Write a Java program to read a file that contains DNA sequences of arbitrary length one per line (note that each DNA sequence is just a String). Your program should sort the sequences in descending order with respect to the number of 'TATA' subsequences present. Finally write the sequences in sorted order into another file

 PROGRAM                       

import java.io.*;

class files

{

String s[]=new String[100];

String str="",m,t;

int x,size=0,i,tem,j=0,chg;

int a[]=new int[100];

int b[]=new int[100];

int c[]=new int[100];

files(String s1,String s2)throws IOException

{

File r=new File(s1);

File w=new File(s2);

FileInputStream fin=new FileInputStream(r);

FileOutputStream fout=new FileOutputStream(w);

do{

i=fin.read();

if(i!=-1)

{

str=str+(char)i;

if((char)i=='\n')

{

s[j]=str;

j++;

size++;

str="";

}

}

}

while(i!=-1);

for(int l=0;l

{

if(s[l]==null)

break;

m=s[l];

t="tata";

b[l]=a[l]=search(m,t);

}

for(int p=0;p

{

for(int q=0;q

{

if(b[q]

{

tem=b[q];

b[q]=b[q+1];

b[q+1]=tem;

}

}

}

for(int h=0;h

{

x=b[h];

c[h]=linear(x,a,size);

}

for(int y=0;y

{

chg=c[y];

byte buf[]=s[chg].getBytes();

fout.write(buf);

}

}

static int linear(int x,int a[],int size)

{

int m,d,item=x,siz=size;

for(d=0;d<=siz;d++)

{

if(item==a[d])

{

m=d;

break;

}

}

return d;

}

static int search(String m,String c)

{

int ch,ma,inc=0;

String pat,main,check;

pat=main=m;

check=c;

do{

pat=main.substring(0,4);

if(pat.equalsIgnoreCase(check))

++inc;

main=main.substring(1);

ch=check.length();

ma=main.length();

}

while(ch

return inc;

}

}

class filehand

{

public static void main(String a[])throws IOException

{

DataInputStream in=new DataInputStream(System.in);

String s1,s2;

System.out.println("enter the read file name :");

s1=in.readLine();

System.out.println("enter the write file name:");

s2=in.readLine();

files f=new files(s1,s2);

System.out.println("successfully writed");

}

}

OUTPUT:

C:\j2sdk1.4.0\bin>javac filehand.java

C:\j2sdk1.4.0\bin>java filehand

enter the read file name :

input.txt

enter the write file name:

output.txt

successfully writed

“Input.txt”

jfjksdf tata fji

fjksdfi tatt fg tata taata tata

jfijsdf tata tjkltj tatta tata tata

“Output.txt”

jfijsdf tata tjkltj tatta tata tata

fjksdfi tatt fg tata taata tata

jfjksdf tata fji