a bunch of tweaks

genetify/controls.css

@@ -108,13 +108,20 @@
 
 /* results table */
 
+#genetify_results {
+    position:absolute; top:0%; right:0%;
+}
+
 #genetify_results_table {
     /*same as control panel*/
     opacity: 0.95;
     font-family:"Lucida Grande", Tahoma, Arial, Verdana, sans-serif;
     font-size:0.9em;
+/*    position: fixed;*/
 
-    position: absolute;
+    /* TODO:  */
+/*    height: 50%;*/
+/*    overflow: scroll;*/
     left: 5%;
     bottom: 20%;
 
@@ -125,6 +132,7 @@
 
 }
 #genetify_results_table th {
+    text-align: center;
     font-weight: bold;
 }
 #genetify_results_table td {
@@ -140,3 +148,12 @@
     text-align: center;
     font-style: italic;
 }
+
+#genetify_results_table td.genetify_col_weight {
+    background-color: rgb(240,240,240);
+}
+
+#genetify_results_table .genetify_col_stddev,
+#genetify_results_table .genetify_col_share {
+    display: none;
+}

genetify/demo/index.php

@@ -23,8 +23,10 @@
 
     <style type="text/css" media="screen">
         /* override controls.css */
-        #genetify_results_table {
+        #genetify_results {
             position: static;
+        }
+        #genetify_results_table {
             width: 200px;
         }
         #genetify_results_table .genetify_gene_row {

genetify/demo/test-sections/combinations.html

@@ -35,7 +35,7 @@
         <td>
             <div class="container">
                 <style type="text/css" media="screen">
-                    .genetify_enabled { display: inline; }
+                    span.genetify_enabled { display: inline; }
                     .picture { width: 200px; height:140px; }
                     .description { font-weight: bold; }
                 </style>

genetify/demo/test.php

@@ -10,6 +10,7 @@
             USE_RESULTS_CACHE: true,
             USE_COOKIE: false,
             LOAD_CONTROLS: true,
+            SHOW_RESULTS: true,
             NAMESPACE: '/genetify/',
             //TODO: change on server
             REMOTE_BASE_URL: '..'
@@ -152,6 +153,7 @@
 	</table>
 
 	<script type="text/javascript" charset="utf-8">
+
         // genetify.vary('elements');
         // genetify.test.printProbs();
 
@@ -163,15 +165,14 @@
 		// console.log(genetify.cookie.read('genetify_genome_page'));
 		// console.log(genetify.cookie.read('genetify_genome'));
 
-        self = genetify.test;
+        // self = genetify.test;
         // self.variants('mygene', ['A', 'B', 'C']);
         // self.variants('.mygene', ['A', 'B']);
         // self.variants('.myothergene', ['A', 'B', 'C']);
         // self.variants('main', ['AdditiveCSSRules', 'Elements']);
 
         // self.results('mygene', ['A', 'B', 'C']);
 
-        // genetify.controls.showResults();
 	</script>
 
     <!-- <a href="#" onclick="genetify.record.goal('adfs',-1); return false;">test error</a>

genetify/genetify.js

@@ -27,8 +27,10 @@ var genetify = {
         USE_COOKIE: true,
         NO_VARYING: false,
         LOAD_CONTROLS: false,
+        SHOW_RESULTS: false,
         NAMESPACE: window.location.pathname
         //TODO: NO_SCANNING
+        //TODO: DEBUG
     },
 
     genome: {},
@@ -66,19 +68,36 @@ var genetify = {
         };
         genetify._addListener(window, 'onclick', warnOnClick);
 
+        //TODO: this causes an error in IE
         // covers case sensitivity bug in Safari
-        genetify.utils.assert(window.document.doctype, 'Document does not have a DOCTYPE');
+        // genetify.utils.assert(window.document.doctype, 'Document does not have a DOCTYPE');
 
         if (window.location.protocol.indexOf('file:') != -1){
             genetify.config.REMOTE_BASE_URL = genetify.config.REMOTE_BASE_URL.replace('file:', 'http:');
         }
 
         if (genetify.config.LOAD_CONTROLS){
-            window.onload = function(){
+            genetify._addListener(window, 'onload', function(){
                 genetify.controls.load();
-            };
+            });
+        }
+
+        if (genetify.config.SHOW_RESULTS){
+            genetify._addListener(window, 'onload', function(){
+                genetify.controls.showResults();
+            });
         }
 
+        genetify._addListener(window, 'onkeydown', function(e){
+            if (e.ctrlKey){
+                var key = e.charCode || e.keyCode;
+                if (key == 71 ){ // g
+                    genetify.controls.load();
+                    genetify.controls.showResults();
+                }
+            }
+        });
+
         genetify._checkQueryString(); //because of links from GA
 
         genetify.cookie.init();
@@ -92,7 +111,9 @@ var genetify = {
             }
 
             // TODO: make this optional as speed optimization
-            genetify._checkCSS(['.v', '.genetify_enabled', '.genetify_disabled']);
+            genetify._addListener(window, 'onload', function(){
+                genetify._checkCSS(['.v', '.genetify_enabled', '.genetify_disabled']);
+            });
             //TODO: parse only CSS after init()
             //TODO: return objects instead of setting
             genetify._registerSystemObjects();
@@ -204,7 +225,7 @@ var genetify = {
             'javascript': '_v',
             'elements': '\\s+v\\s+'
         };
-        var variantNamePattern = '([A-Z0-9_$][a-zA-Z0-9_$]*)';
+        var variantNamePattern = '([A-Z0-9_$][a-zA-Z0-9_$\-]*)';
         for (var p in markerPatternDict){
             var pattern = geneNamePattern + markerPatternDict[p] + variantNamePattern;
             if (p == 'elements'){
@@ -1483,6 +1504,7 @@ genetify.controls = {
             for (var j=0; j < cols.length; j++){
 
                 var extra = ' class="genetify_col_' + rows[0][j] + '"';
+                extra += ' title="The ' + rows[0][j] + ' of variant ' + cols[0] + ' is ' + cols[j] + '"';
 
                 if (cols.length === 1){
                     extra = ' colspan="' + rows[i+1].length + '"';

genetify/init.php

@@ -1,4 +1,6 @@
 <?php
+$start_time = microtime(1);
+
 require_once('CONFIG.php');
 
 $mysqli = new mysqli($DB['host'], $DB['user'], $DB['password'], $DB['database']);

genetify/reader.php

@@ -32,7 +32,7 @@ function get_results($domain, $page){
 
     $sql = "SELECT * FROM result
         WHERE domain_name = '$domain' AND page_name = '$page'
-        ORDER BY gene_name, variant_name = '__original__' DESC, variant_name";
+        ORDER BY gene_name, variant_weight DESC, variant_name = '__original__' DESC, variant_name";
 
     $result = $mysqli->query($sql);
     $rows = array();

genetify/recorder.php

@@ -19,23 +19,23 @@ function test()
     $tests['pageview']['observed'] = file_get_contents($base_url . '/recorder.php?return=text&domain=test.com&page=/test.html&genome=main=Elements,mygene=C,myothergene=__original__&pageview_xid=0&load_time=7&init_time=7&results_time=14&idle_time=86&vary_time=17&vary_call=elements');
 
     //prevent false alarm on first run after install
-    $tests['pageview']['observed'] = str_replace('visitor: 1 rows inserted', '', $tests['pageview']['observed']);
+    $tests['pageview']['observed'] = str_replace('visitor: 1 inserted', '', $tests['pageview']['observed']);
 
     $tests['pageview']['expected'] = '
-page: 1 rows inserted
-genome: 1 rows inserted
-stats_by_genome: 1 rows inserted
-pageview: 1 rows inserted
-gene: 3 rows inserted
-variant: 3 rows inserted
-genome_variant_link: 3 rows inserted
-stats_by_variant: 3 rows inserted';
+page: 1 inserted
+genome: 1 inserted
+stats_by_genome: 1 inserted
+pageview: 1 inserted
+gene: 3 inserted
+variant: 3 inserted
+genome_variant_link: 3 inserted
+stats_by_variant: 3 inserted';
 
     $tests['goal']['observed'] = file_get_contents($base_url . '/recorder.php?goal=test&value=100&pageview_xid=0&return=text');
-    $tests['goal']['expected'] = 'goal: 1 rows inserted
-stats_by_genome: 2 rows inserted
-stats_by_variant: 6 rows inserted
-result: 3 rows inserted';
+    $tests['goal']['expected'] = 'goal: 1 inserted
+stats_by_genome: 2 inserted
+stats_by_variant: 6 inserted
+result: 3 inserted';
 
     $tests['results']['observed'] = file_get_contents($base_url . '/reader.php?callback=genetify.handleResults&domain=test.com&page=/test.html');
     $tests['results']['expected'] = 'genetify.handleResults({"main":{"Elements":{"count":1,"sum":100,"avg":100,"stddev":0,"share":1,"weight":1}},"mygene":{"C":{"count":1,"sum":100,"avg":100,"stddev":0,"share":1,"weight":1}},"myothergene":{"__original__":{"count":1,"sum":100,"avg":100,"stddev":0,"share":1,"weight":1}}})';
@@ -136,13 +136,15 @@ function record_error($message, $line_number, $domain, $page)
 
 function render_status($table)
 {
+    global $start_time;
+
     if (@$_REQUEST['return'] == 'text' || @$_REQUEST['callback']) {
         foreach ($GLOBALS['affected_tables'] as $t => $value) {
-            $lines[] = "$t: $value rows inserted";
+            $lines[] = "$t: $value inserted";
         }
         //TODO: suppress only for auto test
         if (!@$_REQUEST['return'] == 'text') {
-            $lines[] = round(1000 * (microtime(1) - $_SERVER['REQUEST_TIME'])) . 'ms';
+            $lines[] = round(1000 * (microtime(1) - $start_time)) . 'ms';
         }
         callback(@$_REQUEST['callback'] ? implode(', ', $lines) : implode("\n", $lines));
     }