1: <?php
  2: 
  3: namespace webservices\graphs\genome;
  4: /**
  5:  * Return tracks for canvasXpress genome browser
  6:  * go to http://canvasxpress.org/documentation.html#data , scroll down to "tracks"
  7:  */
  8: class Isoform extends \WebService {
  9: 
 10:     /**
 11:      * returns "right" or "left" depending on $strand>0
 12:      * @param int $strand
 13:      * @return String
 14:      */
 15:     private static function strand2dir($strand) {
 16:         return $strand > 0 ? 'right' : 'left';
 17:     }
 18: 
 19:     /**
 20:      * fill up with two spaces between each char to align protein and nucleotide sequences
 21:      * canvasXpress SHOULD be able to do that on its own, but fails in its current version
 22:      * @param String $sequence
 23:      * @return string
 24:      */
 25:     private static function space($sequence) {
 26:         $ret = "";
 27:         for ($i = 0; $i < strlen($sequence); $i++)
 28:             $ret .= $sequence{$i} . '  ';
 29:         return $ret;
 30:     }
 31: 
 32:     /**
 33:      * if strand is left, rewind string
 34:      * @param string $sequence
 35:      * @param int $strand
 36:      * @return string
 37:      */
 38:     private static function rewinds($sequence, $strand) {
 39:         if ($strand < 0)
 40:             return strrev($sequence);
 41:         return $sequence;
 42:     }
 43: 
 44:     /**
 45:      * @inheritDoc
 46:      */
 47:     public function execute($querydata) {
 48:         global $db;
 49: 
 50:         #UI hint
 51:         if (false)
 52:             $db = new \PDO();
 53: 
 54:         $stm_get_features = $db->prepare('SELECT * FROM get_isoform_graph(?)');
 55:         $stm_get_features->execute(array($querydata['query1']));
 56: 
 57:         $return = array();
 58:         $min = 0;
 59:         $max = 0;
 60: 
 61:         $last_row = null;
 62:         
 63:         //before reading this code, read the canvasXpress documentation!
 64: 
 65:         //(feature_id int, type_id int, residues text, seqlen int, fmin int, fmax int, strand smallint);
 66:         while ($row = $stm_get_features->fetch(\PDO::FETCH_ASSOC)) {
 67:             switch ($row['type_id']) {
 68:                 case CV_ISOFORM:
 69:                     $max = $row['seqlen'];
 70:                     $return[] = array(
 71:                         #'name' => 'Isoform',
 72:                         'type' => 'sequence',
 73:                         'subtype' => 'DNA',
 74:                         'data' => array(array(
 75:                                 'id' => $row['name'],
 76:                                 'sequence' => $row['residues'],
 77:                                 'translate' => array(-1, 3),
 78:                                 'dir' => 'right',
 79:                                 'offset' => 1
 80:                         ))
 81:                     );
 82:                     break;
 83:                 case CV_ANNOTATION_REPEATMASKER:
 84:                     // this would look better, but canvasXpress cuts datasets after 8 rows so each bar has to be it's own dataset
 85:                     //if (!isset($return['repeatmasker'])) {
 86:                         $return[] = array(
 87:                             #'name' => 'Repeatmasker',
 88:                             'type' => 'box',
 89:                             'fill' => 'rgb(255,25,51)',
 90:                             'outline' => 'rgb(0,0,0)',
 91:                             'data' => array()
 92:                         );
 93:                         $current_repeatmasker = &$return[count($return)-1];
 94:                     //}
 95:                     
 96:                     $current_repeatmasker['data'][] = array(
 97:                         'id' => $row['name'],
 98:                         'data' => array(array($row['fmin'], $row['fmax'])),
 99:                         'dir' => self::strand2dir($row['strand'])
100:                     );
101:                     break;
102:                 case CV_PREDPEP:
103:                     $last_predpep_row = $row;
104:                     $return[] = array(
105:                         #'name' => 'Predicted Peptides',
106:                         'type' => 'sequence',
107:                         'subtype' => 'DNA',
108:                         'fill' => 'rgb(255,255,51)',
109:                         'outline' => 'rgb(0,0,0)',
110:                         'data' => array(array(
111:                                 'id' => sprintf('predpep %d-%d'
112:                                         , $row['fmin'], $row['fmax']),
113:                                 'sequence' => self::rewinds(self::space($row['residues']), $row['strand']),
114:                                 'offset' => $row['fmin'],
115:                                 'dir' => 'right'#strand2dir($predpep['strand'])
116:                         ))
117:                     );
118:                     break;
119:                 case CV_ANNOTATION_INTERPRO:
120:                     // this would look better, but canvasXpress cuts datasets after 8 rows so each bar has to be it's own dataset
121:                     //if ($last_row['type_id'] != CV_ANNOTATION_INTERPRO) {
122:                         
123:                         $return[] = array(
124:                             #'name' => 'Interpro Domain',
125:                             'type' => 'box',
126:                             'fill' => 'rgb(20,255,51)',
127:                             'outline' => 'rgb(0,0,0)',
128:                             'data' => array()
129:                         );
130:                         $current_interpro = &$return[count($return)-1];
131:                     //}
132:                     $left = $last_predpep_row['fmin'] + ($row['fmin'] - 1) * 3;
133:                     $right = $left + ($row['fmax'] - $row['fmin'] + 1) * 3;
134:                     $current_interpro['data'][] = array(
135:                         'id' => $row['name'],
136:                         'data' => array(array($left, $right)),
137:                         'dir' => self::strand2dir($row['strand'])
138:                     );
139:                     break;
140:             }
141:             $last_row = $row;
142:         }
143:         return array('tracks' => array_values($return), 'min' => $min, 'max' => $max);
144:     }
145: 
146: }
147: 
148: ?>
149: