Example 10
<![CDATA[
<!-- Meaning short title to appear in Hot List etc. -->
<TITLE>
MOOSE - Fast Protein Structure Search by Conformational Likeness
</TITLE>
<!-- Set background color to white -->
<BODY BGCOLOR="#FFFFFF" >
<!-- CGI script to accept input from the form -->
<FORM METHOD="GET"
ACTION="http://xtal1.sdsc.edu/misha/cgi-bin/misha1.cgi">
<P>
<CENTER>
<H2>Fast Protein Structure Search by Conformational Likeness</H2>
<B>Other Queries:</B>
<A HREF="http://db2.sdsc.edu/moose">Moose</A> |
<A HREF="misha.html">Alignment</A><P>
<HR>
<!-- Define a text box that can contain up to 8 characters and with an
initial value of 4HHBA. The value entered will be assigned to the
name value of entity_code1 -->
<B>Entity:</B>
<INPUT NAME = "entity_code1", VALUE="4HHBA", SIZE=8>
<HR></CENTER>
<!-- Define a radio button which is on by default (CHECKED). The value "julia"
will be passed to the CGI and equated with the name "ent_or_frag" -->
<INPUT TYPE="radio" NAME="ent_or_frag" VALUE="julia" CHECKED>
<B> Entity Search </B><P>
<!-- Define a second radio button which is not on. Since the name value is
the same selecting this button will deselect the previous button -->
<INPUT TYPE="radio" NAME="ent_or_frag" VALUE="misha" >
<B> Fragment Search
<!-- Associate two additional text boxes with the radio button.
Note that this is a loose association, that is, values entered here
will not be used unless the button is selected (this is controlled
by the CGI script not the form). -->
From </B>
<INPUT NAME = "entity_frag1", VALUE="10", SIZE=4><B> To </B>
<INPUT NAME = "entity_frag2", VALUE="30", SIZE=4>
<HR>
<!-- Define a scrollable list of options. Since this list lacks the MULTIPLE attribute
the single option selected will be equated with the name variable "mode" .
SIZE = 10 indicates that 10 options on the list will be visible without scrolling.
The OPTION designated as SELECTED is the default. -->
<CENTER>
<B>Select Mode:</B>
<SELECT NAME="mode" SIZE = 10>
<!-- Without the VALUE attribute "mode" is defined by the option value e.g.,
LocalDist -->
<OPTION> LocalDist
<OPTION> LocalAngle
<OPTION> LocalTwist
<OPTION> LocalSurface
<OPTION> LocalPhiPsi
<OPTION SELECTED>LocalSecStr
<OPTION> SeqPAMatrix
<OPTION> FeatSurface
<OPTION> FeatShape
<OPTION> FeatFreq
<!-- Options omitted here -->
</SELECT>
<HR><P>
<B>Length Criterion:</B>
<!-- Define a pop-up list (distinguished from a scrolling list by the lack of a SIZE
attribute). Again the SELECTED OPTION defines the default value. -->
<SELECT NAME="length">
<OPTION VALUE=10 SELECTED> 10%
<OPTION VALUE=50> 50%
<OPTION VALUE=200> 200%
<OPTION VALUE=300> 300%
<OPTION VALUE=1000> Any
</SELECT>
<B>Likeness Criterion:</B>
<!-- A text box as describe above. -->
<INPUT NAME="likeness", VALUE="0.25", size=6>
<P>
<I> Click <A HREF="julia_help.html"><B>here</B></A> for details.</I>
<HR><BR>
<!-- The input type hidden does not appear on the Web form but sends
the value "search" to the CGI with a name value of "query_type".
The VALUE attribute for the submit and reset buttons defines the
text that appears in the buttons. -->
<iINPUT TYPE=hidden NAME="query_type" VALUE="search">
<INPUT TYPE=submit VALUE="EXECUTE QUERY">
<INPUT TYPE=reset VALUE="RESET FORM"><BR>
</CENTER>
</FORM> <!-- End of form -->
<HR>
</BODY>
]]>
<![CDATA[
#!/usr/local/bin/perl
# This script simply takes the input from the Web form (Figure 10–3) and
# converts it to a command string that is executed on the server and the results
# are returned as HTML to the client Web browser.
# Define locations (server dependent) for temporary files.
$SCRATCH_PATH = "/scratch/s1/moose_output";
$SCRATCH_URL = "http://xtal1.sdsc.edu/scratch";
# Include a Perl library which contains a routine to parse the input string from
# the GET operation.
require "cgi-lib.pl";
# Routine from cgi-lib.pl to parse the input stream into array input.
&ReadParse(*input);
# Build a variable "command" from the input parameters. Note that the
# "query_type" is the hidden variable in the above form. In the above form
# the value of "query_type" is "search" hence this part of the script will
# get executed by submitting the above form. This offers a convenient way to have
# a single Perl script process multiple Web forms.
if($input{'query_type'} eq 'search')
# Build the command string from the input array.
{
$ent1=$input{'entity_code1'};
$mode=$input{'mode'};
$length=$input{'length'};
$likeness=$input{'likeness'};
$ent_or_frag=$input{'ent_or_frag'};
$command ="/misc/x1/moose/pon/"."$ent_or_frag"." "."$ent1"." "."$mode".","."$length".","."$likeness";
# Modify the command string for the fragment case.
if($ent_or_frag eq 'misha')
{
$frag1=$input{'entity_frag1'};
$frag2=$input{'entity_frag2'};
$command .=","."$frag1".","."$frag2";
}
# Define the output to be sent back to the Web client.
# First define the content type and header information.
print "Content-type: text/html\n\n";
print "<TITLE>Pure Output</TITLE>\n";
print "<BODY BGCOLOR=\"#ffffff\">\n";
# Execute the command appending an HTML line break to each line.
open (RES, "$command |");
while (<RES>) {
print; print "<BR>";
}
print "</BODY>\n";
}
]]>