Poor data at the left and right ends of the trace can be marked
using the "Left Quality" and "Right Quality" options in the Edit menu.
Alternatively a keyboard shortcut for editing the cutoff is to press
Control L or Control R to edit left or right cutoff
respectively. To select the left cutoff, choose the "Left Quality" option
from the menu. Then click the left mouse button at the required position in the
trace display.
The region from the start of the sequence to this position will
be highlighted in grey. To select the right hand cutoff, choose the
"Right Quality" option in the Edit menu and click the required position in the trace
display. The region between the
left boundary and the end of the sequence will be highlighted. To prevent
accidentally changing the cutoffs once these have been selected, choose the
"Sequence" option in the Edit menu.
If vector sequence has been marked trev will also display these in a similar
fashion to the quality cutoffs except in a peach colour. These cutoffs can be
changed by selecting "Left Vector" and "Right Vector" in the same fashion as
editing the quality cutoffs. Where both quality and vector cutoffs coincide
trev draws the regions by striping between both peach and grey.
If the ability to edit has not been disabled, there will be two windows showing the trace sequence. The original sequence is displayed in the upper window. The window below this, which contains the blue cursor, is the editing window. To edit this sequence, select the "Sequence" option in the Edit menu. The editing cursor is positioned by clicking with the left mouse button within the display. Bases are deleted to the left of the cursor using the delete key of the keyboard. Additional bases are inserted to the left of the cursor. Only A, a, C, c, G, g, T, and t are allowed. It is recommended that edits are entered in lower case to distinguish them from the original bases.
It is often easy to accidently forget which editing mode you are in and adjust a quality or vector clip point by mistake. Trev keeps track of all clip edits and hence these may be "Undone" by selecting "Undo Clipping" from the Edit menu. This will remove the last clip edit. It is not yet possible to undo sequence edits.