Tell me about exec(),biojava...,how to connect database written in c executable file?

problem that i am faceing is that..i have to run about 50mb to 1 gb database using java ..database in in c(executable flatfile)...
it run fine for same databse around 1-10mb..
for bigger databse it is hang...
code i written is////
import java.io.*;
import java.util.*;
import javax.servlet.*;
import javax.servlet.http.*;
/**
* Hello World. This servlet simply says hi.
*
* <P> This is useful for testing the servlet configuration process,
* since this servlet isn't installed.
*/
public class FastaEngine extends HttpServlet {
public void doPost (HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException
{
PrintWriter out;

res.setContentType("text/html");
out = res.getWriter();

String source=req.getParameter("S1");
String v =req.getParameter("libpo");
String databasename =req.getParameter("program");
//String v =req.getParameterValues("libpo");
out.println("<b>Getting the value from text box</b>");
out.println("<H1>"+v+"</H1>");
out.println("<H1>"+databasename+"</H1>");
//building string From various Option
//String command="D:/jithesh/sameer/"+databasename+" - "+ v+" ecoli3.txt ecoli3.txt";
String command="D:/jithesh/sameer/fasta -Q -O output d:/javaproject/ecoli3.txt d:/javaproject/mito.nt";
//D:\\jithesh\\sameer\\Fasta -q -o output salmo.txt swissport
out.println(command);
Date dd1=new Date(System.currentTimeMillis()-24*60*60*1000);
out.println("Time Started:"+dd1);
GregorianCalendar gc1 = new GregorianCalendar();
Date d1 = gc1.getTime();
long l1 = d1.getTime();
/* TAKING QUERY STRING FROM THE TEXT BOX AND WRITING TO THE FILE
OF NAME DEMO.TXT
CODE BEGAIN
*/
char buffer[]=new char[source.length()];
source.getChars(0,source.length(),buffer,0);
//FileReader fr =new FileReader("d:/javaproject/ShowFile.java");
FileWriter wr =new FileWriter("c:/demo2.txt");
for(int i=0;i<buffer.length;i++){
wr.write(buffer[i]);
}
wr.close();
//CODE OF FILE WRITING END.

String s="ASDFSDFDASF";
out.println("<html>");
out.println("<body bgcolor="+"#DBEDFF"+">");
out.println("<p>");
out.println("<hr noshade color="+"#FF0000"+">");
out.println("<H1>Readding The .Exe FileContent......</H1>");
out.println("</body></html>");

//Executing The File And Reading the File
//get Runtime it return the proccess
Runtime rt=Runtime.getRuntime();
//executing the exe file.
//Process pro=rt.exec("D:/jithesh/sameer/Fasta -o ecoli3.txt ecoli3.txt");
Process pro=rt.exec(command);
//reading the file content in byte stream
out.println("Executed");

InputStreamReader isr=new InputStreamReader(pro.getInputStream());
//Storing in the bufferreader.
BufferedReader br= new BufferedReader(isr);
String line;
//Reading the output Content...
while((line=br.readLine())!=null)
// out.println("<br>"+line+"</br>");
out.println("<font color=red><font size="+"1"+">"+"<br>"+line+"</font></br></font>");
GregorianCalendar gc2 = new GregorianCalendar();
Date d2 = gc2.getTime();
long l2 = d2.getTime();
long difference = l2 - l1;
out.println("Elapsed milliseconds: " + difference);

out.println("<html>");
out.println("<body bgcolor="+"#CCCCFF"+">");
out.println("<p>");
out.println("<hr noshade color="+"#FF0000"+">");

out.println("<b>"+"Hello World sameer ....."+source+"</b>");
out.println("<p><a href="+"http://localhost:8080/servlet/FastaOutput"+">see Result of Fasta Engine.....</a></p>");
out.println("</body></html>");
// res.sendRedirect("http://localhost:8080/servlet/RedirectServlet");
Date dd2=new Date(System.currentTimeMillis()-24*60*60*1000);
out.println("<br>TimeComPleted"+dd2+"</br>");
out.println("<br>Elapsed milliseconds: " + difference+"<br>");
}
}
import java.io.*;
import java.util.*;
import javax.servlet.*;
import javax.servlet.http.*;
/**
* Hello World. This servlet simply says hi.
*
* <P> This is useful for testing the servlet configuration process,
* since this servlet isn't installed.
*/
public class FastaEngine extends HttpServlet {
public void doPost (HttpServletRequest req, HttpServletResponse res)
throws ServletException, IOException
{
PrintWriter out;

res.setContentType("text/html");
out = res.getWriter();

String source=req.getParameter("S1");
String v =req.getParameter("libpo");
String databasename =req.getParameter("program");
//String v =req.getParameterValues("libpo");
out.println("<b>Getting the value from text box</b>");
out.println("<H1>"+v+"</H1>");
out.println("<H1>"+databasename+"</H1>");
//building string From various Option
//String command="D:/jithesh/sameer/"+databasename+" - "+ v+" ecoli3.txt ecoli3.txt";
String command="D:/jithesh/sameer/fasta -Q -O output d:/javaproject/ecoli3.txt d:/javaproject/mito.nt";
//D:\\jithesh\\sameer\\Fasta -q -o output salmo.txt swissport
out.println(command);
Date dd1=new Date(System.currentTimeMillis()-24*60*60*1000);
out.println("Time Started:"+dd1);
GregorianCalendar gc1 = new GregorianCalendar();
Date d1 = gc1.getTime();
long l1 = d1.getTime();
/* TAKING QUERY STRING FROM THE TEXT BOX AND WRITING TO THE FILE
OF NAME DEMO.TXT
CODE BEGAIN
*/
char buffer[]=new char[source.length()];
source.getChars(0,source.length(),buffer,0);
//FileReader fr =new FileReader("d:/javaproject/ShowFile.java");
FileWriter wr =new FileWriter("c:/demo2.txt");
for(int i=0;i<buffer.length;i++){
wr.write(buffer[i]);
}
wr.close();
//CODE OF FILE WRITING END.

String s="ASDFSDFDASF";
out.println("<html>");
out.println("<body bgcolor="+"#DBEDFF"+">");
out.println("<p>");
out.println("<hr noshade color="+"#FF0000"+">");
out.println("<H1>Readding The .Exe FileContent......</H1>");
out.println("</body></html>");

//Executing The File And Reading the File
//get Runtime it return the proccess
Runtime rt=Runtime.getRuntime();
//executing the exe file.
//Process pro=rt.exec("D:/jithesh/sameer/Fasta -o ecoli3.txt ecoli3.txt");
Process pro=rt.exec(command);
//reading the file content in byte stream
out.println("Executed");

InputStreamReader isr=new InputStreamReader(pro.getInputStream());
//Storing in the bufferreader.
BufferedReader br= new BufferedReader(isr);
String line;
//Reading the output Content...
while((line=br.readLine())!=null)
// out.println("<br>"+line+"</br>");
out.println("<font color=red><font size="+"1"+">"+"<br>"+line+"</font></br></font>");
GregorianCalendar gc2 = new GregorianCalendar();
Date d2 = gc2.getTime();
long l2 = d2.getTime();
long difference = l2 - l1;
out.println("Elapsed milliseconds: " + difference);

out.println("<html>");
out.println("<body bgcolor="+"#CCCCFF"+">");
out.println("<p>");
out.println("<hr noshade color="+"#FF0000"+">");

out.println("<b>"+"Hello World sameer ....."+source+"</b>");
out.println("<p><a href="+"http://localhost:8080/servlet/FastaOutput"+">see Result of Fasta Engine.....</a></p>");
out.println("</body></html>");
// res.sendRedirect("http://localhost:8080/servlet/RedirectServlet");
Date dd2=new Date(System.currentTimeMillis()-24*60*60*1000);
out.println("<br>TimeComPleted"+dd2+"</br>");
out.println("<br>Elapsed milliseconds: " + difference+"<br>");
}
}