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personId parsed from file... no longer clears extension
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ivp08001 committed Jan 12, 2016
1 parent f784102 commit eb7e8bb
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Showing 3 changed files with 93 additions and 29 deletions.
115 changes: 87 additions & 28 deletions VQI_PathwayEditor.js
Expand Up @@ -29,7 +29,9 @@ var VQI_PathwayEditor = function (parent) {
// Globals
var self = this;
var types = ["bundleOne", "bundleTwo", "gene", "geneProduct", "protein", "rna", "microRNA", "kinase", "ligand", "receptor", "biologicalProcess", "triangle", "rectangle", "circle", "ellipse", "pentagon", "hexagon", "heptagon", "octagon", "star", "diamond", "vee", "rhomboid", "label"];
var states = [];
var personId = "";
var pathName = "";
var states = [];
var stateRecycle = [];
var selectedForQueryNodes = [];
var selectedForEditNodes = [];
Expand Down Expand Up @@ -90,6 +92,7 @@ var VQI_PathwayEditor = function (parent) {
strVar += " <button class=\"btn btn-primary dropdown-toggle\" type=\"button\" data-toggle=\"dropdown\">Process<span class=\"caret\"><\/span><\/button>";
strVar += " <ul class=\"dropdown-menu\">";
strVar += " <li><input id=\"" + parent + "-findpath\" value=\"Find Pathway\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
strVar += " <li><input id=\"" + parent + "-find-paths-all-drop\" value=\"Find All Pathways\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
strVar += " <li><input id=\"" + parent + "-find-object\" value=\"Find Object\" type=\"button\" class=\"btn btn-link disabled\"><\/input><\/li>";
strVar += " <\/ul>";
strVar += " </div>";
Expand Down Expand Up @@ -117,15 +120,15 @@ var VQI_PathwayEditor = function (parent) {
strVar += " <\/div>";
strVar += " <\/nav>";
strVar += " <div id=\"" + parent + "-dialog-table\" title=\"Result\">";
strVar += " <table id=\"" + parent + "-inner-table\" class=\"table table-hover\">";
strVar += " <tr>";
strVar += " <td>name<\/td>";
strVar += " <td>percentage<\/td>";
strVar += " <td>rna distance<\/td>";
strVar += " <td>cnv distance<\/td>";
strVar += " <td>mut distance<\/td>";
strVar += " <\/tr>";
strVar += " <\/table>";
strVar += " <table id=\"" + parent + "-inner-table\" class=\"table table-hover table-condensed\">";
strVar += " <tr>";
strVar += " <td>name<\/td>";
strVar += " <td>percentage<\/td>";
strVar += " <td>rna distance<\/td>";
strVar += " <td>cnv distance<\/td>";
strVar += " <td>mut distance<\/td>";
strVar += " <\/tr>";
strVar += " <\/table>";
strVar += " <\/div>";
strVar += " <div id=\"" + parent + "-dialog-form-save-as-pathway\" title=\"SaveAs\">";
strVar += " <form role=\"form\">";
Expand All @@ -144,6 +147,15 @@ var VQI_PathwayEditor = function (parent) {
strVar += " <input type=\"submit\" class=\"btn btn-default\" tabindex=\"-1\" style=\"position:absolute; top:-1000px\"><\/input>";
strVar += " <\/fieldset>";
strVar += " <\/form>";
strVar += " <\/div>";
strVar += " <div id=\"" + parent + "-dialog-form-configure-pathway\" title=\"Configure Pathway\">";
strVar += " <form role=\"form\">";
strVar += " <div class =\"form-group\">";
strVar += " <label for=\"" + parent + "-configure-person-id\">person-id:<\/label>";
strVar += " <input type=\"text\" class=\"form-control\" name=\"" + parent + "-configure-person-id\" id=\"" + parent + "-configure-person-id\"><br>";
strVar += " <input id=\"" + parent + "-apply-configure-person-id\" value=\"Apply\" type=\"button\" class=\"btn btn-link\"><\/input>";
strVar += " </div>";
strVar += " <\/form>";
strVar += " <\/div>";
strVar += " <div id=\"" + parent + "-dialog-bundle\" title=\"Bundle\">";
strVar += " <form role=\"form\">";
Expand Down Expand Up @@ -306,7 +318,6 @@ var VQI_PathwayEditor = function (parent) {
strVar += " <div id=\"" + parent + "-cy\" style=\"height: 100%;width: 100%;position: absolute; left: 0;\"><\/div>";

document.getElementById(parent).innerHTML = strVar;
sorttable.makeSortable(document.getElementById(parent + '-inner-table'));

$(function () {// on dom ready

Expand All @@ -321,7 +332,8 @@ var VQI_PathwayEditor = function (parent) {
var data = '{"format_version" : "1.0","generated_by" : "cytoscape-3.2.1","target_cytoscapejs_version" : "~2.1","data" :{"shared_name":"","ID":"","BOARDWIDTH":"","BOARDHEIGHT":"","LICENSE":"CC BY 2.0","ORGANISM":"","NAME":"","INSTRUCTION":"","AUTHOR":"","VERSION":"","PATHWAY_TYPE":"original","SUID":205,"__Annotations":[],"selected":true},"elements" : {"nodes" :[],"edges" :[]}}'
var obj = JSON.parse(data);
var title = document.getElementById(parent + "-pathway-title");
title.innerHTML = name;
pathName = name;
title.innerHTML = pathName+"<small>"+personId+"</small>";
removeHeroUnit();
setElements(obj);
save(obj, name);
Expand Down Expand Up @@ -400,6 +412,10 @@ var VQI_PathwayEditor = function (parent) {
function onChangeColoringFile(event) {
var reader = new FileReader();
reader.onload = onColoringReaderLoad;
// personId = event.target.files[0].name.substring(0,event.target.files[0].name.indexOf("."))
personId = event.target.files[0].name;
var title = document.getElementById(parent + "-pathway-title");
title.innerHTML = pathName+"<small>"+personId+"</small>";
reader.readAsText(event.target.files[0]);
saveState();
}
Expand Down Expand Up @@ -523,7 +539,8 @@ var VQI_PathwayEditor = function (parent) {
removeHeroUnit();
var obj = JSON.parse(data);
var title = document.getElementById(parent + "-pathway-title");
title.innerHTML = obj.data.NAME;
pathName= obj.data.NAME;
title.innerHTML = pathName+"<small>"+personId+"</small>";
setElements(obj);
});
}
Expand Down Expand Up @@ -570,7 +587,8 @@ var VQI_PathwayEditor = function (parent) {
function onPathwayReaderLoad(event) {
var obj = JSON.parse(event.target.result);
var title = document.getElementById(parent + "-pathway-title");
title.innerHTML = obj.data.NAME;
pathName = obj.data.NAME;
title.innerHTML = pathName+"<small>"+personId+"</small>";
setElements(obj);
}

Expand Down Expand Up @@ -1171,7 +1189,7 @@ var VQI_PathwayEditor = function (parent) {
s: sid,
d: vid,
json: JSON.stringify(JSON.parse(states[states.length - 1])),
p: "X1728790"
p: personId
}, function (yue_data) {
var result = JSON.parse(yue_data);
var table = document.getElementById(parent + "-inner-table");
Expand All @@ -1180,6 +1198,7 @@ var VQI_PathwayEditor = function (parent) {
for (var n = 0; n < length; n++) {
table.deleteRow(0);
}
table.deleteTHead();

for (var n = 0; n <= result.length; n++) {
var row = table.insertRow();
Expand All @@ -1194,12 +1213,12 @@ var VQI_PathwayEditor = function (parent) {
// Add some text to the new cells:

if (n == 0) {
path.innerHTML = "<i><h3>paths</h3></i>";
rScore.innerHTML = "<i><h3>R-Score</h3></i>";
mScore.innerHTML = "<i><h3>M-Score</h3></i>";
mFdr.innerHTML = "<i><h3>M-FDR</h3></i>";
lowP.innerHTML = "<i><h3>LowP</h3></i>"
consistentLowP.innerHTML = "<i><h3>Consistent Low P</h3></i>"
path.innerHTML = "<i><h5><small>paths</small></h5></i>";
rScore.innerHTML = "<i><h5><small>R-Score</small></h5></i>";
mScore.innerHTML = "<i><h5><small>M-Score</small></h5></i>";
mFdr.innerHTML = "<i><h5><small>M-FDR</small></h5></i>";
lowP.innerHTML = "<i><h5><small>LowP</small></h5></i>"
consistentLowP.innerHTML = "<i><h5><small>Consistent Low P</small></h5></i>"
} else {
var btn = document.createElement("button");
var t = document.createTextNode((n - 1).toString());
Expand All @@ -1220,13 +1239,14 @@ var VQI_PathwayEditor = function (parent) {
}
});
path.appendChild(btn);
rScore.appendChild(document.createTextNode(result[n-1].rscore));
mScore.appendChild(document.createTextNode(result[n-1].mscore));
mFdr.appendChild(document.createTextNode(result[n-1].mFDR));
lowP.appendChild(document.createTextNode(result[n-1].lowp));
consistentLowP.appendChild(document.createTextNode(result[n-1].consistent_lowp));
rScore.innerHTML="<h5><small>"+result[n-1].rscore+"</small></h5>";
mScore.innerHTML="<h5><small>"+result[n-1].mscore+"</small></h5>";
mFdr.innerHTML="<h5><small>"+result[n-1].mFDR+"</small></h5>";
lowP.innerHTML="<h5><small>"+result[n-1].lowp+"</small></h5>";
consistentLowP.innerHTML="<h5><small>"+result[n-1].consistent_lowp+"</small></h5>";
}
}
sorttable.makeSortable(table);
dialogTable.dialog("open");
dialogPathfind.dialog("close");
});
Expand Down Expand Up @@ -1470,16 +1490,25 @@ var VQI_PathwayEditor = function (parent) {
function editNodeCNV() {
var cnv = document.getElementById(parent + "-cnv").value;
selectedForEditNodes.data('cnv', cnv);
dialogNode.dialog("close");
saveState();
}

function editNodeRNA() {
var rna = document.getElementById(parent + "-rna").value;
selectedForEditNodes.data('cnv', rna);
dialogNode.dialog("close");
saveState();
}

function editPersonId() {
id = document.getElementById(parent + "-configure-person-id").value;
setPersonId(id);
}

function setPersonId(id) {
personId = id;
var title = document.getElementById(parent + "-pathway-title")
title.innerHTML = pathName+"<small>"+personId+"</small>";
}

function dialogNewPathwayOpen(event) {
dialogNewPathway.dialog("open");
Expand All @@ -1496,6 +1525,10 @@ var VQI_PathwayEditor = function (parent) {
function dialogPathwaySaveAsOpen(event) {
dialogPathwaySaveAs.dialog("open");
}

function dialogPathwayConfigureOpen(event) {
dialogPathwayConfigure.dialog("open");
}

function findObject(event) {
var val = event.target.value;
Expand Down Expand Up @@ -1935,6 +1968,7 @@ var VQI_PathwayEditor = function (parent) {
$('#' + parent + '-redo').removeClass('disabled');
$('#' + parent + '-duplicate-nodes').removeClass('disabled');
$('#' + parent + '-config-pathway').removeClass('disabled');
$('#' + parent + '-find-paths-all-drop').removeClass('disabled');

// Add processed nodes
cy.add(obj.elements);
Expand Down Expand Up @@ -2247,6 +2281,22 @@ var VQI_PathwayEditor = function (parent) {
close: function () {
}
});

dialogPathwayConfigure = $("#" + parent + "-dialog-form-configure-pathway").dialog({
open: function (event) {
document.getElementById(parent + "-configure-person-id").value = personId;
},
autoOpen: false,
height: 300,
width: 350,
buttons: {
Cancel: function () {
dialogPathwayConfigure.dialog("close");
}
},
close: function () {
}
});

refreshPathwayList();

Expand Down Expand Up @@ -2274,6 +2324,9 @@ var VQI_PathwayEditor = function (parent) {
document.getElementById(parent + '-arrow-type-edge-apply').addEventListener('click', editEdgeArrowType);
document.getElementById(parent + '-line-type-edge-apply').addEventListener('click', editEdgeLineType);
document.getElementById(parent + '-apply-curve-changes').addEventListener('click', toggleEdgeStyle);

//edit pathway settings
document.getElementById(parent + '-apply-configure-person-id').addEventListener('click', editPersonId);

document.getElementById(parent + '-new-pathway').addEventListener('click', dialogNewPathwayOpen);
document.getElementById(parent + '-findpath').addEventListener('click', dialogPathfindOpen);
Expand All @@ -2293,7 +2346,9 @@ var VQI_PathwayEditor = function (parent) {
document.getElementById(parent + '-redo').addEventListener('click', redo);
document.getElementById(parent + '-duplicate-nodes').addEventListener('click', addDuplicateNodes);
document.getElementById(parent + '-find-paths-all').addEventListener('click', findPathsAll);
document.getElementById(parent + '-find-paths-all-drop').addEventListener('click', findPathsAll);
document.getElementById(parent + '-find-paths-one').addEventListener('click', findPathOne);
document.getElementById(parent + '-config-pathway').addEventListener('click', dialogPathwayConfigureOpen);

//search
document.getElementById(parent + '-search-node-name').addEventListener('keyup', search);
Expand All @@ -2312,6 +2367,10 @@ var VQI_PathwayEditor = function (parent) {
self.setDataToSpray = function (data) {
this.sprayData = data;
};

self.setPersonId = function (data) {
setPersonId(data);
};

//external No GUI functions

Expand Down
5 changes: 5 additions & 0 deletions index.php
Expand Up @@ -17,6 +17,7 @@
<input type=button onclick="spray()" value="spray">
<input type=button onclick="findYue()" value="find Yue">
<input type=button onclick="findTham()" value="find Tham">
<input type=button onclick="setPersonId()" value="set Person id">
<input type=button onclick="print()" value="print">
<input type=button onclick="save()" value="save">
<input id="file" type=file value="spray from file">
Expand All @@ -27,6 +28,10 @@
var objVQI_PathwayEditor = new VQI_PathwayEditor("parent");
function load() {
objVQI_PathwayEditor.loadPathwayExternalNoGUI(334);
}
function setPersonId() {
var data = "Hello!";
objVQI_PathwayEditor.setPersonId(data);
}
function findYue() {
objVQI_PathwayEditor.findPathAndScoreExternalYueNoGUI("n0", "n22", function (result) {
Expand Down
2 changes: 1 addition & 1 deletion score_json.txt
Expand Up @@ -7,7 +7,7 @@
"person": "X1728790",
"pathway": 342,
"mscore": 0,
"mFDR": 0.00143,
"mFDR": 0.00356,
"lowp": 1,
"consistent_lowp": 0
},
Expand Down

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