<?php
$feature = $variables['node']->feature;
$aphidcyc_url = "http://aphidcyc.cycadsys.org/__species__/NEW-IMAGE?type=GENE&object=__feat_id__";

$orgs = array(
    'pisum' => 'ACYPI',
    'glycines' => 'APHGL',
    'vitifoliae' => 'DAKVI',
    'noxia' => 'DIUNO',
    'cerasi' => 'MYZCE',
    'persicae' => 'MYZPE_CLONE_O',
    'padi' => 'RHOPA',
    'citrus' => 'ACYPI',
);

$current_org = strtolower($feature->organism_id->genus . ' ' . $feature->organism_id->species);

foreach ($orgs as $needle => $url_chunk) {
    if (preg_match("/.*$needle.*/", $current_org) >= 1) {
        if ($needle == 'persicae' && preg_match('/G006/', $feature->analysisfeature[0]->analysis_id->name) >= 1) {
            $aphidcyc_url = str_replace('__species__', 'MYZPE_CLONE_G006', $aphidcyc_url);
        }
        else {
            $aphidcyc_url = str_replace('__species__', $url_chunk, $aphidcyc_url);
        }
    }
}

if (preg_match('/__species__/', $aphidcyc_url) >= 1) {
    echo 'No metabolic data available at <a href="http://aphidcyc.cycadsys.org">AphidCyc</a> for this feature.';
}
else if (preg_match('/pisum/', $current_org) >= 1 && preg_match('/NCBI/', $feature->analysisfeature[0]->analysis_id->name) >= 1) {
    echo 'No metabolic data available at <a href="http://aphidcyc.cycadsys.org">AphidCyc</a> for this feature.';
}
else if ($feature->type_id->name == 'polypeptide') {
    foreach ($feature->feature_relationship->subject_id as $rel) {
        if ($rel->object_id->type_id->name == 'mRNA' || $rel->object_id->type_id->name == 'transcript') {
            $mrna_feat = chado_expand_var($rel->object_id, 'table', 'feature_relationship');

            if (count($mrna_feat->feature_relationship->subject_id) == 0) {
                // In some cases we might only have mRNA with no genes (brassica napus or transcriptomes
                $url = str_replace('__feat_id__', $mrna_feat->uniquename, $aphidcyc_url);
                echo '<a href="' . $url . '">View metabolic data for ' . $feature->uniquename . ' on AphidCyc</a>';
                break;
            }
            foreach ($mrna_feat->feature_relationship->subject_id as $rel_g) {
                if ($rel_g->type_id->name == 'gene') {
                    $url = str_replace('__feat_id__', $rel_g->uniquename, $aphidcyc_url);
                    echo '<a href="' . $url . '">View metabolic data for ' . $feature->uniquename . ' on AphidCyc</a>';
                    break;
                }
            }
        }
    }
}
else if ($feature->type_id->name == 'mRNA' || $feature->type_id->name == 'transcript') {
    if (count($feature->feature_relationship->subject_id) == 0) {
        // In some cases we might only have mRNA with no genes (brassica napus or transcriptomes)
        $target_id = $feature->uniquename;
        $url = str_replace('__feat_id__', $feature->uniquename, $aphidcyc_url);
        echo '<a href="' . $url . '">View metabolic data for ' . $feature->uniquename . ' on AphidCyc</a>';
    }
    foreach ($feature->feature_relationship->subject_id as $rel) {
        if ($rel->object_id->type_id->name == 'gene') {
            $url = str_replace('__feat_id__', $rel->object_id->uniquename, $aphidcyc_url);
            echo '<a href="' . $url . '">View metabolic data for ' . $feature->uniquename . ' on AphidCyc</a>';
            break;
        }
    }
}
else if ($feature->type_id->name == 'gene') {
    $url = str_replace('__feat_id__', $feature->uniquename, $aphidcyc_url);
    echo '<a href="' . $url . '">View data from metabolic model for ' . $feature->uniquename . '</a>';
}