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Editing

Setting the left and right cutoffs

Poor data at the left and right ends of the trace can be selected using either the "Left Quality" and "Right Quality" options in the Edit menu respectively. A keyboard shortcut for editing the cutoff is to press Control L or Control R to edit left or right cutoff respectively. If selecting the left cutoff, choose the "Left Quality" option and click with the left mouse button within the display at the required right hand boundary. The region from the start of the sequence to this position will be highlighted in grey. To then select the right hand cutoff, choose the "Right Quality" option and mark the left hand boundary. 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 modified bases 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 James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/trev_6.html