Mfind_script.txt

package biomarker1;
/*
a Fastfile class for reading
*/

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;

public class FastaFileConsole {                                                 //a fasta file reader

    ArrayList<Secuencia> secuencias;

    public void use(String path) {
        ArchivoFasta af = new ArchivoFasta();
        this.secuencias = af.AbrirArchivo(path);                                //stablish the path for file read
        int t = af.Tamaño();
        System.out.println("Número de secuencias: " + t);
    }

    public ArrayList armaSeqs() {
        ArrayList seqs = new ArrayList();
        for (int x = 0; x < secuencias.size(); x++) {
            seqs.add((String) secuencias.get(x)._secuencia);                    //build an arrayList with the sequences
        }
        return seqs;
    }

    public ArrayList armaNames() {                                              //build an arrayList with the sequences names
        ArrayList names = new ArrayList();
        for (int x = 0; x < secuencias.size(); x++) {
            names.add((String) secuencias.get(x)._nombre);
        }
        return names;
    }

    public static class Secuencia {

        public String _nombre;
        public String _secuencia;
    }

    public static class ArchivoFasta {

        public ArrayList<Secuencia> secuencias;

        public ArrayList<Secuencia> AbrirArchivo(String ruta) {
            secuencias = new ArrayList<Secuencia>();
            int numero = 1;
            try {
                BufferedReader in = new BufferedReader(new FileReader(ruta));
                String line = null;
                while ((line = in.readLine()) != null) {                        //read the file while there is still a line left
                    int n = line.length();
                    if (n > 0) {
                        boolean i = line.startsWith(">");
                        if (i) {
                            Secuencia _s = new Secuencia();
                            _s._nombre = line;
                            secuencias.add(_s);
                        } else {
                            if (secuencias.get(secuencias.size() - 1)._secuencia == null) {
                                secuencias.get(secuencias.size() - 1)._secuencia = line;
                            } else {
                                secuencias.get(secuencias.size() - 1)._secuencia += line;
                            }
                        }
                    }
                }
                in.close();
            } catch (IOException ex) {
                System.out.println(numero);
                System.out.println(ex.getMessage());
            }
            return secuencias;
        }

        public Secuencia BuscarCadena(int n) {
            if (n < Tamaño()) {                                                 //returns a given sequence with its index number
                return secuencias.get(n);
            } else {
                return null;
            }
        }

        public int Tamaño() {
            return secuencias.size();
        }
    }
}




package biomarker1;

/*
 * Paralell process for microsatellite search
 */


import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.logging.Level;
import java.util.logging.Logger;

public class goParal {

    ArrayList Respaldo = new ArrayList();

    public void primerCorrida(int inic, int finl, int filtro, String subseq, String path) throws InstantiationException, ClassNotFoundException, IllegalAccessException {
        ArrayList seqs = new ArrayList();
        ArrayList workers = new ArrayList();
        ArrayList names = new ArrayList();
        FastaFileConsole FR = new FastaFileConsole();
        panel panel = new panel();
        panel.filtro = filtro;
        panel.subseq = subseq;
        panel.tamanio_final = finl;
        panel.tamanio_inicial = inic;
        panel.path = path;
        panel.actualiza();
        System.out.println(panel.path);

        
        FR.use(panel.path);
        seqs = FR.armaSeqs();
        names = FR.armaNames();

        this.Respaldo = (ArrayList) seqs.clone();

        names.add(">MicroSat");
        final String name1 = (String) names.get(0);                             //saves the first sequence as the problem sequence
        final String S1 = (String) seqs.get(0);
        seqs.remove(0);
        names.remove(0);
        panel.seqs = seqs;
        panel.names = names;
        String SubSeqS1 = "";
        int rangooffsetA = inic;
        int rangooffsetB = finl;
        worker wk1 = new worker();                                              //the parallel readers are named workers
        worker wk2 = new worker();
        ArrayList record = new ArrayList();

        for (int i = rangooffsetA; i <= rangooffsetB; i++) {
            int offset = i;
            int indxI = 0;
            int indxF = indxI + offset;
            System.out.println("longitud actual: " + offset);                   //stablish the microsatellite length 
            int contador = 0;
            Class miclase = Class.forName("biomarker1.worker");
            printer printer = new printer();
            while (indxF <= S1.length()) {
                int c = 0;//**
                while (seqs.size() > 0) {
                    System.out.println("seqs size " + seqs.size());
                    if (indxF <= S1.length()) {
                        SubSeqS1 = S1.substring(indxI, indxF);
                        String sTextoBuscado = SubSeqS1;
                        wk1.setup(sTextoBuscado, (String) seqs.get(seqs.size() - 1), seqs.size() - 1, printer);
                        seqs.remove(seqs.size() - 1);
                        wk2.setup(sTextoBuscado, (String) seqs.get(seqs.size() - 1), seqs.size() - 1, printer);
                        seqs.remove(seqs.size() - 1);
                        wk1.start();                                            //start the work
                        wk2.start();
                        try {
                            wk2.join();
                            wk1.join();
                        } catch (InterruptedException ex) {
                            Logger.getLogger(goParal.class.getName()).log(Level.SEVERE, null, ex);
                        }
                        wk1 = (worker) miclase.newInstance();
                        wk2 = (worker) miclase.newInstance();

                    }

                    System.gc();
                }
                indxI++;
                indxF++;
                while (this.compruebaBusy(workers) > 0) {                       //empty
                }
                workers.clear();
            }
        }
    }

    public void otraCorrida(int inic, int finl, int filtro, String subseq, String path) throws ClassNotFoundException, InstantiationException, IllegalAccessException {
                                                                                //process for a second run
        ArrayList seqs = new ArrayList();
        ArrayList workers = new ArrayList();
        ArrayList names = new ArrayList();
        FastaFileConsole FR = new FastaFileConsole();
        panel panel = new panel();
        panel.filtro = filtro;
        panel.subseq = subseq;
        panel.tamanio_final = finl;
        panel.tamanio_inicial = inic;
        panel.path = path;
        panel.actualiza();
        System.out.println(panel.path);
        seqs = (ArrayList) this.Respaldo.clone();
        System.out.println("segunda vez!!");
        names.add(">Human");
        String name1 = (String) names.get(0);
        String S1 = (String) seqs.get(0);
        seqs.remove(0);
        names.remove(0);
        panel.seqs = seqs;
        panel.names = names;
        String SubSeqS1 = "";

        int rangooffsetA = inic;
        int rangooffsetB = finl;
        ArrayList record = new ArrayList();

        for (int i = rangooffsetA; i <= rangooffsetB; i++) {
            int offset = i;
            int indxI = 0;
            int indxF = indxI + offset;
            int contador = 0;

            String SeqTurno = null;
            Class miclase = Class.forName("biomarker1.worker");
            printer printer = new printer();

            while (indxF <= S1.length()) {
                int c = 0;//**
                while (c <= seqs.size() - 1) {
                    if (this.compruebaBusy(workers) <= 4) {
                        SeqTurno = (String) seqs.get(c);
                        if (indxF <= S1.length()) {                               //creates worker
                            SubSeqS1 = S1.substring(indxI, indxF);
                            String sTextoBuscado = SubSeqS1;
                            worker miobjeto = (worker) miclase.newInstance();
                            miobjeto.setup(sTextoBuscado, SeqTurno, c, printer);
                            miobjeto.start();
                            workers.add(miobjeto);

                            c++;
                        }
                    }
                    System.gc();
                }
                indxI++;
                indxF++;
                while (this.compruebaBusy(workers) > 0) {                       //vacía
                }
                workers.clear();
            }
        }
    }

    public int compruebaBusy(ArrayList Lista) {                                 //validation of busy readers
        Iterator iT = Lista.iterator();
        int c = 0;
        while (iT.hasNext()) {
            worker rd = new worker();
            rd = (worker) iT.next();
            if (rd.isAlive()) {
                c++;
            } else {
                iT.remove();
            }
        }
        return c;
    }
}


package biomarker1;

/**
 * MFind Sofware Rios-Willars
 * This code searches for microsatellites in a multifasta file
 * uses a sliding window and a parallel process for the search
 */

public class Inicio {

    public static void main(String[] args) {          //The begining
        panel panel = new panel();
        panel.setVisible(true);
    }
}


package biomarker1;

/*
* Process for microsatellite count on a given slide window
*/

import java.util.ArrayList;

public class motifCounter {

    ArrayList seqs;
    ArrayList names;

    motifCounter(ArrayList seqs, ArrayList names) {
        this.seqs = seqs;
        this.names = names;
    }

    public String find(String motif) {
        String sTextoBuscado = motif;
        int contador = 0;
        int numSeqTurno = 0;
        String S = "";

        for (Object seq : seqs) {
            contador = 0;
            String SeqTurno = (String) seq;
            String sTexto = SeqTurno;
            while (sTexto.contains(sTextoBuscado)) {
                sTexto = sTexto.substring(sTexto.indexOf(sTextoBuscado) + 1);
                contador++;                                                     //increment the counter while the window containes the microsatellite
            }
            System.out.println("For sequence " + names.get(numSeqTurno) + " And subsequence " + sTextoBuscado + " hit count: " + contador);
            S = S + " \n For sequence " + names.get(numSeqTurno) + " And subsequence " + sTextoBuscado + " hit count: " + contador + "\n";
            numSeqTurno++;
        }
        S = S + "--------------------------\n ";
        return S;
    }
}




package biomarker1;
/*
the graphic inteface
*/

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JFileChooser;

public class panel extends javax.swing.JFrame {

    ArrayList seqs;
    ArrayList names;
    int tamanio_inicial;
    int tamanio_final;
    int filtro;
    String subseq;
    String path;
    goParal goParal = new goParal();

    public panel() {
        initComponents();
        this.setTitle("Mfind");
    }

    @SuppressWarnings("unchecked")
    // <editor-fold defaultstate="collapsed" desc="Generated Code">                          
    private void initComponents() {

        txt_tinicial = new javax.swing.JTextField();
        jLabel1 = new javax.swing.JLabel();
        jLabel3 = new javax.swing.JLabel();
        txt_subseq = new javax.swing.JTextField();
        jLabel4 = new javax.swing.JLabel();
        txt_filtro = new javax.swing.JTextField();
        jScrollPane1 = new javax.swing.JScrollPane();
        jTextArea1 = new javax.swing.JTextArea();
        jButton1 = new javax.swing.JButton();
        btn_reporte = new javax.swing.JButton();
        jButton2 = new javax.swing.JButton();

        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);

        txt_tinicial.setText("4");
        txt_tinicial.setName(""); // NOI18N
        txt_tinicial.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                txt_tinicialActionPerformed(evt);
            }
        });

        jLabel1.setText("Size");

        jLabel3.setText("Find Microsatellites");

        txt_subseq.setText("Type a subsequence..");
        txt_subseq.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                txt_subseqActionPerformed(evt);
            }
        });

        jLabel4.setText("Count hits for this sub sequence");

        txt_filtro.setText("100");
        txt_filtro.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                txt_filtroActionPerformed(evt);
            }
        });

        jTextArea1.setColumns(20);
        jTextArea1.setRows(5);
        jTextArea1.setText("Rios-Willars 2023\n\n1- Select your Fasta File and make sure there is a microSatellite first sequence\n2- Set the microSatellite size \n3- Hit Search Button\n4- Enjoy at Documents\\\\mfind_out.csv");
        jScrollPane1.setViewportView(jTextArea1);

        jButton1.setText("Search");
        jButton1.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                jButton1ActionPerformed(evt);
            }
        });

        btn_reporte.setText("Go");
        btn_reporte.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                btn_reporteActionPerformed(evt);
            }
        });

        jButton2.setText("Select Fasta");
        jButton2.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
                jButton2ActionPerformed(evt);
            }
        });

        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
        getContentPane().setLayout(layout);
        layout.setHorizontalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
                    .addGroup(layout.createSequentialGroup()
                        .addGap(23, 23, 23)
                        .addComponent(jButton2)
                        .addGap(50, 50, 50)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(jLabel1)
                            .addComponent(txt_tinicial, javax.swing.GroupLayout.PREFERRED_SIZE, 50, javax.swing.GroupLayout.PREFERRED_SIZE))
                        .addGap(175, 175, 175)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addGroup(layout.createSequentialGroup()
                                .addGap(226, 226, 226)
                                .addComponent(jLabel4, javax.swing.GroupLayout.PREFERRED_SIZE, 0, javax.swing.GroupLayout.PREFERRED_SIZE))
                            .addGroup(layout.createSequentialGroup()
                                .addComponent(txt_filtro, javax.swing.GroupLayout.PREFERRED_SIZE, 0, javax.swing.GroupLayout.PREFERRED_SIZE)
                                .addGap(1, 1, 1)
                                .addComponent(jLabel3)
                                .addGap(18, 18, 18)
                                .addComponent(jButton1)))
                        .addGap(162, 162, 162)
                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addGroup(layout.createSequentialGroup()
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                                .addComponent(txt_subseq, javax.swing.GroupLayout.PREFERRED_SIZE, 0, javax.swing.GroupLayout.PREFERRED_SIZE)
                                .addGap(292, 292, 292))
                            .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                                .addComponent(btn_reporte, javax.swing.GroupLayout.PREFERRED_SIZE, 0, javax.swing.GroupLayout.PREFERRED_SIZE))))
                    .addGroup(javax.swing.GroupLayout.Alignment.LEADING, layout.createSequentialGroup()
                        .addContainerGap()
                        .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 1063, javax.swing.GroupLayout.PREFERRED_SIZE)))
                .addContainerGap())
        );
        layout.setVerticalGroup(
            layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(layout.createSequentialGroup()
                .addGap(34, 34, 34)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(jLabel4)
                    .addComponent(jLabel1))
                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                    .addComponent(txt_tinicial, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(txt_filtro, javax.swing.GroupLayout.PREFERRED_SIZE, 0, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(txt_subseq, javax.swing.GroupLayout.PREFERRED_SIZE, 1, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jButton1)
                    .addComponent(btn_reporte, javax.swing.GroupLayout.PREFERRED_SIZE, 2, javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addComponent(jButton2)
                    .addComponent(jLabel3))
                .addGap(29, 29, 29)
                .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 533, javax.swing.GroupLayout.PREFERRED_SIZE)
                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
        );

        pack();
    }// </editor-fold>                        
    public void publica(String s) {
        String texto = jTextArea1.getText();
        this.jTextArea1.setText(texto + s);
    }

    public void actualiza() {
        this.txt_filtro.setText(Integer.toString(this.filtro));
        this.txt_subseq.setText(this.subseq);
        this.txt_tinicial.setText(Integer.toString(this.tamanio_inicial));
    }

    private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {                                         
        if (this.path != null) {
            this.filtro = Integer.parseInt(this.txt_filtro.getText());
            this.subseq = this.txt_subseq.getText();
            this.tamanio_inicial = Integer.parseInt(this.txt_tinicial.getText());
            this.tamanio_final = this.tamanio_inicial; //Integer.parseInt(this.txt_tfinal.getText());
            if (goParal.Respaldo.size() == 0) {
                try {
                    goParal.primerCorrida(tamanio_inicial, tamanio_final, filtro, subseq, path);
                    System.out.println("Terminado -- ");
                } catch (InstantiationException ex) {
                    Logger.getLogger(panel.class.getName()).log(Level.SEVERE, null, ex);
                } catch (ClassNotFoundException ex) {
                    Logger.getLogger(panel.class.getName()).log(Level.SEVERE, null, ex);
                } catch (IllegalAccessException ex) {
                    Logger.getLogger(panel.class.getName()).log(Level.SEVERE, null, ex);
                }
            } else {
                try {
                    goParal.otraCorrida(tamanio_inicial, tamanio_final, filtro, subseq, path);
                    System.out.println("Terminado -- ");
                } catch (InstantiationException ex) {
                    Logger.getLogger(panel.class.getName()).log(Level.SEVERE, null, ex);
                } catch (ClassNotFoundException ex) {
                    Logger.getLogger(panel.class.getName()).log(Level.SEVERE, null, ex);
                } catch (IllegalAccessException ex) {
                    Logger.getLogger(panel.class.getName()).log(Level.SEVERE, null, ex);
                }
            }

        } else
            this.jTextArea1.setText("Select you fasta file!");
    }                                        

    private void txt_tinicialActionPerformed(java.awt.event.ActionEvent evt) {                                             
        // TODO add your handling code here:
    }                                            

    private void txt_subseqActionPerformed(java.awt.event.ActionEvent evt) {                                           
        // TODO add your handling code here:
    }                                          

    private void btn_reporteActionPerformed(java.awt.event.ActionEvent evt) {                                            
        if (!"Type a subsequence..".equals(this.txt_subseq.getText()) && !"What are you searching for?".equals(this.txt_subseq.getText()) && this.path != null) {
            motifCounter mC = new motifCounter(seqs, names);
            this.jTextArea1.setText(this.jTextArea1.getText() + " " + mC.find(this.txt_subseq.getText()));
        } else
            this.txt_subseq.setText("What are you searching for?");
    }                                           

    private void jButton2ActionPerformed(java.awt.event.ActionEvent evt) {                                         
        JFileChooser abrirArchivo;
        abrirArchivo = new JFileChooser();
        abrirArchivo.showOpenDialog(this);
        File f = abrirArchivo.getSelectedFile();
        this.jTextArea1.setText(f.getAbsolutePath());
        this.path = f.getAbsolutePath();
    }                                        

    private void txt_filtroActionPerformed(java.awt.event.ActionEvent evt) {                                           
    }                                          
    public static void main(String args[]) {

        java.awt.EventQueue.invokeLater(new Runnable() {
            public void run() {
                new panel().setVisible(true);
            }
        });
    }

    // Variables declaration - do not modify                     
    private javax.swing.JButton btn_reporte;
    private javax.swing.JButton jButton1;
    private javax.swing.JButton jButton2;
    private javax.swing.JLabel jLabel1;
    private javax.swing.JLabel jLabel3;
    private javax.swing.JLabel jLabel4;
    private javax.swing.JScrollPane jScrollPane1;
    private javax.swing.JTextArea jTextArea1;
    private javax.swing.JTextField txt_filtro;
    private javax.swing.JTextField txt_subseq;
    private javax.swing.JTextField txt_tinicial;
    // End of variables declaration                   
}




package biomarker1;
/*
this class builds a csv file with the microsatellite findings
*/

import java.io.FileWriter;
import java.io.PrintWriter;

public class printer {

    boolean busy;

    public void print(String line) {
        busy = true;
        FileWriter fichero = null;
        PrintWriter pw = null;
        try {
            fichero = new FileWriter("C:\\Users\\ernes\\OneDrive\\Documents\\mfind_out.csv", true);  //change the destination if you like. Create it first!!
            pw = new PrintWriter(fichero);
            pw.println(line);
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            try {
                if (null != fichero) {
                    fichero.close();
                }
            } catch (Exception e2) {
                e2.printStackTrace();
            }
            busy = false;
        }
    }
}




package biomarker1;
/*
the class for the parallel reader
*/

import java.io.IOException;
import java.io.RandomAccessFile;
import java.util.logging.Level;
import java.util.logging.Logger;

public class reader extends Thread {

    String S;
    public RandomAccessFile fichero = null;
    int numLines;
    boolean busy;

    public void setup(String archa) throws IOException {
        this.fichero = new RandomAccessFile(archa, "r");
    }

    @Override
    public void run() {                                                         // this is the process that runs in parallel threads
        this.busy = true;
        try {
            fichero.seek(0);
        } catch (IOException ex) {
            Logger.getLogger(reader.class.getName()).log(Level.SEVERE, null, ex);
        }
        String cadena = null;
        try {
            cadena = fichero.readLine();
        } catch (IOException ex) {
            Logger.getLogger(reader.class.getName()).log(Level.SEVERE, null, ex);
        }

        int c = 0;
        while (cadena != null) {
            this.S += cadena;
            c++;
            try {
                cadena = fichero.readLine();
            } catch (IOException ex) {
                Logger.getLogger(reader.class.getName()).log(Level.SEVERE, null, ex);
            }
        }
        try {
            fichero.close();
        } catch (IOException ex) {
            Logger.getLogger(reader.class.getName()).log(Level.SEVERE, null, ex);
        }
        this.busy = false;
    }
}




package biomarker1;
/*
The class for the microsatellite search. this process runs un parallel threads
*/

import static java.lang.Math.random;
import java.util.Random;
import java.util.logging.Level;
import java.util.logging.Logger;

public class worker extends Thread {

    String sproblema;
    String seq;
    boolean busy;
    int archivoNum;
    printer printer;
    int cnt;

    public void setup(String sproblema, String seq, int archivoNum, printer printer) {
        this.sproblema = new String(sproblema);
        this.seq = new String(seq);
        this.archivoNum = archivoNum;
        this.printer = printer;
        this.cnt = 0;
    }

    @Override
    public void run() {
        busy = true;
        boolean done = false;
        Random rn = new Random();
        while (seq.contains(sproblema)) {                                       //validation and count of the microsatellite
            seq = seq.substring(seq.indexOf(sproblema) + 1);
            this.cnt++;
            System.gc();
            done = false;
        }
        this.busy = false;
        String line = " " + sproblema + ", hits: ," + Integer.toString(cnt) + ", Seq Num: ," + archivoNum + " , ";
        System.out.println(line);
        while (done == false) {
            if (printer.busy == false) {
                printer.print(line);
                done = true;
            }
            for (int r = 0; r < rn.nextInt(100); r++) {
            }
        }
    }
}