Text in Graphics Sequence display - 3

Doug Smith 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.


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>From: dsmith at ucsd.edu (Doug Smith)
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>Subject: Text in Graphics Sequence display - 2
>Date: 24 Jan 2000 06:01:52 -0000
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>Hi all,
>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
>>                Frame_sensitive
>>                Strand_sensitive  Show_up_strand  #Colour
>>                Score   Score_by_offset
>>                        Score_by_width
>>                        Score_bounds  UNIQUE  Float  UNIQUE  Float
>>                        Percent
>>                Overlap_mode UNIQUE     Overlap
>>                                        Bumpable
>>                                        Cluster
>>                Width  UNIQUE  Float
>>                Symbol  UNIQUE  Text
>>                Right_priority  UNIQUE  Float
>>                Max_mag UNIQUE Float
>>                Min_mag UNIQUE Float
>>                Show_text
>>        Blastn
>>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.
>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
>displayed !?!
>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 ...
>  -Doug


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