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Public Member Functions

ms_umod_aminoacid Class Reference
[Mascot configuration files module]

Represents an "amino acid" object in unimod.xml. More...

#include <ms_umod_aminoacid.hpp>

List of all members.

Public Member Functions

 ms_umod_aminoacid ()
 Default constructor.
 ms_umod_aminoacid (const ms_umod_aminoacid &src)
 Copying constructor.
virtual ~ms_umod_aminoacid ()
 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_umod_aminoacid *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 dropFullName ()
 Delete the full_name attribute.
void dropMonoMass ()
 Delete the mono_mass attribute.
void dropThreeLetter ()
 Delete the three_letter attribute.
void dropTitle ()
 Delete the title 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.
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.
std::string getFullName () const
 Returns the value of the full_name attribute.
std::string getFullNameSchemaType () const
 Obtain a symbolic name for the full_name attribute 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 a 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.
std::string getThreeLetter () const
 Returns the value of the three_letter attribute.
std::string getThreeLetterSchemaType () const
 Obtain a symbolic name for the three_letter attribute schema type.
std::string getTitle () const
 Returns the value of the title attribute.
std::string getTitleSchemaType () const
 Obtain a symbolic name for the title attribute schema type.
bool haveAvgeMass () const
 Indicates presence of the avge_mass attribute.
bool haveFullName () const
 Indicates presence of the full_name attribute.
bool haveMonoMass () const
 Indicates presence of the mono_mass attribute.
bool haveThreeLetter () const
 Indicates presence of the three_letter attribute.
bool haveTitle () const
 Indicates presence of the title attribute.
ms_umod_aminoacidoperator= (const ms_umod_aminoacid &right)
 C++ style assignment operator.
void setAvgeMass (const double value)
 Set a custom value for the avge_mass attribute.
void setFullName (const char *value)
 Set a custom value for the full_name attribute.
void setMonoMass (const double value)
 Set a custom value for the mono_mass attribute.
void setThreeLetter (const char *value)
 Set a custom value for the three_letter attribute.
void setTitle (const char *value)
 Set a custom value for the title attribute.
bool updateElemRef (const int idx, const ms_umod_elemref *elemref)
 Update the information for a particular element reference object.
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 an "amino acid" object 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.

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 clearElemRefs (  )

Deletes all element reference objects from the list.

Deletes all element references from the list

void copyFrom ( const ms_umod_aminoacid 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 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 dropFullName (  )

Delete the full_name attribute.

Deletes the attribute until it is re-set.

void dropMonoMass (  )

Delete the mono_mass attribute.

Deletes the attribute until is re-set.

void dropThreeLetter (  )

Delete the three_letter attribute.

Deletes the attribute until it is re-set.

void dropTitle (  )

Delete the title attribute.

Deletes the attribute until it is re-set.

double getAvgeMass (  ) const

Returns the value of the avge_mass attribute.

Average mass for the amino acid.

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.
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.
std::string getFullName (  ) const

Returns the value of the full_name attribute.

A full name for the amino acid.

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

Obtain a symbolic name for the full_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.
double getMonoMass (  ) const

Returns the value of the mono_mass attribute.

Monoisotopic mass for the amino acid.

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 a number of element reference objects currently held in memory.

Returns:
total number of chemical element references in the modification 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").
std::string getThreeLetter (  ) const

Returns the value of the three_letter attribute.

A three-letter name for the amino acid.

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

Obtain a symbolic name for the three_letter 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 getTitle (  ) const

Returns the value of the title attribute.

A unique name for the amino acid.

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

Obtain a symbolic name for the title 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 haveAvgeMass (  ) const

Indicates presence of the avge_mass attribute.

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

Indicates presence of the full_name 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 haveThreeLetter (  ) const

Indicates presence of the three_letter attribute.

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

Indicates presence of the title attribute.

Returns:
TRUE if the attribute is present and FALSE otherwise.
ms_umod_aminoacid & operator= ( const ms_umod_aminoacid 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 setFullName ( const char *  value )

Set a custom value for the full_name 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.
void setThreeLetter ( const char *  value )

Set a custom value for the three_letter attribute.

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

Set a custom value for the title 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.
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.
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.

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