PepNovo input file adapter. More...
#include <OpenMS/FORMAT/PepNovoInfile.h>
Public Member Functions | |
| PepNovoInfile () | |
| default constructor More... | |
| PepNovoInfile (const PepNovoInfile &pepnovo_infile) | |
| copy constructor More... | |
| virtual | ~PepNovoInfile () |
| destructor More... | |
| PepNovoInfile & | operator= (const PepNovoInfile &pepnovo_infile) |
| assignment operator More... | |
| bool | operator== (const PepNovoInfile &pepnovo_infile) const |
| equality operator More... | |
| void | store (const String &filename) |
| void | setModifications (const StringList &fixed_mods, const StringList &variable_mods) |
| generates the PepNovo Infile for given fixed and variable modifications * More... | |
| void | getModifications (std::map< String, String > &modification_key_map) const |
| return the modifications. More... | |
Private Member Functions | |
| String | handlePTMs_ (const String &modification, const bool variable) |
Private Attributes | |
| ModificationDefinitionsSet | mods_ |
| std::map< String, String > | mods_and_keys_ |
| TextFile | ptm_file_ |
PepNovo input file adapter.
Creates a PepNovo_PTMs.txt file for PepNovo search.
| PepNovoInfile | ( | ) |
default constructor
| PepNovoInfile | ( | const PepNovoInfile & | pepnovo_infile | ) |
copy constructor
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virtual |
destructor
return the modifications.
the modification unique identifiers are mapped to the keys used in the PepNovo Infile (origin+rounded monoisotopic mass of modification ). (e.g. modification_key_map["K+16"]=="Oxidation (K)" )
retrieves the name of modification, and generates the corresponding line for the PepNovo infile.
| modification | the modification |
| variable | should be set to true if it variable |
| PepNovoInfile& operator= | ( | const PepNovoInfile & | pepnovo_infile | ) |
assignment operator
| bool operator== | ( | const PepNovoInfile & | pepnovo_infile | ) | const |
equality operator
| void setModifications | ( | const StringList & | fixed_mods, |
| const StringList & | variable_mods | ||
| ) |
generates the PepNovo Infile for given fixed and variable modifications *
| fixed_mods | StringList of fixed modifications unique identifiers |
| variable_mods | StringList of variable modifications unique identifiers |
| void store | ( | const String & | filename | ) |
stores the experiment data in a PepNovo input file that can be used as input for PepNovo shell execution
| filename | the file which the input file is stored into |
| Exception::UnableToCreateFile | is thrown if the given file could not be created |
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private |
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private |
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:31 using doxygen 1.8.5 |