Broadcasting

Introduction

Broadcasting is a powerful and unique feature within Genome Workbench that allows communication between different 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.

The following views can communicate with each other:

• Two Tree Views with the same or partially same sets of sequences
• Tree View and Generic Table View
• Tree View and Multiple Sequence Alignment View based on which this tree was created
• Two Graphical Sequence Views open on the same molecule
• Graphical View and Feature Table View

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. Open Project with Trees

Please download the example project from out ftp site

This project contains two trees with the same set of protein sequences but constructed based on multiple alignments created by two different programs (MUSCLE and Crustal Omega). Since the alignments are different, the trees have a slightly different topologies. Broadcasting can help see the differences.

Step 2. Open Trees in Tree View (side by side)

Open both trees using "Tree View" and place views side-by-side. In our example trees are rooted at the midpoint.

Step 3. Select Node by Click

Click on a random terminal node or an internal node in one tree to see the effect of broadcasting on another Tree View. The screenshot below shows how manual selection in one view reflects the automatic broadcast selection in another view. Note that trees have different topologies, but the system knows what to select, in this case using the node attribute "seq-id" (sequence id).
Another aspect is the role of the Active Objects Inspector View (activated by main menu View->Active Objects Inspector). As you can see on the screenshot Active Objects Inspector also receives broadcasting. It shows us the selected Sequence ID (WP_002632591.1) and the tree itself. The Tree object is the main context on the View, and it is also broadcasted.

Step 4. Broadcasting Using Search Queries

Another interesting example of broadcasting in Tree View is using queries. Enter the query: “Thiobacillus” and check the box "All" in the first view. As you can see on the screenshot below the two terminal nodes get selected and broadcasted in the second view. Note: you can use any attribute values for search (they can be seen in tooltips).

Broadcasting works through seq-id matching, but NOT by following the search query criteria (organism in our screenshot). In other words, search finds the terminal nodes with the query organism in the first tree and then matches its seq-id to the corresponding seq-ids in the other tree.

Step 5. Broadcast Options Dialog: Disable Auto and Use Manual Broadcasting

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

To disable auto broadcasting, remove the checkmark from Auto broadcast selection changes checkbox, and close the dialog.

Now automatic broadcasting is disabled, and only manual broadcasting is available. To see how it works, just select any branch in one tree and then click on the Selection broadcasting button in the toolbar – observe that the corresponding branch is selected in the other tree.

Step 6. Broadcasting Based on Attributes Other than Seq-id

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 Broadcast Options dialog/BioTree Settings Tab. The default list of properties is shown in the dialog. 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.

For more information please see the Tree Viewer Broadcasting manual

Step 7. Broadcasting Tree View and Generic Table View

Open any tree in the project in the Generic Table View. Place the Tree view and Generic Table View side by side. Select a line in the Generic Table View and notice the broadcasting to the Tree View.

Step 8. Broadcasting Tree View and MSA View

Now open one of the trees in the project in the Multiple Alignment View. Adjust the MSA View at the bottom of the Tree View. Select a line in the MSA View and notice broadcasting to the Tree view. Screenshot illustrates how the Tree View and Multiple Alignment Views can broadcast sequence ids back and forth.

Chapter 2: Broadcasting in Graphical Sequence View (GSV)

Step 1. Open Same Molecule with Different Versions in GSV

Create a new project and use Open to load GenBank molecules NC_006583.3 and NC_006583.4. Open both molecules with Graphical Sequence View, and use the Broadcast Options dialog as it is shown on the screenshot. Make sure selection broadcasting is enabled and the Policy is Relaxed (we will discuss policies later).

Step 2. Broadcasting by Selected Range

Zoom in into a random area for NC_006583.3 then use mouse selection in the Graphical Sequence View ruler. You can see, the selection is projected into the second view.

A few things need 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 the Selection Broadcasting options: Match at least one id, and ignore versions. If Sequence Matching is set for Exact Match, we will not see the selection in views of alternative versions.

Step 3. Strict Policy Rules

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.

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

Step 4. Visual Range Broadcasting

Open the same molecule (NC_006583.4) twice using Graphical Sequence View. Zoom both views to a different level, then scroll one view to see that the other view is trying to follow the so-called Visual Range (genomic coordinates broadcast from the active view).

Visual Range – the 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.

Visual Range Broadcasting can be disabled using the Broadcast Options Dialog.

Step 5. Broadcasting by Feature Selection

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

Step 6. Broadcasting between GSV and Feature Table View

Select an arbitrary area on the Graphical View of NC_006583.4 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 the Graphical Sequence View.