<commit_before>#Modified August 6, 2009 for CapsDesigner2
#<NAME>, Summer Intern

use strict;
use CXGN::Page;
use CXGN::Page::FormattingHelpers qw/  page_title_html
                                       blue_section_html  /;

#Get input, if this page is loaded from find_caps.pl
our $page = CXGN::Page->new( "CAPS Designer", "Chenwei");
my ($format, $cheap_only, $exclude_seq, $cutno, $seq_data, $seq_select) = $page->get_arguments("format", "cheap", "start", "cutno", "seq_data");#, "seq_select");

my ($intro_content, $input_content);

$intro_content = "<tr><td><p>This tool designs CAPS assays for up to 12 sequences.  Two types of nucleotide inputs are accepted: fasta sequences and clustal alignment.  It generates a list of polymorphic enzymes that cut the sequences into different length products.</p>";
$intro_content .= "<b>Suggestions:</b><ol><li>Low quality nucleotides and \"n\"s at both ends of a sequence generate ambiguity. Please remove them from the input sequences.</li><li>Polymorphic digested fragments of too small sizes are hard to visualize on 1-4% agarose gel, thus not suitable for CAPS experiment.  Please exclude some nucleotides (for example 20) at both ends to avoid the problem.</li></ol></td></tr>";


$input_content = '<form method="post" action="find_caps.pl" name="capsinput">';

#Select input format
$input_content .= '<b>Input format</b><br />';
if ($format eq "clustalw"){
  $input_content .= '<input type="radio" name="format" value="clustalw" checked="checked" />clustal alignment <a target="blank" href="/about/clustal_file.pl">[What is this?]</a><br />';
  $input_content .= '<input type="radio" name="format" value="fasta" />unaligned fasta sequences<br /><br />';
}
else {
  $input_content .= '<input type="radio" name="format" value="clustalw" />clustal alignment <a target="blank" href="/about/clustal_file.pl">[What is this?]</a><br />';
  $input_content .= '<input type="radio" name="format" value="fasta" checked="checked" />unaligned fasta sequences<br /><br />';
}

# #Select sequence pair to analyze
#######NO LONGER NEEDED for CapsDesigner2
# $input_content .= '<b>Sequence pair to analyze</b> <br />Please enter <b>at least two sequences</b>.  Please choose two from the first three sequences to analyze.<br />';
# if ($seq_select == 2) {
#   $input_content .= '<input type="radio" name="seq_select" value="1" />sequence 1 and 2 (default)<br />';
#   $input_content .= '<input type="radio" name="seq_select" value="2" checked="checked" />sequence 1 and 3<br />';
#   $input_content .= '<input type="radio" name="seq_select" value="3" />sequence 2 and 3<br /><br />';
# }
# elsif ($seq_select == 3){
#   $input_content .= '<input type="radio" name="seq_select" value="1" />sequence 1 and 2 (default)<br />';
#   $input_content .= '<input type="radio" name="seq_select" value="2" />sequence 1 and 3<br />';
#   $input_content .= '<input type="radio" name="seq_select" value="3" checked="checked" />sequence 2 and 3<br /><br />';
# }
# else {
#   $input_content .= '<input type="radio" name="seq_select" value="1" checked="checked" />sequence 1 and 2 (default)<br />';
#   $input_content .= '<input type="radio" name="seq_select" value="2" />sequence 1 and 3<br />';
#   $input_content .= '<input type="radio" name="seq_select" value="3" />sequence 2 and 3<br /><br />';
# }

#Text area for input sequences
$input_content .= '<b>Input sequences</b><br />';
$input_content .= "<textarea name=\"seq_data\" rows=\"20\" cols=\"100\">$seq_data</textarea><br /><br /><br /><br />";

#Options low price enzyme
$input_content .= '<b>Options</b><br /><br />';
if ($cheap_only == 1){
  $input_content .= '<input type="checkbox" name="cheap" value = "1" checked="checked" /> Find enzymes priced less than $65/1000u.<br />';
}
else {
  $input_content .= '<input type="checkbox" name="cheap" value = "1" /> Find enzymes priced less than $65/1000u.<br />';
}
<commit_msg>Cleanup caps_input.pl<commit_after>
use strict;
use warnings;
use CXGN::Page;
use CXGN::Page::FormattingHelpers qw/  page_title_html
                                       blue_section_html  /;

#Get input, if this page is loaded from find_caps.pl
our $page = CXGN::Page->new( "CAPS Designer", "Chenwei");
my ($format, $cheap_only, $exclude_seq, $cutno, $seq_data, $seq_select) = $page->get_arguments("format", "cheap", "start", "cutno", "seq_data");#, "seq_select");

my ($intro_content, $input_content);

$intro_content = "<tr><td><p>This tool designs CAPS assays for up to 12 sequences.  Two types of nucleotide inputs are accepted: fasta sequences and clustal alignment.  It generates a list of polymorphic enzymes that cut the sequences into different length products.</p>";
$intro_content .= "<b>Suggestions:</b><ol><li>Low quality nucleotides and \"n\"s at both ends of a sequence generate ambiguity. Please remove them from the input sequences.</li><li>Polymorphic digested fragments of too small sizes are hard to visualize on 1-4% agarose gel, thus not suitable for CAPS experiment.  Please exclude some nucleotides (for example 20) at both ends to avoid the problem.</li></ol></td></tr>";


$input_content = '<form method="post" action="find_caps.pl" name="capsinput">';

#Select input format
$input_content .= '<b>Input format</b><br />';
if ($format eq "clustalw"){
  $input_content .= '<input type="radio" name="format" value="clustalw" checked="checked" />clustal alignment <a target="blank" href="/about/clustal_file.pl">[What is this?]</a><br />';
  $input_content .= '<input type="radio" name="format" value="fasta" />unaligned fasta sequences<br /><br />';
}
else {
  $input_content .= '<input type="radio" name="format" value="clustalw" />clustal alignment <a target="blank" href="/about/clustal_file.pl">[What is this?]</a><br />';
  $input_content .= '<input type="radio" name="format" value="fasta" checked="checked" />unaligned fasta sequences<br /><br />';
}

#Text area for input sequences
$input_content .= '<b>Input sequences</b><br />';
$input_content .= "<textarea name=\"seq_data\" rows=\"20\" cols=\"100\">$seq_data</textarea><br /><br /><br /><br />";

#Options low price enzyme
$input_content .= '<b>Options</b><br /><br />';
if ($cheap_only == 1){
  $input_content .= '<input type="checkbox" name="cheap" value = "1" checked="checked" /> Find enzymes priced less than $65/1000u.<br />';
}
else {
  $input_content .= '<input type="checkbox" name="cheap" value = "1" /> Find enzymes priced less than $65/1000u.<br />';
}

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