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The Settings Menu

The purpose of this menu is to configure the operation of the contig editor. Settings can be saved using the "Save settings" button, but this does not save any tag macros. These may be saved separately using the "Save Macros" option. Settings for the following options can be changed.

Highlight Disagreements

This toggles between the normal sequence display (showing the current base assignments) and one in which those assignments that differ from the consensus are highlighted. It makes scanning for problems by eye much easier.

Several modes of highlighting are available: "By dots" will only display the bases that differ from the consensus, displaying all other bases as full stops if they match or colons if they mismatch but are poor quality. The definition of poor quality here can be adjusted using the "Set quality threshold" option of the Settings menu. The base colours are as normal (ie reflecting tags and quality).

Highlight disagreements "By foreground colour" and "By background colour" displays all base characters, but colours those that differ from the consensus. Bases which differ by are below the difference quality threshold are shaded in light blue while high quality differences are dark blue. This allows easier visual scanning of the context that a difference occurs in, but it may be wise to disable the displaying of tags (hint: control-Q toggles tags on and off).

Finally the "Case sensitive" toggle controls whether upper and lower case bases of the same base type should be considered as differences.

Pack Sequences

This controls whether the editor allocates one row per sequence or whether it is permitted to pack multiple sequences onto a single row, assuming they do not overlap.

The latter allows for a more compact plot which is desirable when dealing with short sequences, however it has the side effect that the reading names can no longer be listed in the names panel to the left.

Hide Annotations

Sometimes we need to see the background shading underneath an annotation, for example to see the base quality or if we have Highlight Disagreements turned on using the by background colour mode. This option simply hides all annotations from display until it is selected again to reveal them once more.

The Control-Q keyboard shortcut has the same effect.


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Last generated on 8 Febuary 2011.