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各種コントローラクラスの作成
● FXMLファイルからイベントハンドルを受取り、メインクラスと結びつけます。

RootController.java 
package sample.controller;

import javafx.event.ActionEvent;
import javafx.scene.control.Alert;
  
public class RootController {
 
    public void siteExit(ActionEvent actionEvent) {
        System.exit(0);
    }
  
    public void siteAbout(ActionEvent actionEvent) {
        Alert alert = new Alert (Alert.AlertType.INFORMATION);
        alert.setTitle("JavaFXSampleFxmlApp");
        alert.setHeaderText("FXMLの切り換えを自由に操作");
        alert.setContentText("データベース操作を目的に応じて画面に表示し、データの処理を視覚的に容易にした。");
        alert.show();
    }
     
    public void siteVersion(ActionEvent actionEvent) {
        Alert alert = new Alert (Alert.AlertType.INFORMATION);
        alert.setTitle("バージョン情報");
        alert.setHeaderText("JavaFXSampleFxmlApp 1.0");
        alert.setContentText("");
        alert.show();
    }
}

IndexController.java 
package sample.controller;

import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import sample.view.Main;

// call Mainクラス
public class IndexController {

  @FXML
  public void toCreate(ActionEvent actionEvent) {   
    Main.getInstance().create();
  }
  @FXML
  public void toSearch(ActionEvent actionEvent) {   
    Main.getInstance().search();
  }  
  @FXML
  public void selectAllView(ActionEvent actionEvent) {                       
      Main.getInstance().selectAllView();
  } 
}

CreateController.java 
package sample.controller;

import java.sql.SQLException;
import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.control.Label;
import javafx.scene.control.TextArea;
import javafx.scene.control.TextField;
import sample.view.Main;
import sample.DBJ.SampleDBJ;

public class CreateController {  
  @FXML
  private TextField nameCreate;
  @FXML
  private TextField addressCreate;
  @FXML
  private TextArea memoCreate;
  @FXML
  private Label createSuccsess;
  
  public void linkSave(ActionEvent actionEvent) {
    String insName = nameCreate.getText();
    String insAddress = addressCreate.getText();
    String insMemo = memoCreate.getText();
    if (insName.isEmpty()) {
      createSuccsess.setText("Name is required input！.");
    } else {
       try {
         SampleDBJ.insertData(insName,insAddress,insMemo);
         createSuccsess.setText(null);
         createSuccsess.setText("Success.");
       } catch (SQLException | ClassNotFoundException ex) {
           Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
       }
    }
  }

  // Show Alldata
  public void linkShowAll(ActionEvent actionEvent) {
      Main.getInstance().selectAllView(); // call Mainクラス
  }

  // Index
  public void linkIndex(ActionEvent actionEvent) {
      Main.getInstance().indexView(); // call Mainクラス
  }
}

SearchController.java 
package sample.controller;

import java.sql.SQLException;
import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.control.Hyperlink;
import javafx.scene.control.Label;
import javafx.scene.control.TableCell;
import javafx.scene.control.TableColumn;
import javafx.scene.control.TableView;
import javafx.scene.control.TextField;
import javafx.util.Callback;
import sample.view.Main;
import sample.Model.SampleModel;
import sample.DBJ.SampleDBJ;

public class SearchController {    
  
  @FXML
  private TableColumn<SampleModel, Integer> idCol;
  @FXML
  private TableColumn<SampleModel, String> nameCol;
  @FXML
  private TableColumn<SampleModel, String> addressCol;
  @FXML
  private TableColumn<SampleModel, String> memoCol;
  @FXML
  private TableColumn<SampleModel, String> created_atCol;
  @FXML
  private TableColumn<SampleModel, String> updated_atCol; 
  @FXML
  private TextField searchName;
  @FXML
  private Label searchError;
  @FXML
  private TableView<SampleModel> table;
  private ObservableList<SampleModel> data;
  
  // 初期化
  public void initialize() {                                 
    /**
    * カラム
    */
    idCol.setCellValueFactory(cellData -> cellData.getValue().IdProperty().asObject());
    nameCol.setCellValueFactory(cellData -> cellData.getValue().NameProperty());
    addressCol.setCellValueFactory(cellData -> cellData.getValue().AddressProperty());
    memoCol.setCellValueFactory(cellData -> cellData.getValue().MemoProperty());
    created_atCol.setCellValueFactory(cellData -> cellData.getValue().Created_atProperty());
    updated_atCol.setCellValueFactory(cellData -> cellData.getValue().Updated_atProperty());          

    /**
    *カラム追加-Hyperlink
    */
    editLink();
    delLink();       
  }  
  
  // nameSearchAction
  public void nameSearchAction(ActionEvent actionEvent) throws SQLException {
    String name = searchName.getText();
    if(name.isEmpty()) {
       searchError.setText("Please input ！.");
       table.setVisible(false);
    } else {
      try {
        searchError.setText(null);
        data = SampleDBJ.searchName(name); // SampleDBJクラス
        table.setItems(data);
        table.setVisible(true); 
      } catch (ClassNotFoundException ex) {
         System.out.println("data not！.");  
      }
    }
  }

　　// Select AllView
  public void toSelectAllView(ActionEvent actionEvent) {
    Main.getInstance().selectAllView();
  }  

  // Index
  public void linkIndex(ActionEvent actionEvent) {
    Main.getInstance().indexView();
  }  
  
  // Edit Link
  private void editLink() {
    TableColumn<SampleModel, Void> edit = new TableColumn("Edit");
    edit.getStyleClass().add("table-Col-Edit");
    Callback<TableColumn<SampleModel, Void>, TableCell<SampleModel, Void>> cellFactory;
    cellFactory = (final TableColumn<SampleModel, Void> param) -> {
      final TableCell<SampleModel, Void> editCell;
      editCell = new TableCell<SampleModel, Void>() {
        private final Hyperlink editLink = new Hyperlink("edit");
        { editLink.getStyleClass().add("editlink");
           editLink.setOnAction((ActionEvent actionEvent) -> {
             // TableViewインスタンスから指定されたインデックスのアイテムの値を取得             
             SampleModel editItems = getTableView().getItems().get(getIndex());
             { Main.getInstance().edit(editItems); } // call Mainクラス
           });
        }                 
        @Override
        public void updateItem(Void item, boolean empty) {
          super.updateItem(item, empty);
          if (!empty) {
            setGraphic(editLink);
          } else {
            setGraphic(null);
          }
        }
      };
        return editCell;
    };
      edit.setCellFactory(cellFactory);
      table.getColumns().add(edit);
  }

  // Delete Link
  private void delLink() {
    TableColumn<SampleModel, Void> del = new TableColumn("Del");
    del.getStyleClass().add("table-Col-Del");  
    Callback<TableColumn<SampleModel, Void>, TableCell<SampleModel, Void>> cellFactory;
    cellFactory = (final TableColumn<SampleModel, Void> param) -> {
      final TableCell<SampleModel, Void> delCell;
      delCell = new TableCell<SampleModel, Void>() {          
        private final Hyperlink delLink = new Hyperlink("del");
        { delLink.getStyleClass().add("dellink");
           delLink.setOnAction((ActionEvent actionEvent)-> {
             SampleModel delItems = getTableView().getItems().get(getIndex());
             int id = delItems.getId(); // getId() - by SampleModelクラス
             try {
               boolean delJudg = SampleDBJ.dataDelete (id); // by SampleDBJクラス
               if (delJudg) {
                 System.out.println("Delete Success.");
               } else {
                 System.out.println("Delete Error！.");
               }
             } catch (SQLException | ClassNotFoundException ex) {
                Logger.getLogger(SelectAllController.class.getName()).log(Level.SEVERE, null, ex);
             }
           });
        };
        @Override
        public void updateItem(Void item, boolean empty) {
          super.updateItem(item, empty);
          if (!empty) {
            setGraphic(delLink);
          } else {
            setGraphic(null);
          }
        }
      };
        return delCell;
    };
      del.setCellFactory(cellFactory);
      table.getColumns().add(del);
  }
}

SelectAllController.java 
package sample.controller;

import java.sql.SQLException;
import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.control.Hyperlink;
import javafx.scene.control.Pagination;
import javafx.scene.control.TableCell;
import javafx.scene.control.TableColumn;
import javafx.scene.control.TableView;
import javafx.scene.layout.AnchorPane;
import javafx.util.Callback;
import sample.view.Main;
import sample.Model.SampleModel;
import sample.DBJ.SampleDBJ;

public class SelectAllController {    
  
  @FXML
  private TableColumn<SampleModel, Integer> idCol;
  @FXML
  private TableColumn<SampleModel, String> nameCol;
  @FXML
  private TableColumn<SampleModel, String> addressCol;
  @FXML
  private TableColumn<SampleModel, String> memoCol;
  @FXML
  private TableColumn<SampleModel, String> created_atCol;
  @FXML
  private TableColumn<SampleModel, String> updated_atCol; 
  @FXML
  private AnchorPane anchor; 
  @FXML
  private Pagination pager; 
  @FXML
  private TableView<SampleModel> table;
  private ObservableList<SampleModel> data;

  private static final int ROWS_PER_PAGE = 5; // レコード数/1ページ当たり  
  
  // ページ区切りコントロール作成とページ・ファクトリの実装
  public AnchorPane dataViewPage() {  
    pager = new Pagination( setPages(), 0 );
    pager.setPageFactory((Integer pageIndex) -> createPage(pageIndex));
    anchor.getChildren().add(pager);   
    AnchorPane.setTopAnchor(pager, 170.0);
    AnchorPane.setRightAnchor(pager, 20.0);
    AnchorPane.setBottomAnchor(pager, 160.0);
    AnchorPane.setLeftAnchor(pager, 20.0);
    return anchor;
  }

  // ページ数
  public int setPages() { 
    int pages = 1;
    if (data.size() % ROWS_PER_PAGE == 0) {
        pages = data.size() / ROWS_PER_PAGE;
    } else if (data.size() > ROWS_PER_PAGE) {
        pages = data.size() / ROWS_PER_PAGE + 1;
    }
    return pages;
  }  

  // オブジェクトtableにデータ・モデルとページを関連付け
  private TableView<SampleModel> createPage(Integer pageIndex) {    
    int fromIndex;
    fromIndex = 0;
    int toIndex;
    toIndex = 0;      
    fromIndex = pageIndex * ROWS_PER_PAGE;
    toIndex = Math.min(fromIndex + ROWS_PER_PAGE, data.size());
    // ListオブジェクトのtableにsetItemsでデータをセット
    table.setItems(FXCollections.observableArrayList(data.subList(fromIndex, toIndex)));       
    // セル高調整
    table.setFixedCellSize(34);
    return table;
  }   

  // 初期化  
  public void initialize() {                                 
    /**
    * カラム
    */
    idCol.setCellValueFactory(cellData -> cellData.getValue().IdProperty().asObject());
    nameCol.setCellValueFactory(cellData -> cellData.getValue().NameProperty());
    addressCol.setCellValueFactory(cellData -> cellData.getValue().AddressProperty());
    memoCol.setCellValueFactory(cellData -> cellData.getValue().MemoProperty());
    created_atCol.setCellValueFactory(cellData -> cellData.getValue().Created_atProperty());
    updated_atCol.setCellValueFactory(cellData -> cellData.getValue().Updated_atProperty());          

    /**
    * カラム追加 - Hyperlink
    */
    seeLink();
    editLink();
    delLink();       

    /**
    * 起動時全データ表示
    */
    allDataView();
  }

  // Create
  public void linkCreate(ActionEvent actionEvent) {
    Main.getInstance().create();
  }  

  // Search
  public void linkSearch(ActionEvent actionEvent) {
    Main.getInstance().search();
  }  
  
  // Index
  public void linkIndex(ActionEvent actionEvent) {
    Main.getInstance().indexView();
  }  
  
  // call DB
  public void allDataView() {    
    try {                     
      data = SampleDBJ.searchAllData();       
      getAllData(data);       
    } catch (SQLException | ClassNotFoundException ex) {
      Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
    }
  }
  
  // after delete 
  public void searchAllReview() {          
    pager.getStyleClass().add("deletepagination"); // css-Initialize Pagination 
    try {                     
      data = SampleDBJ.searchAllData();       
      getAllData(data);       
    } catch (SQLException | ClassNotFoundException ex) {
      Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
    }
  }        
  
  // call AllData
  private void getAllData(ObservableList<SampleModel> data) {               
    // DBデータ有無の判断
    if (data.isEmpty()) {
        System.out.println("data not！.");
    } else {      
        dataViewPage();
    }
  }

  // See Link
  private void seeLink() {
    TableColumn<SampleModel, Void> see = new TableColumn("See");
    see.getStyleClass().add("table-Col-See");
    Callback<TableColumn<SampleModel, Void>, TableCell<SampleModel, Void>> cellFactory;
    cellFactory = (final TableColumn<SampleModel, Void> param) -> {
      final TableCell<SampleModel, Void> editCell;
      editCell = new TableCell<SampleModel, Void>() {
        private final Hyperlink seeLink = new Hyperlink("see");
        { seeLink.getStyleClass().add("seelink");
          seeLink.setOnAction((ActionEvent actionEvent) -> {
            SampleModel seeItems = getTableView().getItems().get(getIndex());
            { Main.getInstance().see(seeItems); } // call Mainクラス
          });
        }                 
        @Override
        public void updateItem(Void item, boolean empty) {
          super.updateItem(item, empty);
          if (!empty) {
            setGraphic(seeLink);
          } else {
             setGraphic(null);
          }
        }
      };
        return editCell;
    };
      see.setCellFactory(cellFactory);
      table.getColumns().add(see);
  }  
  
  // Edit Link
  private void editLink() {
    TableColumn<SampleModel, Void> edit = new TableColumn("Edit");
    edit.getStyleClass().add("table-Col-Edit");
    Callback<TableColumn<SampleModel, Void>, TableCell<SampleModel, Void>> cellFactory;
    cellFactory = (final TableColumn<SampleModel, Void> param) -> {
      final TableCell<SampleModel, Void> editCell;
      editCell = new TableCell<SampleModel, Void>() {
        private final Hyperlink editLink = new Hyperlink("edit");
        { editLink.getStyleClass().add("editlink");
          editLink.setOnAction((ActionEvent actionEvent) -> {
            SampleModel editItems = getTableView().getItems().get(getIndex());
            { Main.getInstance().edit(editItems); } // call Mainクラス
          });
        }                 
        @Override
        public void updateItem(Void item, boolean empty) {
          super.updateItem(item, empty);
          if (!empty) {
            setGraphic(editLink);
          } else {
            setGraphic(null);
          }
        }
      };
        return editCell;
    };
      edit.setCellFactory(cellFactory);
      table.getColumns().add(edit);
  }

  // Delete Link
  private void delLink() {
    TableColumn<SampleModel, Void> del = new TableColumn("Del");
    del.getStyleClass().add("table-Col-Del");  
    Callback<TableColumn<SampleModel, Void>, TableCell<SampleModel, Void>> cellFactory;
    cellFactory = (final TableColumn<SampleModel, Void> param) -> {
      final TableCell<SampleModel, Void> delCell;
      delCell = new TableCell<SampleModel, Void>() {          
        private final Hyperlink delLink = new Hyperlink("del");
        { delLink.getStyleClass().add("dellink");
          delLink.setOnAction((ActionEvent actionEvent)-> {
            SampleModel delItems = getTableView().getItems().get(getIndex());
            int id = delItems.getId(); // getId() - by SampleModelクラス
            try {
              boolean delJudg = SampleDBJ.dataDelete (id); // by SampleDBJクラス
              if (delJudg) {
                searchAllReview();
              } else {
                System.out.println("Delete Error！.");
              }
            } catch (SQLException | ClassNotFoundException ex) {
               Logger.getLogger(SelectAllController.class.getName()).log(Level.SEVERE, null, ex);
            }
          });
        };
        @Override
        public void updateItem(Void item, boolean empty) {
          super.updateItem(item, empty);
          if (!empty) {
            setGraphic(delLink);
          } else {
            setGraphic(null);
          }
        }
      };
        return delCell;
    };
      del.setCellFactory(cellFactory);
      table.getColumns().add(del);
  }
}
package sample.controller;

import java.sql.SQLException;
import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.control.Label;
import javafx.scene.control.TextArea;
import javafx.scene.control.TextField;
import sample.DBJ.SampleDBJ;
import sample.Model.SampleModel;
import sample.view.Main;

public class EditController {

  @FXML
  private Label succsess;
  @FXML
  private TextField idEdit;
  @FXML
  private TextField nameEdit;
  @FXML
  private TextField addressEdit;
  @FXML
  private TextArea memoEdit;
 
  // Edit TextField
  /**
  * @param editItems
  */
  public void editItem(SampleModel editItems) {
    idEdit.setText(Integer.toString(editItems.getId()));
    nameEdit.setText(editItems.getName());
    addressEdit.setText(editItems.getAddress());
    memoEdit.setText(editItems.getMemo());
  }  
  
  // Edit Save
  public void linkSave(ActionEvent actionEvent) throws SQLException, ClassNotFoundException {
      String id_edit = idEdit.getText();
      String address_edit = addressEdit.getText();
      String memo_edit = memoEdit.getText();
      boolean editJudg = SampleDBJ.dataUpdate(id_edit, address_edit, memo_edit);
      if (editJudg) {
        succsess.setText("Succsess.");
      } else {
        succsess.setText("Update Error！.");
      }
  }

  // Show Alldata
  public void linkShowAll(ActionEvent actionEvent) {
    Main.getInstance().selectAllView();
  }

  // Index
  public void linkIndex(ActionEvent actionEvent) {
    Main.getInstance().indexView();
  }
}

SeeController.java 
package sample.controller;

import javafx.event.ActionEvent;
import javafx.fxml.FXML;
import javafx.scene.control.Label;
import javafx.scene.control.TextArea;
import javafx.scene.control.TextField;
import sample.Model.SampleModel;
import sample.view.Main;

public class SeeController {

  @FXML
  private Label idlabel;
  @FXML
  private Label namelabel;
  @FXML
  private TextField addressTxtFld;
  @FXML
  private TextArea memoTxtArea;
   
  // See Item
  /**
  * @param seeItems
  */
  public void seeItem(SampleModel seeItems) {
    idlabel.setText(Integer.toString(seeItems.getId()));
    namelabel.setText(seeItems.getName());
    addressTxtFld.setText(seeItems.getAddress());
    memoTxtArea.setText(seeItems.getMemo());
  }

  // Show Alldata
  public void linkShowAll(ActionEvent actionEvent) {
    Main.getInstance().selectAllView();
  }

  // Index
  public void linkIndex(ActionEvent actionEvent) {
    Main.getInstance().indexView();
  }
}

以上、Fxmlファイルの役割毎にControllerクラスを作成しました。
効率よく一つのControllerクラスにまとめればよいが、かえって複雑かつ膨大な処理を書くことになるかと思います。
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