Hi Tim, On 23/04/2010 Friday, April 23, 09:49, "Tim Carver" <t...@sanger.ac.uk> wrote:
>> * When setting up user options, they don't seem to be recognised correctly >> by the startup dialogue box. For example, specifying the following >> databases in ~/.artemis_options >> >> chado_servers = \ >> 10.211.55.8:5432/pi_broad?lpritc \ >> 10.211.55.8:5432/chado?chado > > The syntax is to give each database a name, e.g.: > > pi_broad 10.211.55.8:5432/pi_broad?lpritc \ D'oh! That's my misreading the tutorial... <looks sheepish> > For model A: > > chado_infer_CDS_UTR=no > > I'm not sure the tutorial is particularly clear. The model used here (in the > pathogen group) uses gene, mRNA, exon, polypep and UTRs - this is model A > (chado_infer_CDS_UTR=no) where the CDS is inferred. The second one stores > just the gene, mRNA, exon and polypep - CDS & UTRs are then implicit. Thanks again - I don't think I was having a good time with reading comprehension yesterday... Apologies for the false alarms. >> * Where the parent feature of another feature has a long digit value as its >> identifier, it is reported in the child feature by ARTEMIS in exponential >> float format, rather than as a string (see exon examples above). >> > > I am guessing the mapping in artemis_sqlmap/Feature.xml needs to set the > java type to string for the uniquename that you are using then. So you could > try changing the template-basicfeature resultmap to: > > <result property="uniqueName" column="uniquename" > javaType="java.lang.String"/> I'll give that a go and recompile, later - I'll let you know if it works. Thanks again for the quick response, L. -- Dr Leighton Pritchard MRSC D131, Plant Pathology Programme, SCRI Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpr...@scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel:+44(0)1382 562731 x2405 ______________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmas...@scri.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ______________________________________________________ _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
