<commit_before>package modloop;
use saliweb::frontend;

use strict;

our @ISA = "saliweb::frontend";

sub new {
    return saliweb::frontend::new(@_, @CONFIG@);
}

sub get_navigation_links {
    my $self = shift;
    my $q = $self->cgi;
    return [
        $q->a({-href=>$self->index_url}, "ModLoop Home"),
        $q->a({-href=>$self->queue_url}, "Current ModLoop queue"),
        $q->a({-href=>$self->help_url}, "Help"),
        $q->a({-href=>$self->contact_url}, "Contact")
#       $q->a({-href=>$self->news_url}, "News"),
        ];
}

sub get_project_menu {
    my $self = shift;
    my $version = $self->version;
    return <<MENU;
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><small>Developer:</small></h4><p><NAME></p>
<h4><small>Acknowledgements:</small></h4>
<p><NAME><br />
<NAME><br />
<br />
<NAME></p>
<p><i>Version $version</i></p>
MENU
}

sub get_footer {
    my $self = shift;
    my $htmlroot = $self->htmlroot;
    return <<FOOTER;
<div id="address">
<center><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=11045621&amp;query_hl=2&amp;itool=pubmed_docsum">
<b><NAME>,  <NAME> and <NAME>, Prot Sci, (2000) <i>9,</i> 1753-1773</b></a>
&nbsp;<a href="http://salilab.org/pdf/082_FiserProteinScience2000.pdf"><img src="$htmlroot/img/pdf.gif" alt="PDF" /></a><br />
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=14668246&amp;query_hl=2&amp;itool=pubmed_docsum">
<b><NAME>, and <NAME>, Bioinformatics, (2003) <i>18,</i> 2500-01</b></a>
&nbsp;<a href="http://salilab.org/pdf/135_FiserBioinformatics2003.pdf"><img src="$htmlroot/img/pdf.gif" alt="PDF" /></a></center>
</div>
FOOTER
}

sub get_index_page {
    my $self = shift;
    my $q = $self->cgi;
    my $greeting = <<GREETING;
<p>ModLoop is a web server for automated modeling of loops in protein
structures. The server relies on the loop modeling routine in MODELLER
that predicts the loop conformations by satisfaction of spatial restraints,
without relying on a database of known protein structures.
<br />&nbsp;</p>
GREETING<commit_msg>Fix journal number and PDF links.<commit_after>package modloop;
use saliweb::frontend;

use strict;

our @ISA = "saliweb::frontend";

sub new {
    return saliweb::frontend::new(@_, @CONFIG@);
}

sub get_navigation_links {
    my $self = shift;
    my $q = $self->cgi;
    return [
        $q->a({-href=>$self->index_url}, "ModLoop Home"),
        $q->a({-href=>$self->queue_url}, "Current ModLoop queue"),
        $q->a({-href=>$self->help_url}, "Help"),
        $q->a({-href=>$self->contact_url}, "Contact")
#       $q->a({-href=>$self->news_url}, "News"),
        ];
}

sub get_project_menu {
    my $self = shift;
    my $version = $self->version;
    return <<MENU;
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h4><small>Developer:</small></h4><p><NAME></p>
<h4><small>Acknowledgements:</small></h4>
<p><NAME><br />
<NAME><br />
<br />
<NAME></p>
<p><i>Version $version</i></p>
MENU
}

sub get_footer {
    my $self = shift;
    my $htmlroot = $self->htmlroot;
    return <<FOOTER;
<div id="address">
<center><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=11045621&amp;query_hl=2&amp;itool=pubmed_docsum">
<b><NAME>,  <NAME> and <NAME>, Prot Sci, (2000) <i>9,</i> 1753-1773</b></a>
&nbsp;<a href="http://salilab.org/pdf/Fiser_ProteinSci_2000.pdf"><img src="$htmlroot/img/pdf.gif" alt="PDF" /></a><br />
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=14668246&amp;query_hl=2&amp;itool=pubmed_docsum">
<b><NAME>, and <NAME>, Bioinformatics, (2003) <i>19,</i> 2500-01</b></a>
&nbsp;<a href="http://salilab.org/pdf/Fiser_ProteinSci_2000.pdf"><img src="$htmlroot/img/pdf.gif" alt="PDF" /></a></center>
</div>
FOOTER
}

sub get_index_page {
    my $self = shift;
    my $q = $self->cgi;
    my $greeting = <<GREETING;
<p>ModLoop is a web server for automated modeling of loops in protein
structures. The server relies on the loop modeling routine in MODELLER
that predicts the loop conformations by satisfaction of spatial restraints,
without relying on a database of known protein structures.
<br />&nbsp;</p>
GREETING
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