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Sourcecode: massxpert version File versions

massXpert::CleaveSpec Class Reference

#include <cleaveSpec.hpp>

Inheritance diagram for massXpert::CleaveSpec:


List of all members.

Detailed Description

The CleaveSpec class provides a cleavage specification.

Cleavage specifications determine the specificity of cleavage in a polymer seuqence using a simple syntax. For example, trypsin is able to cleave after lysyl and arginyl residues. Its cleavage pattern is thus "Lys/;Arg/;-Lys/Pro". Note that a provision can be made: if a lysyl residue is followed by a prolyl residue, then it is not cleaved by trypsin.

A cleavage specification might not be enough information to determine the manner in which a polymer is cleaved. Cleavage rules might be required to refine the specification. A cleavage specification might hold as many cleavage rules as required.

Definition at line 68 of file cleaveSpec.hpp.

Public Member Functions

 CleaveSpec (const CleaveSpec &)
 Constructs a copy of other.
 CleaveSpec (const PolChemDef *, QString, QString=QString())
 Constructs a cleavage specification.
virtual PolChemDefEntityclone () const
 Creates a new polymer chemistry definition entity.
virtual void clone (PolChemDefEntity *) const
 Modifies other to be identical to this.
void clone (CleaveSpec *) const
 Modifies other to be identical to this.
QString * formatXmlClsElement (int, const QString &=QString(" "))
 Formats a string suitable to use as an XML element.
virtual void mold (const PolChemDefEntity &)
 Modifies this to be identical to other.
void mold (const CleaveSpec &)
 Modifies this to be identical to other.
QList< CleaveMotif * > * motifList ()
 Returns the list of motifs.
QString name () const
 Returns the name.
virtual bool operator!= (const PolChemDefEntity &) const
 Tests inequality.
CleaveSpecoperator= (const CleaveSpec &)
 Assigns other to this cleavage specification.
virtual bool operator== (const PolChemDefEntity &) const
 Tests equality.
bool parse ()
 Parses the cleavage specification.
const QString & pattern ()
 Returns the pattern.
const PolChemDefpolChemDef () const
 Returns the polymer chemistry definition.
bool renderXmlClsElement (const QDomElement &, int)
 Parses a cleavage specification XML element.
QList< CleaveRule * > * ruleList ()
 Returns the list of cleavage rules.
void setName (const QString &)
 Sets the name.
void setPattern (const QString &)
 Sets the pattern.
void setPolChemDef (PolChemDef *)
virtual bool validate () const
bool validate ()
 Validates the cleavage specification.
 ~CleaveSpec ()
 Destroys the cleavage specification.

Static Public Member Functions

static int isNameInList (const QString &, const QList< CleaveSpec * > &, CleaveSpec *other=0)
 Searches a cleavage specification in a list.

Protected Attributes

QString m_name
const PolChemDefmp_polChemDef
 Pointer to the reference polymer chemistry definition.

Private Attributes

QList< CleaveMotif * > m_motifList
 List of cleavage motifs.
QString m_pattern
QList< CleaveRule * > m_ruleList
 List of cleavage rules.

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

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