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Public Types | Public Member Functions | Static Public Member Functions

ms_ms1quant_match Class Reference
[Quantitation analysis for Mascot Server and Distiller]

A peptide that has been matched, in quantitation, to a protein hit. More...

#include <ms_ms1quant_match.hpp>

Inherits matrix_science::ms_handle.

List of all members.

Public Types

enum  chargeType {
  CHARGETYPE_ORIGINAL,
  CHARGETYPE_ALL
}
 

Types of charge state used when matching.

More...

Public Member Functions

 ms_ms1quant_match ()
 Default constructor; for standard library collections.
 ms_ms1quant_match (const ms_ms1quant_match_body &body)
 Populated constructor, linked to loaded data.
bool allComponentsIdentified () const
 Check if all the match components were identified by Mascot.
void clearHitRatioOutlier (const std::string &ratioName, int hitId, int memberNumber)
 Clear the match ratio from being an outlier for a hit.
int getChargeState () const
 Get the ion charge state.
ms_ms1quant_charge_state getChargeStateData () const
 Get the charge state data.
chargeType getChargeType () const
 Get whether this charge state has been extrapolated from the charge state of a Mascot match.
ms_ms1quant_match_component getComponent (int index) const
 Get a component associated with this match by its index (1..getNumComponents).
ms_ms1quant_match_component getComponent (std::string componentName) const
 Get a component of the matched peptide.
std::string getConciseLabelFreeVarMods () const
 Get the concise (un-numbered) readable variable modifications.
const ms_matrixgetCorrectionMatrix () const
 Get the correction matrix A, product of J (averagine) and I (impurity).
int getDataSourceId () const
 Get the data source identifier if processed independantly.
double getDisplayIntensity () const
 Get the total intensity of fitted peaks across the XIC peak.
int getFirstXicScanId () const
 Get the first scan of all the scans processed in the search for an XIC peak. Can be a wide region.
const ms_proteingetHit (int index1) const
 Get a protein hit associated with this match by its index (1..getNumHits).
matrix_science::ms_peptide_quant_key getKey () const
 Get a ms_peptide_quant_key code identifying the individual match.
std::string getLabelFreeVarMods () const
 Get the variable modification identifiers, with the labels removed.
int getLastXicScanId () const
 Get the last scan of all the scans processed in the search for an XIC peak. Can be a wide region..
int getNumComponents () const
 Get the number of components associated with this match.
int getNumHits () const
 Get the number of protein hits associated with this match.
int getNumPeptideRatios () const
 Get the number of peptide ratios associated with this match.
ms_ms1quant_match_ratio getPeptideRatio (int index) const
 Get a peptide ratio associated with this match by its index (0..getNumPeptideRatios-1).
ms_ms1quant_match_ratio getPeptideRatio (const std::string &ratioName) const
 Get a peptide ratio value for the ratio name.
std::string getPeptideString () const
 Get the peptide sequence in 1-letter code.
const ms_matrixgetPerfectObservedMatrix () const
 Get the predicted stick spectrum for measured amounts of each component.
const ms_matrixgetPredictionMatrix () const
 Get the predicted stick spectrum for equal amounts of each component.
std::string getReadableLabelFreeVarMods () const
 Get the readable variable modifications.
std::string getVarMods () const
 Get the variable modifications encoded as string of integers.
bool hasComponent (std::string componentName) const
 Returns true if the matched peptide has the component.
bool hasIdentifiedComponent () const
 Check if the match has any component that was identified by Mascot.
bool hasPeptideRatio (const std::string &ratioName) const
 Returns true if the match has a peptide ratio value for the ratio name.
bool isHitRatioExcluded (const std::string &ratioName, int hitId, int memberNumber) const
 Returns true if the match ratio is excluded from a hit.
bool isHitRatioOutlier (const std::string &ratioName, int hitId, int memberNumber) const
 Returns true if the match ratio is an outlier for a hit.
bool isHitRatioUsedForAverage (const std::string &ratioName, int hitId, int memberNumber) const
 Returns true if the match ratio is used in the average quantitation protocol for a hit.
void setHitRatioExcluded (const std::string &ratioName, int hitId, int memberNumber)
 Set the match ratio to be excluded from a hit.
void setHitRatioOutlier (const std::string &ratioName, int hitId, int memberNumber)
 Set the match ratio to be an outlier for a hit.

Static Public Member Functions

static chargeType getCodeFromXml (std::string text)
 Get the charge type code for an XML attribute value.
static std::string getXmlCode (chargeType code)
 Get the XML attribute value for a charge type code.

Detailed Description

A peptide that has been matched, in quantitation, to a protein hit.

Each protein can be matched to a number of peptides. The quantitation ratios of these peptides are used to determine the quantitaion ratio of the protein.

A peptide match can have a number of labelled components (such as 'heavy' and 'light') that are determined by the modifications.

This is stored in XML in a "peptideMatch" entity.


Member Enumeration Documentation

enum chargeType

Types of charge state used when matching.

See Using enumerated values in Perl, Java, Python and C#.

Enumerator:
CHARGETYPE_ORIGINAL 

Charge state found in result file.

CHARGETYPE_ALL 

Match created in all charge states.


Constructor & Destructor Documentation

Default constructor; for standard library collections.

Assigns reasonable default values to all internal members.

ms_ms1quant_match ( const ms_ms1quant_match_body &  body )

Populated constructor, linked to loaded data.

Parameters:
bodyThe data loaded from the result file.

Member Function Documentation

bool allComponentsIdentified (  ) const

Check if all the match components were identified by Mascot.

Tests to see if all the components were identified by Mascot. This method can return false event if hasIdentifiedComponent() returns true, as that method only requires one of the components to have been identified

See also:
hasIdentifiedComponent()
Returns:
True if all the components were identified by Mascot matches, false if not
void clearHitRatioOutlier ( const std::string &  ratioName,
int  hitId,
int  memberNumber 
)

Clear the match ratio from being an outlier for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters:
ratioNameThe name of the ratio.
hitIdProtein hit number.
memberNumberFamily member number.
int getChargeState (  ) const

Get the ion charge state.

Returns:
The ion charge state.
matrix_science::ms_ms1quant_charge_state getChargeStateData (  ) const

Get the charge state data.

Returns:
The charge state data.
ms_ms1quant_match::chargeType getChargeType (  ) const

Get whether this charge state has been extrapolated from the charge state of a Mascot match.

Returns:
CHARGETYPE_ORIGINAL if this charge state was found in the result file, otherwise CHARGETYPE_ALL as it has been extrapolated from the charge state of a Mascot match.
ms_ms1quant_match::chargeType getCodeFromXml ( std::string  text ) [static]

Get the charge type code for an XML attribute value.

Parameters:
textThe string used to encode the charge type in the XML file.
Returns:
The charge type corresponding to the XML encoded string.
ms_ms1quant_match_component getComponent ( int  index ) const

Get a component associated with this match by its index (1..getNumComponents).

Parameters:
indexAn index (1..getNumComponents()) into the components associated with the peptide match.
Returns:
The component.
ms_ms1quant_match_component getComponent ( std::string  componentName ) const

Get a component of the matched peptide.

Parameters:
componentNameThe name of component to be retrieved, e.g. "Heavy".
Returns:
The component.
std::string getConciseLabelFreeVarMods (  ) const

Get the concise (un-numbered) readable variable modifications.

For example: "Dimethyl (KR); Acetyl (K); Methyl (KR)".

Returns:
A semi-colon separated text string.
const matrix_science::ms_matrix & getCorrectionMatrix (  ) const

Get the correction matrix A, product of J (averagine) and I (impurity).

Returns:
The correction matrix
int getDataSourceId (  ) const

Get the data source identifier if processed independantly.

Returns:
The data source identifier, if processed independantly.
double getDisplayIntensity (  ) const

Get the total intensity of fitted peaks across the XIC peak.

Returns:
The total intensity of fitted peaks across the XIC peak.
int getFirstXicScanId (  ) const

Get the first scan of all the scans processed in the search for an XIC peak. Can be a wide region.

Returns:
The identifier of the first scan of all the scans processed in the search for an XIC peak. Can be a wide region.
const matrix_science::ms_protein * getHit ( int  index1 ) const

Get a protein hit associated with this match by its index (1..getNumHits).

Parameters:
index1An index (1..getNumHits()) into the protein hits associated with the peptide match.
Returns:
A protein hit, or null if the index is out of range.

Get a ms_peptide_quant_key code identifying the individual match.

Returns:
The identifier for the match within the quantitation results.
std::string getLabelFreeVarMods (  ) const

Get the variable modification identifiers, with the labels removed.

For example: "00000100000043000009a2000".

Returns:
A string of letters representing the modifications.
int getLastXicScanId (  ) const

Get the last scan of all the scans processed in the search for an XIC peak. Can be a wide region..

Returns:
The identifier of the last scan of all the scans processed in the search for an XIC peak. Can be a wide region.
int getNumComponents (  ) const

Get the number of components associated with this match.

Returns:
The number of components associated with the match.
int getNumHits (  ) const

Get the number of protein hits associated with this match.

Not all peptide matches are associated with every protein. This returns the number of proteins that are matched to this particular peptide and is typically less than the number of proteins in the peptide summary.

Returns:
The number of protein hits associated with the match.
int getNumPeptideRatios (  ) const

Get the number of peptide ratios associated with this match.

Returns:
The number of peptide ratios associated with the match.
matrix_science::ms_ms1quant_match_ratio getPeptideRatio ( const std::string &  ratioName ) const

Get a peptide ratio value for the ratio name.

Peptide ratio data that is independent of the assigned protein hit. To find out whether a match has been accepted or rejected under a particular protein hit, need to look under isHitRatioExcluded().

Parameters:
ratioNameThe name of ratio to be searched for, e.g. "H/L".
Returns:
The peptide match.
matrix_science::ms_ms1quant_match_ratio getPeptideRatio ( int  index ) const

Get a peptide ratio associated with this match by its index (0..getNumPeptideRatios-1).

Parameters:
indexAn index (0..getNumPeptideRatios()-1) into the peptide ratios associated with the match.
Returns:
The peptide ratio.
std::string getPeptideString (  ) const

Get the peptide sequence in 1-letter code.

Returns:
The peptide sequence as a series of 1-letter codes.
const matrix_science::ms_matrix & getPerfectObservedMatrix (  ) const

Get the predicted stick spectrum for measured amounts of each component.

Returns:
The perfect observed matrix.
const matrix_science::ms_matrix & getPredictionMatrix (  ) const

Get the predicted stick spectrum for equal amounts of each component.

Returns:
The prediction matrix
std::string getReadableLabelFreeVarMods (  ) const

Get the readable variable modifications.

For example: "(1) Dimethyl (KR); (6) Acetyl (K); (9) Methyl (KR)".

Returns:
A semi-colon separated text string.
std::string getVarMods (  ) const

Get the variable modifications encoded as string of integers.

Returns:
The variable modifications encoded as string of integers.
std::string getXmlCode ( ms_ms1quant_match::chargeType  code ) [static]

Get the XML attribute value for a charge type code.

Some of the returned values include a substitution string of "%s" or "%d". These are replaced with a specific value in the created XML.

Parameters:
codeThe charge type to get the XML excoding string for.
Returns:
The string used to encode the charge type in the XML file.
bool hasComponent ( std::string  componentName ) const

Returns true if the matched peptide has the component.

Parameters:
componentNameThe name of component to be searched for, e.g. "Heavy".
Returns:
True if the match has the component.
bool hasIdentifiedComponent (  ) const

Check if the match has any component that was identified by Mascot.

Returns:
True if any component of the match has been identified.
bool hasPeptideRatio ( const std::string &  ratioName ) const

Returns true if the match has a peptide ratio value for the ratio name.

Parameters:
ratioNameThe name of ratio to be searched for, e.g. "H/L".
Returns:
True if the ratio exists for the peptide match.
bool isHitRatioExcluded ( const std::string &  ratioName,
int  hitId,
int  memberNumber 
) const

Returns true if the match ratio is excluded from a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters:
ratioNameThe name of the ratio.
hitIdProtein hit number.
memberNumberFamily member number.
Returns:
True if the match ratio is excluded from this hit.
bool isHitRatioOutlier ( const std::string &  ratioName,
int  hitId,
int  memberNumber 
) const

Returns true if the match ratio is an outlier for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters:
ratioNameThe name of the ratio.
hitIdProtein hit number.
memberNumberFamily member number.
Returns:
True if the match ratio is an outlier for the hit.
bool isHitRatioUsedForAverage ( const std::string &  ratioName,
int  hitId,
int  memberNumber 
) const

Returns true if the match ratio is used in the average quantitation protocol for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters:
ratioNameThe name of the ratio.
hitIdProtein hit number.
memberNumberFamily member number.
Returns:
True if the match ratio is used in the average protocol for this hit.
void setHitRatioExcluded ( const std::string &  ratioName,
int  hitId,
int  memberNumber 
)

Set the match ratio to be excluded from a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters:
ratioNameThe name of the ratio.
hitIdProtein hit number.
memberNumberFamily member number.
void setHitRatioOutlier ( const std::string &  ratioName,
int  hitId,
int  memberNumber 
)

Set the match ratio to be an outlier for a hit.

Data for a protein hit to which the peptide match is assigned.

Parameters:
ratioNameThe name of the ratio.
hitIdProtein hit number.
memberNumberFamily member number.

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:53