| OpenMS 2.5.0

Classes | Public Member Functions | Protected Types | Protected Member Functions | List of all members
InclusionExclusionList Class Reference

Provides functionality for writing inclusion or exclusion lists. More...

`#include <OpenMS/ANALYSIS/TARGETED/InclusionExclusionList.h>`

Inheritance diagram for InclusionExclusionList:

## 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 &param)
| 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...

## Detailed Description

Provides functionality for writing inclusion or exclusion lists.

Todo:
  allow modifications (fixed?)

## Member Typedef Documentation

## ◆ WindowList

typedef std::vector<IEWindow> WindowList

protected

## Constructor & Destructor Documentation

## ◆ InclusionExclusionList()

InclusionExclusionList | ( |  | ) |

default constructor

## Member Function Documentation

## ◆ mergeOverlappingWindows_()

void mergeOverlappingWindows_ | ( | WindowList & | list | ) | const

protected

Merges overlapping windows using m/z tolerance.

We employ single linkage clustering to merge windows that:

- are close in m/z
- overlap in RT All clusters found by this are merged such that:
- RT windows are extended
- m/z value is averaged over all windows

## ◆ writeTargets() [1/3]

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).

Exceptions

  Exception::UnableToCreateFile | is thrown if the output file cannot be created

## ◆ writeTargets() [2/3]

void writeTargets | ( | const FeatureMap & | map,
|  | const String & | out_path
| ) |  |

Writes inclusion or exclusion list of given feature map.

Exceptions

  Exception::UnableToCreateFile | is thrown if the output file cannot be created

## ◆ writeTargets() [3/3]

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).

Exceptions

  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

## ◆ writeToFile_()

void writeToFile_ | ( | const String & | out_path,
|  | const WindowList & | windows
| ) |  | const

protected

Writes the windows to the given file.

Format for each window is: <mz>\t<rt_start>\t<rt_stop>\n

Exceptions

  Exception::UnableToCreateFile | when file cannot be created