Possible bug? or HTML rules non-compliance? How to link to GBrowse

sequenceserver
#1

Hi. So I was examining the code (0.8.6) because I aim to create hyperlinks, from the BLAST results to GBrowse. After some time of looking, I found out that construct_standard_sequence_hyperlink(options) as called in line 500 of sequenceserver.rb returns something like this:

xxx--------------------------xxx

gb|EU941459.1|EU941459 PLN Zea mays clone 1453910 mRNA sequence.

xxx--------------------------xxx

Which conflicts with what’s stated at http://www.w3.org/TR/html401/struct/links.html#h-12.2.2 which says
xxx--------------------------xxx

Links and anchors defined by the A element must not be nested; an A element must not contain any other A elements.
xxx--------------------------xxx

Google Chrome does parse it in a way as Jukka K. Korpela says in here: http://stackoverflow.com/questions/13052598/creating-anchor-tag-inside-anchor-tag .
Haven’t tried on another browser yet. I was dumbfounded for around two days why the output does not seem to match with what are being logged.

And this also causes me headache on how to add the link to GBrowse. Any suggestion? So far, I can see variable hint_coordinates as being helpful.

#2

My code for linking to the genome browser (JBrowse) uses something like this–and I think the gbrowse format is similar, perhaps using parameters for ref,start,and end specifically–but with jbrowse the format is /jbrowse/?loc=Chr:Start…End.

matches = options[:sequence_id].match(/^\s*gnl|(\S+)|([^< ]+)/)
hit_coordinates=options[:hit_coordinates]

return “> #{options[:sequence_id]} [<a href=http://hymenopteragenome.org:8080/#{matches[1]}/jbrowse/?loc=#{matches[2]}:#{hit_coordinates[0]}…#{hit_coordinates[1]}>View in JBrowse]
”

Note that our sequence_id ‘matches’ the format “> gnl|Species_Id|Chr_Id <other random info…”. Also, I am not sure about the nested anchor link, but in my customization I had to create the anchor link manually anyways (maybe this is unnecessary but i couldn’t get the anchor links to work otherwise)
Cheers

-Colin