Text in Graphics Sequence display - 3
dsmith at ucsd.edu
Mon Jan 24 09:03:06 EST 2000
RE my following email from yesterday,
I am having troubles getting the 'Sequences and ends' column in the Sequence
Graphics display to work for composite sequences, in either xace-4.7, in
or in AceBrowser.
This is in addition to troubles getting the 'Brief Identifications' to work.
If someone could let me know what tags control these displays, or what methods
are appropriate, and what modifications I need to make in *.wrm files, or
whatever, I would be most appreciative.
>X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to
><news> using -f
>From: dsmith at ucsd.edu (Doug Smith)
>Subject: Text in Graphics Sequence display - 2
>Date: 24 Jan 2000 06:01:52 -0000
>Organization: MRC Human Genome Mapping Project Resource Centre
>X-Trace: niobium.hgmp.mrc.ac.uk 948693713 23600 188.8.131.52 (24 Jan 2000
>X-Complaints-To: news at hgmp.mrc.ac.uk
>X-Received: from biomail.ucsd.edu (biomail.ucsd.edu [184.108.40.206])
> by hgmp.mrc.ac.uk (8.9.3/8.9.3) with ESMTP id GAA15240
> for <acedb at net.bio.net>; Mon, 24 Jan 2000 06:01:50 GMT
>X-Received: from [220.127.116.11] (dt045nba.san.rr.com [18.104.22.168])
> by biomail.ucsd.edu (8.9.3/8.9.3-IH) with ESMTP id WAA13911
> for <acedb at net.bio.net>; Sun, 23 Jan 2000 22:01:48 -0800 (PST)
>X-Sender: dsmith at biomail.ucsd.edu
>X-To: acedb at hgmp.mrc.ac.uk
>To: acedb at hgmp.mrc.ac.uk
>Sender: owner-acedb at hgmp.mrc.ac.uk
>I am still having troubles with Text display in the Sequence Graphics display.
>Hamis McWilliam suggested I do the following:
>>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."
>>Now add this method to all your sequences object that you want to have
>>I hope this helps. Hamish.
>I did this ... and it works ... but, for me, only in part, to wit:
>1. only the Visible information from the *.cds Subsequence objects is
>2. Visible information from other Subsequence objects and from the Sequence
> itself is not displayed.
>Second, this displayed text information appears to be of a 'Text Features'
>... that is, it is removed from the Seq Graphics display when one toggles the
>'Text Features' in 'Columns'
>Perhaps the additional text information should be displayed in the column
>called 'Brief Identifications' ??
>I have not been able to get this column to display anything ...
>If this is what I should be using, how does one use it?
>Does it involve an additional Method to the 'Show_Text' method above?
>If so, what is the Method?
>I appreciate any comments here ...
More information about the Acedb