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+<?PHP
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+/* file: blast_align_image.php
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+ *
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+ * purpose: generate an image of HSPs for a given target
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+ *
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+ * URL paramters:
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+ * acc - target name
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+ * name - query name, false if none
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+ * tsize - target size
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+ * qsize - query size
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+ * hits - each hit represented in URL as:
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+ * targetstart_targetend_hspstart_hspend;
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+ * score - score for each hit
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+ *
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+ * Example: <url>blast_align_image.php?acc=chr2&name=query1&tsize=237068873&qsize=1411&hits=4263001_4262263_1_742;4260037_4259524_895_1411;4260405_4260248_740_897;192158716_192158843_612_742;&scores=722;473;155;51;
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+ *
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+ * history:
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+ * 09/23/10 Carson created
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+ * 04/16/12 eksc adapted into POPcorn code
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+ * 03/12/15 deepak Adapted code into Tripal BLAST
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+ */
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+
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+ /* include_once('../../inc/lib.php');
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+ session_start();
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+ $pc_system = getSystemInfoPC('sequence_search');
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+
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+ $acc = getCGIParamPC('acc', 'GP', '');
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+ $scores = getCGIParamPC('scores', 'GP', '');
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+ $links = getCGIParamPC('links', 'GP', '');
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+ $hits = getCGIParamPC('hits', 'GP', '');
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+ $tsize = intval(getCGIParamPC('tsize', 'GP', ''));
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+ $qsize = intval(getCGIParamPC('qsize', 'GP', ''));
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+ $name = getCGIParamPC('name', 'GP', '');
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+ */
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+ // extract hit information from hit param
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+function generateImage($acc = '', $scores, $hits, $tsize, $qsize, $name, $hit_name) {
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+ $tok = strtok($hits, ";");
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+ $b_hits = Array();
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+ while ($tok !== false) {
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+ $b_hits[] = $tok;
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+ $tok = strtok(";");
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+ }
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+
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+ // extract score information from score param
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+ $tokscr = strtok($scores, ";");
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+ $b_scores = Array();
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+ while ($tokscr !== false) {
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+ $b_scores[] = $tokscr;
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+ $tokscr = strtok(";");
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+ }
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+
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+ // image measurements
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+ $height = 200 + (count($b_hits) * 16);
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+ $width = 520;
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+
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+ $img = imagecreatetruecolor($width, $height);
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+
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+ $white = imagecolorallocate($img, 255, 255, 255);
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+ $black = imagecolorallocate($img, 0, 0, 0);
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+ $darkgray = imagecolorallocate($img, 100, 100, 100);
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+ $strong = imagecolorallocatealpha($img, 202, 0, 0, 15);
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+ $moderate = imagecolorallocatealpha($img, 204, 102, 0, 20);
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+ $present = imagecolorallocatealpha($img, 204, 204, 0, 35);
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+ $weak = imagecolorallocatealpha($img, 102, 204, 0, 50);
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+ $gray = imagecolorallocate($img, 190, 190, 190);
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+ $lightgray = imagecolorallocate($img, 230, 230, 230);
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+
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+ imagefill($img, 0, 0, $lightgray);
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+
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+ // Target coordinates
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+ $maxlength = 300;
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+ $t_length = ($tsize > $qsize)
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+ ? $maxlength : $maxlength - 50;
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+ $q_length = ($qsize > $tsize)
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+ ? $maxlength : $maxlength - 50;
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+
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+ $tnormal = $t_length / $tsize;
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+ $qnormal = $q_length / $qsize;
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+
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+ $t_ystart = 30;
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+ $t_yend = $t_ystart + 20;
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+
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+ $t_xstart = 50;
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+ $t_xend = $t_xstart + $t_length;
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+ $t_center = $t_xstart + ($t_length / 2);
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+
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+ // Target labels
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+ $warn = '"'. $hit_name . '"';
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+ imagestring($img, 5, $t_xstart, $t_ystart-20, $acc.$warn, $black);
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+ imagestring($img, 3, 5, $t_ystart+2, "Target", $black);
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+
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+ // Draw bar representing target
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+ imagefilledrectangle($img, $t_xstart, $t_ystart, $t_xend, $t_yend, $gray);
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+ imagerectangle($img, $t_xstart, $t_ystart, $t_xend, $t_yend, $darkgray);
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+
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+ // query coordinates
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+ $q_maxheight = 250;
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+ $q_ystart = $t_yend + 100;
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+ $q_yend = $q_ystart + 20;
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+
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+ $q_xstart = $t_center - $q_length / 2;
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+ $q_xend = $q_xstart + $q_length;
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+
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+ $q_center = ($q_xend + $q_xstart) / 2;
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+ $q_xwidth = $q_xend - $q_xstart;
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+
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+ // Query labels
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+ imagestring($img, 5, $q_xstart, $q_yend+2, $name, $black);
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+ imagestring($img, 3, $q_xstart, $q_ystart+2, 'Query', $black);
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+
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+ // Draw bar representing query
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+ imagefilledrectangle($img, $q_xstart, $q_ystart, $q_xend, $q_yend, $gray);
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+ imagerectangle($img ,$q_xstart, $q_ystart, $q_xend, $q_yend, $darkgray);
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+
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+ // HSP bars will start here
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+ $hsp_bary = $q_yend + 20;
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+
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+ // Draw solids for HSP alignments
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+ for ($ii=count($b_hits)-1; $ii>=0; $ii--) {
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+ // alignment
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+
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+ $cur_hit = $b_hits[$ii];
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+ $cur_score = intval($b_scores[$ii]);
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+
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+ // set color according to score
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+ $cur_color = $darkgray;
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+ if ($cur_score > 200) {
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+ $cur_color = $strong;
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+ }
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+ else if ($cur_score > 80 && $cur_score <= 200) {
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+ $cur_color = $moderate;
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+ }
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+ else if ($cur_score > 50 && $cur_score <= 80) {
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+ $cur_color = $present;
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+ }
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+ else if ($cur_score > 40 && $cur_score <= 50) {
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+ $cur_color = $weak;
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+ }
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+
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+ $t_start = $tnormal * intval(strtok($cur_hit, "_")) + $t_xstart;
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+ $t_end = $tnormal * intval(strtok("_")) + $t_xstart;
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+ $q_start = $qnormal * intval(strtok("_")) + $q_xstart;
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+ $q_end = $qnormal * intval(strtok("_")) + $q_xstart;
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+
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+ $hit1_array = array($t_start, $t_yend, $t_end, $t_yend, $q_end,
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+ $q_ystart, $q_start, $q_ystart);
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+
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+ // HSP coords
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+ imagefilledpolygon($img, $hit1_array, 4, $cur_color);
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+
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+ }//each hit
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+
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+ // Draw lines over fills for HSP alignments
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+ for ($ii=0; $ii<count($b_hits); $ii++) {
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+ // alignment
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+
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+ $cur_hit = $b_hits[$ii];
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+ $t_start = $tnormal * intval(strtok($cur_hit, "_")) + $t_xstart;
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+ $t_end = $tnormal * intval(strtok("_")) + $t_xstart;
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+ $q_start = $qnormal * intval(strtok("_")) + $q_xstart;
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+ $q_end = $qnormal * intval(strtok("_")) + $q_xstart;
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+
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+ $hit1_array = array($t_start, $t_yend, $t_end, $t_yend, $q_end, $q_ystart,
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+ $q_start, $q_ystart,);
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+
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+ imagerectangle($img, $t_start, $t_ystart, $t_end, $t_yend, $black);
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+ imagerectangle($img, $q_start, $q_ystart, $q_end, $q_yend, $black);
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+ imagepolygon ($img, $hit1_array, 4, $black);
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+
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+ // show HSP
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+
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+ imagestring($img, 3, 2, $hsp_bary, ($acc ."HSP" . ($ii + 1)), $black);
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+
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+ $cur_score = intval($b_scores[$ii]);
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+
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+ // set color according to score
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+ $cur_color = $darkgray;
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+ if ($cur_score > 200) {
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+ $cur_color = $strong;
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+ }
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+ else if ($cur_score > 80 && $cur_score <= 200) {
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+ $cur_color = $moderate;
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+ }
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+ else if ($cur_score > 50 && $cur_score <= 80) {
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+ $cur_color = $present;
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+ }
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+ else if ($cur_score > 40 && $cur_score <= 50) {
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+ $cur_color = $weak;
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+ }
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+
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+ imagefilledrectangle($img, $q_start, $hsp_bary, $q_end, $hsp_bary+10, $cur_color);
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+ $hsp_bary += 15;
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+ }//each hit
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+
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+ // Draw the key
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+
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+ $xchart = 390;
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+ $ychart = 10;
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+ $fontsize = 4;
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+ $yinc = 20;
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+ $ywidth = 7;
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+ $xinc = 10;
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+
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+ imagestring($img, 5, $xchart, $ychart - 5, "Bit Scores", $black);
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+
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+ imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 1) + $ywidth, ">= 200" , $black);
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+ imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 2) + $ywidth, "80 - 200" , $black);
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+ imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 3) + $ywidth, "50 - 80" , $black);
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+ imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 4) + $ywidth, "40 - 50" , $black);
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+ imagestring($img, $fontsize, $xchart + $yinc + $xinc,$ychart + ($yinc * 5) + $ywidth, "< 40" , $black);
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+
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+ imagefilledRectangle($img, $xchart, $ychart + ($yinc * 1) + $xinc, $xchart + $yinc, $ychart + ($yinc * 2), $strong);
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+ imagefilledRectangle($img, $xchart, $ychart + ($yinc * 2) + $xinc, $xchart + $yinc, $ychart + ($yinc * 3), $moderate);
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+ imagefilledRectangle($img, $xchart, $ychart + ($yinc * 3) + $xinc, $xchart + $yinc, $ychart + ($yinc * 4), $present);
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+ imagefilledRectangle($img, $xchart, $ychart + ($yinc * 4) + $xinc, $xchart + $yinc, $ychart + ($yinc * 5), $weak);
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+ imagefilledRectangle($img, $xchart, $ychart + ($yinc * 5) + $xinc, $xchart + $yinc, $ychart + ($yinc * 6), $darkgray);
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+
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+ return $img;
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+ // write out images
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+// header("Content-type: image/png");
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+// imagepng($img);
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+}
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+?>
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ekcannon