Atoms groups. More...

#include <gcp/fragment.h>

Inheritance diagram for gcp::Fragment:

Public Types
enum	Validity { Invalid, Valid, Valid2D, Valid3D }
	The validity state of a Fragment as it is currently evaluated by the framework. The 0.12.x version don't do anything useful with it and all Fragment instances are invalid. More...
enum	FragmentMode { AutoMode, NormalMode, SubscriptMode, SuperscriptMode, ChargeMode, StoichiometryMode }
	Edition mode. More...

Public Member Functions
	Fragment ()
	Fragment (double x, double y)
virtual	~Fragment ()
void	AddItem ()
void	UpdateItem ()
void	SetSelected (int state)
xmlNodePtr	Save (xmlDocPtr xml) const
xmlNodePtr	SaveSelection (xmlDocPtr xml) const
bool	Load (xmlNodePtr node)
bool	OnChanged (bool save)
void	AnalContent ()
void	AnalContent (unsigned start, unsigned &end)
Object *	GetAtomAt (double x, double y, double z=0.)
void	Move (double x, double y, double z=0)
void	Transform2D (gcu::Matrix2D &m, double x, double y)
void	OnChangeAtom ()
Atom *	GetAtom ()
int	GetElementAtPos (unsigned start, unsigned &end)
gccv::Anchor	GetChargePosition (FragmentAtom *pAtom, unsigned char &Pos, double Angle, double &x, double &y)
int	GetAvailablePosition (double &x, double &y)
bool	GetPosition (double angle, double &x, double &y)
bool	Validate ()
double	GetYAlign ()
bool	SetProperty (unsigned property, char const *value)
bool	Analyze ()
void	Update ()
gccv::Item *	GetChargeItem ()
std::string	Name ()
bool	GetCoords (double x, double y, double *z=NULL) const
Validity	GetValid (void) const
void	SetMode (FragmentMode val)
FragmentMode	GetMode (void) const
FragmentMode &	GetRefMode (void)
Public Member Functions inherited from gcp::TextObject
	TextObject (gcu::TypeId Type)
	TextObject (double x, double y, gcu::TypeId Type)
virtual	~TextObject ()
void	GetSize (double &x, double &y)
xmlNodePtr	SaveSelected ()
void	LoadSelected (xmlNodePtr node)
bool	SaveNode (xmlDocPtr xml, xmlNodePtr node) const
bool	IsLocked ()
void	GetSelectionBounds (unsigned &start, unsigned &end)
std::string	GetBuffer ()
virtual std::string	GetProperty (unsigned property) const
void	SelectionChanged (unsigned start, unsigned end)
void	TextChanged (unsigned pos)
gccv::TextTagList	GetTagList (void)
void	SetEditor (TextEditor *val)
TextEditor *	GetEditor (void) const
TextEditor *&	GetRefEditor (void)
gccv::Text *	GetTextItem (void)
Public Member Functions inherited from gcu::Object
	Object (TypeId Id=OtherType)
virtual	~Object ()
TypeId	GetType () const
void	SetId (gchar const *Id)
char const *	GetId () const
virtual void	AddChild (Object *object)
Object *	GetMolecule () const
Object *	GetReaction () const
Object *	GetGroup () const
Document *	GetDocument () const
Application *	GetApplication () const
Object *	GetParentOfType (TypeId Id) const
Object *	GetChild (const gchar *Id) const
Object *	GetFirstChild (std::map< std::string, Object * >::iterator &i)
Object *	GetNextChild (std::map< std::string, Object * >::iterator &i)
Object *	GetDescendant (const char *Id) const
Object *	GetParent () const
void	SetParent (Object *Parent)
bool	SaveChildren (xmlDocPtr xml, xmlNodePtr node) const
void	SaveId (xmlNodePtr node) const
xmlNodePtr	GetNodeByProp (xmlNodePtr node, char const Property, char const Id)
xmlNodePtr	GetNextNodeByProp (xmlNodePtr node, char const Property, char const Id)
xmlNodePtr	GetNodeByName (xmlNodePtr node, char const *Name)
xmlNodePtr	GetNextNodeByName (xmlNodePtr node, char const *Name)
bool	HasChildren () const
unsigned	GetChildrenNumber () const
virtual bool	Build (std::set< Object * > const &Children) throw (std::invalid_argument)
virtual bool	BuildContextualMenu (UIManager uim, Object object, double x, double y)
void	EmitSignal (SignalId Signal)
virtual bool	OnSignal (SignalId Signal, Object *Child)
void	Lock (bool state=true)
Object *	GetFirstLink (std::set< Object * >::iterator &i)
Object *	GetNextLink (std::set< Object * >::iterator &i)
void	Link (Object *object)
void	Unlink (Object *object)
virtual void	OnUnlink (Object *object)
void	GetPossibleAncestorTypes (std::set< TypeId > &types) const
virtual void	OnLoaded ()
void	SetDirty (bool dirty=true)
virtual void	Clear ()
std::string	Identity ()
virtual char const *	HasPropertiesDialog () const
virtual bool	CanSelect () const
virtual void	NotifyEmpty ()
void	ShowPropertiesDialog ()
bool	GetDirty (void) const
Public Member Functions inherited from gccv::TextClient
	TextClient ()
virtual	~TextClient ()
virtual void	InterlineChanged (G_GNUC_UNUSED double interline)
virtual void	JustificationChanged (G_GNUC_UNUSED GtkJustification justification)
Public Member Functions inherited from gccv::ItemClient
	ItemClient ()
virtual	~ItemClient ()
Item *	GetItem (void)

Additional Inherited Members
Static Public Member Functions inherited from gcu::Object
static TypeId	AddType (std::string TypeName, Object (CreateFunc)(), TypeId id=OtherType)
static void	AddAlias (TypeId id, std::string TypeName)
static Object *	CreateObject (const std::string &TypeName, Object *parent=NULL)
static TypeId	GetTypeId (const std::string &Name)
static std::string	GetTypeName (TypeId Id)
static void	AddMenuCallback (TypeId Id, BuildMenuCb cb)
static void	AddRule (TypeId type1, RuleId rule, TypeId type2)
static void	AddRule (const std::string &type1, RuleId rule, const std::string &type2)
static const std::set< TypeId > &	GetRules (TypeId type, RuleId rule)
static const std::set< TypeId > &	GetRules (const std::string &type, RuleId rule)
static void	SetCreationLabel (TypeId Id, std::string Label)
static const std::string &	GetCreationLabel (TypeId Id)
static const std::string &	GetCreationLabel (const std::string &TypeName)
static SignalId	CreateNewSignalId ()
Protected Member Functions inherited from gcu::Object
virtual Dialog *	BuildPropertiesDialog ()
Protected Attributes inherited from gcp::TextObject
double	m_x
double	m_y
double	m_length
double	m_height
int	m_ascent
int	m_InsertOffset
std::string	m_buf
bool	m_bLoading
unsigned	m_StartSel
unsigned	m_EndSel
bool	m_RealSave
gccv::TextTagList	m_TagList
gccv::Text *	m_TextItem

Detailed Description

Atoms groups.

Represents atoms groups displayed as a string. Currntly, the string is not fully parsed, so that some non sense strings might be accepted. Anyway, this will not always be the case in the future.

Definition at line 109 of file fragment.h.

Member Enumeration Documentation

enum gcp::Fragment::FragmentMode

Edition mode.

Current edition mode for the fragment. Used to know how inserted symbolds need to be interpreted.

Enumerator:

AutoMode	Automatic mode, try to guess what each new symbol represent.
NormalMode	New characters are aligned on the base line.
SubscriptMode	New characters are subscripts, but are not related to stoichiometry.
SuperscriptMode	New characters are superscripts, but are not related to charge.
ChargeMode	New characters are interpreted as charge and superscript.
StoichiometryMode	New characters are interpreted as stoichiometry and subscript.

Definition at line 343 of file fragment.h.

enum gcp::Fragment::Validity

The validity state of a Fragment as it is currently evaluated by the framework. The 0.12.x version don't do anything useful with it and all Fragment instances are invalid.

Enumerator:

Invalid	Invalid Fragment or validity not checked.
Valid	Valid Fragment, all symbols in the string can be interpreted.
Valid2D	Valid Fragment, with a known and reasonable 2D structure.
Valid3D	Valid Fragment, with a known and reasonable 3D structure.

Definition at line 318 of file fragment.h.

Constructor & Destructor Documentation

gcp::Fragment::Fragment ( )

The default constructor.

gcp::Fragment::Fragment	(	double	x,
		double	y
	)

Parameters

x	the x position of the new fragment.
y	the y position of the new fragment.

Constructs a new fragment and position it. x and y are the position of the main atom or residue in the fragment.

virtual gcp::Fragment::~Fragment ( )

virtual

The destructor.

Member Function Documentation

void gcp::Fragment::AddItem ( )

virtual

Used to add a representation of the fragment in the view.

Reimplemented from gccv::ItemClient.

void gcp::Fragment::AnalContent ( )

Analyses the whole contents.

void gcp::Fragment::AnalContent	(	unsigned	start,
		unsigned &	end
	)

Parameters

start	the start fo the substring to parse, in bytes.
end	the end fo the substring to parse, in bytes.

Analyses a substring.

bool gcp::Fragment::Analyze ( )

Analyses the text in the fragment. This calls gcp::Fragment::AnalContent() and updates the attribute list.

Atom* gcp::Fragment::GetAtom ( )

inline

Returns: the main atom, which might have a bond.

Definition at line 217 of file fragment.h.

Object* gcp::Fragment::GetAtomAt	(	double	x,
		double	y,
		double	z = `0.`
	)

virtual

Parameters

x	the x coordinate
y	the y coordinate
z	the z coordinate (unused)

Returns: a pointer to the Atom correpoding to the symbol at or near the position defined by the coordinates passed as parameters, if any.

Reimplemented from gcu::Object.

int gcp::Fragment::GetAvailablePosition	(	double &	x,
		double &	y
	)

Parameters

x	the x position.
y	the y position.

This method finds an available position for drawing a charge sign or electrons and returns it as a symbolic value (see POSITION_E, POSITION_N,...). The x and y are updated so that they give the absolute position.

Returns: an available position.

gccv::Item* gcp::Fragment::GetChargeItem ( )

Returns: the gccv::Item used to represent the formal charge of the main atom.

gccv::Anchor gcp::Fragment::GetChargePosition	(	FragmentAtom *	pAtom,
		unsigned char &	Pos,
		double	Angle,
		double &	x,
		double &	y
	)

Parameters

pAtom	the main atom which will get the local charge.
Pos	the approximate position of the charge.
Angle	the angle from horizontal left.
x	the x position of the charge symbol.
y	the y position of the charge symbol.

If pAtom is not the main atom of the fragment, 0 is returned and Pos is not updated. On input Pos can be one of POSITION_E, POSITION_N,... or 0xff, in which case, it will be given a default value. x and y are set to the position where the charge sign should be displayed usding the alignment code returned by this method.

Returns: the anchor for the charge symbol. On error, gccv::AnchorCenter is used as the returned value.

bool gcp::Fragment::GetCoords	(	double *	x,
		double *	y,
		double *	z = `NULL`
	)		const

virtual

Parameters

x	a pointer to the double value which will receive the x coordinate of the Fragment.
y	a pointer to the double value which will receive the y coordinate of the Fragment.
z	a pointer to the double value which will receive the z coordinate of the Fragment or NULL for 2D representations.

Retrieves the coordinates of this Arrow.

Returns: true if successful and false if an error occurs (if x or y is NULL).

Reimplemented from gcu::Object.

int gcp::Fragment::GetElementAtPos	(	unsigned	start,
		unsigned &	end
	)

Parameters

start	the start position of the atomic symbol.
end	the end position of the atomic symbol.

Returns: the atomic number corresponding to the symbol starting at start, if any, or 0. end is updated accordingly.

gcp::Fragment::GetMode ( void ) const

inline

Returns: the current edition mode for the Fragment instance.

Definition at line 395 of file fragment.h.

bool gcp::Fragment::GetPosition	(	double	angle,
		double &	x,
		double &	y
	)

Parameters

angle	the angle at which a charge sign should be displayed.
x	the x position.
y	the y position.

Returns: false and do not update the coordinates.

gcp::Fragment::GetRefMode ( void )

inline

Returns: the current edition mode for the Fragment instance as a reference.

Definition at line 395 of file fragment.h.

gcp::Fragment::GetValid ( void ) const

inline

Returns: the current Fragment::Validity for the Fragment instance.

Definition at line 383 of file fragment.h.

double gcp::Fragment::GetYAlign ( )

virtual

Returns: the y coordinate at half height of a carbon atom symbol if any was present.

Reimplemented from gcu::Object.

bool gcp::Fragment::Load ( xmlNodePtr node )

virtual

Parameters

node	a pointer to the xmlNode containing the serialized fragment.

Used to load a fragment in memory. The Fragment must already exist.

Returns: true on succes, false otherwise.

Reimplemented from gcp::TextObject.

void gcp::Fragment::Move	(	double	x,
		double	y,
		double	z = `0`
	)

virtual

Parameters

x	the x component of the transation vector.
y	the y component of the transation vector.
z	the z component of the transation vector.

Moves the fragment.

Reimplemented from gcp::TextObject.

std::string gcp::Fragment::Name ( )

virtual

Returns: the localized object generic name.

Reimplemented from gcu::Object.

void gcp::Fragment::OnChangeAtom ( )

Called by the framework when the user changes the nature of an atom using the element tool.

bool gcp::Fragment::OnChanged ( bool save )

virtual

Parameters

save	whether the text should be saved for undo/redo operations.

Called after any change in the text.

Implements gcp::TextObject.

xmlNodePtr gcp::Fragment::Save ( xmlDocPtr xml ) const

virtual

Parameters

xml	the xmlDoc used to save the document.

Used to save the fragment to the xmlDoc.

Returns: the xmlNode containing the serialized fragment.

Reimplemented from gcu::Object.

xmlNodePtr gcp::Fragment::SaveSelection ( xmlDocPtr xml ) const

Parameters

xml	the xmlDoc used for clipboard operations.

Saves the currently selected text inside the fragment. This method is used by the framework when editing the fragment.

Returns: the xmlNode containing the serialized selection.

gcp::Fragment::SetMode ( FragmentMode mode )

inline

Parameters

mode	the nexw edition mode.

Sets the current edition mode for the Fragment instance.

Definition at line 395 of file fragment.h.

bool gcp::Fragment::SetProperty	(	unsigned	property,
		char const *	value
	)

virtual

Parameters

property	the property id as defined in objprops.h
value	the property value as a string

Used when loading to set properties for the fragment. This method supports GCU_PROP_POS2D, GCU_PROP_TEXT_TEXT, GCU_PROP_FRAGMENT_ATOM_START, and GCU_PROP_FRAGMENT_ATOM_ID.

Returns: true if the property could be set, or if the property is not relevant, false otherwise.

Reimplemented from gcu::Object.

void gcp::Fragment::SetSelected ( int state )

virtual

Parameters

state the selection state of the fragment.

Used to set the selection state of the fragment inside the widget. The values of state might be gcp::SelStateUnselected, gcp::SelStateSelected, gcp::SelStateUpdating, or gcp::SelStateErasing.

Reimplemented from gccv::ItemClient.

void gcp::Fragment::Transform2D	(	gcu::Matrix2D &	m,
		double	x,
		double	y
	)

virtual

Parameters

m	the Matrix2D of the transformation.
x	the x component of the center of the transformation.
y	the y component of the center of the transformation.

Moves and/or transform an object.

Reimplemented from gcu::Object.

void gcp::Fragment::Update ( )

Changes the order of the symbols if necessary when a bond is at an extremity of the fragment.

void gcp::Fragment::UpdateItem ( )

virtual

Used to update a representation of the fragment in the view.

Reimplemented from gccv::ItemClient.

bool gcp::Fragment::Validate ( )

Validates the contents of the fragment text, and display error messages when necessary.

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

fragment.h

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation