I believe MzXML2Search currently uses the mzParser code which you can find in MSToolkit.
On Tue, Jan 15, 2013 at 10:23 PM, David Zhao <weizhao6...@gmail.com> wrote: > Thanks Jimmy and Eric. I'll look into other alternatives as suggested. My > problems that we have a lot of codes still rely on jrap to parse mzXML > file, but jrap can't seem to parse mzXML generated by ReAdW from the latest > Thermo q exactive instrument ( some scans return negative mz and > intensities). > However, mzxml2search from TPP can parse the mzXML just fine, which makes > me think the jrap is out of date. What parser does mzXML2search use in > this case then? > Thanks, > > David > > On Tuesday, January 15, 2013 9:25:41 PM UTC-8, Eric Deutsch wrote: > >> And if you’re in the market for a Java implementation (like JRAP), then >> I’d recommend jmzreader: >> >> http://code.google.com/p/**jmzreader/<http://code.google.com/p/jmzreader/> >> >> >> >> Cheers, >> >> Eric >> >> >> >> >> >> *From:* spctools...@googlegroups.**com [mailto:spctools...@** >> googlegroups.com] *On Behalf Of *Jimmy Eng >> >> *Sent:* Tuesday, January 15, 2013 9:18 PM >> *To:* spctools...@googlegroups.**com >> >> *Subject:* Re: [spctools-discuss] Re: JRAP question >> >> >> >> At this point, you can probably not worry about jrap not being updated >> because the mzXML format isn't really in flux. But if you want to look for >> alternatives ... >> >> >> >> Quite a few folks here would tell you to look at ProteoWizard >> http://proteowizard.**sourceforge.net/<http://proteowizard.sourceforge.net/> >> >> Possibly look into OpenMS (I honestly have no clue how pertinent this >> is): http://open-ms.sourceforge.**net/ <http://open-ms.sourceforge.net/> >> >> Also MSToolkit: >> https://code.google.com/p/**mstoolkit/<https://code.google.com/p/mstoolkit/> >> >> >> >> Other folks should chime in if there are other parsing libraries out >> there (which I know there are). >> >> >> >> On Tue, Jan 15, 2013 at 7:20 PM, David Zhao <weizh...@gmail.com> wrote: >> >> Thanks Jimmy! So it sounds like jrap is not being updated anymore. If i'd >> like to keep up to date with a mzXML parser, which library should I follow? >> >> Thanks, >> >> >> >> David >> >> >> >> On Tuesday, January 15, 2013 7:14:17 PM UTC-8, Jimmy Eng wrote: >> >> I'm not a jrap user nor do I know what file are associated with what >> versions. But if you are looking for jrap_3.0.jar and >> jakarta-regexp-1.4.jar, you can find them here: http://sashimi.svn.** >> sourceforge.net/viewvc/**sashimi/trunk/jrap/sax2/<http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/sax2/> >> >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to spctools...@googlegroups.**com. >> To unsubscribe from this group, send email to spctools-discu...@** >> googlegroups.com. >> >> For more options, visit this group at http://groups.google.com/** >> group/spctools-discuss?hl=en<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 view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/fGumFv11IeEJ. > > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
