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InclusionExclusionList Class Reference

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

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

Inheritance diagram for InclusionExclusionList:
DefaultParamHandler

List of all members.

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).
void writeTargets (const FeatureMap<> &map, const String &out_path)
 Writes inclusion or exclusion list of given feature map.
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).
Constructors and destructors

 InclusionExclusionList ()
 default constructor

Protected Types

typedef std::vector< IEWindow > WindowList

Protected Member Functions

void mergeOverlappingWindows_ (WindowList &list) const
 Merges overlapping windows using m/z tolerance.
void writeToFile_ (const String &out_path, const WindowList &windows) const
 Writes the windows to the given file.

Detailed Description

Provides functionalty for writing inclusion or exclusion lists.

Todo:
allow modifications (fixed?)

Member Typedef Documentation

typedef std::vector<IEWindow> WindowList [protected]

Constructor & Destructor Documentation

InclusionExclusionList (  ) 

default constructor

Member Function Documentation

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
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
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
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
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
OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1