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import java.awt.Desktop;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.logging.Level;
import java.util.logging.Logger;
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.geometry.Insets;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.ComboBox;
import javafx.scene.control.TextField;
import javafx.scene.layout.GridPane;
import javafx.scene.layout.HBox;
import javafx.scene.layout.StackPane;
import javafx.stage.Stage;

/**
 *
 * @author Devin
 */
public class findSeqs extends Application {

    private Desktop desktop = Desktop.getDesktop();
 
	/**
         * This method was written by CC and modified by DJC, based upon code from StackOverflow user Kip.
         * It takes a string and writes it to a specified file, appending said file.
         * The purpose of this method is to save information and results as they are generated, reducing memory load.
         * 
         * @param content The string to be written
         * @param file The destination file for the string output
         */
	private void writeFile(String content, File file){
                try (FileWriter fw = new FileWriter(file, true)) {
                    fw.write(content);//

                } catch (IOException ex) 
                    {
		     Logger.getLogger(findSeqs.class.getName()).log(Level.SEVERE, null, ex);
		    }
		         
            }

    /**
     * A timestamp, used for generating unique file IDs
     */			 
    final long timeUnique = System.currentTimeMillis();
            
        
    @Override
    public void start(Stage primaryStage) {
        
        final GridPane inputGridPane = new GridPane();		
        
        final ComboBox<String> comboBox1;
        comboBox1 = new ComboBox<String>();
        comboBox1.getItems().addAll("nuccore", "protein", "gene");
        comboBox1.setMinWidth(100);
        comboBox1.setMinHeight(25);
        comboBox1.setValue("protein");
        
        HBox comboBoxSection1;
                comboBoxSection1 = new HBox();
                comboBoxSection1.setSpacing(10);
                comboBoxSection1.getChildren().addAll(comboBox1);        

        TextField txtField1;
        txtField1 = new TextField();
        txtField1.setText("esearch.fcgi? term");
        txtField1.setMinWidth(200);

        TextField txtField2;
        txtField2 = new TextField();
        txtField2.setText("number to retrieve");
        txtField2.setMinWidth(200);
        
        Button btn = new Button();
        btn.setText("Grab sequences");
        btn.setOnAction(new EventHandler<ActionEvent>() {
            
            @Override
              public void handle(ActionEvent e2) {
                System.out.println("Hello World!");
                System.out.println(txtField1.getText());
                
                                        /**
                                         * E-utility URL, built from nucleotide accession, start, and stop values.
                                        */   
                                        URL url;

                                        ArrayList<String> retRecords = new ArrayList<String>();
                                        
                                                try {
                                                    // get URL content

                                                    String a = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=" + comboBox1.getValue() + "&term=" + txtField1.getText() + "&retmax=" + txtField2.getText();
                                                    
                                                    System.out.println("URL: " + a);
                                                    url = new URL(a);
                                                    URLConnection conn = url.openConnection();

                                                    // open the stream and put it into BufferedReader
                                                    BufferedReader br = new BufferedReader(
                                                                       new InputStreamReader(conn.getInputStream()));

                                                    String line;
                                                    while ((line = br.readLine()) != null) {
                           
                                                    if(line.contains("<Id>"))
                                                        {
                                                            line = line.replaceAll("<Id>", "");
                                                            line = line.replaceAll("</Id>", "");
                                                            System.out.println(line);
                                                            
                                                            retRecords.add(line);
                                                        }                                                        
                                                        
                                                    }
                                                    br.close();

                                                    System.out.println("Done");

                                                } catch (MalformedURLException e) {
                                                    e.printStackTrace();
                                                } catch (IOException e) {
                                                    e.printStackTrace();
                                                }
                                                
                                                System.out.println("First Block completed");
                                                
                                                String b = "";
                                                    for (int i = 0; i < retRecords.size(); i++)
                                                    {
                                                        b += retRecords.get(i);
                                                        if (i + 1 < retRecords.size())
                                                        {
                                                            b+= ",";
                                                        }
                                                    }
                                                    
                                                File file1 = new File("output.txt");
                                                writeFile(b, file1);
                                                
            }
        });

        GridPane.setConstraints(txtField1, 0, 0);
        GridPane.setConstraints(txtField2, 0, 1);        
        GridPane.setConstraints(comboBox1, 0, 2);
        GridPane.setConstraints(btn, 0, 3);        
        inputGridPane.setHgap(50);
        inputGridPane.setVgap(50);
        inputGridPane.getChildren().addAll(txtField1, txtField2, comboBox1, btn);
        
        
        StackPane root = new StackPane();
        root.getChildren().add(inputGridPane);      
        
        Scene scene = new Scene(root, 200, 250);
        
        primaryStage.setTitle("Hello World!");
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        launch(args);
    }
    
}