ReferenceManager.cs

using CellexalVR.AnalysisLogic;
using CellexalVR.AnalysisLogic.H5reader;
using CellexalVR.AnalysisObjects;
using CellexalVR.DesktopUI;
using CellexalVR.Filters;
using CellexalVR.Interaction;
using CellexalVR.Menu;
using CellexalVR.Menu.SubMenus;
using CellexalVR.Multiuser;
using CellexalVR.PDFViewer;
using CellexalVR.SceneObjects;
using CellexalVR.Spatial;
using CellexalVR.Tools;
using CellexalVR.Tutorial;
using SQLiter;
using TMPro;
using UnityEditor;
using UnityEngine;
using UnityEngine.XR.Interaction.Toolkit;

namespace CellexalVR.General
{
    /// <summary>
    /// This class just holds a lot of references to other scripts and gameobjects so they won't clutter the inspector so much.
    /// </summary>
    public class ReferenceManager : MonoBehaviour
    {
        public static ReferenceManager instance;

        #region Controller things
        [Header("Controller things")]
        public ActionBasedController rightController;
        public ActionBasedController leftController;
        public GameObject rightControllerScriptAlias;
        public GameObject leftControllerScriptAlias;
        public ControllerModelSwitcher controllerModelSwitcher;
        public GameObject headset;
        public BoxCollider controllerMenuCollider;
        public XRRayInteractor rightLaser;
        public XRRayInteractor leftLaser;
        public LaserPointerController laserPointerController;
        public CellexalRaycast rightRaycast;
        public CellexalRaycast leftRaycast;
        #endregion

        #region Tools
        [Header("Tools")]
        //public SelectionToolHandler selectionToolHandler;
        public SelectionToolCollider selectionToolCollider;
        public GameObject deleteTool;
        public MinimizeTool minimizeTool;
        //public GameObject helpMenu;
        public DrawTool drawTool;
        //public GameObject webBrowser;
        public CaptureScreenshot screenshotCamera;
        public GameObject teleportLaser;
        public VelocityPathTool velocityPathTool;
        #endregion

        #region Menu
        [Header("Menu")]
        public GameObject mainMenu;
        public GameObject frontButtons;
        public GameObject rightButtons;
        public GameObject backButtons;
        public GameObject leftButtons;
        public ToggleArcsSubMenu arcsSubMenu;
        public AttributeSubMenu attributeSubMenu;
        public ColorByIndexMenu indexMenu;
        public ColorByCellStatMenu cellStatMenu;
        public GraphFromMarkersMenu createFromMarkerMenu;
        public SelectionFromPreviousMenu selectionFromPreviousMenu;
        public TextMeshPro cellsEvaluatingText;
        public ColorByGeneMenu colorByGeneMenu;
        public FilterMenu filterMenu;
        public VelocitySubMenu velocitySubMenu;
        public GameObject selectionMenu;
        public FlybyMenu flybyMenu;
        public ColorPickerSubMenu colorPickerSubMenu;
        //public TextMesh currentFlashedGeneText;
        //public TextMesh frontDescription;
        //public TextMesh rightDescription;
        //public TextMesh backDescription;
        //public TextMesh leftDescription;
        public MenuRotator menuRotator;
        public MinimizedObjectHandler minimizedObjectHandler;
        public MenuToggler menuToggler;
        public MenuUnfolder menuUnfolder;
        #endregion

        #region Managers, generators and things
        [Header("Managers, generators and things")]
        public GraphManager graphManager;
        public CellManager cellManager;
        public LineBundler lineBundler;
        public SelectionManager selectionManager;
        public AnnotationManager annotationManager;
        public HeatmapGenerator heatmapGenerator;
        public NetworkGenerator networkGenerator;
        public GraphGenerator graphGenerator;
        public PointCloudGenerator pointCloudGenerator;
        public LegendManager legendManager;
        public InputFolderGenerator inputFolderGenerator;
        public LoaderController loaderController;
        public ConfigManager configManager;
        //public GameObject helperCylinder;
        public InputReader inputReader;
        // public ReportReader reportReader;
        public SQLite database;
        public LogManager logManager;
        public MultiuserMessageSender multiuserMessageSender;
        //public GameObject calculatorCluster;
        public ConsoleManager consoleManager;
        public TurnOffThoseLights turnOffThoseLights;
        public GameObject fpsCounter;
        //public DemoManager demoManager;
        public NewGraphFromMarkers newGraphFromMarkers;
        public NotificationManager notificationManager;
        public TutorialManager tutorialManager;
        public ScreenCanvas screenCanvas;
        //public GameObject helpVideoPlayer;
        public PlayVideo helpVideoManager;
        public VelocityGenerator velocityGenerator;
        public ConvexHullGenerator convexHullGenerator;
        public FilterManager filterManager;
        public ReportManager reportManager;
        public Floor floor;
        public PDFViewer.PDFMesh pdfMesh;
        public AllenReferenceBrain brainModel;
        public GraphLoader graphLoader;

        //h5reader annotator
        public H5ReaderAnnotatorScriptManager h5ReaderAnnotatorScriptManager;

        #endregion

        #region Keyboard
        [Header("Keyboards")]
        public KeyboardHandler geneKeyboard;
        public KeyboardSwitch keyboardSwitch;
        public CorrelatedGenesList correlatedGenesList;
        public PreviousSearchesList previousSearchesList;
        public AutoCompleteList autoCompleteList;
        public ColoringOptionsList coloringOptionsList;
        public KeyboardHandler folderKeyboard;
        //public KeyboardHandler webBrowserKeyboard;
        public SessionHistoryList sessionHistoryList;
        public ReferenceModelKeyboard referenceModelKeyboard;

        #endregion

        #region Filters
        [Header("Filters")]
        public GameObject filterBlockBoard;
        public KeyboardHandler filterNameKeyboard;
        public KeyboardHandler filterOperatorKeyboard;
        public KeyboardHandler filterValueKeyboard;
        public AutoCompleteList filterNameKeyboardAutoCompleteList;
        public CullingFilterManager cullingFilterManager;

        #endregion

        #region SettingsMenu
        [Header("Settings Menu")]
        public SettingsMenu settingsMenu;
        public ColorPicker colorPicker;
        #endregion

        #region Multi-user
        public GameObject spectatorRig;
        public GameObject VRRig;

        #endregion

        private void Awake()
        {
            instance = this;
        }
#if UNITY_EDITOR
        /// <summary>
        /// Attempts to set all references using <see cref="GameObject.Find(string)"/> and <see cref="GameObject.GetComponent(string)"/>.
        /// </summary>
        public void AttemptSetReferences()
        {
            // sorry about this monstrosity
            Undo.RecordObject(this, "ReferenceManager Auto-populate");

            h5ReaderAnnotatorScriptManager = GameObject.Find("H5ReaderTestObjectManager").GetComponent<H5ReaderAnnotatorScriptManager>();
            rightController = GameObject.Find("CellexalOpenXRRig/Camera Offset/RightHand Controller").GetComponent<ActionBasedController>();
            leftController = GameObject.Find("CellexalOpenXRRig/Camera Offset/LeftHand Controller").GetComponent<ActionBasedController>();
            controllerModelSwitcher = GameObject.Find("CellexalOpenXRRig").GetComponent<ControllerModelSwitcher>();

            headset = GameObject.Find("CellexalOpenXRRig/Camera Offset/Main Camera");
            controllerMenuCollider = leftController.GetComponent<BoxCollider>();
            rightLaser = rightController.GetComponentInChildren<XRRayInteractor>();
            leftLaser = leftController.GetComponentInChildren<XRRayInteractor>();
            rightRaycast = rightController.GetComponent<CellexalRaycast>();
            leftRaycast = leftController.GetComponent<CellexalRaycast>();

            selectionToolCollider = rightController.GetComponentInChildren<SelectionToolCollider>(true);
            deleteTool = rightController.GetComponentInChildren<RemovalController>(true).gameObject;
            minimizeTool = rightController.GetComponentInChildren<MinimizeTool>(true);
            drawTool = rightController.GetComponentInChildren<DrawTool>(true);
            //webBrowser = GameObject.Find("WebBrowser");
            screenshotCamera = GameObject.Find("SnapShotCam").GetComponent<CaptureScreenshot>();
            teleportLaser = leftController.gameObject;
            velocityPathTool = rightController.GetComponentInChildren<VelocityPathTool>(true);

            mainMenu = GameObject.Find("MenuHolder/Main Menu");
            arcsSubMenu = mainMenu.GetComponentInChildren<ToggleArcsSubMenu>(true);
            attributeSubMenu = mainMenu.GetComponentInChildren<AttributeSubMenu>(true);
            indexMenu = mainMenu.GetComponentInChildren<ColorByIndexMenu>(true);
            createFromMarkerMenu = mainMenu.GetComponentInChildren<GraphFromMarkersMenu>(true);
            selectionFromPreviousMenu = mainMenu.GetComponentInChildren<SelectionFromPreviousMenu>(true);
            cellsEvaluatingText = mainMenu.transform.Find("Selection Tool Menu/Cells Evaluating Text").GetComponent<TextMeshPro>();
            colorByGeneMenu = mainMenu.GetComponentInChildren<ColorByGeneMenu>(true);
            filterMenu = mainMenu.GetComponentInChildren<FilterMenu>(true);
            velocitySubMenu = mainMenu.GetComponentInChildren<VelocitySubMenu>(true);
            selectionMenu = GameObject.Find("MenuHolder/Main Menu/Selection Tool Menu");
            flybyMenu = mainMenu.GetComponentInChildren<FlybyMenu>();
            colorPickerSubMenu = mainMenu.GetComponentInChildren<ColorPickerSubMenu>(true);
            frontButtons = GameObject.Find("MenuHolder/Main Menu/Front Buttons");
            rightButtons = GameObject.Find("MenuHolder/Main Menu/Right Buttons");
            backButtons = GameObject.Find("MenuHolder/Main Menu/Back Buttons");
            leftButtons = GameObject.Find("MenuHolder/Main Menu/Left Buttons");
            menuRotator = mainMenu.GetComponent<MenuRotator>();
            minimizedObjectHandler = GameObject.Find("MenuHolder/Main Menu/Jail").GetComponent<MinimizedObjectHandler>();
            menuToggler = leftController.GetComponent<MenuToggler>();
            menuUnfolder = mainMenu.GetComponent<MenuUnfolder>();

            GameObject managersParent = GameObject.Find("Managers");
            GameObject generatorsParent = GameObject.Find("Generators");
            graphManager = managersParent.GetComponentInChildren<GraphManager>();
            cellManager = managersParent.GetComponentInChildren<CellManager>();
            lineBundler = managersParent.GetComponentInChildren<LineBundler>();
            selectionManager = managersParent.GetComponentInChildren<SelectionManager>();
            heatmapGenerator = generatorsParent.GetComponentInChildren<HeatmapGenerator>();
            networkGenerator = generatorsParent.GetComponentInChildren<NetworkGenerator>();
            graphGenerator = generatorsParent.GetComponentInChildren<GraphGenerator>();
            pointCloudGenerator = generatorsParent.GetComponentInChildren<PointCloudGenerator>();
            legendManager = managersParent.GetComponentInChildren<LegendManager>();
            cullingFilterManager = managersParent.GetComponentInChildren<CullingFilterManager>();
            inputFolderGenerator = generatorsParent.GetComponentInChildren<InputFolderGenerator>();
            loaderController = GameObject.Find("Tron_Loader").GetComponent<LoaderController>();
            GameObject inputreader = GameObject.Find("InputReader");
            configManager = inputreader.GetComponent<ConfigManager>();
            inputReader = inputreader.GetComponent<InputReader>();
            database = GameObject.Find("SQLiter").GetComponent<SQLiter.SQLite>();
            logManager = inputreader.GetComponent<LogManager>();
            multiuserMessageSender = managersParent.GetComponentInChildren<MultiuserMessageSender>();
            consoleManager = GameObject.Find("Console").GetComponent<ConsoleManager>();
            turnOffThoseLights = GameObject.Find("Light For Testing").GetComponent<TurnOffThoseLights>();
            fpsCounter = GameObject.Find("FPS canvas");
            newGraphFromMarkers = createFromMarkerMenu.GetComponent<NewGraphFromMarkers>();
            notificationManager = managersParent.GetComponentInChildren<NotificationManager>();
            tutorialManager = managersParent.GetComponentInChildren<TutorialManager>();
            helpVideoManager = leftController.GetComponentInChildren<PlayVideo>(true);
            velocityGenerator = generatorsParent.GetComponentInChildren<VelocityGenerator>(true);
            convexHullGenerator = generatorsParent.GetComponentInChildren<ConvexHullGenerator>(true);
            filterManager = managersParent.GetComponentInChildren<FilterManager>(true);
            reportManager = managersParent.GetComponentInChildren<ReportManager>(true);
            floor = GameObject.Find("Floor").GetComponent<Floor>();
            pdfMesh = GameObject.Find("PDFViewer").GetComponentInChildren<PDFMesh>();
            brainModel = GameObject.Find("BrainParent").GetComponent<AllenReferenceBrain>();

            geneKeyboard = GameObject.Find("Keyboard Setup").GetComponent<KeyboardHandler>();
            keyboardSwitch = GameObject.Find("Keyboard Setup").GetComponent<KeyboardSwitch>();
            correlatedGenesList = GameObject.Find("Keyboard Setup/Correlated Genes List").GetComponent<CorrelatedGenesList>();
            previousSearchesList = GameObject.Find("Keyboard Setup/Previous Searches List").GetComponent<PreviousSearchesList>();
            autoCompleteList = GameObject.Find("Keyboard Setup").GetComponent<AutoCompleteList>();
            coloringOptionsList = GameObject.Find("Keyboard Setup/Coloring Options List").GetComponent<ColoringOptionsList>();
            folderKeyboard = GameObject.Find("Tron_Loader/Folder Keyboard").GetComponent<KeyboardHandler>();
            //webBrowserKeyboard = GameObject.Find("WebBrowser/Web Keyboard").GetComponent<KeyboardHandler>();
            annotationManager = keyboardSwitch.GetComponent<AnnotationManager>();
            sessionHistoryList = geneKeyboard.GetComponentInChildren<SessionHistoryList>();

            GameObject filterCreator = GameObject.Find("Filter Creator");
            filterBlockBoard = filterCreator.transform.Find("Filter Block Board").gameObject;
            GameObject keyboardParent = filterBlockBoard.transform.Find("Keyboards").gameObject;
            filterNameKeyboard = keyboardParent.GetComponentInChildren<FilterNameKeyboardHandler>(true);
            filterOperatorKeyboard = keyboardParent.GetComponentInChildren<OperatorKeyboardHandler>(true);
            filterValueKeyboard = keyboardParent.GetComponentInChildren<NumericalKeyboardHandler>(true);
            filterNameKeyboardAutoCompleteList = filterNameKeyboard.gameObject.GetComponentInChildren<AutoCompleteList>(true);
            referenceModelKeyboard = brainModel.GetComponentInChildren<ReferenceModelKeyboard>(true);

            settingsMenu = GameObject.Find("Settings Menu").GetComponent<SettingsMenu>();
            colorPicker = settingsMenu.transform.Find("Color Picker/Content").GetComponent<ColorPicker>();

            spectatorRig = GameObject.Find("SpectatorRig");
            VRRig = GameObject.Find("CellexalOpenXRRig");

            UnityEditor.PrefabUtility.ApplyPrefabInstance(gameObject, UnityEditor.InteractionMode.AutomatedAction);
            UnityEditor.PrefabUtility.SaveAsPrefabAssetAndConnect(gameObject, "Assets/Prefabs/Environment/InputReader.prefab", UnityEditor.InteractionMode.AutomatedAction);
        }
#endif
    }

#if UNITY_EDITOR
    [UnityEditor.CustomEditor(typeof(ReferenceManager))]
    public class ReferenceManagerEditor : UnityEditor.Editor
    {
        private ReferenceManager instance;

        void OnEnable()
        {
            instance = (ReferenceManager)target;
        }

        public override void OnInspectorGUI()
        {
            if (GUILayout.Button("Auto-populate references"))
            {
                instance.AttemptSetReferences();
                serializedObject.Update();
                serializedObject.ApplyModifiedProperties();
            }
            DrawDefaultInspector();
        }

        public void SaveFields()
        {
            serializedObject.Update();
            serializedObject.ApplyModifiedProperties();
        }

    }
#endif
}