ALiX is a software package designed primarily to analyze freely-diffusing single-molecule FRET data.

It is developed as a research tool and has no pretense to meet the needs of all single-molecule FRET experimentalists.

ALiX is comprised of a main window divided into (from top to bottom):
  • a title bar,
  • a menu bar,
  • one of several Pages (or Tabs) in which different controls and indicators allow the user to interact and process data,
  • a status bar.

Finally, additional windows can be opened to provide user with information, allow specific settings to be entered or perform special analysis tasks.

These different components are briefly described in the next few sections. Further details can be found in the respective pages of the manual.

1.1. Title bar

The title bar changes each time a new file is opened. The new title reads "ALiX: path_of_the_file_loaded_in_memory".
This provides a quick way of checking which file is being analyzed from any page within the software.

The close box in the upper right of the window does exactly what it says: It closes the window and consequently quits ALiX (there is a warning dialog window preventing accidentally quitting ALiX). Child windows that become useless without the original data are automatically closed, while others may remained opened, such as the Notebook window. Note that as long as such a window remains open, the application is still considered running, even though there is no way to re-open the main ALiX window.

1.2. Menu bar

5 menus are available: File, Windows, Pages, Analysis and Help. Their description, function and associated shortcuts are described in the corresponding page of the manual.
Note that there are contextual menus (accessible via a mouse right-button click) for most objects found in the various windows and pages.

1.3. Pages

The number of accessible pages depends on the type of the file opened. For instance, when analyzing data from a ns-ALEX experiment, the us Alternation Periods page is not accessible, but the Nanotime Display and Nanotime Analysis pages are, while the opposite is true if the data belongs to a us-ALEX experiment.
Pages can be accessed either by clicking on the corresponding label in the ALiX Pages table of content located to the left of the window, or by selecting them in the Pages menu. A third way to switch from one page to another automatically is by checking one of the Switch to... checkboxes found on some pages. This option allows the user to be automatically moved to the next relevant page (according to the workflow diagram shown in ALiX Workflow) after a particular analysis step has been completed.

1.4. Status bar

At the bottom of the main ALiX window is a box reserved for succinct messages to the user, when the occasion requires it.
The rest of the lower part of the window is reserved for a task progress bar, which only shows up when a CPU intensive task is underway. On its right, an Abort button is present when the progress bar is visible, allowing the user to interrupt a computation (or loading, or any time consuming process). Note that not all lengthy tasks will show a progress bar and the Abort button, but instead will show a "busy" animated icon next to the message box. Currently there is no option to interrupt this kind of tasks but to force quit the application.
Status LED are located on the far right of the status bar. They indicate which step of the analysis have been completed. Hovering the mouse over a LED reveals a tip strip indicating its function.

1.5 Additional windows

Additional windows can be opened, such as the About ALiX window, the ALiX Settings window, ALiX Burst Inspector window, etc. There are different ways to access these windows, including the Windows menu, buttons on some Pages, and user-triggered actions, which will automatically open a window. These different windows are described in detail in the
ALiX Windows section of the manual.