Comments (2)
Hi @jaygray0919,
Thank you for your kind words, I'm sure @spond will appreciate it when he sees this issue.
Have you seen the github page that loads a Newick file?
Specifically, you want to use the built-in JavaScript FileReader object.
This is the relevant code in the script portion of index.html :
$("#newick_file").on ("change", function (e) {
var files = e.target.files; // FileList object
if (files.length == 1) {
var f = files[0];
var reader = new FileReader();
reader.onload = (function(theFile) {
return function(e) {
var res = d3.layout.newick_parser (e.target.result);
if (res["json"]) {
if (!("children" in res["json"])) {
res["error"] = "Empty tree";
}
}
var warning_div = d3.select ("#main_display").insert ("div", ":first-child");
if (res["error"]) {
warning_div.attr ("class", "alert alert-danger alert-dismissable")
.html ("<strong>Newick parser error for file " + f.name +": </strong> In file " + res["error"]);
} else {
default_tree_settings ();
tree (res).svg (svg).layout();
warning_div.attr ("class", "alert alert-success alert-dismissable")
.html ("Loaded a tree from file <strong>" + f.name +": </strong>");
}
warning_div.append ("button")
.attr ("type", "button")
.attr ("class", "close")
.attr ("data-dismiss", "alert")
.attr ("aria-hidden", "true")
.html ("×");
};
})(f);
reader.readAsText(f);
}
});
Basically, you read the file by using the readAsText
method. The reader.onload
callback is executed once the file has been read as text, the file contents are stored in e.target.result
, and we pass that into d3.layout.newick_parser
.
It might be worthwhile to incorporate some of this code into a method called readNewickFromFile
directly into phylotree.js.
Best,
Steven
from phylotree.js.
TY - will work on this next.
We've worked with several Newick parsers; none compare to your implementation.
/jg
from phylotree.js.
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from phylotree.js.