Update the gitigonore
Updated Git Ignore for building with FLASH BUILDER
Cleaning up Flash BUILDER .settings/ folder
 Include a new MAGE BAR View component,
A new MAGE BAR MEDIATOR for interfacing the component with the Magelet Backends
Register the MAGE BAR MEDIATOR in the APPLICATION MEDIATOR
Created a MAGE PARAMETERS MODEL - A mage parameter object for holding all the parameter information
Created a MAGE PARAMETER DIALOG - A graphical MODAL FORM for inputing the parameters
Created a MAGE RESULTS DIALOG - A graphical SIMPLE FORM for displaying the MAGE results
Added getting and seeting functions to the Application Facade for holding, loading and saving infomration to the Mage Parameter Object
 Also update the server address for compatibility with magelet
[MageProperties.as] Created and Restructured
Refactored what was once the MageParameters.as file in Model to become a data store for all MageRelated data
Changed the applicationFacade so that it stores a mageProperties object and has getters and setters for them
Created a MageConstants.as class with static functions that hold all constants related to Mage, this is where all the GUI bounds and static key terms are held
Amended both MageResultsDialog and MagePropertiesDialog to work with new Mage Properties and MageConstants keeping it general
[MageBar] Reorganized and Added Functionality
[MageBar] Removed the drop down menu, formatted the three buttons to have + -  and +_ symbols
[MageBarMediator] Added event listeners to all the three mutation buttons
Added functionality to the insertion button (not complete yet)
Added functionality for refreshing interface information and adding / clearing error strings
[MageConstants] Added some constants that pertain to the MageBar Mediator etc...
[MageBar Mediator] Extended Functionality
Both the deletion and mismatch buttons now have the functionality that insertion had.
Deletion will check for a valid selection
Mismatch will checj for a valid selection
Both will display error strings
[MageConstants] Added a few constants
[MageProperties] The model now has a record function for adding recording a mutation
[MageRecordDialog] Created a dialog for viewing individual records
[MageMutationRecordDialog] - Dialog shown after user clicks on the insertion/deletion/mismatch button
[MageViewResultDialog] - Dialog shown after clicking magebar.magerecords buttons
[mageProperties] Added a queuing system to for mutation records
[mageBar] Added new button for viewing stored mage records.
[mageBarMediator] Added functionality for all the three mutation buttons and the viewResults button.
[MageBarMediator] Corrected deletion methods
[MageMutationRecordDialog] Accomadated deletion mutation exceptions
Added icons
Restructuring the GUI for Mage Editor

Removed - All dialogs except the parameters dialog

[MageParametersDialogForm.mxml] Stripped Old User Input Method
Added new batch IO processing method.
Added upload, preview and save functionality for the parameter
input

[MageTargetDialogForm.mxml] Similar to the parameter dialog
this form will allow a user to upload, preview and save changes
to an INPUTtarg.txt file

[TargetUploader.as] & [ParameterUploader.as]
	These are just files for uploading and mutating state
	To avoid complexity, two files where made

[MageBar.mxml]  Changed the look, removed unncessary old buttons

[mageBarMediator.as] Removed old functionality and added new
upload dialog functionality

[mageProperties.as] Removed old data members/ getters/setters and helper
functions and replaced with ones for uploading target/parameters.
Added Communication Functionality

MageBarMediator -> Add functionality for
communicating with server for batch IO processing
Added Variable POST response

mageProperties -> now class name is MageProperties

MageBar -> Added dropdown combo box

Dialogs -> Changed to uneditable textbox with single
preview and save button. This prevented reformatting of
the original file and problems occuring when sending
the file to the server.

ParameterUploader -> refactoring changes

TargetUploader -> Refactoring changes

ApplicationFacade -> Refactoring changes

Oligo.as -> For use with returned resutls
Added Logging Console Feature

MainContentPanel.mxml -> Added a vertical box divider to include
a textarea where we can have an auto scrolling text box that
displays, like a console, a log of all the user's inputs.

MainContentPanelMediator -> Added a datamember status for the console.
The console is just a string that grows and autoscrolls, therefore there
might be issues if the textarea grows too large.

Integrated a notification for the MainContentPanel that updates the
console when received.

Notifications -> Added a constant UPDATE STATUS notifications

MageBarMediator -> Added a wrapper function to send notifications
to update the status console.

Oligo -> Will use this for working with features

--- Future Work ----

The next step would be to use the post response variables to pass
an array of genbank files which can be used to load and edit a sequence
Restructured the features and Colors

pie/featureRender \		 all had identical color functions
rail/featureRender |-> which nows support insertion, deletion
seq/featureRender /    merlin and optmage oligos

featureDialogForm.mxml -> created the feature type listed above
Integrated Auto Genbank Loading

MageBar.as -> added new Merlin button and functionality to the combobox

MageBarMediator.as -> Added Merlin Button Click and load handlers
	The Click works similar to the previous, the Load splits the result
	into individual oligos / Populates mageBar's combobox

MageProperties.as -> Added getters/setters and merlinResults Data field

Oligo.as -> Created new Oligo.as class as a container for the genbank
	string, to be parser on the fly everytime the oligo is selected
Updated Names on Oligo

Integrated the Oligo Names for cleaner viewing
Added Plotting Functionality

Added working plotting functionality.
All three plots are displayed simulatneously at once and the resultant plotting is shown.

ApplicationFacade.as -> Added an update Charts function as a hack to get
the MainContentPanelMediator to be able to sync with the MageBar

MageBar.mxml -> integrated the updateCharts function into the oligo selection combox
changes

MageBarMediator -> Updated the onMerlinResonse Function to load the plot
data from the response

Oligo.as -> Added more getters/setters and fields for dealing with the chart
plotting data.

Notifications.as -> Added UPDATE_CHARTS notification

TODO: Still need to show the optMAGE vs Merlin points on the graph
Added optmage and merlin positions

Added positions for optMage and Merlin to the graph
Added axis renderer to reduce the number of ticks...
Changed the url from localhost to cidar1