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Commit 37a55320 authored by Jerome Mariette's avatar Jerome Mariette
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add krona view

parent 01ec1ee9
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ui/nG6/class.tx_nG6_eid.php
View file @ 37a55320
......@@ -242,6 +242,141 @@ class tx_nG6_eid {
}
}
print tx_nG6_utils::get_octet_string_representation($full_size);
// If asked the krona page
} else if ($type == 'get_krona') {
$myFile = "/tmp/tmp.txt";
$fh = fopen($myFile, 'w');
$nb_file = trim(t3lib_div::_GP('nb_file'));
$max = intval($nb_file) - 1;
$data_folder = trim(t3lib_div::_GP('data_folder'));
$doc = new DomDocument();
$data_root = $doc->createElement('data');
$data_root = $doc->appendChild($data_root);
$magnitude = $doc->createElement('magnitude');
$magnitude->setAttribute("attribute", "g");
$magnitude = $data_root->appendChild($magnitude);
$magnitudet = $doc->createTextNode('');
$magnitudet = $magnitude->appendChild($magnitudet);
$color = $doc->createElement('color');
$color->setAttribute("attribute", "g");
$color->setAttribute("valueStart", "0");
$color->setAttribute("valueEnd", "40");
$color->setAttribute("hueStart", "120");
$color->setAttribute("hueEnd", "360");
$color = $data_root->appendChild($color);
$colort = $doc->createTextNode('');
$colort = $color->appendChild($colort);
$attributes = $doc->createElement('attributes');
$attributes->setAttribute("g", "Grams");
$attributes->setAttribute("dva", "DVA (%)");
$attributes = $data_root->appendChild($attributes);
$attributest = $doc->createTextNode('');
$attributest = $attributes->appendChild($attributest);
$datasets = $doc->createElement('datasets');
$datasets->setAttribute("names", "Brand X,Brand Y");
$datasets = $data_root->appendChild($datasets);
$datasetst = $doc->createTextNode('');
$datasetst = $datasets->appendChild($datasetst);
foreach (range(0, $max) as $i) {
$file_path = trim(t3lib_div::_GP('file_path_'.(string)$i));
$file_path = $data_folder."/".$file_path;
$file_name = trim(t3lib_div::_GP('file_name_'.(string)$i));
// If the file exists
if (file_exists($file_path)) {
$lines = file($file_path);
// Loop through our array
foreach ($lines as $line_num => $line) {
if ($line != "") {
$mparts = explode("\t", $line);
if ($mparts[0] != "taxlevel" and $mparts[0] != "0") {
// If this guy doesnt exist yet
$id_searched = str_replace(".", "_", "node_".$mparts[1]);
if (count($doc->getElementById($id_searched)) == 0) {
$parentl = implode("_", array_slice(explode(".", $mparts[1]), 0, -1));
// If no parent yet, this is the root
/*if (count($doc->getElementById(str_replace(".", "_", "node_".$parentl))) == 0) {
$current_node = $doc->createElement('node');
$current_node->setAttribute("id", "node_"+str_replace("\.", "_", $mparts[1]));
$current_node->setAttribute("name", $mparts[2]);
$current_node->setAttribute("g", $mparts[4]);
$current_node = $dom->getElementById("data_root").appendChild($current_node);
$current_nodet = $doc->createTextNode('');
$current_nodet = $current_node->appendChild($current_nodet);
} else {
$current_node = $doc->createElement('node');
$current_node->setAttribute("id", "node_"+str_replace("\.", "_", $mparts[1]));
$current_node->setAttribute("name", $mparts[2]);
$current_node->setAttribute("g", $mparts[4]);
$current_node = $dom->getElementById("node_"+$parentl).appendChild($current_node);
$current_nodet = $doc->createTextNode('');
$current_nodet = $current_node->appendChild($current_nodet);
}*/
}
}
}
}
}
}
$xml_string = $doc->saveXML();
fwrite($fh, $xml_string);
fclose($fh);
$val = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">';
$val .= '<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="fr" lang="fr">';
$val .= '<head>';
$val .= '</head>';
$val .= '<body>';
$val .= '<div id="options" style="position:absolute;left:0;top:0"></div>';
$val .= '<div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"></div>';
$val .= '<canvas id="canvas" width="100%" height="100%">This browser does not support HTML5</canvas><div>';
$val .= '<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" visibility="hide"/>';
$val .= '<script name="tree" src="http://krona.sourceforge.net/krona-1.1.js"></script>';
$val .= '<data id="data_root">';
$val .= '<magnitude attribute="g"></magnitude>';
$val .= '<color attribute="g" valueStart="0" valueEnd="40" hueStart="120" hueEnd="360"></color>';
$val .= '<attributes g="Grams" dva="DVA (%)"></attributes>';
$val .= '<datasets names="Brand X,Brand Y"></datasets>';
$val .= '<node id="data1" name="Granola serving" g="55,55">';
$val .= '<node id="data2" name="Fats" g="8,6" dva="12">';
$val .= '<node id="data3" name="Saturated fat" g="2,1" dva="10"></node>';
$val .= '<node id="data4" name="Unsaturated fat" g="6,5">';
$val .= '<node name="Monounsaturated fat" g="3,1"></node>';
$val .= '<node name="Polyunsaturated fat" g="3,4"></node>';
$val .= '</node>';
$val .= '</node>';
$val .= '<node name="Carbohydrates" g="39,41" dva="13">';
$val .= '<node name="Sugars" g="3,5"></node>';
$val .= '<node name="Dietary fiber" g="4,8" dva="16"></node>';
$val .= '</node>';
$val .= '<node name="protein" g="5,6"></node>';
$val .= '</node>';
$val .= '</data>';
$val .= '</div>';
$val .= '</body>';
$val .= '</html>';
print $val;
}
}
......
ui/nG6/pi1/analyzes/MothurClassifyAnalyse.js
View file @ 37a55320
......@@ -541,6 +541,98 @@ $(function () {
}
return data;
}
$(".phylogeny-krona-view-btn").click(function() {
if ($(":checked[id^=chk_sample_]").size() == 0) {
$("#user_information_dialog").dialog("option", "title", $("#information_error_title").val());
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>" + $("#information_dialog_zero_check").val() + "</div>").dialog("open");
var buttons = {};
buttons[$("#ok_btn_label").val()] = function(){ $(this).dialog("close"); }
$("#user_information_dialog").dialog('option', 'buttons', buttons);
} else {
$("#img_dialog").dialog("option", "title", "nG6 - " + $("#analyse_name").val());
$("#img_dialog").dialog("option", "width", 1000);
$("#img_dialog").dialog("option", "height", 700);
var url_val = "index.php?eID=tx_nG6&type=get_krona";
var ind = 0;
$(":checked[id^=chk_sample_]").each(function(){
index = $(this).attr("id").split("_")[2];
var file_basename = $("#phylogeny_file_"+index).val().split("/");
file_basename = file_basename[file_basename.length-1];
url_val += "&file_path_" + ind + "=" + file_basename;
url_val += "&file_name_" + ind + "=" + $("#sample_id_"+index).html();
ind++;
});
url_val += "&nb_file="+ind+"&data_folder="+$("#analysis_folder").val();
$("#img_dialog").html('<iframe frameborder="0" src="'+url_val+'" style="width:100%; height:100%;"></iframe>').dialog("open");
//$("#frameDemo").contents().find("a").css("background-color","#BADA55");
/*var ajax = new Array();
var samples = new Array();
var index = "";
$(":checked[id^=chk_sample_]").each(function(){
index = $(this).attr("id").split("_")[2];
ajax.push($.ajax($("#phylogeny_file_"+index).val()));
samples.push($("#sample_id_"+index).html());
});
/*$.when.apply($, ajax).done(function(){
/*var data_names = '';
/*for (sample in samples) {
data_names += samples[sample] + ","
}
data_names = data_names.substring(0,data_names.length-1);
var data_val = $('<data><magnitude attribute="g"></magnitude><color attribute="g" valueStart="0" valueEnd="40" hueStart="120" hueEnd="360"></color><attributes g="Grams" dva="DVA (%)"></attributes><datasets names="' + data_names + '"></datasets><node id="data_root" name="data_root" g="500"></node></data>');
// for each taxonomy files
/*for( var i = 0; i < arguments.length; i++ ) {
var lines = arguments[i][0].split("\n");
var lines = arguments[0].split("\n");
for (j=0; j<lines.length; j++) {
if (lines[j] != "") {
mparts = lines[j].split("\t");
if (mparts[0] != "taxlevel" && mparts[0] != "0") {
// If this guy doesnt exist yet
if (data_val.find("#node_"+mparts[1].replace(/\./g, '_')).length == 0) {
parentl = mparts[1].split(".").slice(0,-1).join("_");
// If no parent yet, this is the root
if (data_val.find("#node_"+parentl).length == 0) {
data_val.find("#data_root").append('<node id="node_'+mparts[1].replace(/\./g, '_')+'" name="'+mparts[2]+'" g="'+mparts[4]+'"></node>');
} else {
data_val.find("#node_"+parentl).append('<node id="node_'+mparts[1].replace(/\./g, '_')+'" name="'+mparts[2]+'" g="'+mparts[4]+'"></node>');
}
}
}
}
}
}
var datav = "<data>" + data_val.html() + "</data>"
datav = datav.replace(/"/g,'&#34;');*/
/*var data_val = '<data id="data_root">';
data_val += '<magnitude attribute="g"></magnitude>';
data_val += '<color attribute="g" valueStart="0" valueEnd="40" hueStart="120" hueEnd="360"></color>';
data_val += '<attributes g="Grams" dva="DVA (%)"></attributes>';
data_val += '<datasets names="Brand X,Brand Y"></datasets>';
data_val += '<node id="data1" name="Granola serving" g="55,55">';
data_val += '<node id="data2" name="Fats" g="8,6" dva="12">';
data_val += '<node id="data3" name="Saturated fat" g="2,1" dva="10"></node>';
data_val += '<node id="data4" name="Unsaturated fat" g="6,5">';
data_val += '<node name="Monounsaturated fat" g="3,1"></node>';
data_val += '<node name="Polyunsaturated fat" g="3,4"></node>';
data_val += '</node>';
data_val += '</node>';
data_val += '<node name="Carbohydrates" g="39,41" dva="13">';
data_val += '<node name="Sugars" g="3,5"></node>';
data_val += '<node name="Dietary fiber" g="4,8" dva="16"></node>';
data_val += '</node>';
data_val += '<node name="protein" g="5,6"></node>';
data_val += '</node>';
data_val += '</data>';
data_val = data_val.replace(/"/g,'&#34;');*/
//});
}
});
$(".phylogeny-tree-view-btn").click(function() {
if ($(":checked[id^=chk_sample_]").size() == 0) {
......
ui/nG6/pi1/analyzes/MothurClassifyAnalyse.tpl
View file @ 37a55320
......@@ -30,6 +30,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=results}
<div id="user_information_dialog" title=""></div>
<input type="hidden" id="analyse_name" value="{$analyse.name}"/>
<input type="hidden" id="data_folder" value="{$data_folder}"/>
<input type="hidden" id="analysis_folder" value="{$data_folder|cat:$analyse.directory}"/>
<input type="hidden" id="nb_sequences" value="{$llang.MothurClassifyAnalyse_nb_sequences}"/>
<input type="hidden" id="sequences" value="{$llang.MothurClassifyAnalyse_sequences}"/>
<input type="hidden" id="click_to_view" value="{$llang.MothurClassifyAnalyse_click_to_view}"/>
......@@ -80,7 +82,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<tr>
<th align="left" colspan="10">
{$llang.toolbar_title}
<button type="button" class="btn pill-l phylogeny-bar-view-btn"><span><span>{$llang.MothurClassifyAnalyse_barview_button}</span></span></button><button type="button" class="btn pill-c phylogeny-tree-view-btn"><span><span>{$llang.MothurClassifyAnalyse_treeview_button}</span></span></button><button type="button" class="btn pill-r venn-view-btn"><span><span>{$llang.MothurClassifyAnalyse_vennview_button}</span></span></button>
<button type="button" class="btn pill-l phylogeny-bar-view-btn"><span><span>{$llang.MothurClassifyAnalyse_barview_button}</span></span></button><button type="button" class="btn pill-c phylogeny-krona-view-btn"><span><span>{$llang.MothurClassifyAnalyse_kronaview_button}</span></span></button><button type="button" class="btn pill-r venn-view-btn"><span><span>{$llang.MothurClassifyAnalyse_vennview_button}</span></span></button>
</th>
</tr>
</tfoot>
......
ui/nG6/pi1/class.tx_nG6_pi1.php
View file @ 37a55320
......@@ -300,6 +300,7 @@ class tx_nG6_pi1 extends tslib_pibase {
$smarty->assign('analyse', $analyse);
$analysis_size = tx_nG6_db::get_analysis_size($this->piVars['analyze_id'], $this->conf['data']);
$smarty->assign('analyse_size', tx_nG6_utils::get_octet_string_representation($analysis_size));
$smarty->assign('data_folder', $this->conf["data"]);
// Then select analyse results
$results = tx_nG6_db::select_analyse_results($this->piVars['analyze_id']);
......
ui/nG6/pi1/locallang.xml
View file @ 37a55320
......@@ -331,7 +331,7 @@
<label index="MothurClassifyAnalyse_results_title">Classifying results</label>
<label index="MothurClassifyAnalyse_nb_classified_sequences">Number of sequences</label>
<label index="MothurClassifyAnalyse_barview_button">Bar view</label>
<label index="MothurClassifyAnalyse_treeview_button">Tree view</label>
<label index="MothurClassifyAnalyse_kronaview_button">Krona view</label>
<label index="MothurClassifyAnalyse_nb_sequences">Number of sequences</label>
<label index="MothurClassifyAnalyse_click_to_view">Click to view ###CATEGORY###</label>
<label index="MothurClassifyAnalyse_sequences">sequences</label>
......@@ -684,7 +684,7 @@
<label index="MothurClassifyAnalyse_params_title">Commandes et paramètres mothur utilisées</label>
<label index="MothurClassifyAnalyse_nb_classified_sequences">Nombre de séquences</label>
<label index="MothurClassifyAnalyse_barview_button">Bar view</label>
<label index="MothurClassifyAnalyse_treeview_button">Tree view</label>
<label index="MothurClassifyAnalyse_kronaview_button">Krona view</label>
<label index="MothurClassifyAnalyse_nb_sequences">Nombre de séquences</label>
<label index="MothurClassifyAnalyse_sequences">séquences</label>
<label index="MothurClassifyAnalyse_click_to_view">Cliquez pour voir la distribution de ###CATEGORY###</label>
......
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