column configuration and queries

janety janety at u.washington.edu
Thu Mar 9 19:38:24 EST 2000


Hi everybody

I am having trouble with column configuration of the Gmap display and am
hoping someone can tell me what stupid mistake I am making.

I have a query which works fine via the query commands window, but when
I use it to try to configure a column I get nothing displayed.

The query is
Find Chrom_Band Positive_BAC; follow Positive_BAC

The model I am using is based on the chromosome 6 model at Sanger:

?Chrom_Band Map  ?Map XREF Chrom_Band #Map_position  // position on
vertical maps
            Display     Black
                        Dark 
                        NOR
                        Centromere  // special flag for waisted drawing
                        p_Telomere      // special flag for drawing
                        q_Telomere  // special flag for drawing
            Contains ?Chrom_Band XREF Contained_in
            Contained_in ?Chrom_Band XREF Contains
            Contains_breakpoint ?Hybrid XREF Breaks_in_band
            Positive Positive_locus  ?Locus XREF In_situ
                     Positive_sequence      ?Sequence XREF In_situ
                     Positive_clone         ?Clone XREF In_situ
                     Positive_cosmid  ?Cosmid XREF In_situ
                     Positive_fosmid  ?Fosmid XREF In_situ
                     Positive_YAC           ?YAC XREF In_situ
                     Positive_BAC           ?BAC XREF In_situ
                     Positive_PAC           ?PAC XREF In_situ
                     Positive_STS           ?STS XREF In_situ
                     Positive_cDNA          ?cDNA XREF In_situ
                     Positive_probe         ?Probe XREF In_situ
                     Positive_pool_probe ?Pool XREF In_situ
                     Positive_hybrid ?Hybrid XREF Chrom_band
            OMIM   ?OMIM       XREF Chrom_Band

and In_situ is a Positive tag in the BAC class 

I want to be able to enter my Positive In_situ results, and have BACs
displayed on the map according to those results. Am I not getting the
BACs displayed as I haven't specified a map position for them? My
Chrom_bands have a map position (Ends Left and Right) - shouldn't the
BAC acquire these positions via the Positive magic tag? I think there is
something fundamental I've failed to understand about mapping in ace.

thanks for any help

Janet Young

------------------------------------------------------------------- 
                         Dr. Janet Young 
Dept. Molecular Biotechnology 
University of Washington             tel: (206) 685 9254 
Health Sciences Building             fax: (206) 685 7301 
PO BOX 357730                        email: janety at u.washington.edu 
Seattle, WA 98195, USA
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