Genoverse functions

The following are functions that exist in the Genoverse object. Any of these can have before/after hooks added to them, or be overwritten by supplying them as properties in configuration.

Initialization

genoverse.init()

Called once the Genoverse instance is created. Sets initial properties of the instance and calls functions to creates its DOM elements, event handlers, tracks and highlights, and set the starting location.

genoverse.addDomElements(width)

Creates the DOM elements required by the instance of Genoverse

Argument	Type	Description
width	Integer	The width for the container DOM element (usually this should be the initial value of genoverse.width)

genoverse.addUserEventHandlers()

Creates the event handlers required for users to interact with the instance of Genoverse

Configuration

genoverse.loadConfig()

If genoverse.saveable is true, configuration will be loaded from window[genoverse.storageType].getItem(genoverse.saveKey). This configuration contains the user's previous tracks, their ordering, heights, and any other track configuration settings. If no configuration exists, the default set of tracks will be used instead.

genoverse.saveConfig()

If genoverse.saveable is true, the user's current tracks, their ordering, heights, and any other track configuration settings will be saved to window[genoverse.storageType].getItem(genoverse.saveKey).

genoverse.resetConfig()

If genoverse.saveable is true, removes all tracks and unremovable highlights, adds the default set of tracks, and removes the value in genoverse.saveKey from window[genoverse.storageType].

Changing browser location

genoverse.moveTo(chr, start, end [, update, keepLength])

See the api documentation

genoverse.move(delta)

Move the browser region a number of pixels left or right. This will be translated into a new chromosomal location based on the current value of genoverse.scale (width of the browser's containing DOM element in pixels / size of genomic region being viewed).

Note: genoverse.moveTo should be used instead to change the location of a Genoverse instance externally.

Argument	Type	Description
delta	Integer	The number of pixels to move the browser region by (> 1 for left to right, < 1 for right to left)

genoverse.setRange(start, end [, update, keepLength ])

Sets genoverse.start and genoverse.end, moving the browser region in the process.

Note: genoverse.moveTo should be used instead to change the location of a Genoverse instance externally.

Argument	Type	Description
start	Integer	A number between 1 and genoverse.chromosomeSize
end	Integer	A number between start and genoverse.chromosomeSize
update	Boolean or undefined	If true, the URL will be updated with the new start and end
keepLength	Boolean or undefined	if true, the new viewpoint will have the same zoom level as before (end - start remains unchanged), centered on the given start and end.

genoverse.setScale()

Sets genoverse.scale to (width of the browser's containing DOM element in pixels / size of genomic region being viewed). If the scale changes, forces all tracks to draw new images at the new scale.

Track interactions

genoverse.addTracks

See the api documentation

genoverse.addTrack

See the api documentation

genoverse.removeTracks

See the api documentation

genoverse.removeTrack

See the api documentation

genoverse.updateTrackOrder(e, ui)

Called when a user moves track labels to reorder tracks in the browser. Set the moved track's order property such that it is between the order properties of its new immediate siblings. genoverse.sortTracks is then called to update the position of the track's image element.

See jQuery UI sortable update event for argument details.

genoverse.sortTracks

Reorders the tracks' DOM elements based on each track's order property, lowest first.

Highlight interactions

genoverse.addHighlights(highlights)

See the api documentation

genoverse.addHighlight(highlight)

See the api documentation

URL interactions

genoverse.updateURL

If genoverse.urlParamTemplate is set, the URL will be updated to reflect the current browser region. This will be done either by using window.history.pushState, or by updating window.location.hash, depending on the value of genoverse.useHash.

genoverse.popState

Called by window.onpopstate or window.onhashchange to update the browser region if the user uses the back or forward buttons in their web browser.

genoverse.getCoords

Returns an object in the form { chr: '1', start: 123, end: 456 } by parsing the URL using the value of genoverse.urlParamTemplate.

If the URL does not match genoverse.urlParamTemplate, or contains coordinates which do not match the defined genoverse.genome, return the initial coordinates defined by chr, start, and end in the instance's configuration.

genoverse.getQueryString

Returns a string of genoverse.urlParamTemplate with the placeholders replaced with their relevant values, to be used in updating the URL. If genoverse.useHash is false, this will be appended to any existing value of window.location.search such that other parameters are unchanged.

Popup menus

genoverse.makeMenu(features [, event, track ])

Creates a popup menu for one or more features. If more than one feature is provided, the popup will contain one link per feature which each create another popup for that feature

Argument	Type	Description
features	Feature object or array of feature objects	The feature(s) to make the menu for
event	jQuery event or undefined	The click event that created the menu, used to position the menu at the mouse pointer
track	Genoverse.Track instance or undefined	The track which was clicked on

genoverse.makeFeatureMenu(feature [, event, track ])

Called by genoverse.makeMenu to create a popup menu for a single feature

Argument	Type	Description
feature	Feature object	The feature to make the menu for
event	jQuery event or undefined	The click event that created the menu, used to position the menu at the mouse pointer
track	Genoverse.Track instance or undefined	The track which was clicked on

genoverse.insertPropertiesIntoMenu(menuProperties, menuEl, contentEl, feature [, track ])

Called by genoverse.makeFeatureMenu, creates the HTML for a popup menu. This includes one or more <table> elements, as well as titles and focus and highlight links where relevant (see controller.populateMenu for futher details).

If the popup menu is for a track's feature, menuProperties will be the value returned by controller.populateMenu. If not, it will be the feature that genoverse.makeFeatureMenu was called with.

Argument	Type	Description
menuProperties	Object or Array of Objects	The properties of the feature to create the popup for
feature	Object	The feature to create the popup for
menuEl	jQuery selector	The element containing the popup menu
contentEl	jQuery selector	The element containing the popup menu's content
track	Genoverse.Track instance or undefined	The track which was clicked on to create the popup

genoverse.closeMenus([ track ])

See the api documentation

User events

genoverse.setDragAction(action)

See the api documentation

genoverse.setWheelAction(action)

See the api documentation

genoverse.startDragScroll(e)

Initializes a scroll action

Argument	Type	Description
e	jQuery event	The user event which starts a scroll operation

genoverse.stopDragScroll([ update ])

Ends a scroll action

Argument	Type	Description
update	Boolean or undefined	If not false, will update the URL to the new location (providing the URL is changeable by the instance of Genoverse)

genoverse.startDragSelect(e)

Initializes a select action

Argument	Type	Description
e	jQuery event	The user event which starts a select operation

genoverse.stopDragSelect(e)

Ends a select action, showing an actions menu for the selected region

Argument	Type	Description
e	jQuery event	The user event which ends a select operation

genoverse.cancelSelect()

Hides the region selection element

genoverse.dragSelect(e)

Resizes the region selection element based on a mousemove event

Argument	Type	Description
e	jQuery event	The mousemove event

genoverse.keydown(e)

If the shift key is pressed, region selection is enabled while it is held down (nothing happens if genoverse.dragAction was already "select"). If the escape key is pressed, any popup menus (for track features or the region select menu) are hidden.

Argument	Type	Description
e	jQuery event	The keydown event

genoverse.keyup(e)

If the shift key is released, region selection is disabled if it was enabled by pressing the key initially (nothing happens if genoverse.dragAction was already "select").

Argument	Type	Description
e	jQuery event	The keyup event

genoverse.mousedown(e)

Starts a scroll or select action by calling genoverse.startDragScroll(e) or genoverse.startDragSelect(e), based on the value of genoverse.dragAction

Argument	Type	Description
e	jQuery event	The mousedown event

genoverse.mouseup(e)

Ends the current scroll or select action by calling genoverse.stopDragScroll(update) or genoverse.stopDragSelect(e), as applicable

Argument	Type	Description
e	jQuery event	The mouseup event

genoverse.mousemove(e)

If a scroll action is taking place, moves the browser region as the mouse moves. If a region select is taking place, changes the size of the selected region as the mouse moves. If genoverse.dragAction is "select" and a region select is not taking place, moves the region select element (a dotted red vertical line) to the location of the mouse pointer.

Argument	Type	Description
e	jQuery event	The mousemove event

genoverse.mousewheelZoom(e, delta)

Performs zoom in and zoom out operations

Argument	Type	Description
e	jQuery event	The user event which will cause a zoom operation
delta	1 or -1	1 for zoom in, -1 for zoom out

genoverse.zoomIn([ x ])

Calls genoverse.setRange to zoom in, halving the size of the browser region (e.g. 100-200 becomes 125-175). If an x argument is provided, the zoom will step towards that point, instead of directly inward. xis the difference between the x coordinate of a mousewheel zoom event and the left offset of the browser images on the page.

Argument	Type	Description
x	Integer or undefined	The point to zoom towards

genoverse.zoomOut([ x ])

Calls genoverse.setRange to zoom out, doubling the size of the browser region (e.g. 100-200 becomes 50-250). If an x argument is provided, the zoom will step towards that point, instead of directly outward. xis the difference between the x coordinate of a mousewheel zoom event and the left offset of the browser images on the page.

Argument	Type	Description
x	Integer or undefined	The point to zoom towards

Misc

genoverse.on()

See the api documentation

genoverse.once()

See the api documentation

genoverse.reset()

See the api documentation

genoverse.destroy()

See the api documentation

genoverse.setWidth(width)

See the api documentation

genoverse.getChromosomeSize(chr)

If genoverse.genome is an object, returns the size of the chromosome in the genome, else returns genoverse.chromosomeSize

Argument	Type	Description
chr	String	The name of the chromosome

genoverse.getSelectorPosition()

Returns an object in the form { start: 1, end: 2, left: 1, width, 1 } representing the position of the region selector DOM element. start and end are the genomic coordinates selected by the region, left and width are the CSS positional values of the element.

genoverse.onTracks(functionName [, arg1, arg2, ...argN ])

Calls the function functionName on all tracks in the instance of Genoverse, with the arguments provided

Argument	Type	Description
functionName	String	The name of the function to call. This function can be in Genoverse.Track, Genoverse.Track.Controller, Genoverse.Track.Model, or Genoverse.Track.View
args	Anything	A list of arguments to be passed to the function being called