[BioC] Change in URL for PFAM links in GOstats (PFAMHyperGResult)

[Marc Carlson]

Thank you Wade,

The changes have been made and should propogate within a day or so.

  Marc


On 02/23/2011 09:54 AM, Davis, Wade wrote:
> Dear Biocore Team (and users of GOstats):
>
> It appears that the Sanger URL format has changed for the Pfam site, which causes broken links when using summary() with option htmlLinks=TRUE. Below is a comparison of the old and new URLs for the same accession number.
>
> OLD
> http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF07974
>
> NEW
> http://pfam.sanger.ac.uk/family?acc=PF07974
>
> The latest development version of GOstats (2.17.1) that I looked at (below) shows the old form so I thought I would pass along.
>
> Thanks for all your hard work with Bioconductor. It is greatly appreciated!
>
>
> -------------------------------------------------------------------------
>
> showMethods(summary, class = "PFAMHyperGResult", includeDefs = TRUE)
>
> Function: summary (package base)
> object="PFAMHyperGResult"
> function (object, ...)
> {
>     .local <- function (object, pvalue = pvalueCutoff(object),
>         categorySize = NULL, htmlLinks = FALSE)
>     {
>         PFAM_URL <- "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s"
>         df <- callNextMethod(object = object, pvalue = pvalue,
>             categorySize = categorySize)
>         if (nrow(df) == 0) {
>             df$Term <- character(0)
>             return(df)
>         }
>         pfamIds <- df[[1]]
>         if (htmlLinks) {
>             pfamIdUrls <- sapply(pfamIds, function(x) sprintf(PFAM_URL,
>                 x))
>             pfamTerms <- paste("<a href=\"", pfamIdUrls, "\">",
>                 pfamIds, "</a>", sep = "")
>         }
>         else {
>             pfamTerms <- pfamIds
>         }
>         df$Term <- pfamTerms
>         df
>     }
>     .local(object, ...)
> }
>
>
> --------------------------------------------------------------------------
>
>
> J. Wade Davis, PhD
> Assistant Professor
> 187 Galena DC 018.0
> University of Missouri
> Columbia, MO 65212
> Phone: (573) 882-0770
> Fax: (573) 884-4196
> MU Biostatistics Group<http://som.missouri.edu/Research/BioStat/Default.aspx>
>
>
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>
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