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 [[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. | + | 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. |
| + | |||
| + | ==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== | ==Getting the software== | ||
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| *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/] | *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== | ==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 | ||
Current revision
Contents |
[edit]
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.
[edit]
RAMP in the TPP
- MzXML2Search – RAMP
- ASAPRatio – RAMP
- Xpress – RAMP
- Libra – RAMP
- SpectraST – cRAMP
- pep3D -RAMP
- MS/MS spectrum viewer - RAMP
[edit]
External Projects
- muxQuant (M. Palmblad)
[edit]
Getting the software
- stable: You can also look in the latest stable/official source release, under /trans_proteomic_pipeline/src/Parsers/ramp/
- Latest (bleeding edge) is in the SVN trunk: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Parsers/ramp/
[edit]
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.
[edit]
