#!/usr/bin/perl

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# SCRIPT NAME:  Page_MINE.cgi
# FUNCTION:     A HOME page 
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# MINE: Molecular INformation Explorer
# Copyright 2000 Dawn Field.  All rights reserved.
# The CGI-PERL scripts belonging to MINE
# may be used and modified freely, but I do
# request that this copyright notice remain attached
# to this file/source code.  If you make modifications
# please do not distribute unless
# you fully document the modifications.

# file was edited from another directory

	
use  CGI;
require "CGI-MINE.pl";

        #################
        # START EACH MINE CGI SCRIPT
        #################
	# this redirects the error messages to the user's screen
	# and is useful for debugging CGI scripts!
	open (STDERR, ">&STDOUT");         # print errors to screen
	$| = 1;                            # flush the print buffer continuously
	# make a new query object using CGI.pm module
	$query = new CGI;
	# print the required header and start the web page
	print $query->header;   
	print $query->start_html(-title=>'MINE Welcome page',
				-BGCOLOR=>'white'
				);
	# Each time a script is invoked for the first time (or $action undef),
	# log the visit in the custom MINE server log (see CGI-MINE.pl)
	# (put this after the header incase an error message is printed)
	# check value of $action
	$action = $query->param('action');
	if ($action eq undef) {&log();}


if (!-e "MINE_Customization_File") {
        &table_top();
        print "<P><P><B>NOTE:</b> You are currently using the \"MINE_Customization_File.default\" file.  You should copy this
        file to \"MINE_Customization_File\" and customize the global variables found within it to suit your database.
        Go to the <a href=\"Page_MINE_FAQ.cgi#customizing mine once installed\">FAQ</a>, if you need help setting up this file.";
        &table_bottom();
}

	#######
	# START THE WEBPAGE
	#######
	&menu;
	# print the MINE menu
#	&footer;
	# start the basic gray table used for formatting MINE pages
	&table_top();
	# put the main title of your page here
	print "<hr><P><center><b><i><font face=\"Arial, Helvetica, sans-serif\"
	size=+3>Welcome to \"MINE\"</font></i></b><br>";


	# print "<font face=\"Arial, Helvetica, sans-serif\" size=\"3\">";

        $demo_file = <*0001.db> ||<*001.db>;
        $demo_blast_report = <*0001.db*blast.html>||<*001.db*blast.html>;

	print <<MESSAGE;
	You have entered the portion of the $database_name where you can actually see and use the
	scripts used to store the primary data and do basic data-mining (e.g. blast).  We refer to these scripts collectively
	as the Molecular INformation Explorer project, or "MINE".  Go here to the 
	<a href="Page_MINE_FAQ.cgi#what is mine">MINE FAQ</a> 
	to see why or to read a bit about the 
	<a href="Page_MINE_FAQ.cgi#the purpose of the mine project and the pfsbw25 encyclopaedia">purpose</a> or
	<a href="Page_MINE_FAQ.cgi#the philosophy of mine">philosophy</a>
	 of this open-source project.
	To return to the $database_name homepage select 
	<a href="$database_welcome_page">HOME</a>
	 from the above menu.

	<P>Here are a few of the things you can do using the MINE options in the above MINE navigation menu:

	<p><b>Directly View all the primary sequence files and related analysis files (i.e. blast reports).<br></b>
	Select <a href="Page_Database_Log.cgi">Data Log</a> and then click on a file 
	(<a href="Page_View.cgi?file=$demo_file">$demo_file</a> or 
	<a href="$demo_blast_report">$demo_blast_report</a>).

	<P><b>Do a blast search against the $database_name</b>:
        <br>Select <a href="Page_Do_Blast_Searches.cgi">Blast</a> and the "SELF_blast_database" option which contains all sequences
	in the $database_name.

        <P><b>Use the search engine to search all entries and to create lists of subsets of 
	sequences that match particular criteria (e.g. G+C or sequence length).  Or use the display function to see a
	particular subset of stored
	information about all files in the database, for example the top blast matches for each entry.
If you select "MORE Search Parameters" you can concatenate searches to generate progressively complex and refined searches.</b>
        <br>Select <a href="Page_Search_and_Display.cgi">Search</a>, pick a display format, and then fill in the search options.
</center><P><hr>
MESSAGE

	# end table
	&table_bottom();
	print "</center>";


        # PRINT BOTTOM OF EACH WEB PAGE
        # if $show_source is set to 1 show a link
        # at the bottom of each script to the source
        # code - pass the name of this script to the
        # function in CGI-MINE.pl
        if ($show_source) {
                $script_name = $query->script_name();
                &source ($script_name);
        }	# ATTACH the MINE copywrite
	&mine_cp;
	print $query->end_html;
        #################
        # END WEBPAGE
        #################






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# FUNCTIONS
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