Side Panel

When an element is open for viewing, options for configuring that view are available in the Side Panel. The settings for a given view can be saved and re-used, as described in Side Panel view settings.

The Side Panel is organized into palettes, where related settings are grouped (figure 2.10). The specific palettes and options depend on the data type and the view that is open. The buttons in the top right side of each palette can be used for expanding the contents for viewing (Image sidepanel_expand_16_n_p), or collapsing (Image sidepanel_collapse_16_n_p). Using the buttons at the bottom left side of the Side Panel, all the palettes can be expanded (Image sidepanel_expand_16_n_p) or collapsed (Image sidepanel_collapse_16_n_p).

Image sidepanel-sequenceditor
Figure 2.10: Side Panel settings for a nucleotide sequence. The Annotation layout palette is expanded, while the remaining palettes are collapsed. In the bottom left corner of the Side Panel are buttons for expanding, collapsing and re-docking all palettes.

Palettes can be placed at a different level in the Side Panel or undocked to be viewed anywhere on the screen (figure 2.11). For this, click on the palette name and while keeping the mouse depressed, drag the palette up and down, or drag it outside the CLC Workbench.

Image sidepanel-sequenceditor-detached
Figure 2.11: The Annotation types and Motifs palettes have been undocked. The Nucleotide info palette has been moved at the top of the Side Panel. The background color of nucleotides reflects the quality scores.

A palette can be re-docked by clicking on its tab name and dragging it back into the Side Panel. A red highlight indicates where it will be placed. Alternatively, clicking on the (Image sidepanelreturn_16_n_p) button at the top left of the floating palette will place it at the bottom of the Side Panel. All floating palettes can be re-docked by clicking on the (Image detach_16_n_p) button at the bottom of the Side Panel.

The whole Side Panel can be hidden or revealed using buttons at the top right: (Image hide_sidepanel) to hide the Side Panel and (Image sidepanel_left_16_n_p) to reveal it, if it was hidden. The keyboard shortcut Ctrl + U (Image command_key_web + U on Mac) can also be used for these actions.

Changing the colors

Where color settings are offered, you have the option to use a fixed color or a gradient. For example, in figure 2.11, each annotation type is displayed using a fixed color, while the quality scores are displayed using a gradient. The color/gradient used can be changed by clicking on it.

A fixed color can be chosen from a predefined set of swatches (figure 2.12) or defined by setting the:

Image choose_color
Figure 2.12: Clicking on the color of the mRNA annotation type opens a dialog where the color can be changed.

A gradient can be chosen from a predefined set of gradients (figure 2.13) or customized by setting:

Image customize_gradient
Figure 2.13: Clicking on the gradient of the quality scores opens a dialog where the gradient can be changed.

Gradients settings can be reused, making it easy to apply the same gradient consistently across different views. This is done using buttons in the 'Configure gradient' dialog (figure 2.13):