Broadcasting

Introduction

Broadcasting is a powerful and unique feature within Genome Workbench that allows the sharing and communicating of selected and context objects between multiple active views. Users interact with the focused view, and that view lets the other open views know what is happening. Depending on contexts, views can broadcast sequence ids, selected locations on molecules, visual ranges, nodes of trees, etc.

Other open views listen for these broadcast events and may respond by highlighting relevant objects, such as sequence ids. If two open views are of the same type, e.g. graphical sequence views open on the same molecule, the non-focused view can ‘follow’ the current selections and visual range of the active view. This is especially useful when views are configured to show different characteristics of the molecule such as different tracks, different zoom levels and/or different display options.

Chapter 1: Broadcasting between Tree Views

Broadcasting is supported between phylogenetic tree views. This can be very useful for finding similarities or differences between two open trees. Clicking on nodes or selecting groups of nodes in one tree will result in matching nodes, such as nodes with matching sequence ids, being highlighted in the other tree.

Step 1

Shared IDs project

Step 2

The project contains two trees, please open both of them using "Tree View" and place views side-by-side. For the second tree: 'get_snp_17_2_asn' use the context menu to change layout style to Circular.

Two bio-trees

Step 3

Click on a random node in one tree to see effect of broadcasting on another Tree View. As data supporting both treee views are not equal please try selecting another node if you do not see the desired effect.

Effect of broadcasting on another tree view

The screenshot above shows how manual selection in one view reflects in automatic broadcast selection in another view. Note that the partner view contains a different tree with very different topology, but the system knows what to select, in this case using the node attribute "seq-id" (sequence id). Tree node tooltips on the screenshots display lists of available attributes.

Another aspect is the role of Active Objects Inspector (activated by main menu View->Active Objects Inspector). As you can see on the screenshot Active Objects Inspector also receives broadcasting. It shows us selected Sequence ID (SRR404994) and the tree itself. The Tree object is the main context on the View and it is also broadcast.

Step 4

Another interesting example of broadcasting in Tree View is using queries. Enter the query: "dist >= 11" and check-box "All" in the first view to select more than one node.

Select more than one node

As you can see on the screenshot the multi-node selection gets broadcast and reflected in the second view. The second view topology is different and broadcasting works through seq-id matching, NOT by following the query criteria (distance).

Step 5

You can use Tools/Broadcast Options menu (in the main menu bar on the top of the screen) to bring up the Broadcast Options dialog. Sometimes it is necessary to disable the broadcasting or use manual broadcasting of selections.

Global broadcast options dialog

Selection broadcasting button in the toolbar - use it when automatic broadcasting is disabled.

Selection broadcasting button

Step 6

If you want to broadcast selections between trees based on attributes other than seq-id, then configure the attributes for broadcasting between trees using the phylogenetic tree "Properties" dialog. To open this dialog, right-click in one of the tree views and select "Settings…".

Context menu settings

When the dialog opens, select the "Broadcast Parameters" tab to show the below options.

The default list of properties is shown below. When broadcasting is enabled, selection is based on the first property in the list that is present in both trees. In the above examples, that property was seq-id. To update the list, use the icons on the right to add, change, delete or reorder the properties. These updates will apply to all tree broadcasting and will be saved between sessions. If either of the trees do not have any properties in the list, no broadcast selections will occur. Changing these properties will not affect broadcasting between trees and other non-tree views, such as the graphical view.

Properties dialog

For more information please see the Tree Viewer Broadcasting manual

Step 7

Open tree object "FDA_Salmonella_1_asn" using Generic Table View. Place the Tree view and Generic Table view side by side. Select a line in Generic Table view and notice broadcasting to Tree view.

Properties dialog

Chapter 2: Broadcasting in Graphical Sequence View

Step 1

Create a new project and use Open to load GenBank molecules NC_006583.2 and NC_006583.3. Open both molecules with Graphical Sequence View, and use Broadcast Options dialog as it is shown on the screenshot. Make sure selection broadcasting is enabled and Policy is Relaxed (we will discuss policies later).

Broadcast options dialog

Step 2

Zoom in into a random area for NC_006583.2 then use mouse selection in the Graphical Sequence View ruler. You can see, selection is projected into the second view.

Selection projected into second view

Something needs to be explained here. These are different versions of the same molecule, and location broadcasting works only if we use specific settings for Sequence Matching in Selection Broadcasting options: Match at least one id, ignore versions. If Sequence Matching is set for Exact Match, we will not see selection in views of alternative versions.

Step 3

Now use broadcast dialog to set Strict policy rules. You can see that the current policy setting is reflected in the status bar and selection broadcasting does not translate between different versions of molecules.

Set strict policy rules

Please note: selection is not broadcasted and not cleared from other views when we are dealing with different versions.

Step 4

Open the same molecule (NC_006583.2) twice using Graphical Sequence View. Zoom both views to a different level, then scroll one view to see the other view is try to follow the so called Visual Range (genomic cordinates broadcast from the active view).

Visual Range – part of the viewed sequence currently visible on the view after all zooming and scrolling. Numerical values of visual range as sequence coordinates can be seen in the ruler bar on top of the Graphical Sequence View.

Second view following visual range

Visual Range Broadcasting can be disabled using Broadcast Options Dialog.

Disabling visual range broadcasting

Step 5

If you select a few objects (Ctrl + Mouse click) in one view - this gets broadcasted and selected in others.

Selected objects broadcasted in other views

Step 6

Select an arbitrary area on a Graphical View of NC_006583.2 and open a Feature Table View on it. Place the Feature Table and Graphical views side-by-side. Row selection in the Feature Table View should be reflected in the Graphical View.

Note: Make sure to turn on feature tracks in Graphical Sequence View.

Feature table and graphical views

Step 7

Broadcasting between different views can also be illustrated with MAV tree project

Broadcasting illustrated with MAV tree project

Screenshot illustrates how the Tree View and Multiple Alignment Views can broadcast sequence ids back and forth.

Support Center

Last updated: 2017-11-04T03:25:26Z