Provides functionalty for writing inclusion or exclusion lists. More...
#include <OpenMS/ANALYSIS/TARGETED/InclusionExclusionList.h>
 
  
 | Classes | |
| struct | IEWindow | 
| class | WindowDistance_ | 
| Determine distance between two spectra.  More... | |
| Public Member Functions | |
| void | writeTargets (const std::vector< FASTAFile::FASTAEntry > &fasta_entries, const String &out_path, const IntList &charges, const String rt_model_path) | 
| Writes inclusion or exclusion list of tryptic peptides of the given proteins (tab-delimited).  More... | |
| void | writeTargets (const FeatureMap<> &map, const String &out_path) | 
| Writes inclusion or exclusion list of given feature map.  More... | |
| void | writeTargets (const std::vector< PeptideIdentification > &pep_ids, const String &out_path, const IntList &charges) | 
| Writes inclusion or exclusion list of given peptide ids (tab-delimited).  More... | |
| Constructors and destructors | |
| InclusionExclusionList () | |
| default constructor  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Protected Types | |
| typedef std::vector< IEWindow > | WindowList | 
| Protected Member Functions | |
| void | mergeOverlappingWindows_ (WindowList &list) const | 
| Merges overlapping windows using m/z tolerance.  More... | |
| void | writeToFile_ (const String &out_path, const WindowList &windows) const | 
| Writes the windows to the given file.  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () | 
| This method is used to update extra member variables at the end of the setParameters() method.  More... | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
| Additional Inherited Members | |
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
Provides functionalty for writing inclusion or exclusion lists.
| 
 | protected | 
default constructor
| 
 | protected | 
Merges overlapping windows using m/z tolerance.
We employ single linkage clustering to merge windows that:
| void writeTargets | ( | const std::vector< FASTAFile::FASTAEntry > & | fasta_entries, | 
| const String & | out_path, | ||
| const IntList & | charges, | ||
| const String | rt_model_path | ||
| ) | 
Writes inclusion or exclusion list of tryptic peptides of the given proteins (tab-delimited).
| Exception::UnableToCreateFile | is thrown if the output file cannot be created | 
| void writeTargets | ( | const FeatureMap<> & | map, | 
| const String & | out_path | ||
| ) | 
Writes inclusion or exclusion list of given feature map.
| Exception::UnableToCreateFile | is thrown if the output file cannot be created | 
| void writeTargets | ( | const std::vector< PeptideIdentification > & | pep_ids, | 
| const String & | out_path, | ||
| const IntList & | charges | ||
| ) | 
Writes inclusion or exclusion list of given peptide ids (tab-delimited).
| Exception::UnableToCreateFile | is thrown if the output file cannot be created | 
| Exception::InvalidSize | is thrown if a peptide id contains more than one hit | 
| Exception::MissingInformation | is thrown if a peptide id contains no RT information | 
| 
 | protected | 
Writes the windows to the given file.
Format for each window is: <mz>\t<rt_start>\t<rt_stop>\n
| Exception::UnableToCreateFile | when file cannot be created | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |