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Setting the left and right cutoffs

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.

Editing the sequence

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.

Undoing clip edits

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.

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This page is maintained by staden-package. Last generated on 22 October 2002.