bioinformatics-java-toolkits/ORF_Testing.java at main · mmqkafi/bioinformatics-java-toolkits · GitHub

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package bioinformatics;
/*
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
*/
public class ORF_Testing {/*
	public static void main(String[] args) throws IOException {
		BufferedReader br = new BufferedReader( new FileReader( args[0]));
		ORF_Testing orf_testing = new ORF_Testing();

		String lines ;
		while( (lines = br.readLine()) != null ) {
			if ( lines.startsWith(">")) {
				continue ;
			}
			else {
				orf_testing.ORF(lines);
			}
	}br.close();
}	*/
public String ORF(String lines) {

	 String seq = lines;


         /*
     if ( seq.indexOf("ATG") != -1  )
     {
    	 System.out.println(seq.indexOf("ATG"));
    	 System.out.println("Start codon found");

     }
     if ( seq.indexOf("TAA") != -1  )
     {
    	 System.out.println(seq.indexOf("TAA"));
    	 System.out.println("Stop codon found");

     }
     */
     if ( seq.indexOf("ATG") != -1  && seq.indexOf("TAA") != -1 ) {
     int start = seq.indexOf("ATG");
     int stop = seq.indexOf("TAA");

     System.out.println(seq.indexOf("ATG"));
	 System.out.println("Start codon found");
	 System.out.println(seq.indexOf("TAA"));
	 System.out.println("Stop codon found");


     if ( stop > start ) {

     String orf_sequence = seq.substring(start + 3, stop);
     System.out.println("ORF Seq: " + orf_sequence);
     System.out.println("");
     }


     }

		return  "";
	}


}