#!/usr/bin/perl
# License information (the MIT license)
# Copyright (c) 2003 Christian Rees, Janos Demeter, John Matese, Gavin
# Sherlock; Stanford University
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
use strict;
# uncomment the following two lines of you installed the GeneXplorer
# libraries in a lib directory at the same level as your DOCUMENT_ROOT
# (html) directory
#use File::Basename;
#use lib dirname($ENV{DOCUMENT_ROOT})."/lib";
use Microarray::CdtDataset;
use Microarray::Explorer;
use Microarray::Config;
use CGI qw/:html3 :standard :netscape/;
use CGI::Carp qw/fatalsToBrowser/;
{ #MAIN
my $action = param('a');
my $name = param('n')|| &WrapUp("You did not supply a value for the 'n' parameter! Please, provide the name of your dataset!");
# you need to edit the construction of the Microarray::Config object
# such that your rootpath and rooturl are passed in
my $config = new Microarray::Config(rootpath => '<rootpath>',
rooturl => '<rooturl>');
my $dataset = &CreateDataset('config' => $config,
'name' => $name);
defined $dataset || &WrapUp("The dataset $name could not be created");
my $explorer = &CreateExplorer('config' => $config,
'name' => $name,
'dataset' => $dataset);
# dispatch logic
# when no action requested print frameset to window
my $target = "_top";
# check for requested action and direct to appropriate frame
if($action){
$target = 'z' if $action eq 'z' || $action eq 'c' || $action eq 's';
$target = 'r' if $action eq 'r';
$target = 't' if $action eq 't';
}
# print header for the targeted frame ...
print header (-target => $target);
if ( $target eq "_top" ) {
$explorer->print_frameset(); # or for the whole document
exit;
}
# Do what was requested ...
$explorer->toolbar if $action eq 't';
$explorer->radar if $action eq 'r';
$explorer->zoom if $action eq 'z';
$explorer->search_feature if $action eq 's';
$explorer->neighbors if $action eq 'c';
exit;
}
#####################################################################
sub CreateDataset {
#####################################################################
# this particular gx client knows where the data and images should
# reside (by design), and constructs the fully qualified paths based
# one just the name (and optional project)
my (%args) = @_;
# construct the data path
my $dataPath = $args{'config'}->gxDataPath; # default for this client
# construct the image path
my $imagePath = $args{'config'}->gxHtmlPath; # default for this client
# create a new dataset object
my $dataset = Microarray::CdtDataset->new(name => $args{'name'},
datapath => $dataPath,
imagepath => $imagePath,
config => $args{'config'});
return $dataset;
}
#####################################################################
sub CreateExplorer {
#####################################################################
# this particular gx client knows where the data and images should
# reside (by design), and constructs the fully qualified paths based
# on just the name
my (%args) = @_;
# create a new explorer object
my $displayConfig = "default.display_config"; # How display configs are treated needs to be revisited
my $explorer = Microarray::Explorer->New({ dataset => $args{'dataset'},
config => $args{'config'},
displayConfig => $displayConfig});
return $explorer;
}
#####################################################################
sub WrapUp {
#####################################################################
# This subroutine handles
my $message = shift;
print header(-type => 'text/html');
print start_html(-title => "Missing Name for GeneXplorer");
$message = br.table({-cellpadding => 3,
-width => '95%'},
Tr(
td({#-colspan => '2',
-height => '20',
-bgcolor => 'beige'},
font({-face => 'arial,sans-serif',
-size => 3}, b($message)
), "\n"
), "\n"
), "\n"
)."\n";
print $message, br;
print end_html();
exit;
}
=pod
=head1 Abstract
The gx script is a client of the Microarray::Explorer class.
Microarray::Explorer functions as a web viewer for
Microarray::CdtDataset objects. Following the Model/View/Controller
concept, the Microarray::Explorer class is the View, the
Microarray::CdtDataset class is the Model, and this script, gx, is the
controller, dealing with the dispatch logic.
=head2 Intended Behaviour
Explorer will display the dataset object in a web browser in a frameset
of 3 frames.
The frames are: - radar frame - left side of the window
- toolbar frame - top of right side of window
- zoom frame - lower part of right side of window
=head3 Radar frame
The radar frame displays the whole dataset as an image map. The genes
(clones, ...) are shown are the rows of the image, while the experiments
are shown as the columns. Clicking the image will have 2 effects:
- the expression patterns for the next XXX genes starting at
position of the click are displayed in the zoom frame
- the top of a small bracket on the right side of the radar
frame is positioned at the height of the click and the bracket
shows the XXX genes selected and magnified on the zoom frame.
The size of the image is maximized both horizontally and vertically.
=head3 Toolbar frame
The toolbar allows actions on either the radar frame or the zoom frame.
For the radar frame it allows a simple customization: changing the width of
the radar image. Selecting any of the allowed percentages changes the current
width of the image proprotionately.
For the zoom frame, it provides a search tool. The various fields of annotations
or all of them for the genes can be searched for a string. The string can be
entered in a text field. The string may contain more than one terms, spaces
are interpreted as term separators. The terms are conbined using logical 'AND'.
The hits resulting from the search are displayed in the zoom frame, as expression
patterns.
The number of hits displayed in the zoom window is limited to 200 hits and the
length of each term in te search string should be at least 2 characters long.
In addition, the toolbar frame contains an Info Box that displays various textual
information dependent on the position of the mouse pointer over the zoom frame.
It can display:
- gene information in the NAME field when the mouse is positioned
over an image row
- experiment info, if positioned above the experiment image map
- correlation of a genes expression pattern to that of the top
gene in to zoom window displaying correlations, when the pointer
is above is above the correlation image.
=head3 Zoom frame
The zoom frame displays expression patterns and annotations for genes in the
dataset. It can display genes selected from:
- radar frame; it displays a given number of genes starting from the
genes whose image was clicked on
- the toolbar; the result of the search performed using the searchtool
is displayed here
- the zoom frame itself; when a row is clicked on in the radar frame,
the genes with the highest correlation in their expression pattern
are displayed
Information about various elements in the zoom frame is displayed in the Info Box
in the toolbar, dependent on the position of the mouse:
- experiment info
- gene info
- correlation value
=head2 Parameters
'n' = name; name of dataset to use
'a' = action; action to perform
'seed' = seed;
'q' = query (the string to use for the search)
'f' = field (the field to search)
'rx' = column width in pxl in radar frame
'ry' = column height in pxl in radar frame
'zy' = column height in pxl in zoom frame
'ry' = column width in pxl in zoom frame
possible values for action:
---------------------------
'c' = correlate
- print the most correlated gene expression vectors
(neighbors) for gene provided in param('seed')
's' = search
- Do a search using the string provided in param('q')
to search the field(s) provided in param('f')
'z' = zoom
- print a zoom frame (currently arround the mouseclick
x/y coordinates
'r' = radar
- print a radar frame
't' = toolbar
- print a toolbar frame
=head1 Authors
Original work: Christian Rees
Re-write: Janos Demeter
jdemeter@genome.stanford.edu
=cut