JavaScript Sequence Alignment Viewer
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README.md

JavaScript Sequence Alignment Viewer (JSAV) V1.10

JSAV is a simple JavaScript sequence alignment viewer

Look at index.html and index2.html for example usage information

The main user entry point is:

    printJSAV(divId, sequenceArray, options);

Where:

  • divId is the name of a div that will be created
  • sequenceArray is an array of sequence objects - these contain id and sequence fields
  • options is an object describing options - see below

The options for controlling the display are:

  • sortable - Should the sorting options be displayed (default: false)
  • width - The width of the selection slider with units (default: '400px')
  • height - The height of the selection slider with units. This is actually a font size and the actualy slider height is relative to this (default: '6pt')
  • selectable - Should selection checkboxes be displayed for each sequence
  • deletable - Makes it possible to delete sequences
  • deleteLabel - Label for the delete button
  • highlight - Array of ranges to highlight (e.g. [24,34,50,56] would highlight positions 24-34 and 50-56)
  • submit - URL for submitting selected sequences
  • submitLabel - Label for submit button
  • idSubmit - URL for submitting a single sequence where its id/label has been clicked. See also idSubmitAttribute which allows other attributes to be passed
  • idSubmitClean - Remove non-alpha characters from sequence before submitting
  • idSubmitAttribute - Specifies which attribute of the sequence object should be passed to a URL specified with idSubmit. Default is 'sequence'
  • action - Function to call using selected sequences - the function will be passed the divId and array of sequence objects
  • actionLabel - Label for action button
  • dotify - Repeated residues in the alignment are replaced with dots
  • nocolour or nocolor - Repeated residues are not coloured
  • toggleDotify - Display a checkbox to toggle the dotify mode
  • toggleDotifyLabel - Label for dotify checkbox toggle
  • toggleNocolour or toggleNocolor - Display a checkbox to toggle the nocolour-dotify mode
  • toggleNocolourLabel or toggleNocolorLabel - Label for nocolour checkbox toggle
  • fasta - Create a FASTA export button
  • fastaLabel - Label for FASTA export button
  • consensus - Display consensus sequence
  • colourScheme or colorScheme - Default colour scheme - valid options depend on the css, but are currently taylor, clustal, zappo, hphob, helix, strand, turn, buried
  • selectColour or selectColor - Display a pull-down to choose the colour scheme.
  • colourChoices or colorChoices - Array of colour scheme names - only used if the user has added to the CSS
  • plainTooltips - disable JQuery tool-tips
  • callback - name of a function to be called whenever the display is refreshed. The divId is passed into this function.
  • scrollX - Specify a width for the sequence display div and make it scrollable (e.g. "500px") Use "100%" to make it the width of the screen (or containing div)
  • scrollY - Specify a height for the sequence display div and make it scrollable (e.g. "500px")
  • labels - Array of residue labels
  • autoLabels - Generate sequential labels automatically

The Sequence Object

The sequence object must contain two fields:

  • id which contains an identifier that is displayed along side the sequence
  • sequence which is the 1-letter code sequence (with dashes as necessary for the alignment)

In addition it may contain any other required fields that will be passed around but are not used by JSAV itself. For example some sort of accession code that might be required by an 'action' run from JSAV.

CSS Control

The overall JSAV component is wrapped in a div with the ID specified in the call. Within this there are two divs

  • the first displays the alignment and has class='JSAVDisplay'
  • the second displays the controls and has class='JSAVControls'

Prerequisites

You must have JQuery and JQuery-UI installed - simply download them from http://www.jqueryui.com/ and access the two JavaScript files and the CSS file from your HTML. You can customize the look and feel of the slider and the confirmation/alert boxes by choosing a different (or customized) JQuery-UI theme.

Your code should include these with something like:

<link href="external/jquery.css" rel="stylesheet" />
<script type='text/javascript' src='external/jquery-1.10.2.min.js'></script>
<script type='text/javascript' src='external/jquery-ui-1.10.4.custom.min.js'></script>

alternatively, you could access the JQuery code from Google APIs:

<link rel="stylesheet" href="//ajax.googleapis.com/ajax/libs/jqueryui/1.10.4/themes/smoothness/jquery-ui.css" />
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
<script src="//ajax.googleapis.com/ajax/libs/jqueryui/1.10.4/jquery-ui.min.js"></script>

Note that this must appear before including the JSAV.js code and CSS:

<link href="JSAV.css" rel="stylesheet" />
<script type='text/javascript' src='JSAV.js'></script>

Optional styling

By default, JQuery tooltips are enabled. As above, these can be disabled using the plainTooltips option.

The tooltips are fully compatible with the tooltipster package which gives more attractive tooltips. If you wish to use this, simply download the package from https://github.com/iamceege/tooltipster/archive/master.zip and add the following lines to your HTML:

<link href="external/tooltipster-master/css/tooltipster.css" rel="stylesheet" />
<script type='text/javascript' src='external/tooltipster-master/js/jquery.tooltipster.min.js'></script>
<script>
function enableTooltipster()
{
    $(document).ready(function() {
        $('.tooltip').tooltipster();
    });
enableTooltipster();
</script>

Note that this must appear after including the JSAV.js code and CSS (unless you also remember to set the options.plainTooltips option).

The enableTooltipster() function must be called whenever the display is refreshed. This is achieved by adding the option:

    options.callback = "enableTooltipster";

Note

In future, the slider may be replaced with http://refreshless.com/nouislider/ which works better on touchscreens.

Contributing to JSAV

Contributions to JSAV through pull requests are encouraged. If you contribute, you acknowledge that you transfer copyright in your modifications to University College London and Dr. Andrew C.R. Martin.