Right, i will start again and take on board what you said.

Im going to leave the BlastTool.cgi as the first port of call, then just split up the modules.

What in effect i need to do, as the finished article, is to wrap the software so that other java applications can input their params and get output back. But still have the capability to produce output to a web browser

Another question then: If i have input from both command line and web page, can i get the input the same way or do i have to use an if statement eg. 

  $html = new CGI;  # create a new instance of CGI 
  $seq = $html->param('Sequence_input');
  
  if($seq eq "")
  {
    GetOptions( "sequence=s" => \$seq);
  }

[download]

monkPaul.

In reply to Re: Passing and recieving params by MonkPaul
in thread Passing and recieving params by MonkPaul

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