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Public Member Functions

ms_umod_composition Class Reference
[Mascot configuration files module]

Represents the composition type in unimod.xml. More...

#include <ms_umod_composition.hpp>

Inheritance diagram for ms_umod_composition:
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List of all members.

Public Member Functions

 ms_umod_composition ()
 Default constructor.
 ms_umod_composition (const ms_umod_composition &src)
 Copying constructor.
 ms_umod_composition (const ms_quant_composition &src, const ms_umod_configfile &umodFile)
 Copying constructor.
virtual ~ms_umod_composition ()
 Destructor.
void appendElemRef (const ms_umod_elemref *elemref)
 Adds a new element reference object at the end of the list.
void clearElemRefs ()
 Deletes all element reference objects from the list.
void copyFrom (const ms_quant_composition *right, const ms_umod_configfile &umodFile)
 Copies all content from another object.
void copyFrom (const ms_umod_composition *right)
 Copies all content from another instance.
void defaultValues ()
 Call this member if you want to start again.
bool deleteElemRef (const int idx)
 Remove an element reference object from the list in memory.
void dropAvgeMass ()
 Delete the avge_mass attribute.
void dropCompositionString ()
 Delete the composition attribute.
void dropMonoMass ()
 Delete the mono_mass attribute.
double getAvgeMass () const
 Returns the value of the avge_mass attribute.
std::string getAvgeMassSchemaType () const
 Obtain a symbolic name for the avge_mass attribute schema type.
std::string getCompositionString () const
 Returns the value of the composition attribute.
std::string getCompositionStringSchemaType () const
 Obtain a symbolic name for the composition attribute schema type.
const ms_umod_elemrefgetElemRef (const int idx) const
 Returns a read-only pointer to an element reference object by its number.
std::string getElemRefSchemaType () const
 Obtain a symbolic name for the element's schema type.
double getMonoMass () const
 Returns the value of the mono_mass attribute.
std::string getMonoMassSchemaType () const
 Obtain a symbolic name for the mono_mass attribute schema type.
int getNumberOfElemRefs () const
 Returns the number of element reference objects currently held in memory.
virtual std::string getSchemaType () const
 Returns name of the schema type that can be used to validate this element.
bool haveAvgeMass () const
 Indicates presence of the avge_mass attribute.
bool haveCompositionString () const
 Indicates presence of the composition attribute.
bool haveMonoMass () const
 Indicates presence of the mono_mass attribute.
bool isSameAs (const ms_umod_composition &right) const
 Returns true if instances contain the same information.
ms_umod_compositionoperator= (const ms_umod_composition &right)
 C++ style assignment operator.
void setAvgeMass (const double value)
 Set a custom value for the avge_mass attribute.
void setCompositionString (const char *value)
 Set a custom value for the composition attribute.
void setMonoMass (const double value)
 Set a custom value for the mono_mass attribute.
bool updateElemRef (const int idx, const ms_umod_elemref *elemref)
 Update the information for a particular element reference object.
void updateMasses (const ms_umod_configfile &umodFile, const ms_quant_component &quantComp)
 Recalculates all deltas with isotope substitution according to selected component in quantification.xml.
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

Represents the composition type in unimod.xml.

This type is used for modification delta and ignore elements in unimod.xml.


Constructor & Destructor Documentation

Default constructor.

Assigns reasonable default values to all internal members.

Copying constructor.

Parameters:
srcanother instance of this class to copy the content from.
ms_umod_composition ( const ms_quant_composition src,
const ms_umod_configfile umodFile 
)

Copying constructor.

Parameters:
srcanother object to copy the content from.
umodFilean instance of a Unimod file object to extract element masses.

Member Function Documentation

void appendElemRef ( const ms_umod_elemref elemref )

Adds a new element reference object at the end of the list.

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

Parameters:
elemrefan instance of element reference object to copy the content from.
void copyFrom ( const ms_umod_composition right )

Copies all content from another instance.

Parameters:
rightanother instance of this class to copy the content from.
void copyFrom ( const ms_quant_composition right,
const ms_umod_configfile umodFile 
)

Copies all content from another object.

Parameters:
rightanother object to copy the content from.
umodFilea Unimod file object to obtain element masses from.
void defaultValues (  )

Call this member if you want to start again.

This will reset all internal values to their defaults, as if the object had been freshly created with the default constructor.

Reimplemented in ms_umod_neutralloss.

bool deleteElemRef ( const int  idx )

Remove an element reference object from the list in memory.

Parameters:
idxnumber of the element reference for deletion from 0 to (getNumberOfElemRefs() - 1).
Returns:
TRUE if the object has been found and successfully deleted and FALSE otherwise.
void dropAvgeMass (  )

Delete the avge_mass attribute.

Deletes the attribute until is re-set.

void dropCompositionString (  )

Delete the composition attribute.

Deletes the attribute until it is re-set.

void dropMonoMass (  )

Delete the mono_mass attribute.

Deletes the attribute until is re-set.

double getAvgeMass (  ) const

Returns the value of the avge_mass attribute.

Average mass for the object.

Returns:
current value of the attribute.
std::string getAvgeMassSchemaType (  ) const

Obtain a symbolic name for the avge_mass 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 getCompositionString (  ) const

Returns the value of the composition attribute.

A composition string for the object.

Returns:
current value of the attribute.
std::string getCompositionStringSchemaType (  ) const

Obtain a symbolic name for the composition 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_umod_elemref * getElemRef ( const int  idx ) const

Returns a read-only pointer to an element reference object by its number.

Retrieves an element reference object from the list by its number.

Parameters:
idxnumber of the reference from 0 to (getNumberOfElemRefs() - 1).
Returns:
a read-only pointer to the retrieved object. See Maintaining object references: two rules of thumb.
std::string getElemRefSchemaType (  ) 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.
double getMonoMass (  ) const

Returns the value of the mono_mass attribute.

Monoisotopic mass for the object.

Returns:
current value of the attribute.
std::string getMonoMassSchemaType (  ) const

Obtain a symbolic name for the mono_mass 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.
int getNumberOfElemRefs (  ) const

Returns the number of element reference objects currently held in memory.

Returns:
total number of chemical element references in the composition object.
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, "umod:nameType").

Reimplemented in ms_umod_neutralloss.

bool haveAvgeMass (  ) const

Indicates presence of the avge_mass attribute.

Returns:
TRUE if the attribute is present and FALSE otherwise.
bool haveCompositionString (  ) const

Indicates presence of the composition attribute.

Returns:
TRUE if the attribute is present and FALSE otherwise.
bool haveMonoMass (  ) const

Indicates presence of the mono_mass attribute.

Returns:
TRUE if the attribute is present and FALSE otherwise.
bool isSameAs ( const ms_umod_composition right ) const

Returns true if instances contain the same information.

Compares the element symbols and number of symbols that make up the composition regardless of storage order. Element symbols may be specified in the composition but have a count of zero and so do not affect the total mass values.

Parameters:
rightanother instance of this class to compare.
Returns:
true if the two compositions are equivalent.
ms_umod_composition & operator= ( const ms_umod_composition right )

C++ style assignment operator.

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

Set a custom value for the avge_mass attribute.

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

Set a custom value for the composition attribute.

Parameters:
valuea new value for the attribute.
void setMonoMass ( const double  value )

Set a custom value for the mono_mass attribute.

Parameters:
valuea new value for the attribute.
bool updateElemRef ( const int  idx,
const ms_umod_elemref elemref 
)

Update the information for a particular element reference object.

Parameters:
idxnumber of the element reference for updating from 0 to (getNumberOfElemRefs() - 1).
elemrefan object to copy the content from.
Returns:
TRUE if the element reference has been found and successfully updated and FALSE otherwise.
void updateMasses ( const ms_umod_configfile umodFile,
const ms_quant_component quantComp 
)

Recalculates all deltas with isotope substitution according to selected component in quantification.xml.

The method updates masses according to the selected isotope substitution. Masses are recalculated only in the current modification object, not in the whole Unimod file object umodFile. The Unimod file object is used only to retrieve masses of elements and their isotopes.

Parameters:
umodFileUnimod file object.
quantCompcomponent object from quantitation.xml.
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.

Reimplemented in ms_umod_neutralloss.

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.

Reimplemented in ms_umod_neutralloss.


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