MultiSearchRevised.java

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class MultiSearchRevised 
{
    public static void main(String[] args) 
    {
        String filePath ="C:\\Users\\sami0\\OneDrive\\Documents\\Downloads\\KEGGdatabase.txt"; // Change this to the path of your file
        String charactersToSearch = "agtc"; // Characters you want to search for

        // Initialize counters for each character
        int countA = 0, countT = 0, countC = 0, countG = 0, countat = 0, countgc = 0;

        try (BufferedReader br = new BufferedReader(new FileReader(filePath))) 
        {
            String line;

            String wordToFind1 = "at";
            String regex1 = Pattern.quote(wordToFind1) ; 
            Pattern pattern1 = Pattern.compile(regex1);

            String wordToFind2 = "gc";
            String regex2 = Pattern.quote(wordToFind2) ; 
            Pattern pattern2 = Pattern.compile(regex2);

            Pattern pattern = Pattern.compile("[" + charactersToSearch + "]"); // Create regex pattern
             
            for(int i=1;i<=30;i++)
            {
            while ((line = br.readLine()) != null) 
            {
                if (line.trim().isEmpty())
                    {
                       break;
                    }

                    Matcher matcher1 = pattern1.matcher(line);
                    while(matcher1.find()) 
                    {
                        countat++;
                    }

                    Matcher matcher2 = pattern2.matcher(line);
                    while(matcher2.find()) 
                    {
                        countgc++;
                    }

                Matcher matcher = pattern.matcher(line);
                while (matcher.find()) 
                {

                    char foundChar = matcher.group().charAt(0);
                    //System.out.println(foundChar);
                    switch (foundChar) 
                    {
                        case 'a': 
                        countA++; break; 
                        case 't': 
                        countT++; break;
                        case 'c': 
                        countC++; break; 
                        case 'g': 
                        countG++; break;
                    }
                }
            }
            float totl=countA+countT+countC+countG;
            float perA=(countA/totl)*100;
            float perT=(countT/totl)*100;
            float perC=(countC/totl)*100;
            float perG=(countG/totl)*100;
            // Display the count of each character
        
            System.out.println("Sequence "+i);
            System.out.println("Total content : " + totl );
            System.out.print("A content : " + countA+"       " );
            System.out.println("A content(%) : " + perA + "%");
            System.out.print("T content : " + countT +"       ");
            System.out.println("T content(%) : " + perT + "%");
            System.out.print("C content : " + countC +"       ");
            System.out.println("C content(%) : " + perC + "%");
            System.out.print("G content : " + countG +"       ");
            System.out.println("G content(%) : " + perG + "%"); 
            System.out.println("No. of AT dimers : " + countat );
            System.out.println("No. of GC dimers : " + countgc );
            System.out.println();
            
            countA = 0;
            countT = 0;
            countC = 0;
            countG = 0;
            countat = 0;
            countgc = 0;
    }
}
        catch (IOException e) 
        {
            e.printStackTrace();
        }
    }
}