Class Biojs.ProteinPortafolio

Version 1.0.0.

Extends Biojs.

Defined in: Biojs.ProteinPortafolio.js.

Class Summary
Constructor Attributes	Constructor Name and Description
	Biojs.ProteinPortafolio(options) ProteinPortafolio component shows the description of a protein as well as its PDB alignments if there is any.

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)
	getAlignmentsByPdb(pdb) Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).
	getCurrentAlignment()
	setProtein(accession) Sets the protein accession which changes everything to reflect the new protein information
	setSize(size) Change the font size.

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

Event Summary
Event Attributes	Event Name and Description
	onClick(actionPerformed)
	onPdbSelected(actionPerformed)

Class Detail

Biojs.ProteinPortafolio(options)

ProteinPortafolio component shows the description of a protein as well as its PDB alignments if there is any. Component shows the PDBLogos of the selected alignment and ables to play with the sequence and the 3D draw of the alignment.
Author: John Gomez.

var instance = new Biojs.ProteinPortafolio({
		target : "YourOwnDivId",
		accession : 'P99999'
});

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

Options detailed:
{string} target: Identifier of the DIV tag where the component should be displayed.
{string} [fontFamily='"Andale: mono", courier, monospace'] Font list to be applied to the component content.
{string} [fontColor="white"]: HTML color code for the font.
{string} [backgroundColor="#7BBFE9"]: Background color for the entire div content.
{Object} [selectionFontColor="white"]: This color will be used to change the font color of selected text.
{Object} [: selectionBackgroundColor="yellow"] This color will be used to change the background of selected text.
{string} [pdb3DIcon='../biojs/css/images/3d.png']: The only PDB icon is able to defines the 3D structure. Set source URL for 3D icon

Requires:: jQuery Core 1.6.4; Raphael 2.1.0; PDBLogos; Sequence; Protein3DWS; jMol 12.0.48; Protein3D CSS; ProteinPortafolio CSS

Field Detail

<inner> eventTypes

Array containing the supported event names

<inner> opt

Default values for the options

Method Detail

constructor(options)

Parameters:
options

{Object} getAlignmentsByPdb(pdb)

Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).

// Get the alignments matching with bases 4, 8 and 100.
alert ( instance.getAlignmentsByPdb("2F73") );

Parameters:
{string} pdb: identifier.

Returns:: {Object} .

getCurrentAlignment()

setProtein(accession)

Sets the protein accession which changes everything to reflect the new protein information

instance.setProtein("P07148");

instance.setProtein("P12345");

Parameters:
{string} accession: The new protein identifier

setSize(size)

Change the font size. Do nothing it no value is provided.

instance.setSize("72px");

Parameters:
{string} size Optional: The new font size in pixels.

Event Detail

onClick(actionPerformed)

instance.onClick(
   function( objEvent ) {
      alert("The character " + objEvent.selected + " was clicked.");
   }
);

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.
{int} selected: Selected character.

onPdbSelected(actionPerformed)

instance.onPdbSelected(
   function( e ) {
      alert("Selected " + e.alignmentId + " alignment.");
   }
);

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} alignmentId: Identifier .
{string} pdbId: Selected pdb entry.
{int} start: Start position of the alignment.
{int} end: End position of the alignment.

Classes

Class Biojs.ProteinPortafolio