barChartGrouping;
+    }
+
+    public StackedBar getStackedBar() {
+        return stackedBar;
+    }
+
+    public TreeView getTreeView() {
+        return treeView;
+    }
+
+    public ProfilePlot getProfilePlot() {
+        return profilePlot;
+    }
+
+    public PieChartViz getPieChartViz() {
+        return pieChartViz;
+    }
+
+    public ColorSchemeStackedBarChart getColorScheme() {
+        return colorScheme;
+    }
+
+    public TabPane getTabPane() {
+        return tabPane;
+    }
+
+    public TabPane getStatsTabpane() {
+        return statsTabpane;
+    }
+
+    public Menu getMenuGraphics() {
+        return menuGraphics;
+    }
+
+    public HashMap<String, List<String>> getTreeMap_path_to_root() {
+        return treeMap_path_to_root;
+    }
+
+    public int getProfilePlotID() {
+        return profilePlotID;
+    }
+
+    public TreeItem<String> getTree_root() {
+        return tree_root;
+    }
+
+    public LogClass getLogClass() {
+        return logClass;
+    }
+}