OpenMS
2.6.0
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Provides functionality 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 | |
Constructors and destructors | |
InclusionExclusionList () | |
default constructor More... | |
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... | |
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 | |
Static Public Member Functions inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") |
Writes all parameters to meta values. More... | |
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 functionality for writing inclusion or exclusion lists.
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protected |
default constructor
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protected |
Merges overlapping windows using m/z tolerance.
We employ single linkage clustering to merge windows that:
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< 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 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 |
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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 |