#include <ProteomeData.hpp>
Inheritance diagram for pwiz::proteome::Protein:
Public Member Functions | |
| Protein (const std::string &id, size_t index, const std::string &description, const std::string &sequence) | |
| bool | empty () const |
 Public Member Functions inherited from pwiz::proteome::Peptide | |
| Peptide (const std::string &sequence="", MODIFICATION_PARSING_ARGUMENTS) | |
| Peptide (const char *sequence, MODIFICATION_PARSING_ARGUMENTS) | |
| Peptide (std::string::const_iterator begin, std::string::const_iterator end, MODIFICATION_PARSING_ARGUMENTS) | |
| Peptide (const char *begin, const char *end, MODIFICATION_PARSING_ARGUMENTS) | |
| Peptide (const Peptide &) | |
| Peptide & | operator= (const Peptide &) |
| virtual | ~Peptide () |
| const std::string & | sequence () const |
| returns the sequence of amino acids making up the peptide | |
| chemistry::Formula | formula (bool modified=false) const |
| if modified = false: returns the composition formula of sequence()+water if modified = true: returns the composition formula of sequence()+modifications()+water throws an exception if modified = true and any modification has only mass information | |
| double | monoisotopicMass (int charge=0, bool modified=true) const |
| if charge = 0: returns neutral mass if charge > 0: returns charged m/z if modified = false: returns the monoisotopic mass of sequence()+water if modified = true: returns the monoisotopic mass of sequence()+modifications()+water | |
| double | molecularWeight (int charge=0, bool modified=true) const |
| if charge = 0: returns neutral mass if charge > 0: returns charged m/z if modified = false: returns the molecular weight of sequence()+water if modified = true: returns the molecular weight of sequence()+modifications()+water | |
| ModificationMap & | modifications () |
| the map of sequence offsets (0-based) to modifications; modifications can be added or removed from the peptide with this map | |
| const ModificationMap & | modifications () const |
| the map of sequence offsets (0-based) to modifications | |
| Fragmentation | fragmentation (bool monoisotopic=true, bool modified=true) const |
| returns a fragmentation model for the peptide; fragment masses can calculated as mono/avg and as modified/unmodified | |
| bool | operator== (const Peptide &rhs) const |
| returns true iff peptide sequences and modifications are equal | |
| bool | operator< (const Peptide &rhs) const |
| returns true iff this peptide has a lesser sequence length, sequence, modifications length, or modifications | |
Public Attributes | |
| std::string | id |
| size_t | index |
| std::string | description |
Detailed Description
Definition at line 36 of file ProteomeData.hpp.
Constructor & Destructor Documentation
| pwiz::proteome::Protein::Protein | ( | const std::string & | id, |
| size_t | index, | ||
| const std::string & | description, | ||
| const std::string & | sequence | ||
| ) |
Member Function Documentation
| bool pwiz::proteome::Protein::empty | ( | ) | const |
Member Data Documentation
| std::string pwiz::proteome::Protein::id |
Definition at line 42 of file ProteomeData.hpp.
Referenced by pwiz::proteome::TextWriter::operator()(), pwiz::tradata::TextWriter::operator()(), and testProtein().
| size_t pwiz::proteome::Protein::index |
Definition at line 43 of file ProteomeData.hpp.
Referenced by SelectedIndexPredicate::accept(), and pwiz::proteome::TextWriter::operator()().
| std::string pwiz::proteome::Protein::description |
Definition at line 44 of file ProteomeData.hpp.
Referenced by pwiz::proteome::TextWriter::operator()().
The documentation for this struct was generated from the following file:
- /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/proteome/ProteomeData.hpp
