Lorikeet Reference
=====================================

Lorikeet is a JQuery plugin to render MS/MS spectra annotated with fragment ions. 
The spectrum is interactive with zoom capabilities, selection of fragment types,
switching annotations on and off etc. The plugin can, optionally, also render a MS1 
spectrum below the MS/MS spectrum, with options to highlight the precursor peak 
for the MS/MS scan, as well as any other precursor peaks.  


Files required for the plugin to work:
1. specview.js -- this file has the plugin's rendering functions
2. aminoacid.js
3. ion.js
4. peptide.js
5. jquery.flot.js -- this is a modified version of the flot (http://code.google.com/p/flot/) 
                     plotting library for JQuery.  It is base off of subversion revision 263.
6. jquery.flot.selection.js -- part of the flot package.  This is also from revision 263.


Other Dependencies:
1. JQuery core library (tested with version 1.4.2)
2. JQuery UI library (tested with version 1.8.4)

A NOTE ABOUT Internet Explorer
---------------------------------------
The flot JQuery plugin makes use of the canvas element of HTML5.  This element is not 
supported in the current versions of IE. It should be supported in IE9. 
For the viewer to work on IE the ExplorerCanvas script has to be included in the page.
This script brings the canvas functionality to IE. 

    <!--[if IE]><script language="javascript" type="text/javascript" src="../js/excanvas.min.js"></script><![endif]-->



Examples:
---------------------------------------
Please see the following examples of using the Lorikeet plugin in a html page:
1. example_use.html 	-- MS/MS spectrum only
2. example_use2.html 	-- MS/MS and MS1 spectra


Stylesheet:
---------------------------------------
The stylesheet lorikeet.css contains the necessary styling for the Lorikeet plugin.


Usage:
---------------------------------------
The following fragment has to be included in the HTML file where the viewer should be
displayed.  The id of the div can be any id that is unique on the page.
	<div id="lorikeet"></div>

The following fragment has to be included in a script element on the page.  This is 
typically included in the window.onload function.  $("#lorikeet") is the JQuery way
of referring to a DOM element with the id "lorikeet". 
	$("#lorikeet").specview(options);
	

API Documentation:
---------------------------------------
Lorikeet has only a single method that renders the viewer! 

    specview(options)

    options is a set of key/value pairs that configure and provide data to the viewer.

Options:
	{
	    "sequence": null,
		"staticMods": [],
		"variableMods": [],
		"ntermMod": 0, // additional mass to be added to the n-term
		"ctermMod": 0, // additional mass to be added to the c-term
		"peaks": [],
		"massError": 0.5, 
		"scanNum": null,
		"fileName": null,
		"charge": null,
		"precursorMz": null,
		"ms1peaks": null,
		"ms1scanLabel": null,
		"precursorPeaks": null,
		"precursorPeakClickFn": null,
		"zoomMs1": false,
		"width": 750, 	  // width of the ms/ms plot
		"height": 450, 	  // height of the ms/ms plot
		"extraPeakSeries": [],
		"showIonTable": true,
        "showViewingOptions": true,
        "showOptionsTable": true,
        "showSequenceInfo": true,
        "labelImmoniumIons": true,
        "labelPrecursorPeak": true,
        "labelReporters": false,
        "showMassErrorPlot": false,
        "massErrorPlotDefaultUnit": 'Da'
    }
    
    The required options(key/value pairs) are:
    ------------------------------------------
    1. sequence: the sequence of the peptide
    2. peaks: an array of peaks in the MS/MS scan.  
              Example: [ [602.17,209860.34], [691.67,33731.58],[871.42,236841.11],[888.50,1005389.56] ]
    
    Other options (not required):
    ----------------------------
    1. charge: The charge of the precursor. This information is displayed at the top of the scan.
    2. precursorMz: The m/z of the precursor. This information is displayed at the top of the scan.
                    This value is required for labeling the precursor peak in the MS1 scan if 
                    it is rendered, and also marking the precursor peak in the MS/MS scan.
    3. scanNum:  The scan number of the MS/MS scan. This information is displayed at the top of the scan.
    4. fileName: Name of the file that contains the MS/MS scan. This information is displayed at the top of the scan.
    5. staticMods: An array of static modifications. Each modification is a set of key/value pairs.
                   Example: [{"modMass":57.0,"aminoAcid":"C"}];
    4. variableMods: An array of variable modifications. Each modification is a set of key/value pairs.
                   Example: [ {index: 14, modMass: 16.0, aminoAcid: 'M'} ] // index is the index (1-based) 
                                                                           // of the modification in the sequence.
    5. ntermMod: additional mass to be added to the N-terminus.
    6. ctermMod: additional mass to be added to the C-terminus.  
    7. massError: mass tolerance used for labeling peaks in the MS/MS scan.                                                                         
    8. ms1Peaks:  peaks in the MS1 scan. Format is the same as the "peaks" option.
    9. precursorPeaks:  Any precursor peaks in the MS1 scan that will be highlighted. 
                        Same format is the same as the "peaks" option.
    10. zoomMs1: If the value is "true" the MS1 scan, upon initialization, is zoomed around the peak 
                 that is the closest match to the "precursorMz" option. Default is "false".  
    11. ms1scanLabel: Label for the MS1 scan.
    12. precursorPeakClickFn: This is the function that will be called when a precursor peak is clicked.
    13. width: width of the MS/MS plot area. Default is 750.
    14. height: height of the MS/MS plot area. Default is 450. 
    15. extraPeakSeries: An array of user defined peak series.  Each series should be a set of key value pairs.
                  Example: {data: [[10.0,2.0],[20.0,3.0]], color: "#00aa00",labelType: 'mz',labels: ['one','two']}
                  		   "labelType" should not be used if custom labels are provided as value to the "labels" key.
                           If "labelType" is 'mz', custom labels are ignored.
    16. showIonTable: Show a table with theoretical fragment ion masses to the right of the annotated MS/MS scan.
                      Default is true.
    17. showViewingOptions: Show zooming and other options at the bottom of the MS/MS scan. Default is true.
    18. showOptionsTable: Show a table with all the available options to the left of the annotated MS/MS scan.
                          Default is true.
    19. showSequenceInfo: Show sequence, m/z, filename, scan number, charge etc. at the top of the MS/MS scan.
                          Default is true.
    20. labelImmoniumIons: Label immonium ions in the MS/MS scan. Default is true.
                           Example file: example_precursor_immonium.html
    21. labelPrecursorPeaks: Label precursor ion if found in the MS/MS scan. Default is true.
                             Example file: example_precursor_immonium.html
    22. labelReporters: Label reporter ions such as iTRAQ and TMT. Default is false.
                        Example file: example_itraq.html
    23. showMassErrorPlot: Display a plot showing the mass errors for annoated peaks. Default is false.
                           Example file: example_mass_error_plot.html
    24. massErrorPlotDefaultUnit: Unit for mass error plot. Default is 'Da'.  Set to 'ppm' to see mass error in
                                  parts per million.
}