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CATUI Main Application Window

Table of Contents

1. Windowing Framework and Entity Management (Back to Top)

The main CATUI Application window is currently split into two parts, the Data Source List Pane and the Data Source Tabbed View Pane.

1a. Data Source List Pane (Back to Top)

The CATUI provides for the visualization and manipulation of different biological data elements/sources utilized in RNA comparative analysis. The biological data sources currently supported by the CATUI are discussed here. The data sources can be organized into three groups:
  1. Sequence Alignments
  2. Structure Diagrams (2-D)
  3. Structure Models (3-D)
The Data Source List Pane (on the left side of the main CATUI window) organizes any data sources loaded into the CATUI according to these groupings. In the screen capture below, two data sources are loaded into the CATUI, one is a Sequence Alignment and the other is a Secondary Structure Model.
Note: Workspaces are simply pre-defined sets of data sources and are discussed below.

CATUI Data Source Pane

Multiple visualizations of any data source can be opened simultaneously in the CATUI. Each visualization is considered to be a separate view of the data source. All open views are tracked on the Data Source Pane. In the screen capture below, each data source loaded has a single open view.

CATUI Data Source Pane

The CATUI automatically determines which views are supported by any data source. In the following screen capture, an RNA single secondary structure diagram data source capable of supporting three different views.

CATUI Data Source Pane

1b. Data Source Tabbed View Pane (Back to Top)

When any view is opened on a data source, it is initially added to the Data Source Tabbed View Pane as an additional tab. In the screen capture below, we show two data sources loaded into the CATUI Application; a sequence alignment and a secondary structure. Each data source has a single open view which appears in the view pane.

CATUI Data Source Tab Pane

1c. Floating Windows (Back to Top)

Any open view can be undocked from the Data Source Tabbed View Pane and converted into a floating window by clicking on the "push-pin" icon at the left hand side of the tab. The floating window can be re-docked to Data Source Tabbed View Pane by clicking the "push-pin" icon in the far left corner of the floating window. The combined floating/tabbed architecture allows the user the freedom to size and position windows appropriate for their particular analysis task and leverage dual screen setups as well as large, widescreen monitors (e.g., 30").
  • To undock a window:
CATUI Floating Windows
CATUI Floating Windows

2. Workspaces (Back to Top)

The CATUI Application supports the simultaneous visualization of different of biological data sources utilized in comparative analysis such as: sequence alignments, 2D secondary structures, and 3D structures. Because these different data sources are typically stored in separate locations (files) and varying formats, but are related, the CATUI provides a workspace mechanism to associate different data sources together.

Through a workspace, a user can open hundreds of data sources simultaneously. Users can easily modify a workspace to add or remove data sources at anytime. Multiple workspaces can be opened simultaneously if desired.

2a. Creating a new Workspace (Back to Top)

  • Right-click on Workspace and select Create New Workspace
  • Enter a workspace name and select a folder to store the workspace file in the Dialog
  • In this example, I am creating a workspace named DocumentationWorkspace and saving it in C:\
  • Note: Currently there is a bug and you must select a different folder than is initially suggested as a target location for the new workspace. This will be fixed in a future version of the CATUI.
  • The new, empty workspace, DocumentationWorkspace is in the main window under Workspaces. The three data source categories: Sequence Alignments, Structure Diagrams and Molecular Structure (3D) appear under the workspace. We can now add data sources to the workspace.
  • To save the workspace, close the CATUI application.

2b. Opening an existing Workspace (Back to Top)

  • Right-click on Workspace and select Open Workspace

2c. Adding Data Sources to a Workspace (Back to Top)

  • Open an existing workspace or create a new workspace.
  • Select the data source container and open the new data source. In the screen-capture below, we add a sequence alignment to the workspace.
  • When you close the CATUI, the data source will be mapped to the workspace.
  • Note: The paths for file-based data sources are stored in the workspace, so moving the file will break the workspace.

2d. Adding a Data Source to a Workspace that is already Open in the CATUI (Back to Top)

  • Open a data source such as a sequence alignment or a 2D structure model in the CATUI.
  • Note: This option only applies to file-based data sources, not those from to an rCAD database.
  • Open an existing workspace or create a new workspace
  • Right-click on the Workspace and select Add Open Data File
  • Select the open data source to add to the workspace.

2e. Removing a Data Source from a Workspace (Back to Top)

  • Open an existing workspace that has at least one data source associated with it.
  • Right-click on the data source to remove from the workspace and select Close

2f. Other Workspace Options (Back to Top)

  • Open All Data Sources: When a workspace with data sources associated is opened, initially the data sources are not loaded into memory. All data sources can be loaded into memory by right-clicking on the workspace and selecting Open All Data Sources.
  • Close All Views: All views on any data sources associated with a workspace can be closed at once by right-clicking on the workspace and selecting Close All Views.

Last edited Dec 11, 2009 at 10:07 PM by kjdoshi, version 18


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