Matrix Science header
Public Types | Public Member Functions

ms_quant_method Class Reference
[Mascot configuration files module]

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

#include <ms_quant_method.hpp>

List of all members.

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_componentgetComponentByName (const char *name) const
 Returns a component object by its name or a null value in case of not found.
const ms_quant_componentgetComponentByNumber (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_integrationgetIntegration () 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_modgroupgetModificationGroupByName (const char *name) const
 Returns a modification group object by its name or a null value in case of not found.
const ms_quant_modgroupgetModificationGroupByNumber (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_normalisationgetNormalisation () 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_outliersgetOutliers () 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_protocolgetProtocol () 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_qualitygetQuality () 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_ratiogetReportRatioByName (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_ratiogetReportRatioByNumber (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_methodoperator= (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

Enum used by isMethodCompatible()

See Using enumerated values 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

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_method ( const ms_quant_method src )

Copying constructor.

Parameters:
srcanother instance of this class to copy the content from.

Member Function Documentation

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:
iteman instance of component object to copy content from.
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:
exclusionan string value for the element.
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:
iteman instance of modification group object to copy content from.
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:
iteman instance of report_ratio element object to copy content from.
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:
seqan string value for the element.
void copyFrom ( const ms_quant_method right )

Copies all content from another instance.

Parameters:
rightanother instance of this class to copy the content from.
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.

bool deleteComponentByName ( const char *  name )

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

Parameters:
namename of the component for deletion.
Returns:
TRUE if the component has been found and successfully deleted and FALSE otherwise.
bool deleteComponentByNumber ( const int  idx )

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

Parameters:
idxnumber of the component for deletion from 0 to (getNumberOfComponents() - 1).
Returns:
TRUE if the component has been found and successfully deleted and FALSE otherwise.
bool deleteExclusion ( const int  idx )

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

Parameters:
idxnumber 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.
bool deleteModificationGroupByName ( const char *  name )

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

Parameters:
namename of the modification group for deletion.
Returns:
TRUE if the modification group has been found and successfully deleted and FALSE otherwise.
bool deleteModificationGroupByNumber ( const int  idx )

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

Parameters:
idxnumber 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.
bool deleteReportRatioByName ( const char *  name )

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

Parameters:
namename of the report_ratio element for deletion.
Returns:
TRUE if the report_ratio element has been found and successfully deleted and FALSE otherwise.
bool deleteReportRatioByNumber ( const int  idx )

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

Parameters:
idxnumber 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.
bool deleteSeq ( const int  idx )

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

Parameters:
idxnumber 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.
void dropComp (  )

Delete the comp element.

Disables the element until it is re-set.

void dropConstrainSearch (  )

Delete the constrain_search attribute.

Disables the attribute until it is re-set.

void dropDescription (  )

Delete the description attribute.

Disables the attribute until it is re-set.

void dropIntegration (  )

Delete the integration element.

Deletes the element until it is re-set.

void dropMinNumPeptides (  )

Delete the min_num_peptides attribute.

Disables the attribute until it is re-set.

void dropName (  )

Delete the name attribute.

Disables the attribute until it is re-set.

void dropNormalisation (  )

Delete the normalisation element.

Deletes the element until it is re-set.

void dropOutliers (  )

Delete the outliers element.

Deletes the element until it is re-set.

void dropProteinRatioType (  )

Delete the protein_ratio_type attribute.

Disables the attribute until it is re-set.

void dropProtocol (  )

Delete the protocol element.

Deletes the element until it is re-set.

void dropProtScoreType (  )

Delete the prot_score_type attribute.

Disables the attribute until it is re-set.

void dropQuality (  )

Delete the quality element.

Deletes the element until it is re-set.

void dropReportDetail (  )

Delete the report_detail attribute.

Disables the attribute until it is re-set.

void dropRequireBoldRed (  )

Delete the require_bold_red attribute.

Disables the attribute until it is re-set.

void dropShowSubSets (  )

Delete the show_sub_sets attribute.

Disables the attribute until it is re-set.

void dropSigThresholdValue (  )

Delete the sig_threshold_value attribute.

Disables the attribute until it is re-set.

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].
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:
namename of the component to find.
Returns:
a read-only pointer to a component object. See Maintaining object references: two rules of thumb.
const ms_quant_component * getComponentByNumber ( const int  idx ) const

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

Parameters:
idxnumber 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.
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.
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.
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.
std::string getDescription (  ) const

Returns the value of the description attribute.

Returns:
free text string for description.
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.
std::string getExclusion ( const int  idx ) const

Returns a exclusion element object by its number.

Parameters:
idxnumber of the exclusion element from 0 to (getNumberOfExclusions() - 1).
Returns:
a string copy of the exclusion element.
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.
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.
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.
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:
localDefVectorvector to fill with ms_quant_localdef* object pointers.
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
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.
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:
namename of the modification group to find.
Returns:
a read-only pointer to a modification group object. See Maintaining object references: two rules of thumb.
const ms_quant_modgroup * getModificationGroupByNumber ( const int  idx ) const

Returns a modification group object by its number.

Parameters:
idxnumber 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.
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.
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.
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.
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.
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.
int getNumberOfComponents (  ) const

Returns the number of nested components.

Returns:
total number of nested components.
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.
int getNumberOfModificationGroups (  ) const

Returns the number of nested modification groups.

Returns:
total number of nested modification groups.
int getNumberOfReportRatios (  ) const

Returns the number of nested report_ratio elements.

Returns:
total number of nested report_ratio elements.
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.
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.
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.
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
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.
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.
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.
std::string getProtScoreType (  ) const

Returns the value of the prot_score_type attribute.

Returns:
either "standard" or "mudpit" type.
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.
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.
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.
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.
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:
namename 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.
const ms_quant_ratio * getReportRatioByNumber ( const int  idx ) const

Returns a report_ratio element object by its number.

Parameters:
idxnumber 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.
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.
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.
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").
std::string getSeq ( const int  idx ) const

Returns a seq element object by its number.

Parameters:
idxnumber of the seq element from 0 to (getNumberOfSeqs() - 1).
Returns:
a string copy of the seq element.
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.
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().
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.
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
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.
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.
bool haveConstrainSearch (  ) const

Indicates whether the constrain_search attribute is present.

Returns:
TRUE if present and FALSE otherwise.
bool haveDescription (  ) const

Indicates whether the description attribute is present.

Returns:
TRUE if present and FALSE otherwise.
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.
bool haveMinNumPeptides (  ) const

Indicates whether the min_num_peptides attribute is present.

Returns:
TRUE if present and FALSE otherwise.
bool haveName (  ) const

Indicates whether the name attribute is present.

Returns:
TRUE if present and FALSE otherwise.
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.
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.
bool haveProteinRatioType (  ) const

Indicates whether the protein_ratio_type attribute is present.

Returns:
TRUE if present and FALSE otherwise.
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.
bool haveProtScoreType (  ) const

Indicates whether the prot_score_type attribute is present.

Returns:
TRUE if present and FALSE otherwise.
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.
bool haveReportDetail (  ) const

Indicates whether the report_detail attribute is present.

Returns:
TRUE if present and FALSE otherwise.
bool haveRequireBoldRed (  ) const

Indicates whether the require_bold_red attribute is present.

Returns:
TRUE if present and FALSE otherwise.
bool haveShowSubSets (  ) const

Indicates whether the show_sub_sets attribute is present.

Returns:
TRUE if present and FALSE otherwise.
bool haveSigThresholdValue (  ) const

Indicates whether the sig_threshold_value attribute is present.

Returns:
TRUE if present and FALSE otherwise.
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
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]otheris the other method to compare with this one.
[out]reasonStrRefis 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.
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
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.
ms_quant_method & operator= ( const ms_quant_method right )

C++ style assignment operator.

Parameters:
rightanother instance of this class to copy the content from.
Returns:
reference to the current object
void setComp ( const char *  value )

Set a custom value for the comp element.

Parameters:
valuea new value for the element.
void setConstrainSearch ( const bool  value )

Set a custom value for the constrain_search attribute.

Parameters:
valuea new value for the attribute.
void setDescription ( const char *  value )

Set a custom value for the description attribute.

Parameters:
valuea new value for the attribute.
void setIntegration ( const ms_quant_integration integration )

Supply custom content for the integration element.

Parameters:
integrationan object to copy the content from.
void setMinNumPeptides ( const int  value )

Set a custom value for the min_num_peptides attribute.

Parameters:
valuea new value for the attribute.
void setName ( const char *  value )

Set a custom value for the name attribute.

Parameters:
valuea new value for the attribute.
Examples:
config_quantitation.cpp.
void setNormalisation ( const ms_quant_normalisation normalisation )

Supply custom content for the normalisation element.

Parameters:
normalisationan object to copy the content from.
void setOutliers ( const ms_quant_outliers outliers )

Supply custom content for the outliers element.

Parameters:
outliersan object to copy the content from.
void setProteinRatioType ( const char *  value )

Set a custom value for the protein_ratio_type attribute.

Parameters:
valuea new value for the attribute.
void setProtocol ( const ms_quant_protocol protocol )

Supply custom content for the protocol element.

Parameters:
protocolan object to copy the content from.
void setProtScoreType ( const char *  value )

Set a custom value for the prot_score_type attribute.

Parameters:
valuea new value for the attribute.
void setQuality ( const ms_quant_quality quality )

Supply custom content for the quality element.

Parameters:
qualityan object to copy the content from.
void setReportDetail ( const bool  value )

Set a custom value for the report_detail attribute.

Parameters:
valuea new value for the attribute.
void setRequireBoldRed ( const bool  value )

Set a custom value for the require_bold_red attribute.

Parameters:
valuea new value for the attribute.
void setShowSubSets ( const char *  value )

Set a custom value for the show_sub_sets attribute.

Parameters:
valuea new value for the attribute.
void setSigThresholdValue ( const char *  value )

Set a custom value for the sig_threshold_value attribute.

Parameters:
valuea new value for the 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.

Parameters:
namename of the component for updating.
compan object to copy the content from.
Returns:
TRUE if the component has been found and successfully updated and FALSE otherwise.
bool updateComponentByNumber ( const int  idx,
const ms_quant_component comp 
)

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

Parameters:
idxnumber of the component for updating from 0 to (getNumberOfComponents() - 1).
compan object to copy the content from.
Returns:
TRUE if the component has been found and successfully updated and FALSE otherwise.
bool updateExclusion ( const int  idx,
const char *  exclusion 
)

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

Parameters:
idxnumber of the exclusion element for updating from 0 to (getNumberOfExclusions() - 1).
exclusionnew string value for the element.
Returns:
TRUE if the exclusion element has been successfully updated and FALSE otherwise.
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:
namename of the modification group for updating.
modgroupan object to copy the content from.
Returns:
TRUE if the modification group has been found and successfully updated and FALSE otherwise.
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:
idxnumber of the modification group for updating from 0 to (getNumberOfModificationGroups() - 1).
modgroupan object to copy the content from.
Returns:
TRUE if the modification group has been found and successfully updated and FALSE otherwise.
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:
namename of the report_ratio element for updating.
ratioan object to copy the content from.
Returns:
TRUE if the report_ratio element has been found and successfully updated and FALSE otherwise.
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:
idxnumber of the report_ratio element for updating from 0 to (getNumberOfReportRatios() - 1).
ratioan object to copy the content from.
Returns:
TRUE if the report_ratio element has been found and successfully updated and FALSE otherwise.
bool updateSeq ( const int  idx,
const char *  seq 
)

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

Parameters:
idxnumber of the seq element for updating from 0 to (getNumberOfSeqs() - 1).
seqa new string value for the element.
Returns:
TRUE if the seq element has been successfully updated and FALSE otherwise.
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:
pSchemaFileObja 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.
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:
pSchemaFileObja 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:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:54