diff --git a/bigscape.py b/bigscape.py
index e575d930107f66deccd66241e6dc64c657fab111..1968732f50d234990ff1eb1c2adb0376badfd6a7 100644
--- a/bigscape.py
+++ b/bigscape.py
@@ -1148,6 +1148,7 @@ def clusterJsonBatch(bgcs, outputFileBase,matrix,cutoffs=[1.0],damping=0.8,clust
bgc2simIdx = dict(zip(bgcs, range(len(bgcs))))
pfam_domain_categories = os.path.join(os.path.dirname(os.path.realpath(__file__)), "Pfam-A.clans.tsv")
pfam_descrs = generatePfamDescriptionsMatrix(pfam_domain_categories)
+ pfam_colors = generatePfamColorsMatrix(os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv"))
# Get info on all BGCs to export to .js for visualization
bs_data = []
@@ -1200,16 +1201,13 @@ def clusterJsonBatch(bgcs, outputFileBase,matrix,cutoffs=[1.0],damping=0.8,clust
entry = line.split('\t')
orf = entry[-1].strip().split(':')[0]
pfamID = entry[5].split('.')[0]
- pfamDescr = pfam_descrs.get(pfamID,None)
- if pfamDescr:
- orfDict[orf]["domains"].append({'code': '{} : {}'.format(pfamID,pfamDescr),'start':int(entry[3]),'end':int(entry[4]),'bitscore': float(entry[1])})
- else:
- orfDict[orf]["domains"].append({'code': entry[5], 'start': int(entry[3]), 'end': int(entry[4]), 'bitscore': float(entry[1])})
+ orfDict[orf]["domains"].append({'code': pfamID, 'start': int(entry[3]), 'end': int(entry[4]), 'bitscore': float(entry[1])})
bgcJsonDict[bgcName]['orfs'] = list(orfDict.values())
bs_data = [bgcJsonDict[clusterNames[int(bgc)]] for bgc in bgcs]
## Write html output folder structure (and update bigscape_classes.js) for this module
## Write {modulename}/bgcs.js
+ ## Write js/pfams.js
assert htmlFolder != None
module_name = outputFileBase.split(os.path.sep)[-1]
module_html_path = os.path.join(html_folder, "networks", module_name)
@@ -1217,6 +1215,16 @@ def clusterJsonBatch(bgcs, outputFileBase,matrix,cutoffs=[1.0],damping=0.8,clust
with open(os.path.join(module_html_path, "bs_data.js"), "w") as bs_data_js:
bs_data_js.write("var bs_data={};\n".format(json.dumps(bs_data, indent=4, separators=(',', ':'), sort_keys=True)))
add_to_bigscape_classes_js(module_name, className, ["cutoff{:4.2f}".format(cutoff) for cutoff in cutoffs], htmlFolder)
+ with open(os.path.join(html_folder, "js", "pfams.js"), "w") as pfams_js:
+ pfam_json = {}
+ for pfam_code in pfam_colors:
+ pfam_obj = {}
+ pfam_obj["col"] = pfam_colors[pfam_code]
+ pfam_obj["desc"] = ""
+ if pfam_code in pfam_descrs:
+ pfam_obj["desc"] = pfam_descrs[pfam_code]
+ pfam_json[pfam_code] = pfam_obj
+ pfams_js.write("var pfams={};\n".format(json.dumps(pfam_json, indent=4, separators=(',', ':'), sort_keys=True)))
for cutoff in cutoffs:
simMatrix = lil_matrix((len(bgcs), len(bgcs)), dtype=np.float32)
diff --git a/functions.py b/functions.py
index 8f25d9d763c8fb000a3688be79975b7c2e8a0147..85c29b6bc49f1acd272314a5315520bfca5d0e48 100644
--- a/functions.py
+++ b/functions.py
@@ -541,6 +541,30 @@ def generatePfamDescriptionsMatrix(pfam_domain_categories):
return pfam_descriptions
+def generatePfamColorsMatrix(pfam_domain_colors):
+ '''
+
+ :param pfam_domain_colors: tab-delimited file
+ :return: dictionary with pfam ID as key and rgb colors as value
+ '''
+ pfam_colors = {}
+
+ if os.path.isfile(pfam_domain_colors):
+ print(" Found file with Pfam domain colors")
+ with open(pfam_domain_colors, "r") as cat_handle:
+ for line in cat_handle:
+ # handle comments and empty lines
+ if line[0] != "#" and line.strip():
+ row = line.strip().split("\t")
+ domain = row[0]
+ rgb = row[-1]
+ pfam_colors[domain] = rgb
+ else:
+ print(" File pfam_domain_colors was NOT found")
+
+ return pfam_colors
+
+
def copy_html_template(html_folder):
if (os.path.isdir(html_folder)):
shutil.rmtree(html_folder)
diff --git a/html_template/js/arrower.js b/html_template/js/arrower.js
index 39cdfa93a02ce7f465c309e2f726c4cba6f58175..aafabb9e3e8b35078654531671b6f953ec4284ea 100755
--- a/html_template/js/arrower.js
+++ b/html_template/js/arrower.js
@@ -1,296 +1,308 @@
/* Copyright 2017 Satria Kautsar */
var Arrower = {
- version: "0.0.0",
- required: [
- "jquery",
- "svg.js"
- ],
- tooltip_id: "arrower-tooltip-1234567890"
+ version: "0.0.0",
+ required: [
+ "jquery",
+ "svg.js",
+ "pfams.js"
+ ],
+ tooltip_id: "arrower-tooltip-1234567890"
};
+if (pfams === undefined) {
+pfams = {};
+}
Arrower.drawClusterSVG = (function(cluster, height = 40) {
- var container = document.createElement("div");
- var draw = SVG(container).size('100%', height).group();
- var scale = (function(val) { return parseInt(val / (1000 / height)); })
+var container = document.createElement("div");
+var draw = SVG(container).size('100%', height).group();
+var scale = (function(val) { return parseInt(val / (1000 / height)); })
- // draw line
- draw.line(0, parseInt(height / 2), scale(cluster.end - cluster.start), parseInt(height / 2)).stroke({width: 1});
- var width = scale(cluster.end - cluster.start);
-
- if (cluster.hasOwnProperty("orfs")) {
- // draw arrows
- for (var i in cluster.orfs) {
- var orf = cluster.orfs[i];
- var orf_color = "white";//"gray";
- if (orf.hasOwnProperty("color")) {
- orf_color = orf.color;
- }
- var pol = draw.polygon(Arrower.toPointString(Arrower.getArrowPoints(orf, cluster, height, scale)))
- .fill(orf_color)
- .stroke({width: 1})
- .addClass("arrower-orf");
- $(pol.node).mouseover({orf: orf}, function(handler){
- var start = handler.data.orf.start;
- var end = handler.data.orf.end;
- Arrower.showToolTip("ORF: " + handler.data.orf.id + "<br/>" + start + " - " + end, handler);
- $(handler.target).css("stroke-width", "3px");
- $(handler.target).css("stroke", "red");
- handler.stopPropagation();
- });
- $(pol.node).mouseleave(function(handler){
- $(handler.target).css("stroke-width", "1px");
- $(handler.target).css("stroke", "black");
- $("#" + Arrower.tooltip_id).css("display", "none");
- });
+// draw line
+draw.line(0, parseInt(height / 2), scale(cluster.end - cluster.start), parseInt(height / 2)).stroke({width: 1});
+var width = scale(cluster.end - cluster.start);
- if (orf.hasOwnProperty("domains")) {
- // draw domains
- for (var j in orf.domains) {
- var domain = orf.domains[j];
- var color = "gray";
- if (domain.hasOwnProperty("color")) {
- color = domain.color;
- }
- var dom = draw.polygon(Arrower.toPointString(Arrower.getDomainPoints(domain, orf, cluster, height, scale)))
- .fill(color)
- .stroke({width: 1})
- .addClass("arrower-domain");
- $(dom.node).mouseover({domain: domain}, function(handler){
- var start = handler.data.domain.start;
- var end = handler.data.domain.end;
- Arrower.showToolTip("Domain: " + handler.data.domain.code + " (" + domain.bitscore + ")" + "<br/>" + start + " - " + end, handler);
- $(handler.target).css("stroke-width", "3px");
- $(handler.target).css("stroke", "red");
- handler.stopPropagation();
- });
- $(dom.node).mouseleave(function(handler){
- $(handler.target).css("stroke-width", "1px");
- $(handler.target).css("stroke", "black");
- $("#" + Arrower.tooltip_id).css("display", "none");
- });
+if (cluster.hasOwnProperty("orfs")) {
+ // draw arrows
+ for (var i in cluster.orfs) {
+ var orf = cluster.orfs[i];
+ var orf_color = "white";//"gray";
+ if (orf.hasOwnProperty("color")) {
+ orf_color = orf.color;
+ }
+ var pol = draw.polygon(Arrower.toPointString(Arrower.getArrowPoints(orf, cluster, height, scale)))
+ .fill(orf_color)
+ .stroke({width: 1})
+ .addClass("arrower-orf");
+ $(pol.node).mouseover({orf: orf}, function(handler){
+ var start = handler.data.orf.start;
+ var end = handler.data.orf.end;
+ Arrower.showToolTip("ORF: " + handler.data.orf.id + "<br/>" + start + " - " + end, handler);
+ $(handler.target).css("stroke-width", "3px");
+ $(handler.target).css("stroke", "red");
+ handler.stopPropagation();
+ });
+ $(pol.node).mouseleave(function(handler){
+ $(handler.target).css("stroke-width", "1px");
+ $(handler.target).css("stroke", "black");
+ $("#" + Arrower.tooltip_id).css("display", "none");
+ });
+
+ if (orf.hasOwnProperty("domains")) {
+ // draw domains
+ for (var j in orf.domains) {
+ var domain = orf.domains[j];
+ var color = "gray";
+ if (domain.hasOwnProperty("color")) {
+ color = domain.color;
+ } else if (pfams.hasOwnProperty(domain.code)) {
+ color = "rgb(" + pfams[domain.code]["col"] + ")";
}
+ var dom = draw.polygon(Arrower.toPointString(Arrower.getDomainPoints(domain, orf, cluster, height, scale)))
+ .fill(color)
+ .stroke({width: 1})
+ .addClass("arrower-domain");
+ $(dom.node).mouseover({domain: domain}, function(handler){
+ var start = handler.data.domain.start;
+ var end = handler.data.domain.end;
+ var dom_desc = "";
+ if (handler.data.domain.hasOwnProperty("desc")) {
+ dom_desc = handler.data.domain.color;
+ } else if (pfams.hasOwnProperty(handler.data.domain.code)) {
+ dom_desc = pfams[handler.data.domain.code]["desc"];
+ }
+ Arrower.showToolTip("Domain: " + handler.data.domain.code + " " + dom_desc + " (" + handler.data.domain.bitscore + ")" + "<br/>" + start + " - " + end, handler);
+ $(handler.target).css("stroke-width", "3px");
+ $(handler.target).css("stroke", "red");
+ handler.stopPropagation();
+ });
+ $(dom.node).mouseleave(function(handler){
+ $(handler.target).css("stroke-width", "1px");
+ $(handler.target).css("stroke", "black");
+ $("#" + Arrower.tooltip_id).css("display", "none");
+ });
}
}
}
+}
- $(draw.node).parent().mouseover({domain: domain}, function(handler){
- var bgc_desc = "<b>BGC: " + cluster.id + "</b>";
- if (cluster.hasOwnProperty("desc")) {
- bgc_desc += "<br /> " + cluster["desc"];
- }
- Arrower.showToolTip(bgc_desc, handler);
- });
- $(draw.node).parent().mouseleave(function(handler){
- $("#" + Arrower.tooltip_id).css("display", "none");
- });
+$(draw.node).parent().mouseover({domain: domain}, function(handler){
+ var bgc_desc = "<b>BGC: " + cluster.id + "</b>";
+ if (cluster.hasOwnProperty("desc")) {
+ bgc_desc += "<br /> " + cluster["desc"];
+ }
+ Arrower.showToolTip(bgc_desc, handler);
+});
+$(draw.node).parent().mouseleave(function(handler){
+ $("#" + Arrower.tooltip_id).css("display", "none");
+});
- $(container).find("svg").attr("width", width + "px");
- return $(container).find("svg")[0];
+$(container).find("svg").attr("width", width + "px");
+return $(container).find("svg")[0];
});
Arrower.getOrfPoints = (function(orf, cluster, height, scale){
- var x_points = [
- scale(orf.start),
- (orf.strand === 0) ?
- (scale(orf.start) + scale(orf.end - orf.start))
- : ((scale(orf.end - orf.start) > (height / 2)) ?
- (scale(orf.start) + Math.max(scale(orf.end - orf.start - ((orf.end - orf.start) / 4)), (scale(orf.end - orf.start) - parseInt(height / 2))))
- : scale(orf.start)),
+var x_points = [
+ scale(orf.start),
+ (orf.strand === 0) ?
(scale(orf.start) + scale(orf.end - orf.start))
- ];
- var y_points = [
- (orf.strand === 0) ?
- ((height / 2) - (height / 3))
- : ((height / 2) - (height / 3)) - (height / 5),
- ((height / 2) - (height / 3)),
- (height / 2),
- ((height / 2) + (height / 3)),
- (orf.strand === 0) ?
- ((height / 2) + (height / 3))
- : ((height / 2) + (height / 3)) + (height / 5)
- ];
+ : ((scale(orf.end - orf.start) > (height / 2)) ?
+ (scale(orf.start) + Math.max(scale(orf.end - orf.start - ((orf.end - orf.start) / 4)), (scale(orf.end - orf.start) - parseInt(height / 2))))
+ : scale(orf.start)),
+ (scale(orf.start) + scale(orf.end - orf.start))
+];
+var y_points = [
+ (orf.strand === 0) ?
+ ((height / 2) - (height / 3))
+ : ((height / 2) - (height / 3)) - (height / 5),
+ ((height / 2) - (height / 3)),
+ (height / 2),
+ ((height / 2) + (height / 3)),
+ (orf.strand === 0) ?
+ ((height / 2) + (height / 3))
+ : ((height / 2) + (height / 3)) + (height / 5)
+];
- return { x: x_points, y: y_points };
+return { x: x_points, y: y_points };
});
Arrower.getArrowPoints = (function(orf, cluster, height, scale) {
- var points = [];
- var pts = Arrower.getOrfPoints(orf, cluster, height, scale);
+var points = [];
+var pts = Arrower.getOrfPoints(orf, cluster, height, scale);
- points.push({ // blunt start
- x: pts.x[0],
- y: pts.y[1]
- });
- points.push({ // junction top
- x: pts.x[1],
- y: pts.y[1]
- });
- points.push({ // junction top-top
- x: pts.x[1],
- y: pts.y[0]
- });
- points.push({ // pointy end
- x: pts.x[2],
- y: pts.y[2]
- });
- points.push({ // junction bottom-bottom
- x: pts.x[1],
- y: pts.y[4]
- });
- points.push({ // junction bottom
- x: pts.x[1],
- y: pts.y[3]
- });
- points.push({ // blunt end
- x: pts.x[0],
- y: pts.y[3]
- });
+points.push({ // blunt start
+ x: pts.x[0],
+ y: pts.y[1]
+});
+points.push({ // junction top
+ x: pts.x[1],
+ y: pts.y[1]
+});
+points.push({ // junction top-top
+ x: pts.x[1],
+ y: pts.y[0]
+});
+points.push({ // pointy end
+ x: pts.x[2],
+ y: pts.y[2]
+});
+points.push({ // junction bottom-bottom
+ x: pts.x[1],
+ y: pts.y[4]
+});
+points.push({ // junction bottom
+ x: pts.x[1],
+ y: pts.y[3]
+});
+points.push({ // blunt end
+ x: pts.x[0],
+ y: pts.y[3]
+});
- if (orf.strand < 0) {
- points = Arrower.flipHorizontal(points, scale(orf.start), (scale(orf.start) + scale(orf.end - orf.start)));
- }
+if (orf.strand < 0) {
+ points = Arrower.flipHorizontal(points, scale(orf.start), (scale(orf.start) + scale(orf.end - orf.start)));
+}
- return points;
+return points;
});
Arrower.getDomainPoints = (function(domain, orf, cluster, height, scale) {
- var points = [];
- var arrow_pts = Arrower.getArrowPoints(orf, cluster, height, scale);
- if (orf.strand < 0) {
- arrow_pts = Arrower.flipHorizontal(arrow_pts, scale(orf.start), (scale(orf.start) + scale(orf.end - orf.start)));
- }
- arrow_pts.splice(3, 0, arrow_pts[3]); // convert into bluntish-end arrow
- var domain_x = {
- start: (scale(orf.start) + scale(domain.start * 3)),
- end: (scale(orf.start) + scale(domain.end * 3))
- };
+var points = [];
+var arrow_pts = Arrower.getArrowPoints(orf, cluster, height, scale);
+if (orf.strand < 0) {
+ arrow_pts = Arrower.flipHorizontal(arrow_pts, scale(orf.start), (scale(orf.start) + scale(orf.end - orf.start)));
+}
+arrow_pts.splice(3, 0, arrow_pts[3]); // convert into bluntish-end arrow
+var domain_x = {
+ start: (scale(orf.start) + scale(domain.start * 3)),
+ end: (scale(orf.start) + scale(domain.end * 3))
+};
- var getY = function(x) {
- var m = Math.abs(arrow_pts[5].y - arrow_pts[4].y) / Math.abs(arrow_pts[5].x - arrow_pts[4].x);
- return (m * (x - arrow_pts[4].x));
- }
+var getY = function(x) {
+ var m = Math.abs(arrow_pts[5].y - arrow_pts[4].y) / Math.abs(arrow_pts[5].x - arrow_pts[4].x);
+ return (m * (x - arrow_pts[4].x));
+}
- for (var i in arrow_pts) {
- var apt = arrow_pts[i];
- var new_point = {};
- new_point.x = apt.x < domain_x.start ? domain_x.start : (apt.x > domain_x.end ? domain_x.end : apt.x);
- new_point.y = (new_point.x < arrow_pts[1].x) ?
- Math.min(Math.max(apt.y, arrow_pts[0].y), arrow_pts[7].y)
- :((new_point.x == arrow_pts[1].x) ?
- apt.y
- :(i < 4 ?
- (arrow_pts[3].y + getY(new_point.x))
- :(arrow_pts[3].y - getY(new_point.x))));
- points.push(new_point);
- }
+for (var i in arrow_pts) {
+ var apt = arrow_pts[i];
+ var new_point = {};
+ new_point.x = apt.x < domain_x.start ? domain_x.start : (apt.x > domain_x.end ? domain_x.end : apt.x);
+ new_point.y = (new_point.x < arrow_pts[1].x) ?
+ Math.min(Math.max(apt.y, arrow_pts[0].y), arrow_pts[7].y)
+ :((new_point.x == arrow_pts[1].x) ?
+ apt.y
+ :(i < 4 ?
+ (arrow_pts[3].y + getY(new_point.x))
+ :(arrow_pts[3].y - getY(new_point.x))));
+ points.push(new_point);
+}
- if (orf.strand < 0) {
- points = Arrower.flipHorizontal(points, scale(orf.start), (scale(orf.start) + scale(orf.end - orf.start)));
- }
+if (orf.strand < 0) {
+ points = Arrower.flipHorizontal(points, scale(orf.start), (scale(orf.start) + scale(orf.end - orf.start)));
+}
- return points;
+return points;
});
Arrower.flipHorizontal = (function(points, leftBound, rightBound) {
- var new_points = [];
+var new_points = [];
- for(var i in points) {
- var point = points[i];
- if ((point.x < leftBound) || (point.x > rightBound)) {
- throw "Error flipping points";
- }
- new_points.push({ x: rightBound - (point.x - leftBound), y: point.y });
+for(var i in points) {
+ var point = points[i];
+ if ((point.x < leftBound) || (point.x > rightBound)) {
+ throw "Error flipping points";
}
+ new_points.push({ x: rightBound - (point.x - leftBound), y: point.y });
+}
- return new_points;
+return new_points;
});
Arrower.toPointString = (function(points) {
- points_string = "";
+points_string = "";
- for(var i in points) {
- var point = points[i];
- if (i > 0) {
- points_string += ", ";
- }
- points_string += parseInt(point.x) + "," + parseInt(point.y);
+for(var i in points) {
+ var point = points[i];
+ if (i > 0) {
+ points_string += ", ";
}
+ points_string += parseInt(point.x) + "," + parseInt(point.y);
+}
- return points_string;
+return points_string;
});
Arrower.getRandomCluster = (function() {
- function random(min, max) {
- min = Math.ceil(min);
- max = Math.floor(max);
- return Math.floor(Math.random() * (max - min)) + min;
- }
- var cl_start = 23000;
- var cl_end = 23000 + random(5000, 50000);
+function random(min, max) {
+ min = Math.ceil(min);
+ max = Math.floor(max);
+ return Math.floor(Math.random() * (max - min)) + min;
+}
+var cl_start = 23000;
+var cl_end = 23000 + random(5000, 50000);
- var orfs = [];
- var num_orfs = random(5, 20);
- for (var i = 0; i < num_orfs; i++) {
- var pos1 = random(i * ((cl_end - cl_start) / num_orfs), (i + 1) * ((cl_end - cl_start) / num_orfs));
- var pos2 = random(i * ((cl_end - cl_start) / num_orfs), (i + 1) * ((cl_end - cl_start) / num_orfs));
- if (Math.abs(pos1 - pos2) < 200) {
- continue;
- }
- var orf_start = Math.min(pos1, pos2);
- var orf_end = Math.max(pos1, pos2);
- var orf_strand = Math.random() > 0.5? 1 : -1;//random(-1, 2);
- var orf_type = Math.random() > 0.5? "biosynthetic" : "others";
- var orf_domains = [];
- var num_domains = random(0, 4);
- for (var j = 0; j < num_domains; j++) {
- var dpos1 = random(j * ((orf_end - orf_start) / num_domains), (j + 1) * ((orf_end - orf_start) / num_domains));
- var dpos2 = random(j * ((orf_end - orf_start) / num_domains), (j + 1) * ((orf_end - orf_start) / num_domains));
- var dom_start = Math.min(dpos1, dpos2);
- var dom_end = Math.max(dpos1, dpos2);
- orf_domains.push({
- code: "RAND_DOM_" + i + "_" + j,
- start: dom_start,
- end: dom_end,
- bitscore: random(30, 300),
- color: "rgb(" + random(0, 256) + "," + random(0, 256) + "," + random(0, 256) + ")",
- });
- }
- orfs.push({
- id: "RAND_ORF_" + i,
- desc: "Randomly generated ORF",
- start: orf_start,
- end: orf_end,
- strand: orf_strand,
- domains: orf_domains
+var orfs = [];
+var num_orfs = random(5, 20);
+for (var i = 0; i < num_orfs; i++) {
+ var pos1 = random(i * ((cl_end - cl_start) / num_orfs), (i + 1) * ((cl_end - cl_start) / num_orfs));
+ var pos2 = random(i * ((cl_end - cl_start) / num_orfs), (i + 1) * ((cl_end - cl_start) / num_orfs));
+ if (Math.abs(pos1 - pos2) < 200) {
+ continue;
+ }
+ var orf_start = Math.min(pos1, pos2);
+ var orf_end = Math.max(pos1, pos2);
+ var orf_strand = Math.random() > 0.5? 1 : -1;//random(-1, 2);
+ var orf_type = Math.random() > 0.5? "biosynthetic" : "others";
+ var orf_domains = [];
+ var num_domains = random(0, 4);
+ for (var j = 0; j < num_domains; j++) {
+ var dpos1 = random(j * ((orf_end - orf_start) / num_domains), (j + 1) * ((orf_end - orf_start) / num_domains));
+ var dpos2 = random(j * ((orf_end - orf_start) / num_domains), (j + 1) * ((orf_end - orf_start) / num_domains));
+ var dom_start = Math.min(dpos1, dpos2);
+ var dom_end = Math.max(dpos1, dpos2);
+ orf_domains.push({
+ code: "RAND_DOM_" + i + "_" + j,
+ start: dom_start,
+ end: dom_end,
+ bitscore: random(30, 300),
+ color: "rgb(" + random(0, 256) + "," + random(0, 256) + "," + random(0, 256) + ")",
});
}
+ orfs.push({
+ id: "RAND_ORF_" + i,
+ desc: "Randomly generated ORF",
+ start: orf_start,
+ end: orf_end,
+ strand: orf_strand,
+ domains: orf_domains
+ });
+}
- var cluster = { start: cl_start, end: cl_end, orfs: orfs, desc: 'Randomly generated Cluster'};
- return cluster;
+var cluster = { start: cl_start, end: cl_end, orfs: orfs, desc: 'Randomly generated Cluster'};
+return cluster;
});
Arrower.drawRandomClusterSVG = (function(cluster) {
- return Arrower.drawClusterSVG(Arrower.getRandomCluster());
+return Arrower.drawClusterSVG(Arrower.getRandomCluster());
});
Arrower.showToolTip = (function(html, handler){
- var divTooltip = $("#" + Arrower.tooltip_id);
- if (divTooltip.length < 1) {
- divTooltip = $("<div id='" + Arrower.tooltip_id + "'>");
- divTooltip.css("background-color", "white");
- divTooltip.css("border", "1px solid black");
- divTooltip.css("color", "black");
- divTooltip.css("font-size", "small");
- divTooltip.css("padding", "0 5px");
- divTooltip.css("pointer-events", "none");
- divTooltip.css("position", "fixed");
- divTooltip.appendTo($(document.body));
- }
- divTooltip.html(html);
- divTooltip.css("cursor", "default");
- divTooltip.css("top", handler.pageY + "px");
- divTooltip.css("left", handler.pageX + "px");
- divTooltip.css("display", "block");
+var divTooltip = $("#" + Arrower.tooltip_id);
+if (divTooltip.length < 1) {
+ divTooltip = $("<div id='" + Arrower.tooltip_id + "'>");
+ divTooltip.css("background-color", "white");
+ divTooltip.css("border", "1px solid black");
+ divTooltip.css("color", "black");
+ divTooltip.css("font-size", "small");
+ divTooltip.css("padding", "0 5px");
+ divTooltip.css("pointer-events", "none");
+ divTooltip.css("position", "fixed");
+ divTooltip.appendTo($(document.body));
+}
+divTooltip.html(html);
+divTooltip.css("cursor", "default");
+divTooltip.css("top", handler.pageY + "px");
+divTooltip.css("left", handler.pageX + "px");
+divTooltip.css("display", "block");
});
diff --git a/html_template/networks/index_html b/html_template/networks/index_html
index 37fd5f3c65303f757564db387b5d17716ef51d83..75ce78996c97dfbedf79d9d9ed2928b680b1badd 100644
--- a/html_template/networks/index_html
+++ b/html_template/networks/index_html
@@ -1,10 +1,10 @@
<!DOCTYPE html>
<html>
<head>
- <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
- <meta http-equiv='cache-control' content='no-cache'>
- <meta http-equiv='expires' content='0'>
- <meta http-equiv='pragma' content='no-cache'>
+ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ <meta http-equiv='cache-control' content='no-cache'>
+ <meta http-equiv='expires' content='0'>
+ <meta http-equiv='pragma' content='no-cache'>
<title>BiG-SCAPE Result</title>
<link rel="stylesheet" type="text/css" href="../../../css/style.css">
</head>
@@ -15,8 +15,9 @@
<script type="text/javascript" src="../../../js/jquery-3.2.1.min.js"></script>
<script type="text/javascript" src="../../../js/vivagraph.js"></script>
<script type="text/javascript" src="../../../js/svg.js"></script>
- <script type="text/javascript" src="../../../js/arrower.js"></script>
<script type="text/javascript" src="../../../js/fuse.min.js"></script>
+ <script type="text/javascript" src="../../../js/pfams.js"></script>
+ <script type="text/javascript" src="../../../js/arrower.js"></script>
<script type="text/javascript" src="../../../js/bigscape.js"></script>
<script type="text/javascript" src="../bs_data.js"></script>
<script type="text/javascript" src="bs_networks.js"></script>