#!/usr/bin/perl ############################################## ############################################## # SCRIPT NAME: Page_Code_Documentation.cgi # FUNCTION: Document the Code ############################################## # 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. 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', -bgcolor=>'#D1DFC4' ); # 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();} $debug = ""; # "1" to print, "0" to hide print statements ####### # START THE WEBPAGE ####### # print the MINE menu &menu; # start the basic gray table used for formatting MINE pages # &table_top(); # put the main title of your page here # print "Scripts

"; # print the list of scripts and their brief descriptions using traditional html in a text block (HTML_TEXT) print $var =<

MINE Menu
 
description
 
script name
 
source code
Submit
Create a brand new sequence entry
Page_Submit_new_data.cgi
 
source
Edit
Edit a sequence entry
Page_Edit_a_File.cgi
 
source
Translate & Convert
Translate and convert sequences
Page_Change_Format.cgi
 
source
View Data Log
View all sequence and results files in a simple browser window
Page_Database_Log.cgi
 
source
Statistics
View how many sequence entries are in the database
Page_Database_Statistics.cgi
 
source
Blast
Blast interface (manager has access to batch blasting from stored files)
Page_Do_Blast_Searches.cgi
 
source
G+C & More
Calculate G+C, sequence length and other features for all sequence entries in the database
Page_Analysis.cgi
 
source
Remote Tools
A list of remote tools for more specialized analysis of individual sequences
Page_Tools.cgi
 
source
Search Engine
Create complex queries and display information from matching files
Page_Search_and_Display.cgi
 
source
All Scripts
This page. A list of all the scripts in MINE.
Page_Code_Documentation.cgi
 
source
Link MINE
Collections of related links with annotation. Can easily be edited to add new links.
Page_Link_MINE.cgi
 
source
Manual
The beginnings of a User's Manual for MINE.
Page_Documentation.cgi
 
source
Comments
A simple
Page_Comments.cgi
 
source
Web Log
View summaries of all visits to MINE scripts (visits to all scripts are logged)
Page_Web_Log_Reader.cgi
 
source
Admin
A set of automated tasks that help the Curator in set-up and maintenance of the database.
Page_Make_Source_ADMIN.cgi
 
source
"MINE"
 
HOME
The home page for this specific MINE database.
Page_MINE.cgi
 
source
FAQ
FAQ about the MINE code
Page_MINE_FAQ.cgi
 
source
MINE
MINE Homepage:
http://mariecurie2.imm.ox.ac.uk/MINE/
 
Website
Essential Files not in Menu         CGI-MINE.pl
text
MINE_Preferences
text
MINE_Customization File
text
Essential Externals
CGI.pm
Perl module
Optional Externals Required for full functionality
Blastall
Application
Bioperl
Perl package
HTML_TEXT #&table_bottom(); # 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 #################