ProteoWizard

This is copy of the ProteoWizard code used to learn and explore the project. See the official ProteoWizard page for details. The orignal code is available at http://proteowizard.sourceforge.net.

License

Apache License Version 2.0 - see LICENSE for details.

Installation and compilation

git clone git@github.com:lgatto/proteowizard.git
cd proteowizard
./quickbuild.sh

$cat BUILDING 
BUILDING PROTEOWIZARD

Run "quickbuild.sh" to build ProteoWizard. (Use "quickbuild.bat" for Windows.) 

Use the "--help" switch for some useful hints on building ProteoWizard.

Open doc/index.html in a browser for more detailed info on
ProteoWizard, known issues, etc.

Technical documentation

See [./pwiz/doc/technical/index.html]

Directory Layout

[root]
    build   [everything is built here]
    doc     [documentation]
    example_data [some example data files]
    libraries    [3rd party library archives]
    pwiz       [main source tree -- all Apache licensed]
    pwiz_aux   [non-Apache licensed contributed code]
    pwiz_tools [source code for tools]

Projects

Here is an outline of the various ProteoWizard projects, organized by dependency level. There may be dependencies within a given level, but there should never be any up-level dependencies. Unless otherwise noted, all projects are cross-platform. Each project's source files are contained in the subdirectory of pwiz of the same name.

level 0 (pwiz/utility)

• math: Mathematics classes (linear algebra, statistics, special mathematical functions)
• misc: Miscellaneous standalone utility classes (Base64, SHA-1, 2D drawing, unit testing)
• minimxml: XML parsing and writing
• proteome: Chemical formula, peptide, and isotope calculations.
• vendor_api: Vendor-specific API wrappers (Windows only)

level 1 (pwiz/data):

• msdata: Mass spec file format abstraction layer.
• ident: identification file format abstraction layer.
• misc: Library containing classes for handling FT transient data, complex frequency data, MS1 peak data.
• vendor_readers: Vendor-specific Reader implementations

level 2 (pwiz/analysis):

• chromatogram_processing: Chromatogram analysis
• frequency: Library of routines for frequency-domain peak detection.
• passive: Event-driven analysis modules
• peakdetect: General interface for peak detection
• peptideid: Modules handling peptide id info abstraction and parsing
• spectrum_processing: Spectrum analysis

level 3 (pwiz_tools):

• commandline: Command-line tools
• SeeMS: Graphic data visualization program (Windows only)

Code Conventions

A code module consists of an interface (Foo.hpp), implementation (Foo.cpp), and a unit test (FooTest.cpp). The interface should be self-documenting, with optional inclusion of comment markup for automated documentation tools (e.g. Doxygen). The unit test serves two purposes:

• To exercise the module's interface and validate its behavior independent of other modules.
• To document the intended usage of the code module.

Clients of a code module should never need to look at the implementation for questions about usage.

ProteoWizard Data Access Layer Design

The ProteoWizard data access layer library is pwiz/msdata, and the interface and data structure definitions are in MSData.hpp.

The data model is a one-to-one translation from mzML data elements to C++ structs. The root mzML element correspondes to an MSData struct, and the sub-elements correspond to structs with similar names. SpectrumList has a virtual interface, which allows for lazy evaluation backed by a data file.

The mzML controlled vocabulary (CV) is parsed at compile time, generating cv.hpp and cv.cpp. This allows CV terms to be used in a typesafe manner, and also makes the various CV relations and synonyms available to C++ client code.

Mapping from the various structs to mzML is done in the IO module, and diff calculations in Diff. Serializer_mzML and Serializer_mzXML allow serializations to/from iostreams in mzML and mzXML formats, respectively.

MSDataFile is a subclass of MSData that adds file I/O handling. MSDataFile::Reader provides a generic interface for file readers. By default, Readers for mzML, mzXML, and Thermo RAW files are provided. On instantiation with a filename, MSDataFile finds a Reader that will accept the file, and uses that Reader to fill in the internal data structures.

Sandbox

./pwiz/sandox with code initially from ./pwiz/doc/technical/hello_pwiz.

Notes

identdata

• IdentData: mzIdentML structure.

• IdentDataFile: IdentData object plus file I/O.

• Reader: interface for file readers.

• DefaultReaderList: reader classes for mzid, pepXML, protXML.

• MascotReader: Mascot file reader.

• Serializer_*: write mzid, pepXML, protXML and Text (tab delimited) files.

• examples: generate example files.

• IO: XML read/write.

• References: functions for resolving references from objects into the internal MSData lists

• Pep2MzIdent: Translates data from a MinimumPepXML object into a IdentData object tree when a translation is known.

• Other: DelimReader, DelimWriter, Diff, KwCVMap, MzidPredicates, TextWriter, Version.