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stevenweaver avatar stevenweaver commented on August 17, 2024

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 ("&times;");
        };
      })(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.

jaygray0919 avatar jaygray0919 commented on August 17, 2024

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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