Class Biojs.Chromosome

Version 1.0.1.

Extends Biojs.

Defined in: Biojs.Chromosome.js.

Class Summary
Constructor Attributes	Constructor Name and Description
	Biojs.Chromosome(options) This component allow to visualize a chromosome and its bands.

Field Summary
Field Attributes	Field Name and Description
<inner>	eventTypes Array containing the supported event names
<inner>	opt Default values for the options

Method Summary
Method Attributes	Method Name and Description
	constructor(options)
	moveSelectorToCoordinates(from, to) Move the Selector to a specific place in the chromosome

Methods borrowed from class Biojs:: addListener, extend, getId, listen, raiseEvent, setEventHandlers, setOptions

Event Summary
Event Attributes	Event Name and Description
	onBandSelection(actionPerformed)
	onDASLoadFail(actionPerformed)
	onModelLoaded(actionPerformed)
	onSelectorChanged(actionPerformed)

Class Detail

Biojs.Chromosome(options)

This component allow to visualize a chromosome and its bands. The bands can be recovered from a DAS source or directly from a javascript model.
Author: Gustavo A. Salazar.

					var instance= new Biojs.Chromosome({
						target: "YourOwnDivId",
						dasSource: "http://www.ensembl.org/das/Homo_sapiens.NCBI36.karyotype/",
						dasSegment: "8"
					});

Parameters:
{Object} options: An object with the options for the Chromosome component.

Options detailed:
{string} target: Identifier of the DIV tag where the component should be displayed.
{string} dasSource: URL of the DAS source to obtain the band's information. For example Ensembl provides the human chromosome information as a DAS source in the URL http://www.ensembl.org/das/Homo_sapiens.NCBI36.karyotype/
{string} dasSegment: DAS segment to query, in case of chromosomes is the chromosome id (eg. 8). Optionally DAS sources can be queried for a spwcific region of the chromosome(eg. 8:43100000,49100001)
{Object} model: Alternatively to DAS, This component can receive directly a javascript object containing the relevant information. Here is an example of the object structure using JSON notation: { "id": "8", "start": 1, "stop": 199999, "bands": [ { "label": "p11", "type": "acen", "start": 1, "stop": "100000" }, { "label": "q11", "type": "gpos75", "start": 100001, "stop": "199999" } ] }
{boolean} [includeSelector]: Include an area selector that interacts with the coordinate position of the chromosome. default true.

Requires:: jQuery Core 1.7.2; jsdas 0.1.6; Chromosome CSS; Biojs AreaSelector; jQuery UI 1.8.2; jQuery UI CSS 1.8.2; jquery.watcher.js; Selector CSS

Field Detail

<inner> eventTypes

Array containing the supported event names

<inner> opt

Default values for the options

Method Detail

constructor(options)

Parameters:
options

moveSelectorToCoordinates(from, to)

Move the Selector to a specific place in the chromosome

instance.moveSelectorToCoordinates(10000000,20000000);

Parameters:
{integer} from: initial chromosome coordinate to locate the selector
{integer} to: final chromosome coordinate to locate the selector

Event Detail

onBandSelection(actionPerformed)

					instance.onBandSelection(function( objEvent ) {
						alert("The band " + objEvent.band_id + " of the chromosome " + objEvent.chromosome_id + " has been selected\n[" + objEvent.band_start + "," + objEvent.band_stop + "]");
					});

Parameters:
{function} actionPerformed: A function which receives an Biojs.Event object as argument.

Event object data:
{Object} source: The component which did triggered the event.
{string} type: The name of the event.
{string} chromosome_id: Id of the chromosome that the selected band belongs.
{string} band_id: Id of the band that has been selected.
{integer} band_start: Coordinate of the first nucleotide of the selected band
{integer} band_stop: Coordinate of the last nucleotide of the selected band
{string} band_type: type of the band selected (eg. acen, gpos50, gneg).

onDASLoadFail(actionPerformed)

					instance.onDASLoadFail(function( objEvent ) {
						alert("The DAS source "+objEvent.dasSource+" with information of the segment "+objEvent.dasSegment+" couldn't be loaded");
					});

Parameters:
{function} actionPerformed: A function which receives an Biojs.Event object as argument. Triggered when the model couldn't be loaded

Event object data:
{Object} source: The component which did triggered the event.
{string} type: The name of the event.
{string} dasSource: URL of the DAS source queried
{string} dasSegment: URL of the DAS source queried

onModelLoaded(actionPerformed)

					instance.onModelLoaded(function( objEvent ) {
						alert("The model for the chromosome "+objEvent.model.id+" has been loaded");
					});

Parameters:
{function} actionPerformed: A function which receives an Biojs.Event object as argument. Triggered when he model has been loaded

Event object data:
{Object} source: The component which did triggered the event.
{string} type: The name of the event.
{Object} model: The model after been displayed

onSelectorChanged(actionPerformed)

					instance.onSelectorChanged(function( objEvent ) {
						alert("The selector has move to the region \n[" + objEvent.selector_start + "," + objEvent.selector_stop + "]");
					});

Parameters:
{function} actionPerformed: A function which receives an Biojs.Event object as argument. Is triggered when the the coordinates of the selector have been changed.

Event object data:
{Object} source: The component which did triggered the event.
{string} type: The name of the event.
{string} chromosome_id: Id of the chromosome that the selected band belongs.
{integer} selector_start: Coordinate of the left side of the selector
{integer} selector_stop: Coordinate of the right side of the selector

Classes

Class Biojs.Chromosome