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massXpert::Oligomer Class Reference

#include <oligomer.hpp>

Inheritance diagram for massXpert::Oligomer:

massXpert::Sequence massXpert::Ionizable massXpert::PropListHolder massXpert::PolChemDefEntity massXpert::Ponderable

List of all members.


Detailed Description

The Oligomer class provides an oligomer.

An oligomer is a stretch of monomers belonging to a polymer. It is characterized by: \

The start index cannot be less than 0 and greater than the size of the polymer minus one, and the end index follows the same rule.

Derived from Ponderable, an oligomer is also characterized by a monoisotopic mass and an average mass.

All computations about an oligomer(fragmentation, composition, for example, isoelectric point, ...) can only be performed by referring to the sequence of its "enclosing" polymer. Therefore, an oligomer should never exist after the destruction of its enclosing polymer.

Definition at line 82 of file oligomer.hpp.


Public Member Functions

virtual bool accountMasses (double *=0, double *=0, int=1) const
 Increments the masses in the arguments.
bool addCrossLink (CrossLink *)
void appendCoordinates (const Coordinates &)
int appendCoordinates (CoordinateList *)
void appendMonomerText (const QString &)
 Appends text to the sequence text.
bool appendProp (Prop *)
const Monomerat (int) const
 Returns the monomer at index index.
const MonomeratLeftEnd () const
const MonomeratRightEnd () const
QString avg (const QLocale &, int=10) const
 Returns the average mass as a string.
double avg () const
 Returns the average mass.
virtual bool calculateMasses (const CalcOptions *calcOptions, const IonizeRule *ionizeRule=0)
 Calculates the masses(mono and avg).
virtual bool calculateMasses ()
 Calculates the masses(mono and avg).
virtual int charge () const
 Returns the ionization charge of this Ionizable.
quint16 checksum (int=-1, int=-1, bool=false) const
void clearMasses ()
 Clears the monoisotopic and average masses by setting both to 0.
virtual void clone (PropListHolder *) const
virtual PropListHolderclone () const
virtual void clone (Ponderable *) const
 Modifies other to be identical to this.
virtual void clone (PolChemDefEntity *) const
 Modifies other to be identical to this.
virtual void clone (Ionizable *) const
 Modifies other to be identical to this.
virtual Ionizableclone () const
 Creates a new Ionizable.
QString comment () const
QList< CrossLink * > * crossLinkList ()
void debugPutStdErr ()
void decrementAvg (double)
 Decrements the average mass by mass.
void decrementMono (double)
 Decrements the monoisotopic mass by mass.
virtual int deionize ()
 Deionizes this Ionizable.
void empty ()
bool encompasses (const Monomer *) const
bool encompasses (int) const
bool encompassIndex (int) const
int endIndex () const
 Returns the end index.
bool findForwardMotif (Sequence *, const PolChemDef *, int *)
void incrementAvg (double)
 Increments the average mass by mass.
void incrementMass (double, MassType)
void incrementMono (double)
 Increments the monoisotopic mass by mass.
QString indicesAsText () const
bool insertMonomerAt (const Monomer *, int)
 Inserts the monomer at index index.
virtual int ionize (const IonizeRule &)
 Ionizes this Ionizable.
virtual int ionize ()
 Ionizes this Ionizable.
const IonizeRuleionizeRule () const
 Returns the IonizeRule as a constant reference.
IonizeRuleionizeRule ()
 Returns the IonizeRule as a pointer.
bool isIonized () const
 Returns the ionization status of this Ionizable.
bool isLeftMostCoordinates (Coordinates *) const
virtual bool isModified ()
 Tells if the oligomer contains at least one modified monomer.
bool isRightMostCoordinates (Coordinates *) const
int leftMostCoordinates (QList< int > &) const
int makeMonomerList (const PolChemDef *, bool=true, QList< int > *=0)
 Creates a list of monomers from the string sequence.
virtual int makeMonomerText ()
 Creates the string representation of the sequence.
double mass (MassType) const
void masses (double *=0, double *=0) const
 Updates the arguments with the monoisotopic and average masses.
virtual void mold (const PropListHolder &)
virtual void mold (const Ponderable &)
 Modifies this to be identical to other.
virtual void mold (const PolChemDefEntity &)
 Modifies this to be identical to other.
virtual void mold (const Ionizable &)
 Modifies this to be identical to other.
virtual double molecularMass (MassType)
QString mono (const QLocale &, int=10) const
 Returns the monoisotopic mass as a string.
double mono () const
 Returns the monoisotopic mass.
const MonomermonomerAt (int) const
int monomerIndex (const Monomer *)
const QList< const Monomer * > & monomerList () const
 Returns the sequence as a list of monomers.
QList< const Monomer * > * monomerListPtr ()
 Returns the sequence as a list of monomers.
QString * monomerText (const CoordinateList &, bool, bool) const
QString * monomerText (int, int, bool) const
QString * monomerText ()
 Returns the sequence as a string of monomer codes.
QString name () const
 Returns the name.
int nextCode (QString *, int *, QString *, int)
 Returns the next code occurring in the sequence.
 Oligomer (const Oligomer &)
 Constructs a copy of other.
 Oligomer (const PolChemDef *, const QString &=QString(), double=0, double=0, int=-1, int=-1)
 Constructs an oligomer.
 Oligomer (Polymer *, const QString &=QString(), double=0, double=0, int=-1, int=-1)
 Constructs an oligomer.
 Oligomer (const PolChemDef *, const QString &=QString(), const Ponderable &=Ponderable(), int=-1, int=-1)
 Constructs an oligomer.
 Oligomer (Polymer *, const QString &=QString(), const Ponderable &=Ponderable(), int=-1, int=-1)
 Constructs an oligomer.
 Oligomer (const PolChemDef *, const QString &=QString(), const Ponderable &=Ponderable(), const IonizeRule &=IonizeRule(), bool=false, int=-1, int=-1)
 Constructs an oligomer.
 Oligomer (Polymer *, const QString &=QString(), const Ponderable &=Ponderable(), const IonizeRule &=IonizeRule(), bool=false, int=-1, int=-1)
 Constructs an oligomer.
virtual bool operator!= (const Ponderable &) const
 Inquality operator.
virtual bool operator!= (const PolChemDefEntity &) const
 Tests inequality.
virtual bool operator!= (const Ionizable &) const
virtual bool operator== (const Ponderable &) const
 Equality operator.
virtual bool operator== (const PolChemDefEntity &) const
 Tests equality.
virtual bool operator== (const Ionizable &) const
const PolChemDefpolChemDef () const
 Returns the polymer chemistry definition.
const Polymerpolymer () const
 Returns the polymer.
QString positionsAsText () const
virtual bool prepareMonomerRemoval (const Monomer *)
Propprop (const QString &, int *=0)
int propIndex (const QString &, Prop *=0)
QList< Prop * > & propList ()
const QList< Prop * > & propList () const
int propListSize () const
double & ravg ()
 Returns a reference to the average mass.
virtual bool removeMonomerAt (int)
 Removes the monomer at index index.
bool removeProp (const QString &)
bool removeProp (Prop *)
int rightMostCoordinates (QList< int > &) const
double & rmono ()
 Returns a reference to the monoisotopic mass.
bool setAvg (const QString &, const QLocale &)
 Sets the average mass to mass.
void setAvg (double)
 Sets the average mass to mass.
int setCharge (int)
 Sets the charge of this Ionizable.
void setComment (QString comment)
void setCoordinates (const CoordinateList &)
void setCoordinates (const Coordinates &)
void setEndIndex (int)
 Sets the end index.
void setIonizeRule (IonizeRule &)
void setMass (double, MassType)
void setMasses (double, double)
 Sets the monoisotopic and average masses.
bool setMono (const QString &, const QLocale &)
 Sets the monoisotopic mass to mass.
void setMono (double)
 Sets the monoisotopic mass to mass.
void setMonomerText (const QString &)
 Sets the sequence text.
void setName (const QString &)
 Sets the name.
void setPolChemDef (PolChemDef *)
void setStartEndIndices (int, int)
 Sets the start and end indices.
void setStartIndex (int)
 Sets the start index.
int size () const
 Returns the size of the sequence.
int size ()
int startIndex () const
 Returns the start index.
void unspacifyMonomerText ()
 Removes all spaces, carriage returns and linefeeds.
virtual bool validate () const
bool validate ()
bool validate (const PolChemDef *)
virtual ~Oligomer ()
 Destroys the oligomer.

Static Public Member Functions

static int deionize (Ionizable *)
static int ionize (Ionizable *, const IonizeRule &)
 Ionizes ionizable.

Protected Attributes

double m_avg
 Average mass.
QString m_comment
QList< CrossLink * > m_crossLinkList
IonizeRule m_ionizeRule
 IonizeRule that is used to ionize this Ionizable.
bool m_isIonized
 Indicates if this Ionizable has been effectively ionized.
double m_mono
 Monoisotopic mass.
QList< const Monomer * > m_monomerList
 List of monomers in the sequence. Empty upon creation.
QString m_monomerText
 Sequence in the form of a string of concatenated monomer codes.
QString m_name
 Name.
QList< Prop * > m_propList
const PolChemDefmp_polChemDef
 Pointer to the reference polymer chemistry definition.
const QPointer< Polymermp_polymer
 Polymer in which this oligomer spans a region.

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

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