Hi Betina, If you haven't overridden the Apollo default (e.g. by defining your own name adapter and/or display preferences class) then I think it's quite possible that the analysis name plus the genomic coordinates _is_ the id/display name of the feature in question. I think this is what Apollo uses in the chado JDBC adapter when it doesn't have anything better to use (and no database-specific alternative has been provided via one of the files I just mentioned--I forget which one, probably the display preferences file.) If you select "Show labels" for the tier in question you should be able to see if this is the case.
Jonathan On Tue, Jun 30, 2009 at 11:32 AM, Betina Porcel <[email protected]>wrote: > Hi everybody! > Here the problem: I'm using (still!) Apollo1.10.0 connected to a Chado DB, > and I'm having problems when trying to get additional information for a > feature via the web. My Apollo is linked to the GBrowse, as shown in the > xxx.tiers file > > [Type] > tiername : Gene Integration > typename : Gaze > resulttype : Gaze:XXXX_wss_Gaze > color : 0,0,255 > usescore : true > glyph : DrawableResultFeatureSet > column : SCORE > column : GENOMIC_RANGE > column : query_frame > sortbycolumn : GENOMIC_RANGE > weburl : > https://www.genoscope.cns.fr/secure-nda/XXXXX/cgi-bin/gbrowse/XXXX/?name= > > 1) launch apollo on my Linux (Java version: 1.6.0_04) -> OK > 2) search for my gene model -> OK > > But when selecting the gene model feature, it doesn't always get the right > link using the "Get info for this feature via web" > > when working, it points out on the > https://www.genoscope.cns.fr/secure-nda/XXXXX/cgi-bin/gbrowse/XXXX/?name=GSCHCT00011788001 > > but sometimes just get > > > https://www.genoscope.cns.fr/secure-nda/XXXXX/cgi-bin/gbrowse/XXXX/?name=Gaze:164606-163765 > > so, the name (in the analysis table from Chado) and the start-end of the > genomic region (instead of the gene model ID). > > Any ideas why this can happen? > > > Thanks a lot!! > > Betina > -------------------------------------------------- > Betina Porcel > Analyse de séquences de génomes eucaryotes > (Coordination Plateforme d'Annotation Experte) > Genoscope - Institut de Génomique - CEA > 2, rue Gaston Crémieux CP5706 > 91057 Evry CEDEX France > Tel: +33 (0)1 60 87 25 20 > Fax: +33 (0)1 60 87 25 14 > E-mail: [email protected] > -------------------------------------------------- > > > > _______________________________________________ > apollo mailing list > [email protected] > http://mail.fruitfly.org/mailman/listinfo/apollo >
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