CSC

Editing Toggles and Settings

The editor has a variety of boolean values for determining editing and display modes. Most take an optional value parameter to explicitly set the value of the boolean. With no value parameter specified the boolean is toggled instead.

set_reveal ?value?

This sets the editor 'cutoffs' mode. A setting of 1 indicates that cutoff data is to be displayed in the lightColour colour. A setting of 0 indicates that no cutoff data is to be displayed.

set_insert ?value?

This command sets the editor insert/replace mode. A value of 1 sets the editor to insert mode. A value of 0 sets the editor to replace mode.

superedit modes

This command sets which editing actions should be allowed. The modes argument should be a Tcl list of 10 values, each 0 (disabled) or 1 (enabled). The values in order repesent insert any to read, delete any from read, insert to consensus, delete dash from consensus, delete any from consensus, replace base in consensus, shift readings, transpose any bases, can use uppercase edits, and replacement mode. The replacement mode is 0 for editing by base type and 1 for edit by confidence value.

auto_save ?value?

This command sets the auto-save mode. A value of 1 enables auto-saving. A value of 0 disables it.

show_differences ?value?

This command set the show differences mode. A value of 1 will display only those bases that disagree with the consensus. All other bases are displayed as a fullstop. A value of 0 shows all bases.

compare_strands ?value?

This command sets the compare strands mode. A value of 1 will make the editor compute the consensus separately for the positive and negative strands. Strands that disagree are given a final consensus character of '-'. A value of 0 will use the normal single consensus mode.

join_lock ?value?

This command sets the scroll locking between two editors forming a join editor. A value of 1 will mean that scrolling (not cursor movement) in one contig will also scroll the other contig.

show_quality value

This commands sets the quality display mode. With a value of 1 and a positive quality cutoff value all qualities values are displayed as grey scales using the 10 qualColourn configuration options.