An object of this class represent a single quantitation method from quantitation.xml. More...

#include <ms_quant_method.hpp>

Inherits ms_xml_IValidatable.

Public Types
enum	METHOD_COMPATIBLE { COMPATIBLE , COMPATIBLE_DIFF_PROTOCOL , COMPATIBLE_DIFF_NUM_COMPONENTS , COMPATIBLE_MISSING_COMPONENT , COMPATIBLE_DIFF_NUM_MOD_GROUPS , COMPATIBLE_MISSING_MOD_GROUP , COMPATIBLE_DIFF_NUM_LOCAL_MODS , COMPATIBLE_DIFF_LOCAL_MOD , COMPATIBLE_DIFF_NUM_MODS , COMPATIBLE_MISSING_MOD , COMPATIBLE_MISSING_INTEGRATION , COMPATIBLE_MISSING_INTEGRATION_PARAM , COMPATIBLE_DIFF_INTEGRATION_PARAM , COMPATIBLE_DIFF_NUM_ISOTOPES }
	Enum used by isMethodCompatible() More...

Public Member Functions
	ms_quant_method ()
	Default constructor.

	ms_quant_method (const ms_quant_method &src)
	Copying constructor.

virtual	~ms_quant_method ()
	Destructor.

void	appendComponent (const ms_quant_component *item)
	Adds a new component at the end of the list.

void	appendExclusion (const char *exclusion)
	Adds a new `exclusion` element at the end of the list.

void	appendModificationGroup (const ms_quant_modgroup *item)
	Adds a new modification group at the end of the list.

void	appendReportRatio (const ms_quant_ratio *ratio)
	Adds a new `report_ratio` element at the end of the list.

void	appendSeq (const char *seq)
	Adds a new `seq` element at the end of the list.

void	clearComponents ()
	Deletes all components from the list.

void	clearExclusions ()
	Deletes all `exclusion` elements from the list.

void	clearModificationGroups ()
	Deletes all modification groups from the list.

void	clearReportRatios ()
	Deletes all `report_ratio` elements from the list.

void	clearSeqs ()
	Deletes all `seq` elements from the list.

void	copyFrom (const ms_quant_method *right)
	Copies all content from another instance.

void	defaultValues ()
	Call this member if you want to start again.

bool	deleteComponentByName (const char *name)
	Remove a component from the list in memory by its unique name.

bool	deleteComponentByNumber (const int idx)
	Remove a component from the list in memory by its index.

bool	deleteExclusion (const int idx)
	Remove a `exclusion` element from the list in memory by its index.

bool	deleteModificationGroupByName (const char *name)
	Remove a modification group from the list in memory by its unique name.

bool	deleteModificationGroupByNumber (const int idx)
	Remove a modification group from the list in memory by its index.

bool	deleteReportRatioByName (const char *name)
	Remove a `report_ratio` element from the list in memory by its unique name.

bool	deleteReportRatioByNumber (const int idx)
	Remove a `report_ratio` element from the list in memory by its index.

bool	deleteSeq (const int idx)
	Remove a `seq` element from the list in memory by its index.

void	dropComp ()
	Delete the `comp` element.

void	dropConstrainSearch ()
	Delete the `constrain_search` attribute.

void	dropDescription ()
	Delete the `description` attribute.

void	dropIntegration ()
	Delete the `integration` element.

void	dropMinNumPeptides ()
	Delete the `min_num_peptides` attribute.

void	dropName ()
	Delete the `name` attribute.

void	dropNormalisation ()
	Delete the `normalisation` element.

void	dropOutliers ()
	Delete the `outliers` element.

void	dropProteinRatioType ()
	Delete the `protein_ratio_type` attribute.

void	dropProtocol ()
	Delete the `protocol` element.

void	dropProtScoreType ()
	Delete the `prot_score_type` attribute.

void	dropQuality ()
	Delete the `quality` element.

void	dropReportDetail ()
	Delete the `report_detail` attribute.

void	dropRequireBoldRed ()
	Delete the `require_bold_red` attribute.

void	dropShowSubSets ()
	Delete the `show_sub_sets` attribute.

void	dropSigThresholdValue ()
	Delete the `sig_threshold_value` attribute.

std::string	getComp () const
	Returns the value of the `comp` element.

const ms_quant_component *	getComponentByName (const char *name) const
	Returns a component object by its name or a null value in case of not found.

const ms_quant_component *	getComponentByNumber (const int idx) const
	Returns a component object by its number (0..n-1).

std::string	getComponentSchemaType () const
	Obtain a symbolic name for the component element schema type.

std::string	getCompSchemaType () const
	Obtain a symbolic name for the `comp` element schema type.

std::string	getConstrainSearchSchemaType () const
	Obtain a symbolic name for the `constrain_search` attribute schema type.

std::string	getDescription () const
	Returns the value of the `description` attribute.

std::string	getDescriptionSchemaType () const
	Obtain a symbolic name for the `description` attribute schema type.

std::string	getExclusion (const int idx) const
	Returns a `exclusion` element object by its number.

std::string	getExclusionSchemaType () const
	Obtain a symbolic name for the `exclusion` element schema type.

const ms_quant_integration *	getIntegration () const
	Returns a pointer to the `integration` element.

std::string	getIntegrationSchemaType () const
	Obtain a symbolic name for the `integration` element schema type.

void	getLocalModifications (std::vector< const ms_quant_localdef * > &localDefVector)
	Returns all local modification definitions within method and components.

int	getMinNumPeptides () const
	Returns the value of the `min_num_peptides` attribute.

std::string	getMinNumPeptidesSchemaType () const
	Obtain a symbolic name for the `min_num_peptides` attribute schema type.

const ms_quant_modgroup *	getModificationGroupByName (const char *name) const
	Returns a modification group object by its name or a null value in case of not found.

const ms_quant_modgroup *	getModificationGroupByNumber (const int idx) const
	Returns a modification group object by its number.

std::string	getModificationGroupSchemaType () const
	Obtain a symbolic name for the modification group element schema type.

std::string	getName () const
	Returns the value of the `name` attribute.

std::string	getNameSchemaType () const
	Obtain a symbolic name for the "name attribute" schema type.

const ms_quant_normalisation *	getNormalisation () const
	Returns a pointer to the `normalisation` element.

std::string	getNormalisationSchemaType () const
	Obtain a symbolic name for the `normalisation` element schema type.

int	getNumberOfComponents () const
	Returns the number of nested components.

int	getNumberOfExclusions () const
	Returns the number of nested `exclusion` elements.

int	getNumberOfModificationGroups () const
	Returns the number of nested modification groups.

int	getNumberOfReportRatios () const
	Returns the number of nested `report_ratio` elements.

int	getNumberOfSeqs () const
	Returns the number of nested `seq` elements.

const ms_quant_outliers *	getOutliers () const
	Returns a pointer to the `outliers` element.

std::string	getOutliersSchemaType () const
	Obtain a symbolic name for the `outliers` element schema type.

std::string	getProteinRatioType () const
	Returns the value of the `protein_ratio_type` attribute.

std::string	getProteinRatioTypeSchemaType () const
	Obtain a symbolic name for the `protein_ratio_type` attribute schema type.

const ms_quant_protocol *	getProtocol () const
	Returns a pointer to the `protocol` element.

std::string	getProtocolSchemaType () const
	Obtain a symbolic name for the `protocol` element schema type.

std::string	getProtScoreType () const
	Returns the value of the `prot_score_type` attribute.

std::string	getProtScoreTypeSchemaType () const
	Obtain a symbolic name for the `prot_score_type` attribute schema type.

const ms_quant_quality *	getQuality () const
	Returns a pointer to the `quality` element.

std::string	getQualitySchemaType () const
	Obtain a symbolic name for the `quality` element schema type.

std::string	getReportDetailSchemaType () const
	Obtain a symbolic name for the `report_detail` attribute schema type.

const ms_quant_ratio *	getReportRatioByName (const char *name) const
	Returns a `report_ratio` element object by its name or a null value in case of not found.

const ms_quant_ratio *	getReportRatioByNumber (const int idx) const
	Returns a `report_ratio` element object by its number.

std::string	getReportRatioSchemaType () const
	Obtain a symbolic name for the `report_ratio` element schema type.

std::string	getRequireBoldRedSchemaType () const
	Obtain a symbolic name for the `require_bold_red` attribute schema type.

virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.

std::string	getSeq (const int idx) const
	Returns a `seq` element object by its number.

std::string	getSeqSchemaType () const
	Obtain a symbolic name for the element's schema type.

std::string	getShowSubSets () const
	Returns the value of the `show_sub_sets` attribute.

std::string	getShowSubSetsSchemaType () const
	Obtain a symbolic name for the `show_sub_sets` attribute schema type.

std::string	getSigThresholdValue () const
	Returns the value of the `sig_threshold_value` attribute.

std::string	getSigThresholdValueSchemaType () const
	Obtain a symbolic name for the `sig_threshold_value` attribute schema type.

bool	haveComp () const
	Indicates whether the `comp` element is present.

bool	haveConstrainSearch () const
	Indicates whether the `constrain_search` attribute is present.

bool	haveDescription () const
	Indicates whether the `description` attribute is present.

bool	haveIntegration () const
	Indicates whether the `integration` element is present.

bool	haveMinNumPeptides () const
	Indicates whether the `min_num_peptides` attribute is present.

bool	haveName () const
	Indicates whether the `name` attribute is present.

bool	haveNormalisation () const
	Indicates whether the `normalisation` element is present.

bool	haveOutliers () const
	Indicates whether the `outliers` element is present.

bool	haveProteinRatioType () const
	Indicates whether the `protein_ratio_type` attribute is present.

bool	haveProtocol () const
	Indicates whether the `protocol` element is present.

bool	haveProtScoreType () const
	Indicates whether the `prot_score_type` attribute is present.

bool	haveQuality () const
	Indicates whether the `quality` element is present.

bool	haveReportDetail () const
	Indicates whether the `report_detail` attribute is present.

bool	haveRequireBoldRed () const
	Indicates whether the `require_bold_red` attribute is present.

bool	haveShowSubSets () const
	Indicates whether the `show_sub_sets` attribute is present.

bool	haveSigThresholdValue () const
	Indicates whether the `sig_threshold_value` attribute is present.

bool	isConstrainSearch () const
	Returns the value of the `constrain_search` attribute.

int	isMethodCompatible (const ms_quant_method &other, std::string &reasonStrRef) const
	Methods are compatible if the protocol and selected other values are identical.

bool	isReportDetail () const
	Returns the value of the `report_detail` attribute.

bool	isRequireBoldRed () const
	Returns the value of the `require_bold_red` attribute.

ms_quant_method &	operator= (const ms_quant_method &right)
	C++ style assignment operator.

void	setComp (const char *value)
	Set a custom value for the `comp` element.

void	setConstrainSearch (const bool value)
	Set a custom value for the `constrain_search` attribute.

void	setDescription (const char *value)
	Set a custom value for the `description` attribute.

void	setIntegration (const ms_quant_integration *integration)
	Supply custom content for the `integration` element.

void	setMinNumPeptides (const int value)
	Set a custom value for the `min_num_peptides` attribute.

void	setName (const char *value)
	Set a custom value for the `name` attribute.

void	setNormalisation (const ms_quant_normalisation *normalisation)
	Supply custom content for the `normalisation` element.

void	setOutliers (const ms_quant_outliers *outliers)
	Supply custom content for the `outliers` element.

void	setProteinRatioType (const char *value)
	Set a custom value for the `protein_ratio_type` attribute.

void	setProtocol (const ms_quant_protocol *protocol)
	Supply custom content for the `protocol` element.

void	setProtScoreType (const char *value)
	Set a custom value for the `prot_score_type` attribute.

void	setQuality (const ms_quant_quality *quality)
	Supply custom content for the `quality` element.

void	setReportDetail (const bool value)
	Set a custom value for the `report_detail` attribute.

void	setRequireBoldRed (const bool value)
	Set a custom value for the `require_bold_red` attribute.

void	setShowSubSets (const char *value)
	Set a custom value for the `show_sub_sets` attribute.

void	setSigThresholdValue (const char *value)
	Set a custom value for the `sig_threshold_value` attribute.

bool	updateComponentByName (const char name, const ms_quant_component comp)
	Update the information for a specific component refering to it by its unique name.

bool	updateComponentByNumber (const int idx, const ms_quant_component *comp)
	Update the information for a specific component refering to it by its index.

bool	updateExclusion (const int idx, const char *exclusion)
	Update the information for a specific `exclusion` element refering to it by its index.

bool	updateModificationGroupByName (const char name, const ms_quant_modgroup modgroup)
	Update the information for a specific modification group refering to it by its unique name.

bool	updateModificationGroupByNumber (const int idx, const ms_quant_modgroup *modgroup)
	Update the information for a specific modification group refering to it by its index.

bool	updateReportRatioByName (const char name, const ms_quant_ratio ratio)
	Update the information for a specific `report_ratio` element refering to it by its unique name.

bool	updateReportRatioByNumber (const int idx, const ms_quant_ratio *ratio)
	Update the information for a specific `report_ratio` element refering to it by its index.

bool	updateSeq (const int idx, const char *seq)
	Update the information for a specific `seq` element refering to it by its index.

virtual std::string	validateDeep (const ms_xml_schema *pSchemaFileObj) const
	Performs validation of all child elements in addition to 'shallow' validation.

virtual std::string	validateShallow (const ms_xml_schema *pSchemaFileObj) const
	Performs simple validation of the top-level elements only.

Detailed Description

An object of this class represent a single quantitation method from quantitation.xml.

Examples: config_quantitation.cpp.

Member Enumeration Documentation

◆ METHOD_COMPATIBLE

enum METHOD_COMPATIBLE

Enum used by isMethodCompatible()

See Using enumerated values and static const ints in Perl, Java, Python and C#. The description for each of the enums is the human readable text for each of the 'error' codes

Enumerator
COMPATIBLE	Methods are compatible.
COMPATIBLE_DIFF_PROTOCOL	Methods 'x' and 'y' are incompatible: Different protocols ('p1' and 'p2') for the methods.
COMPATIBLE_DIFF_NUM_COMPONENTS	Methods 'x' and 'y' are incompatible: Different number of components ('c1' and 'c2').
COMPATIBLE_MISSING_COMPONENT	Methods 'x' and 'y' are incompatible: Component 'c1' is missing from method 'y'.
COMPATIBLE_DIFF_NUM_MOD_GROUPS	Methods 'x' and 'y' are incompatible: Different number of modification groups ('mg1' and 'mg2') for component/method 'Z'.
COMPATIBLE_MISSING_MOD_GROUP	Methods 'x' and 'y' are incompatible: Modification group mg is missing from component 'c'.
COMPATIBLE_DIFF_NUM_LOCAL_MODS	Methods 'x' and 'y' are incompatible: Different number of local modification definitions ('mg1' and 'mg2') for modification group 'mg'.
COMPATIBLE_DIFF_LOCAL_MOD	Methods 'x' and 'y' are incompatible: Local modification 'lm' definition differs.
COMPATIBLE_DIFF_NUM_MODS	Methods 'x' and 'y' are incompatible: Different number of modifications ('mg1' and 'mg2') for modification group 'mg'.
COMPATIBLE_MISSING_MOD	Methods 'x' and 'y' are incompatible: Modification 'mod' is missing from modification group 'mg'.
COMPATIBLE_MISSING_INTEGRATION	Methods 'x' and 'y' are incompatible: One method has integration parameters and the other has none.
COMPATIBLE_MISSING_INTEGRATION_PARAM	Methods 'x' and 'y' are incompatible: "Method 'x' has integration parameter 'p' but method 'y' does not.
COMPATIBLE_DIFF_INTEGRATION_PARAM	Methods 'x' and 'y' are incompatible: Method 'x' has integration parameter 'p1'='v1' but method 'y' has 'p2'='v2'.
COMPATIBLE_DIFF_NUM_ISOTOPES	Methods 'x' and 'y' are incompatible: Different number of isotopes ('mg1' and 'mg2') for component 'c1'.

Constructor & Destructor Documentation

◆ ms_quant_method() [1/2]

ms_quant_method ( )

Default constructor.

Assigns reasonable default values to all internal members.

◆ ms_quant_method() [2/2]

ms_quant_method ( const ms_quant_method & src )

Copying constructor.

Parameters

src	another instance of this class to copy the content from.

Member Function Documentation

◆ appendComponent()

void appendComponent ( const ms_quant_component * item )

Adds a new component at the end of the list.

Creates a new component object, copies all content from the object supplied as a parameter and adds it at the end of the components list.

Parameters

item	an instance of component object to copy content from.

◆ appendExclusion()

void appendExclusion ( const char * exclusion )

Adds a new exclusion element at the end of the list.

Creates a new exclusion element object and adds it at the end of the exclusion elements list.

Parameters

exclusion an string value for the element.

◆ appendModificationGroup()

void appendModificationGroup ( const ms_quant_modgroup * item )

Adds a new modification group at the end of the list.

Creates a new modification group object, copies all content from the object supplied as a parameter and adds it at the end of the methods list.

Parameters

item	an instance of modification group object to copy content from.

◆ appendReportRatio()

void appendReportRatio ( const ms_quant_ratio * item )

Adds a new report_ratio element at the end of the list.

Creates a new report_ratio element object, copies all content from the object supplied as a parameter and adds it at the end of the "report_ratio" elements list.

Parameters

item	an instance of `report_ratio` element object to copy content from.

◆ appendSeq()

void appendSeq ( const char * seq )

Adds a new seq element at the end of the list.

Creates a new seq element object and adds it at the end of the "seq" elements list.

Parameters

seq	an string value for the element.

◆ copyFrom()

void copyFrom ( const ms_quant_method * right )

Copies all content from another instance.

Parameters

right another instance of this class to copy the content from.

◆ defaultValues()

void defaultValues ( )

Call this member if you want to start again.

All internal values are reset to their defaults, as if the object had been freshly created with the default constructor.

◆ deleteComponentByName()

bool deleteComponentByName ( const char * name )

Remove a component from the list in memory by its unique name.

Parameters

name	name of the component for deletion.

Returns: TRUE if the component has been found and successfully deleted and FALSE otherwise.

◆ deleteComponentByNumber()

bool deleteComponentByNumber ( const int idx )

Remove a component from the list in memory by its index.

Parameters

idx	number of the component for deletion from 0 to (getNumberOfComponents() - 1).

Returns: TRUE if the component has been found and successfully deleted and FALSE otherwise.

◆ deleteExclusion()

bool deleteExclusion ( const int idx )

Remove a exclusion element from the list in memory by its index.

Parameters

idx	number of the `exclusion` element for deletion from 0 to (getNumberOfExclusions() - 1).

Returns: TRUE if the exclusion element has been found and successfully deleted and FALSE otherwise.

◆ deleteModificationGroupByName()

bool deleteModificationGroupByName ( const char * name )

Remove a modification group from the list in memory by its unique name.

Parameters

name	name of the modification group for deletion.

Returns: TRUE if the modification group has been found and successfully deleted and FALSE otherwise.

◆ deleteModificationGroupByNumber()

bool deleteModificationGroupByNumber ( const int idx )

Remove a modification group from the list in memory by its index.

Parameters

idx	number of the modification group for deletion from 0 to (getNumberOfModificationGroups() - 1).

Returns: TRUE if the modification group has been found and successfully deleted and FALSE otherwise.

◆ deleteReportRatioByName()

bool deleteReportRatioByName ( const char * name )

Remove a report_ratio element from the list in memory by its unique name.

Parameters

name	name of the `report_ratio` element for deletion.

Returns: TRUE if the report_ratio element has been found and successfully deleted and FALSE otherwise.

◆ deleteReportRatioByNumber()

bool deleteReportRatioByNumber ( const int idx )

Remove a report_ratio element from the list in memory by its index.

Parameters

idx	number of the `report_ratio` element for deletion from 0 to (getNumberOfReportRatios() - 1).

Returns: TRUE if the report_ratio element has been found and successfully deleted and FALSE otherwise.

◆ deleteSeq()

bool deleteSeq ( const int idx )

Remove a seq element from the list in memory by its index.

Parameters

idx	number of the `seq` element for deletion from 0 to (getNumberOfSeqs() - 1).

Returns: TRUE if the seq element has been found and successfully deleted and FALSE otherwise.

◆ dropComp()

void dropComp ( )

Delete the comp element.

Disables the element until it is re-set.

◆ dropConstrainSearch()

void dropConstrainSearch ( )

Delete the constrain_search attribute.

Disables the attribute until it is re-set.

◆ dropDescription()

void dropDescription ( )

Delete the description attribute.

Disables the attribute until it is re-set.

◆ dropIntegration()

void dropIntegration ( )

Delete the integration element.

Deletes the element until it is re-set.

◆ dropMinNumPeptides()

void dropMinNumPeptides ( )

Delete the min_num_peptides attribute.

Disables the attribute until it is re-set.

◆ dropName()

void dropName ( )

Delete the name attribute.

Disables the attribute until it is re-set.

◆ dropNormalisation()

void dropNormalisation ( )

Delete the normalisation element.

Deletes the element until it is re-set.

◆ dropOutliers()

void dropOutliers ( )

Delete the outliers element.

Deletes the element until it is re-set.

◆ dropProteinRatioType()

void dropProteinRatioType ( )

Delete the protein_ratio_type attribute.

Disables the attribute until it is re-set.

◆ dropProtocol()

void dropProtocol ( )

Delete the protocol element.

Deletes the element until it is re-set.

◆ dropProtScoreType()

void dropProtScoreType ( )

Delete the prot_score_type attribute.

Disables the attribute until it is re-set.

◆ dropQuality()

void dropQuality ( )

Delete the quality element.

Deletes the element until it is re-set.

◆ dropReportDetail()

void dropReportDetail ( )

Delete the report_detail attribute.

Disables the attribute until it is re-set.

◆ dropRequireBoldRed()

void dropRequireBoldRed ( )

Delete the require_bold_red attribute.

Disables the attribute until it is re-set.

◆ dropShowSubSets()

void dropShowSubSets ( )

Delete the show_sub_sets attribute.

Disables the attribute until it is re-set.

◆ dropSigThresholdValue()

void dropSigThresholdValue ( )

Delete the sig_threshold_value attribute.

Disables the attribute until it is re-set.

◆ getComp()

std::string getComp ( ) const

Returns the value of the comp element.

See haveComp() method for more information on how to use this.

Returns: a composition qualifier in Mascot notation, e.g. *[C].

◆ getComponentByName()

const ms_quant_component * getComponentByName ( const char * name ) const

Returns a component object by its name or a null value in case of not found.

Parameters

name	name of the component to find.

Returns: a read-only pointer to a component object. See Maintaining object references: two rules of thumb.

◆ getComponentByNumber()

const ms_quant_component * getComponentByNumber ( const int idx ) const

Returns a component object by its number (0..n-1).

Parameters

idx	number of the component from 0 to (getNumberOfComponents() - 1).

Returns: a read-only pointer to a component object. See Maintaining object references: two rules of thumb.

◆ getComponentSchemaType()

std::string getComponentSchemaType ( ) const

Obtain a symbolic name for the component element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getCompSchemaType()

std::string getCompSchemaType ( ) const

Obtain a symbolic name for the comp element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getConstrainSearchSchemaType()

std::string getConstrainSearchSchemaType ( ) const

Obtain a symbolic name for the constrain_search attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getDescription()

std::string getDescription ( ) const

Returns the value of the description attribute.

Returns: free text string for description.

◆ getDescriptionSchemaType()

std::string getDescriptionSchemaType ( ) const

Obtain a symbolic name for the description attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getExclusion()

std::string getExclusion ( const int idx ) const

Returns a exclusion element object by its number.

Parameters

idx	number of the `exclusion` element from 0 to (getNumberOfExclusions() - 1).

Returns: a string copy of the exclusion element.

◆ getExclusionSchemaType()

std::string getExclusionSchemaType ( ) const

Obtain a symbolic name for the exclusion element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getIntegration()

const ms_quant_integration * getIntegration ( ) const

Returns a pointer to the integration element.

See haveIntegration() for more information.

Returns: a pointer to the object that represents theintegration" element (or a null value if not present). See Maintaining object references: two rules of thumb.

◆ getIntegrationSchemaType()

std::string getIntegrationSchemaType ( ) const

Obtain a symbolic name for the integration element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getLocalModifications()

void getLocalModifications ( std::vector< const ms_quant_localdef * > & localDefVector )

Returns all local modification definitions within method and components.

Method currently only valid for C++ due to vector of object pointers.

Parameters

localDefVector vector to fill with ms_quant_localdef* object pointers.

◆ getMinNumPeptides()

int getMinNumPeptides ( ) const

Returns the value of the min_num_peptides attribute.

Minimum number of peptide matches for reporting quantitation at protein level.

Returns: minimum number of peptide matches

◆ getMinNumPeptidesSchemaType()

std::string getMinNumPeptidesSchemaType ( ) const

Obtain a symbolic name for the min_num_peptides attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getModificationGroupByName()

const ms_quant_modgroup * getModificationGroupByName ( const char * name ) const

Returns a modification group object by its name or a null value in case of not found.

Parameters

name	name of the modification group to find.

Returns: a read-only pointer to a modification group object. See Maintaining object references: two rules of thumb.

◆ getModificationGroupByNumber()

const ms_quant_modgroup * getModificationGroupByNumber ( const int idx ) const

Returns a modification group object by its number.

Parameters

idx	number of the modification group from 0 to (getNumberOfModificationGroups() - 1).

Returns: a read-only pointer to a modification group object. See Maintaining object references: two rules of thumb.

◆ getModificationGroupSchemaType()

std::string getModificationGroupSchemaType ( ) const

Obtain a symbolic name for the modification group element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getName()

std::string getName ( ) const

Returns the value of the name attribute.

Returns: a descriptive name that will appear in drop down lists, etc.

Examples: config_quantitation.cpp.

◆ getNameSchemaType()

std::string getNameSchemaType ( ) const

Obtain a symbolic name for the "name attribute" schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

Examples: config_quantitation.cpp.

◆ getNormalisation()

const ms_quant_normalisation * getNormalisation ( ) const

Returns a pointer to the normalisation element.

See haveNormalisation() for more information.

Returns: a pointer to the object that represents the normalisation element (or a null value if not present). See Maintaining object references: two rules of thumb.

◆ getNormalisationSchemaType()

std::string getNormalisationSchemaType ( ) const

Obtain a symbolic name for the normalisation element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getNumberOfComponents()

int getNumberOfComponents ( ) const

Returns the number of nested components.

Returns: total number of nested components.

◆ getNumberOfExclusions()

int getNumberOfExclusions ( ) const

Returns the number of nested exclusion elements.

Exclude peptides from quantitation if they contain modifications from this group.

Returns: total number of nested exclusion elements.

◆ getNumberOfModificationGroups()

int getNumberOfModificationGroups ( ) const

Returns the number of nested modification groups.

Returns: total number of nested modification groups.

◆ getNumberOfReportRatios()

int getNumberOfReportRatios ( ) const

Returns the number of nested report_ratio elements.

Returns: total number of nested report_ratio elements.

◆ getNumberOfSeqs()

int getNumberOfSeqs ( ) const

Returns the number of nested seq elements.

Sequence qualifier in Mascot notation, e.g. *-TSL.

Returns: total number of nested seq elements.

◆ getOutliers()

const ms_quant_outliers * getOutliers ( ) const

Returns a pointer to the outliers element.

See haveOutliers() for more information.

Returns: a pointer to the object that represents theoutliers" element (or a null value if not present). See Maintaining object references: two rules of thumb.

◆ getOutliersSchemaType()

std::string getOutliersSchemaType ( ) const

Obtain a symbolic name for the outliers element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getProteinRatioType()

std::string getProteinRatioType ( ) const

Returns the value of the protein_ratio_type attribute.

Method of calculating the ratio for the protein from the individual peptide ratios.

Returns: protein ratio type

◆ getProteinRatioTypeSchemaType()

std::string getProteinRatioTypeSchemaType ( ) const

Obtain a symbolic name for the protein_ratio_type attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getProtocol()

const ms_quant_protocol * getProtocol ( ) const

Returns a pointer to the protocol element.

See haveProtocol() for more information.

Returns: a pointer to the object that represents the protocol element (or a null value if not present). See Maintaining object references: two rules of thumb.

◆ getProtocolSchemaType()

std::string getProtocolSchemaType ( ) const

Obtain a symbolic name for the protocol element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getProtScoreType()

std::string getProtScoreType ( ) const

Returns the value of the prot_score_type attribute.

Returns: either "standard" or "mudpit" type.

◆ getProtScoreTypeSchemaType()

std::string getProtScoreTypeSchemaType ( ) const

Obtain a symbolic name for the prot_score_type attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getQuality()

const ms_quant_quality * getQuality ( ) const

Returns a pointer to the quality element.

See haveQuality() for more information.

Returns: a pointer to the object that represents thequality" element (or a null value if not present). See Maintaining object references: two rules of thumb.

◆ getQualitySchemaType()

std::string getQualitySchemaType ( ) const

Obtain a symbolic name for the quality element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getReportDetailSchemaType()

std::string getReportDetailSchemaType ( ) const

Obtain a symbolic name for the report_detail attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getReportRatioByName()

const ms_quant_ratio * getReportRatioByName ( const char * name ) const

Returns a report_ratio element object by its name or a null value in case of not found.

Parameters

name	name of the `report_ratio` element to find.

Returns: a read-only pointer to a report_ratio element object. See Maintaining object references: two rules of thumb.

◆ getReportRatioByNumber()

const ms_quant_ratio * getReportRatioByNumber ( const int idx ) const

Returns a report_ratio element object by its number.

Parameters

idx	number of the `report_ratio` element from 0 to (getNumberOfReportRatios() - 1).

Returns: a read-only pointer to a report_ratio element object. See Maintaining object references: two rules of thumb.

◆ getReportRatioSchemaType()

std::string getReportRatioSchemaType ( ) const

Obtain a symbolic name for the report_ratio element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getRequireBoldRedSchemaType()

std::string getRequireBoldRedSchemaType ( ) const

Obtain a symbolic name for the require_bold_red attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getSchemaType()

std::string getSchemaType ( ) const

virtual

Returns name of the schema type that can be used to validate this element.

Additional information about the current object can be retrieved from the associated XML schema file. Every element in an XML document is defined with a named type, which you can use to find out what kind of limits (numerical or otherwise) are defined for values of that type.

See also: validateShallow(), validateDeep()

Returns: a symbolic fully qualified type name (for example, "mqm:nameType").

◆ getSeq()

std::string getSeq ( const int idx ) const

Returns a seq element object by its number.

Parameters

idx	number of the `seq` element from 0 to (getNumberOfSeqs() - 1).

Returns: a string copy of the seq element.

◆ getSeqSchemaType()

std::string getSeqSchemaType ( ) const

Obtain a symbolic name for the element's schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getShowSubSets()

std::string getShowSubSets ( ) const

Returns the value of the show_sub_sets attribute.

Returns: A floating point number (represented as a string) between 0 and 1 showing how many subset proteins to display. See also ms_mascotresults::setSubsetsThreshold().

◆ getShowSubSetsSchemaType()

std::string getShowSubSetsSchemaType ( ) const

Obtain a symbolic name for the show_sub_sets attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getSigThresholdValue()

std::string getSigThresholdValue ( ) const

Returns the value of the sig_threshold_value attribute.

Mascot score significance threshold as a probabliltiy, default 0.05.

Returns: significant threshold

◆ getSigThresholdValueSchemaType()

std::string getSigThresholdValueSchemaType ( ) const

Obtain a symbolic name for the sig_threshold_value attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ haveComp()

bool haveComp ( ) const

Indicates whether the comp element is present.

The comp element can be missing for the current method object. In order to be qualified as valid composition qualifier it must be at least 4 characters long. Therefore, an empty string returned by getComp() is not a valid value for the element. Always check whether the comp element is present in the document before retrieving its value.

Returns: TRUE if present and FALSE otherwise.

◆ haveConstrainSearch()

bool haveConstrainSearch ( ) const

Indicates whether the constrain_search attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveDescription()

bool haveDescription ( ) const

Indicates whether the description attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveIntegration()

bool haveIntegration ( ) const

Indicates whether the integration element is present.

The integration element describes method and parameters to be used to integrate precursor over time. If missing, no integration is performed.

Returns: TRUE if present and FALSE if missing.

◆ haveMinNumPeptides()

bool haveMinNumPeptides ( ) const

Indicates whether the min_num_peptides attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveName()

bool haveName ( ) const

Indicates whether the name attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveNormalisation()

bool haveNormalisation ( ) const

Indicates whether the normalisation element is present.

Method of normailising ratios for a complete data set. If missing, no normalisation is performed.

Returns: TRUE if present and FALSE otherwise.

◆ haveOutliers()

bool haveOutliers ( ) const

Indicates whether the outliers element is present.

Method and parameters to be used to remove outliers. If missing, no outlier removal is performed.

Returns: TRUE if present and FALSE otherwise.

◆ haveProteinRatioType()

bool haveProteinRatioType ( ) const

Indicates whether the protein_ratio_type attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveProtocol()

bool haveProtocol ( ) const

Indicates whether the protocol element is present.

The protocol element describes how the quantitative information is obtained.

Returns: TRUE if present and FALSE otherwise.

◆ haveProtScoreType()

bool haveProtScoreType ( ) const

Indicates whether the prot_score_type attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveQuality()

bool haveQuality ( ) const

Indicates whether the quality element is present.

This element specifies quality thresholds for selecting individual spectra or matches.

Returns: TRUE if present and FALSE otherwise.

◆ haveReportDetail()

bool haveReportDetail ( ) const

Indicates whether the report_detail attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveRequireBoldRed()

bool haveRequireBoldRed ( ) const

Indicates whether the require_bold_red attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveShowSubSets()

bool haveShowSubSets ( ) const

Indicates whether the show_sub_sets attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ haveSigThresholdValue()

bool haveSigThresholdValue ( ) const

Indicates whether the sig_threshold_value attribute is present.

Returns: TRUE if present and FALSE otherwise.

◆ isConstrainSearch()

bool isConstrainSearch ( ) const

Returns the value of the constrain_search attribute.

If any modification group specifies exclusive mode, then apply this constraint during the search so that only matches that can be used for quantitation will be returned.

Returns: true if constraint applies to the search, false otherwise

◆ isMethodCompatible()

int isMethodCompatible	(	const ms_quant_method &	other,
		std::string &	reasonStrRef
	)		const

Methods are compatible if the protocol and selected other values are identical.

Result files with 'compatible' quantitation methods can be combined. It is also possible to apply a modified method to an existing results file when creating an ms_ms2quantitation object as long as the methods are 'compatible'.

See ms_quant_method::METHOD_COMPATIBLE for a list of reasons why the methods may not be compatible.

See Multiple return values in Perl, Java, Python and C#.

Parameters

[in]	other	is the other method to compare with this one.
[out]	reasonStrRef	is set to a human readable string if the methods are not compatible.

Returns: ms_quant_method::COMPATIBLE if the quantitation methods are compatible otherwise returns one of the error codes.

◆ isReportDetail()

bool isReportDetail ( ) const

Returns the value of the report_detail attribute.

This attribute defines whether to display quantitation results at the peptide match level.

Returns: true if quantitation results are displayed, false otherwise

◆ isRequireBoldRed()

bool isRequireBoldRed ( ) const

Returns the value of the require_bold_red attribute.

Returns: TRUE if only show proteins that contain a least one "bold red" peptide match.

◆ operator=()

ms_quant_method & operator= ( const ms_quant_method & right )

C++ style assignment operator.

Parameters

right another instance of this class to copy the content from.

Returns: reference to the current object

◆ setComp()

void setComp ( const char * value )

Set a custom value for the comp element.

Parameters

value a new value for the element.

◆ setConstrainSearch()

void setConstrainSearch ( const bool value )

Set a custom value for the constrain_search attribute.

Parameters

value a new value for the attribute.

◆ setDescription()

void setDescription ( const char * value )

Set a custom value for the description attribute.

Parameters

value a new value for the attribute.

◆ setIntegration()

void setIntegration ( const ms_quant_integration * integration )

Supply custom content for the integration element.

Parameters

integration an object to copy the content from.

◆ setMinNumPeptides()

void setMinNumPeptides ( const int value )

Set a custom value for the min_num_peptides attribute.

Parameters

value a new value for the attribute.

◆ setName()

void setName ( const char * value )

Set a custom value for the name attribute.

Parameters

value a new value for the attribute.

Examples: config_quantitation.cpp.

◆ setNormalisation()

void setNormalisation ( const ms_quant_normalisation * normalisation )

Supply custom content for the normalisation element.

Parameters

normalisation an object to copy the content from.

◆ setOutliers()

void setOutliers ( const ms_quant_outliers * outliers )

Supply custom content for the outliers element.

Parameters

outliers an object to copy the content from.

◆ setProteinRatioType()

void setProteinRatioType ( const char * value )

Set a custom value for the protein_ratio_type attribute.

Parameters

value a new value for the attribute.

◆ setProtocol()

void setProtocol ( const ms_quant_protocol * protocol )

Supply custom content for the protocol element.

Parameters

protocol an object to copy the content from.

◆ setProtScoreType()

void setProtScoreType ( const char * value )

Set a custom value for the prot_score_type attribute.

Parameters

value a new value for the attribute.

◆ setQuality()

void setQuality ( const ms_quant_quality * quality )

Supply custom content for the quality element.

Parameters

quality an object to copy the content from.

◆ setReportDetail()

void setReportDetail ( const bool value )

Set a custom value for the report_detail attribute.

Parameters

value a new value for the attribute.

◆ setRequireBoldRed()

void setRequireBoldRed ( const bool value )

Set a custom value for the require_bold_red attribute.

Parameters

value a new value for the attribute.

◆ setShowSubSets()

void setShowSubSets ( const char * value )

Set a custom value for the show_sub_sets attribute.

Parameters

value a new value for the attribute.

◆ setSigThresholdValue()

void setSigThresholdValue ( const char * value )

Set a custom value for the sig_threshold_value attribute.

Parameters

value a new value for the attribute.

◆ updateComponentByName()

bool updateComponentByName	(	const char *	name,
		const ms_quant_component *	comp
	)

Update the information for a specific component refering to it by its unique name.

Parameters

name	name of the component for updating.
comp	an object to copy the content from.

Returns: TRUE if the component has been found and successfully updated and FALSE otherwise.

◆ updateComponentByNumber()

bool updateComponentByNumber	(	const int	idx,
		const ms_quant_component *	comp
	)

Update the information for a specific component refering to it by its index.

Parameters

idx	number of the component for updating from 0 to (getNumberOfComponents() - 1).
comp	an object to copy the content from.

Returns: TRUE if the component has been found and successfully updated and FALSE otherwise.

◆ updateExclusion()

bool updateExclusion	(	const int	idx,
		const char *	exclusion
	)

Update the information for a specific exclusion element refering to it by its index.

Parameters

idx	number of the `exclusion` element for updating from 0 to (getNumberOfExclusions() - 1).
exclusion	new string value for the element.

Returns: TRUE if the exclusion element has been successfully updated and FALSE otherwise.

◆ updateModificationGroupByName()

bool updateModificationGroupByName	(	const char *	name,
		const ms_quant_modgroup *	modgroup
	)

Update the information for a specific modification group refering to it by its unique name.

Parameters

name	name of the modification group for updating.
modgroup	an object to copy the content from.

Returns: TRUE if the modification group has been found and successfully updated and FALSE otherwise.

◆ updateModificationGroupByNumber()

bool updateModificationGroupByNumber	(	const int	idx,
		const ms_quant_modgroup *	modgroup
	)

Update the information for a specific modification group refering to it by its index.

Parameters

idx	number of the modification group for updating from 0 to (getNumberOfModificationGroups() - 1).
modgroup	an object to copy the content from.

Returns: TRUE if the modification group has been found and successfully updated and FALSE otherwise.

◆ updateReportRatioByName()

bool updateReportRatioByName	(	const char *	name,
		const ms_quant_ratio *	ratio
	)

Update the information for a specific report_ratio element refering to it by its unique name.

Parameters

name	name of the `report_ratio` element for updating.
ratio	an object to copy the content from.

Returns: TRUE if the report_ratio element has been found and successfully updated and FALSE otherwise.

◆ updateReportRatioByNumber()

bool updateReportRatioByNumber	(	const int	idx,
		const ms_quant_ratio *	ratio
	)

Update the information for a specific report_ratio element refering to it by its index.

Parameters

idx	number of the `report_ratio` element for updating from 0 to (getNumberOfReportRatios() - 1).
ratio	an object to copy the content from.

Returns: TRUE if the report_ratio element has been found and successfully updated and FALSE otherwise.

◆ updateSeq()

bool updateSeq	(	const int	idx,
		const char *	seq
	)

Update the information for a specific seq element refering to it by its index.

Parameters

idx	number of the `seq` element for updating from 0 to (getNumberOfSeqs() - 1).
seq	a new string value for the element.

Returns: TRUE if the seq element has been successfully updated and FALSE otherwise.

◆ validateDeep()

std::string validateDeep ( const ms_xml_schema * pSchemaFileObj ) const

virtual

Performs validation of all child elements in addition to 'shallow' validation.

The current object can be checked against an XML schema. When using this method all possible checks are performed. However, this is not a substitute for the schema: some schema-defined constraint are not applied (unique fields, foreign keys etc.).

In order to make sure that current object is free from all syntax errors validate it as a part of the whole document.

See also: validateShallow(), getSchemaType()

Parameters

pSchemaFileObj a valid schema object instance to validate against.

Returns: user-friendly description of any errors found during validation or an empty string if no errors detected.

Examples: config_quantitation.cpp.

◆ validateShallow()

std::string validateShallow ( const ms_xml_schema * pSchemaFileObj ) const

virtual

Performs simple validation of the top-level elements only.

The current object can be checked against some basic constraints in a schema without looking at children element types. When using this method only the current object and children derived from standard types (for example, restrictions with enumerations) are checked. For more thorough validation, use validateDeep().

See also: getSchemaType()

Parameters

pSchemaFileObj a valid schema object instance to validate against.

Returns: user-friendly description of any errors found during validation or an empty string if no errors detected.

Examples: config_quantitation.cpp.

The documentation for this class was generated from the following files:

ms_quant_method.hpp
ms_quant_method.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ METHOD_COMPATIBLE

Constructor & Destructor Documentation

◆ ms_quant_method() [1/2]

◆ ms_quant_method() [2/2]

Member Function Documentation

◆ appendComponent()

◆ appendExclusion()

◆ appendModificationGroup()

◆ appendReportRatio()

◆ appendSeq()

◆ copyFrom()

◆ defaultValues()

◆ deleteComponentByName()

◆ deleteComponentByNumber()

◆ deleteExclusion()

◆ deleteModificationGroupByName()

◆ deleteModificationGroupByNumber()

◆ deleteReportRatioByName()

◆ deleteReportRatioByNumber()

◆ deleteSeq()

◆ dropComp()

◆ dropConstrainSearch()

◆ dropDescription()

◆ dropIntegration()

◆ dropMinNumPeptides()

◆ dropName()

◆ dropNormalisation()

◆ dropOutliers()

◆ dropProteinRatioType()

◆ dropProtocol()

◆ dropProtScoreType()

◆ dropQuality()

◆ dropReportDetail()

◆ dropRequireBoldRed()

◆ dropShowSubSets()

◆ dropSigThresholdValue()

◆ getComp()

◆ getComponentByName()

◆ getComponentByNumber()

◆ getComponentSchemaType()

◆ getCompSchemaType()

◆ getConstrainSearchSchemaType()

◆ getDescription()

◆ getDescriptionSchemaType()

◆ getExclusion()

◆ getExclusionSchemaType()

◆ getIntegration()

◆ getIntegrationSchemaType()

◆ getLocalModifications()

◆ getMinNumPeptides()

◆ getMinNumPeptidesSchemaType()

◆ getModificationGroupByName()

◆ getModificationGroupByNumber()

◆ getModificationGroupSchemaType()

◆ getName()

◆ getNameSchemaType()

◆ getNormalisation()

◆ getNormalisationSchemaType()

◆ getNumberOfComponents()

◆ getNumberOfExclusions()

◆ getNumberOfModificationGroups()

◆ getNumberOfReportRatios()

◆ getNumberOfSeqs()

◆ getOutliers()

◆ getOutliersSchemaType()

◆ getProteinRatioType()

◆ getProteinRatioTypeSchemaType()

◆ getProtocol()

◆ getProtocolSchemaType()

◆ getProtScoreType()

◆ getProtScoreTypeSchemaType()

◆ getQuality()

◆ getQualitySchemaType()

◆ getReportDetailSchemaType()

◆ getReportRatioByName()

◆ getReportRatioByNumber()