CSC

Miscellaneous Commands

xview ?position?

yview ?position?

These commands are used to query and change the horizontal and vertical position of the information displayed in the editor's window. Without specifying the optional position argument the current value is returned. Specifying position sets the position and updates the editor display.

align

Aligns the data covered by the selection with the consensus sequence. The sequence is then padded automatically.

configure ?option? ?value option value ...?

Reconfigures the editor. NB: not all configuration options allowed at startup operate correctly when reconfiguring. (This is a bug.)

dump_contig filename from to line_length

Saves the contig display to a file within a specified region. The output consists of the data and settings of the current display.

edits_made

Queries whether edits have been made. Returns 1 if they have, 0 if they have not.

find_read identifier

Converts a reading identifier to an internal editor sequence number.

get_displayed_annos

Returns a list of the displayed annotation types.

get_extents

Returns the start and end of the displayable contig positions. If cutoff data is shown this will also include the cutoff data beyond the normal contig ends.

get_hidden_reads

This returns the hidden reads as a list of reading name identifiers.

get_name ?gel_number?

Returns the gel name from a given internal reading number, or for the reading underneath the editing cursor.

get_number ?xpos ypos?

Returns the editor's internal reading number covering the screen coordinate (xpos,ypos). If no xpos and ypos are specified then the position of the editing cursor is used.

get_read_number ?xpos ypos?

Returns the reading number covering the screen coordinate (xpos,ypos). If no xpos and ypos are specified then the position of the editing cursor is used.

hide_read

This command toggles the 'hidden' status of a reading. Hidden readings are not used to compute the consensus.

io

This returns the IO handle used for this editor.

join

Performs a join in the join editor.

join_align

Performs an alignment (and pads automatically) on the overlapping region in a join editor.

join_mode

Queries whether the editor is part of a join editor. Returns 1 if it is and 0 if it is not.

join_percentage

Returns the percentage mismatch of the overlap for a join editor.

save

Saves the database, but doesn't quit.

set_displayed_annos ?type ...?

Sets the displayed annotation types to those specified. All other are turned off.

shuffle_pads

Realigns pads along the total length of the consensus.

undo

Undoes the last compound operation (from a list of changes).

write_mode

This toggles the editor between read-write and read-only mode.