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Matrix Science Mascot Parser toolkit
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Matrix Science Mascot Parser toolkit
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Linkers element in crosslinking.xml
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#include <ms_crosslinking_linkers.hpp>
Inherits ms_xml_IValidatable.
Public Member Functions | |
| ms_crosslinking_linkers () | |
| Default constructor. | |
| ms_crosslinking_linkers (const ms_crosslinking_linkers &src) | |
| Copying constructor. | |
| virtual | ~ms_crosslinking_linkers () |
| Destructor. | |
| void | appendLinker (const ms_crosslinking_linker *item) |
| Adds a new linker code at the end of the list. | |
| void | clearLinkers () |
| Deletes all linker codes from the list. | |
| void | copyFrom (const ms_crosslinking_linkers *right) |
| Copies all content from another instance. | |
| void | defaultValues () |
| Call this member if you want to start again. | |
| bool | deleteLinkerByNumber (const int idx) |
| Remove a linker code from the list in memory by its index. | |
| const ms_crosslinking_linker * | getLinkerByNumber (const int idx) const |
| Returns a linker code object by its number. | |
| std::string | getLinkerSchemaType () const |
| Obtain a symbolic name for the linker element schema type. | |
| int | getNumberOfLinkers () const |
| Returns the number of linker. | |
| virtual std::string | getSchemaType () const |
| Returns name of the schema type that can be used to validate this element. | |
| ms_crosslinking_linkers & | operator= (const ms_crosslinking_linkers &right) |
| C++ style assignment operator. | |
| bool | updateLinkerByNumber (const int idx, const ms_crosslinking_linker *linker) |
| Update the information for a specific linker code 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. | |
Linkers element in crosslinking.xml
The linkers element groups together specificities of a single linker.
In Mascot 2.7, the restrictions are:
For example, it is possible to specify Xlink:DSS (K) and Xlink:DSS (Protein N-term) for searching, as it is a single linker with two specificities. It is not possible to select two different linkers, like Xlink:DSS and Xlink:DSSO.
Default constructor.
Assigns reasonable default values to all internal members.
| ms_crosslinking_linkers | ( | const ms_crosslinking_linkers & | src | ) |
Copying constructor.
| src | another instance of this class to copy the content from. |
| void appendLinker | ( | const ms_crosslinking_linker * | item | ) |
Adds a new linker code at the end of the list.
Creates a new linker code object, copies all content from the object supplied as a parameter and adds it at the end of the methods list.
| item | an instance of a linker object to copy content from. |
| void copyFrom | ( | const ms_crosslinking_linkers * | right | ) |
Copies all content from another instance.
| right | another 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 deleteLinkerByNumber | ( | const int | idx | ) |
Remove a linker code from the list in memory by its index.
| idx | number of the linker code for deletion from 0 to (getNumberOfLinkers() - 1). |
| const ms_crosslinking_linker * getLinkerByNumber | ( | const int | idx | ) | const |
Returns a linker code object by its number.
| idx | number of the linker code from 0 to (getNumberOfLinkers() - 1). |
| std::string getLinkerSchemaType | ( | ) | const |
Obtain a symbolic name for the linker element schema type.
The obtained type name can be used to get a corresponding type description object from ms_xml_schema.
| int getNumberOfLinkers | ( | ) | const |
Returns the number of linker.
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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.
| ms_crosslinking_linkers & operator= | ( | const ms_crosslinking_linkers & | right | ) |
C++ style assignment operator.
| right | another instance of this class to copy the content from. |
| bool updateLinkerByNumber | ( | const int | idx, |
| const ms_crosslinking_linker * | linker | ||
| ) |
Update the information for a specific linker code refering to it by its index.
| idx | number of the linker code for updating from 0 to (getNumberOfLinkers() - 1). |
| linker | an object to copy the content from. |
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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.
| pSchemaFileObj | a valid schema object instance to validate against. |
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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().
| pSchemaFileObj | a valid schema object instance to validate against. |
1.9.6