biojs-vis-blasterjs

Authors

Aitor Blanco Míguez (aiblanco@uvigo.es)
Dr. Florentino Fernández Riverola (riverola@uvigo.es)
Dr. Anália Maria Garcia Lourenço (analia@uvigo.es)
Dr. Borja Sánchez García (borja.sanchez@csic.es)
Thomas Roder (roder.thomas@gmail.com)

Description

A free to use, open source Javascript BLAST alignments viewer library created by SING group.

How to cite

Blanco-Míguez A, Fdez-Riverola F, SánchezB, Lourenço A (2018) BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results. PLoS ONE 13(10): e0205286. https://doi.org/10.1371/journal.pone.0205286

Requeriments

Bootstrap 3 (http://getbootstrap.com/)
HTML2CANVAS ([http://html2canvas.hertzen.com/])

Accepted files

BLAST text and XML output files (-outfmt 0 and 5)

You can check NCBI BLAST user manual.

Getting Started

Install the module with: npm install biojs-vis-blasterjs

<head>
    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css"
          integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" crossorigin="anonymous"/>
    <link rel="stylesheet" type="text/css" href="css/blasterjs-colors-nucleotides.css"
          id="stylesheet-blasterjs-nucleotides"/>
    <link rel="stylesheet" type="text/css" href="css/blasterjs-colors-proteins.css"
          id="stylesheet-blasterjs-proteins"/>
    ...
</head>
<body>
...
<input type="file" id="blastinput"/>
<div id="blast-multiple-alignments"></div>
<div id="blast-alignments-table"></div>
<div id="blast-single-alignment"></div>
...
<script src="https://cdnjs.cloudflare.com/ajax/libs/html2canvas/1.4.1/html2canvas.min.js"></script>
<script type="text/javascript" src="js/blaster.js"></script>
<script type="text/javascript">

    // activate the appropriate stylesheet
    document.getElementById('stylesheet-blasterjs-nucleotides').disabled = true
    document.getElementById('stylesheet-blasterjs-proteins').disabled = false

    // start blasterjs
    let blasterjs = require("biojs-vis-blasterjs")
    let instance = new blasterjs({
        input: "blastinput",
        multipleAlignments: "blast-multiple-alignments",
        alignmentsTable: "blast-alignments-table",
        singleAlignment: "blast-single-alignment"
    })
</script>
</body>

Custom options:

Get alignments via String instead of input form:

...
<script type="text/javascript">
    var alignments = "...";

    var blasterjs = require("biojs-vis-blasterjs");
    var instance = new blasterjs({
        string: alignments,
        multipleAlignments: "blast-multiple-alignments",
        alignmentsTable: "blast-alignments-table",
        singleAlignment: "blast-single-alignment",
    });
</script>
...

Define a custom callback on alignment table item click event:

...
<script type="text/javascript">
    var blasterjs = require("biojs-vis-blasterjs");
    var instance = new blasterjs({
        input: "blastinput",
        multipleAlignments: "blast-multiple-alignments",
        alignmentsTable: "blast-alignments-table",
        singleAlignment: "blast-single-alignment",
        callback: function (alignment) { ...
        }
    });
</script>
...

Institution

[© SING - Sistemas Informáticos de Nueva Generación 2015]
Department of Computer Science, University of Vigo
ESEI - Escuela Superior de Ingeniería Informática Edificio politécnico
Campus Universitario As Lagoas s/n
32004 Ourense, Spain
Tel: +34 988 387 013
Fax: +34 988 387 001

Contributing

All contributions are welcome.

Support

If you have any problem or suggestion please open an issue here.

License

GNU General Public License v3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

MrTomRod / biojs-vis-blasterjs