Plant Bioinformatics Group

View settings

Using the overview window:

Click the overview button on the toolbar (this is a toggle button which shows/hides the overview). A separate window with a miniature version of the main canvas will appear. When a genome is zoomed in, a slightly opaque red rectangle will be visible on top of its representation in the overview window and this can be moved up and down with the mouse to scroll the genome on the main canvas up and down. It also lets the user see at a glance which chromosome of the genome is currently showing on the main canvas.

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Filtering homology links by score (e.g. BLAST e-value):

Using the score cut-off spinner on the toolbar, users can set a threshold for the homology score in use beyond which they will not be shown. Links will be filtered in real-time as the spinner value is changed with the up and down arrows or by entering a new value and pressing Enter.

In Strudel format datasets it is expected that the score is a BLAST generated e-Value. For MAF format this is the score that accompanies each block of alignments.



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Manual override of feature and label display:

In order to control clutter on screen Strudel automatically controls when it displays features. This behaviour can be overridden by the user with the help of the "Always show all features" button which is found next to the zoom control at the bottom of the main canvas. When selected, this button forces the permanent display of features at all times for the currently selected genome.

To force the continuous display of all feature labels, right click over a chromosome and select the "Show all labels" item from the context menu. This toggles the display of all labels for this chromosome on and off. Only one chromosome per genome can be selected for this at any one time.

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Exporting the current view as an image:

Click on the export image button on the toolbar and a save image dialog will appear. Choose a file name and location and click the Save button in the dialog.

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Customising the colour schemes:

Click on the customise colours button on the toolbar and the customise colours dialog will appear. You can swap between colour schemes by selecting a scheme from the combo box. On the left you can see a list of colours and on the right you can see a preview of the colour scheme. To customise a colour scheme, double click on the colour for the element of the scheme you wish to change in the list and a colour chooser dialog will be displayed. Select your chosen colour, using the controls in one of the tabs, then press the OK button. You will now see the updated preview. Once you have finished customising a colour scheme, press the apply button to have the main view updated with the new colour scheme. The modified colour scheme will be saved as part of your preferences automatically. Reset to defaults in the dialog reverts a colour scheme back to its original colours.

The background colour scheme is normally a gradient between Background Gradient Start and Background Gradient End. To achieve a single colour background you should set both Background Gradient Start and Background Gradient End to the same colour.

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Configuring other view settings:

The configure view settings button brings up the following dialog which lets the user configure several view settings at once:

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