Hello Dave, Thanks for the suggestion and research. We are planning on developing a completely new prot-xml viewer within the next few months, since the current one has severe limitations when dealing with very large files.
In the meantime, David and I have just checked in a version of protxml2html that performs about 4-5 times faster than the previous one (still using xsltproc). It would be interesting to see if this speed-up holds with other xslt engines; we may tweak this a bit more in the next few weeks before the full re-write. Cheers, --Luis On Wed, Dec 2, 2009 at 9:17 AM, dctrud <[email protected]> wrote: > Brian, > > The Ubuntu libsaxonb-java package in the universe repository installs > the script /usr/bin/saxonb-xslt which fires up saxonb under Java. It > expects filenames to be specified as the TPP does to Xalan, i.e. > > saxonb-xslt <xml file> <xsl file> > > ... so it will work if you just replace references to /usr/bin/ > xsltproc with /usr/bin/saxonb-xslt in the pl scripts. > > My quick tests were done on a command-line xslt transform. Actual > performance when using protxml2html.pl via a web browser doesn't > improve as much since the resulting html is still huge, and takes time > to transfer and for the browser to display. It does seem very useful > for getting huge results files out into text format quickly by > invoking protxml2html on the command line though. Another thing to > note is that on very small files xsltproc is probably still faster due > to the overhead of starting up a JVM for Saxon. > > The commercial Saxon-EE is very impressive with its 28x speed-up, but > the free speedup of 7.5x with saxonb is still very nice. I also tested > Saxon-HE (new open source version that is replacing Saxonb, but not > packaged for Ubuntu), and it's about the same as saxonb. > > DT > > On Dec 2, 4:53 pm, Brian Pratt <[email protected]> wrote: > > Impressive! I'm unclear, though, on the practicalities of how it > replaces > > xsltproc (which is an executable) - presumably there's a script that > invokes > > java? In which case we have a TPP java dependency we didn't have before > - > > not that this is necessarily an insurmountable problem, and one we'll > > probably have to address sooner than later anyway. > > > > Brian Pratt > > > > On Wed, Dec 2, 2009 at 4:28 AM, dctrud <[email protected]> wrote: > > > Have obtained a Saxon-EE evaluation to try it. Same .prot.xml file, > > > same server - 35.04s (3.5% of the xsltproc run-time). Down side is > > > that it costs 300 GBP per server. > > > > > DT > > > > > On Dec 2, 10:45 am, dctrud <[email protected]> wrote: > > > > I've just done a quick comparison of the speeds of various XSLT > > > > processors for transforming .prot.xml to html. There is a marked > > > > difference between the processors, and xsltproc which is the TPP > > > > default is not the quickest. > > > > > > Tests performed on Ubuntu 9.0x 64-bit on a DELL R600 Dual Xeon 5500 > > > > 32GB RAM. All processors are installed from their Ubuntu packages. > > > > Input document was a large 200Mb .prot.xml file resulting from OMSSA > > > > search of the 72-run MaxQuant dataset downloaded from > ProteomeCommons: > > > > > > xsltproc - 1011.96s > > > > xalan - 1206.95 > > > > saxon-xslt - 491.95s > > > > saxonb-xslt - 132.19s > > > > > > saxonb-xslt works for me as a direct replacement for xsltproc in the > > > > $xsltproc definition in protxml2html.pl > > > > > > I've not tried the commercial Saxon-SA / Saxon-EE from Saxonica.com, > > > > but they are supposedly faster still. > > > > > > DT > > > > > -- > > > > > You received this message because you are subscribed to the Google > Groups > > > "spctools-discuss" group. > > > To post to this group, send email to [email protected] > . > > > To unsubscribe from this group, send email to > > > [email protected]<spctools-discuss%[email protected]> > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > > . > > > For more options, visit this group at > > >http://groups.google.com/group/spctools-discuss?hl=en. > > > > > > -- > > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
