The Side Panel is shown to the right of all views that are opened inCLC Genomics Workbench.
By using the settings in theSide Panelyou can specify how the layout and contents of the view.
Figure5.8is an example of theSide Panelof a sequence view.
Figure 5.8: The Side Panel of a sequence contains several groups: Sequence layout, Annotation types, Annotation layout, etc. Several of these groups are present in more views. E.g. Sequence layout is also in the Side Panel of alignment views.
By clicking the black triangles or the corresponding headings, the groups can be expanded or collapsed. An example is shown in figure5.9where theSequence layout is expanded.
The content of the groups is described in the sections where the functionality is explained. E.g.
Sequence Layoutfor sequences is described in chapter11.1.1.
When you have adjusted a view of e.g. a sequence, your settings in theSide Panelcan be saved.
When you open other sequences, which you want to display in a similar way, the saved settings can be applied. The options for saving and applying are available in the top of the Side Panel (see figure5.10).
To save and apply the saved settings, click ( ) seen in figure5.10. This opens a menu, where the following options are available:
Figure 5.9:The Sequence layout is expanded.
Figure 5.10: At the top of the Side Panel you can: Expand all groups, Collapse all preferences, Dock/Undock preferences, Help, and Save/Restore preferences.
• Save Settings.This brings up a dialog as shown in figure5.11where you can enter a name for your settings. Furthermore, by clicking the checkboxAlways apply these settings, you can choose to use these settings every time you open a new view of this type. If you wish to change which settings should be used per default, open the Preferences dialog (see section5.2).
• Delete Settings.Opens a dialog to select which of the saved settings to delete.
• Apply Saved Settings. This is a submenu containing the settings that you have previously saved. By clicking one of the settings, they will be applied to the current view. You will also see a number of pre-defined view settings in this submenu. They are meant to be examples of how to use the Side Panel and provide quick ways of adjusting the view to common usages. At the bottom of the list of settings you will see CLC Standard Settings which represent the way the program was set up, when you first launched it.
Figure 5.11:The save settings dialog.
Figure 5.12:Applying saved settings.
The settings are specific to the type of view. Hence, when you save settings of a circular view, they will not be available if you open the sequence in a linear view.
If you wish to export the settings that you have saved, this can be done in thePreferencesdialog under theViewtab (see section5.2.2).
The remaining icons of figure 5.10 are used to; Expand all groups, Collapse all groups, and Dock/Undock Side Panel. Dock/Undock Side Panel is to make the Side Panel"floating" (see below).
5.6.1 Floating Side Panel
The Side Panel of the views can be placed in the right side of a view, or it can be floating (see figure5.13).
Figure 5.13:The floating Side Panel can be moved out of the way, e.g. to allow for a wider view of a table.
By clicking the Dock icon ( ) the floating Side Panel reappear in the right side of the view. The size of the floating Side Panel can be adjusted by dragging the hatched area in the bottom right.
Printing
Contents
6.1 Selecting which part of the view to print . . . 199
6.2 Page setup. . . 200
6.2.1 Header and footer . . . 201
6.3 Print preview. . . 201 CLC Genomics Workbenchoffers different choices of printing the result of your work.
This chapter deals with printing directly fromCLC Genomics Workbench. Another option for using the graphical output of your work, is to export graphics (see chapter7.5) in a graphic format, and then import it into a document or a presentation.
All the kinds of data that you can view in the View Area can be printed. The CLC Genomics Workbench uses a WYSIWYG principle: What You See Is What You Get. This means that you should use the options in the Side Panel to change how your data, e.g. a sequence, looks on the screen. When you print it, it will look exactly the same way on print as on the screen.
For some of the views, the layout will be slightly changed in order to be printer-friendly.
It is not possible to print elements directly from theNavigation Area. They must first be opened in a view in order to be printed. To print the contents of a view:
select relevant view|Print ( ) in the toolbar This will show a print dialog (see figure6.1).
In this dialog, you can:
• Select which part of the view you want to print.
• AdjustPage Setup.
• See a printPreviewwindow.
These three options are described in the three following sections.
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Figure 6.1:The Print dialog.