biovisualize/index.html

## index.html
<!DOCTYPE html>
<html>
<head>
<script type="text/javascript" src="http://mbostock.github.com/d3/d3.js"></script>
<script type="text/javascript" src="svg_slides.js"></script>

<script type="text/javascript">

    // There are probably better ways of loading the SVG, but this is one example I found

    d3.xml("test.svg", "image/svg+xml", function(xml) {
        var importedNode = document.importNode(xml.documentElement, true);
        d3.select("body").node().appendChild(importedNode);

        svg=d3.select("body").select("svg")
            .attr("height","100%")
            .attr("width","100%");
        slides = svg_slides(svg,1500);

        // Lets test the slide scales - put a bouncing ball on slide id 3
        s = slides[3];
        circle = svg.append("svg:circle")
            .attr("cx",s.scale_x(500)).attr("cy",s.scale_y(500))
            .attr("r",20)
            .style("fill","steelblue");

        next = 500;

        function bounce() {
            next = -next;
            circle.transition().duration(2500).attr("cx",s.scale_x(500+next))
            .each("end",bounce);
        }

        bounce();
    });

</script>
</head>
<body></body>
</html>

## svg_slides.js
/*  This is a basic attempt to use d3 to process transitional slides from SVG files (i.e. Inkscape)
    The main objective here was to keep everything as simple as possible

    To create a slide, simply create a rectangle in inkscape where you set the object ID to "slide_" + a number
    This number can be either integer or float, so "slide_1","slide_2" and "slide_3.56" all work.

    The script sorts the slide-numbers and transitions between slides based on the final sorted order.

    It is easy to add slides into a pre-existing ordering, simply by chosing a floating number in the middle of the two
    Example: If we want to add slide between "slide_2" and "slide_3" we simply add a rectancle called "slide_2.5"

    Keyboard definitions:
        Right arrow:    next slide
        Left arrow:     previous slide
        Home:           first slide
        End:            last slide

    Please be aware that you need to remove any layer transition is the svg file (or put the layer transition to 0,0)

    Each slide has a scale_x and scale_y functions that have pre-set range to the slide boundaries and a default
    domain of [0,1000], allowing the user to position objects easily onto each slide.


    ziggy.jonsson.nyc@gmail.com
*/


function svg_slides(svg,delay) {
    var slides={},
        slide = 0,
        delay = delay ? delay : 3500;

    svg.attr("preserveAspectRatio","xMidYid meet");

    rects = svg.selectAll("rect")[0];

    for (i=0;i<rects.length;i++) {
        id = rects[i].id;
        console.log(id);
        if (id.slice(0,6)=='slide_') {
            slides[id.slice(6)]=rects[i]
            rects[i].scale_x = d3.scale.linear().range([rects[i].x.baseVal.value,rects[i].x.baseVal.value+rects[i].width.baseVal.value]).domain([0,1000]);
            rects[i].scale_y = d3.scale.linear().range([rects[i].y.baseVal.value,rects[i].y.baseVal.value+rects[i].height.baseVal.value]).domain([0,1000]);
            }

    }

    keys = Object.keys(slides).sort();
    slides.keys = keys;

    function next_slide()  {
        svg.transition().duration(delay).attr("viewBox",slides[keys[slide]].x.baseVal.value+" "+slides[keys[slide]].y.baseVal.value+" "+slides[keys[slide]].width.baseVal.value+" "+slides[keys[slide]].height.baseVal.value);
    }

    d3.select("body").on("touchmove", function() { if(slide<keys.length-1) {slide++; console.log(slide);}});

    d3.select(window).on("keydown", function() {
        switch (d3.event.keyCode) {
          case 37: {if (slide>0) {slide=slide-1; console.log(slide);next_slide()};break}
          case 39: {if(slide<keys.length-1) {slide++; console.log(slide);next_slide()};break}
          case 36: {slide = 0;next_slide();break}
          case 35: {slide = keys.length -1; next_slide();break}
        }

     });

    // Start with the first slide
    next_slide();
    return slides
}

## test.svg

      
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              test.svg
            
          
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	<!DOCTYPE html>
	<html>
	<head>
	<script type="text/javascript" src="http://mbostock.github.com/d3/d3.js"></script>
	<script type="text/javascript" src="svg_slides.js"></script>

	<script type="text/javascript">

	// There are probably better ways of loading the SVG, but this is one example I found

	d3.xml("test.svg", "image/svg+xml", function(xml) {
	var importedNode = document.importNode(xml.documentElement, true);
	d3.select("body").node().appendChild(importedNode);

	svg=d3.select("body").select("svg")
	.attr("height","100%")
	.attr("width","100%");
	slides = svg_slides(svg,1500);

	// Lets test the slide scales - put a bouncing ball on slide id 3
	s = slides[3];
	circle = svg.append("svg:circle")
	.attr("cx",s.scale_x(500)).attr("cy",s.scale_y(500))
	.attr("r",20)
	.style("fill","steelblue");

	next = 500;

	function bounce() {
	next = -next;
	circle.transition().duration(2500).attr("cx",s.scale_x(500+next))
	.each("end",bounce);
	}

	bounce();
	});

	</script>
	</head>
	<body></body>
	</html>
	/* This is a basic attempt to use d3 to process transitional slides from SVG files (i.e. Inkscape)
	The main objective here was to keep everything as simple as possible

	To create a slide, simply create a rectangle in inkscape where you set the object ID to "slide_" + a number
	This number can be either integer or float, so "slide_1","slide_2" and "slide_3.56" all work.

	The script sorts the slide-numbers and transitions between slides based on the final sorted order.

	It is easy to add slides into a pre-existing ordering, simply by chosing a floating number in the middle of the two
	Example: If we want to add slide between "slide_2" and "slide_3" we simply add a rectancle called "slide_2.5"

	Keyboard definitions:
	Right arrow: next slide
	Left arrow: previous slide
	Home: first slide
	End: last slide

	Please be aware that you need to remove any layer transition is the svg file (or put the layer transition to 0,0)

	Each slide has a scale_x and scale_y functions that have pre-set range to the slide boundaries and a default
	domain of [0,1000], allowing the user to position objects easily onto each slide.


	ziggy.jonsson.nyc@gmail.com
	*/


	function svg_slides(svg,delay) {
	var slides={},
	slide = 0,
	delay = delay ? delay : 3500;

	svg.attr("preserveAspectRatio","xMidYid meet");

	rects = svg.selectAll("rect")[0];

	for (i=0;i<rects.length;i++) {
	id = rects[i].id;
	console.log(id);
	if (id.slice(0,6)=='slide_') {
	slides[id.slice(6)]=rects[i]
	rects[i].scale_x = d3.scale.linear().range([rects[i].x.baseVal.value,rects[i].x.baseVal.value+rects[i].width.baseVal.value]).domain([0,1000]);
	rects[i].scale_y = d3.scale.linear().range([rects[i].y.baseVal.value,rects[i].y.baseVal.value+rects[i].height.baseVal.value]).domain([0,1000]);
	}

	}

	keys = Object.keys(slides).sort();
	slides.keys = keys;

	function next_slide() {
	svg.transition().duration(delay).attr("viewBox",slides[keys[slide]].x.baseVal.value+" "+slides[keys[slide]].y.baseVal.value+" "+slides[keys[slide]].width.baseVal.value+" "+slides[keys[slide]].height.baseVal.value);
	}

	d3.select("body").on("touchmove", function() { if(slide<keys.length-1) {slide++; console.log(slide);}});

	d3.select(window).on("keydown", function() {
	switch (d3.event.keyCode) {
	case 37: {if (slide>0) {slide=slide-1; console.log(slide);next_slide()};break}
	case 39: {if(slide<keys.length-1) {slide++; console.log(slide);next_slide()};break}
	case 36: {slide = 0;next_slide();break}
	case 35: {slide = keys.length -1; next_slide();break}
	}

	});

	// Start with the first slide
	next_slide();
	return slides
	}