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Classes


Class Biojs.ProteinPortafolio


Version 1.0.0.

Extends Biojs.

Defined in: Biojs.ProteinPortafolio.js.

Class Summary
Constructor Attributes Constructor Name and Description
 
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>  
Array containing the supported event names
<inner>  
opt
Default values for the options
Method Summary
Method Attributes Method Name and Description
 
constructor(options)
 
Get the available alignments for the current protein filtered by selection (PDB files containing a part of the requested region).
 
 
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, removeListener, 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.

Documentation generated by JsDoc Toolkit 2.3.2 on Thu Apr 17 2014 17:42:43 GMT+0100 (BST)