Software:RAMP

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RAMP: '''R'''andom '''A'''ccess '''M'''inimal '''P'''arser RAMP: '''R'''andom '''A'''ccess '''M'''inimal '''P'''arser
-C/C++ parser for mzXML files. Contained in the TPP source tree. See Sashimi SVN for details.+C/C++ parser for [[Formats:mzXML|mzXML]] (and mzData) files. The RAMP parser code is contained in the TPP source tree. RAMP is heavily used in the TPP; this allows programs to seamlessly adapt to revisions to the [[Formats:mzXML|mzXML]] format, as well as handle other formats such as mzData. RAMP itself is C-language code; "cRAMP" is a C++ wrapper.
-==Related project==+==RAMP in the TPP==
 + 
 +*[[Software:MzXML2Search|MzXML2Search]] – RAMP
 +*[[Software:ASAPRatio|ASAPRatio]] – RAMP
 +*[[Software:XPRESS|Xpress]] – RAMP
 +*[[Software:Libra|Libra]] – RAMP
 +*[[Software:SpectraST|SpectraST]] – cRAMP
 +*[[Software:Pep3D|pep3D]] -RAMP
 +*MS/MS spectrum viewer - RAMP
 + 
 +==External Projects==
 +*[http://dx.doi.org/10.1021/pr0705340 muxQuant] (M. Palmblad)
 + 
 +==Getting the software==
 +*stable: You can also look in the latest stable/official [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 source release], under /trans_proteomic_pipeline/src/Parsers/ramp/
 +
 +*stable (svn): [http://sashimi.svn.sourceforge.net/viewvc/sashimi/tags/release_3-4-0/ [http://sashimi.svn.sourceforge.net/viewvc/sashimi/tags/release_3-4-0/]
 +
 +*Latest (bleeding edge) is in the SVN trunk: [http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Parsers/ramp/ http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Parsers/ramp/]
 + 
 +==History and Design Decisions==
 + 
 +RAMP was developed at time when full XML parsing libraries (such as xerces) were heavyweight and slow, and not suited for the fast, random-access parsing of large spectral files in proteomics applications. As such, the code is string-based ASCII processing rather than true XML parsing. This unfortunately also makes RAMP fairly dependent on the whitespace in mzXML, and occasionally the order of attributes within elements.
 + 
 +==Related projects==
*[[Software:JRAP|JRAP]]-- java mzXML parser *[[Software:JRAP|JRAP]]-- java mzXML parser
*[[Software:RAP|RAP]]-- earlier xerces-based mzXML parser, retired. *[[Software:RAP|RAP]]-- earlier xerces-based mzXML parser, retired.
 +*X!Tandem uses a custom SAX-based parser

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Contents

RAMP

RAMP: Random Access Minimal Parser

C/C++ parser for mzXML (and mzData) files. The RAMP parser code is contained in the TPP source tree. RAMP is heavily used in the TPP; this allows programs to seamlessly adapt to revisions to the mzXML format, as well as handle other formats such as mzData. RAMP itself is C-language code; "cRAMP" is a C++ wrapper.

RAMP in the TPP

External Projects

Getting the software

  • stable: You can also look in the latest stable/official source release, under /trans_proteomic_pipeline/src/Parsers/ramp/

History and Design Decisions

RAMP was developed at time when full XML parsing libraries (such as xerces) were heavyweight and slow, and not suited for the fast, random-access parsing of large spectral files in proteomics applications. As such, the code is string-based ASCII processing rather than true XML parsing. This unfortunately also makes RAMP fairly dependent on the whitespace in mzXML, and occasionally the order of attributes within elements.

Related projects

  • JRAP-- java mzXML parser
  • RAP-- earlier xerces-based mzXML parser, retired.
  • X!Tandem uses a custom SAX-based parser
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