text in graphics Sequence display

Hamish McWilliam Hamish.McWilliam at bbsrc.ac.uk
Fri Oct 29 11:09:58 EST 1999

> I am having troubles bringing up text features in the Sequence graphics
> display using xace on our Unix machine, and I note the same problem with
> both WebAce and AceBrowser.
> I thought that tags under the 'Visible' tag of the ?Sequence model were
> automatically displayed in the Sequence graphics display.  This is the
> case for MacAce, but not so for xace, WebAce, or AceBrowser.

This was the case for versions pre 4.7 (don't know about 4.6).
> It appears that some parameter needs to be set.
> I perused through the display.wrm and options.wrm files but could not
> find what parameter needs to be set.

I found the following worked for me (thanks to R. Durbin for this one).

Update ?Method in models.wrm:

?Method Remark ?Text
        Display Colour  #Colour
                Strand_sensitive  Show_up_strand  #Colour
                Score   Score_by_offset
                        Score_bounds  UNIQUE  Float  UNIQUE  Float
                Overlap_mode UNIQUE     Overlap
                Width  UNIQUE  Float
                Symbol  UNIQUE  Text
                Right_priority  UNIQUE  Float
                Max_mag UNIQUE Float
                Min_mag UNIQUE Float

Show_text is the important bit here (see ACEDB 4.7 models.wrm).

Also add the following to ?Sequence

          Method UNIQUE ?Method

Now define a Method object which makes the Visible stuff display, e.g.

Method : Default_Sequence
Remark "A default display method for sequences."
Display Show_Text

Now add this method to all your sequences object that you want to have
text annotation.

I hope this helps. Hamish.

Hamish P. McWilliam
Brassica and Oilseeds Research
John Innes Center
Norwich Research Park
Colney Lane

Tel: 01603-452571 x2553
WWW: http://jiio10.jic.bbsrc.ac.uk/
God invented Brownian motion to stir his coffee.

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