CCellDesignerImporter.h File Reference

#include <vector>
#include <list>
#include <map>
#include <string>
#include <utility>
#include <limits>
#include "copasi/copasi.h"
#include <sbml/packages/layout/sbml/BoundingBox.h>
#include <sbml/packages/layout/sbml/Curve.h>
#include <sbml/packages/layout/sbml/Dimensions.h>
#include <sbml/packages/layout/sbml/LineSegment.h>
#include <sbml/packages/layout/sbml/Point.h>
#include <sbml/packages/render/sbml/Text.h>
#include "copasi/utilities/CCopasiNode.h"

Classes
class	CCellDesignerImporter
struct	CellDesignerSpecies
struct	CompartmentAlias
struct	CompartmentAnnotation
struct	ConnectScheme
struct	DoubleLine
struct	EditPoints
struct	Line
struct	LineDirection
struct	LinkTarget
struct	Paint
struct	Protein
struct	ProteinModification
struct	ReactantLink
struct	ReactionAnnotation
struct	ReactionModification
struct	SpeciesAlias
struct	SpeciesAnnotation
struct	SpeciesIdentity
struct	SpeciesModification
struct	SpeciesState
struct	UsualView

Enumerations
enum	CONNECTION_POLICY { POLICY_UNDEFINED , POLICY_DIRECT , POLICY_SQUARE }
enum	DIRECTION_VALUE { DIRECTION_UNDEFINED , DIRECTION_UNKNOWN , DIRECTION_HORIZONTAL , DIRECTION_VERTICAL }
enum	MODIFICATION_LINK_TYPE {   UNDEFINED_ML_TYPE , CATALYSIS_ML_TYPE , UNKNOWN_CATALYSIS_ML_TYPE , INHIBITION_ML_TYPE ,   UNKNOWN_INHIBITION_ML_TYPE , TRANSPORT_ML_TYPE , HETERODIMER_ASSOCIATION_ML_TYPE , TRANSCRIPTIONAL_ACTIVATION_ML_TYPE ,   TRANSCRIPTIONAL_INHIBITION_ML_TYPE , TRANSLATIONAL_ACTIVATION_ML_TYPE , TRANSLATIONAL_INHIBITION_ML_TYPE , PHYSICAL_STIMULATION_ML_TYPE ,   MODULATION_ML_TYPE , TRIGGER_ML_TYPE , BOOLEAN_LOGIC_GATE_AND_ML_TYPE , BOOLEAN_LOGIC_GATE_OR_ML_TYPE ,   BOOLEAN_LOGIC_GATE_NOT_ML_TYPE , BOOLEAN_LOGIC_GATE_UNKNOWN_ML_TYPE }
enum	MODIFICATION_TYPE {   UNDEFINED_MTYPE , CATALYSIS_MTYPE , UNKNOWN_CATALYSIS_MTYPE , INHIBITION_MTYPE ,   UNKNOWN_INHIBITION_MTYPE , TRANSPORT_MTYPE , HETERODIMER_ASSOCIATION_MTYPE , TRANSCRIPTIONAL_ACTIVATION_MTYPE ,   TRANSCRIPTIONAL_INHIBITION_MTYPE , TRANSLATIONAL_ACTIVATION_MTYPE , TRANSLATIONAL_INHIBITION_MTYPE , PHYSICAL_STIMULATION_MTYPE ,   MODULATION_MTYPE }
enum	PAINT_SCHEME { PAINT_UNDEFINED , PAINT_COLOR , PAINT_GRADIENT }
enum	POSITION {   POSITION_UNDEFINED , POSITION_N , POSITION_E , POSITION_S ,   POSITION_W , POSITION_NE , POSITION_NW , POSITION_SE ,   POSITION_SW , POSITION_NNE , POSITION_ENE , POSITION_ESE ,   POSITION_SSE , POSITION_SSW , POSITION_WSW , POSITION_WNW ,   POSITION_NNW }
enum	POSITION_TO_COMPARTMENT {   UNDEFINED_POSITION , OUTER_SURFACE , TRANSMEMBRANE , INNER_SURFACE ,   INSIDE , INSIDE_MEMBRANE }
enum	REACTION_TYPE {   UNDEFINED_RTYPE , STATE_TRANSITION_RTYPE , KNOWN_TRANSITION_OMITTED_RTYPE , UNKNOWN_TRANSITION_RTYPE ,   CATALYSIS_RTYPE , UNKNOWN_CATALYSIS_RTYPE , INHIBITION_RTYPE , UNKNOWN_INHIBITION_RTYPE ,   TRANSPORT_RTYPE , HETERODIMER_ASSOCIATION_RTYPE , DISSOCIATION_RTYPE , TRUNCATION_RTYPE ,   TRANSCRIPTIONAL_ACTIVATION_RTYPE , TRANSCRIPTIONAL_INHIBITION_RTYPE , TRANSLATIONAL_ACTIVATION_RTYPE , TRANSLATIONAL_INHIBITION_RTYPE ,   TRANSCRIPTION_RTYPE , TRANSLATION_RTYPE }
enum	SPECIES_CLASS {   UNDEFINED_CLASS , PROTEIN_CLASS , GENE_CLASS , RNA_CLASS ,   ANTISENSE_RNA_CLASS , PHENOTYPE_CLASS , ION_CLASS , SIMPLE_MOLECULE_CLASS ,   DRUG_CLASS , UNKNOWN_CLASS , COMPLEX_CLASS , SQUARE_CLASS ,   OVAL_CLASS , SQUARE_NW_CLASS , SQUARE_NE_CLASS , SQUARE_SW_CLASS ,   SQUARE_SE_CLASS , SQUARE_N_CLASS , SQUARE_E_CLASS , SQUARE_W_CLASS ,   SQUARE_S_CLASS , DEGRADED_CLASS , TRUNCATED_CLASS , RECEPTOR_CLASS ,   CHANNEL_CLASS }
enum	SPECIES_MODIFICATION_TYPE {   UNDEFINED_MOD_TYPE , PHOSPHORYLATED_MOD_TYPE , ACETYLATED_MOD_TYPE , UBIQUITINATED_MOD_TYPE ,   METHYLATED_MOD_TYPE , HYDROXYLATED_MOD_TYPE , DONTCARE_MOD_TYPE , UNKNOWN_MOD_TYPE ,   GLYCOSYLATED_MOD_TYPE , MYRISTOYLATED_MOD_TYPE , PALMYTOYLATED_MOD_TYPE , PRENYLATED_MOD_TYPE ,   PROTONATED_MOD_TYPE , SUFLATED_MOD_TYPE , EMPTY_MOD_TYPE }

Enumeration Type Documentation

CONNECTION_POLICY

enum CONNECTION_POLICY

Enumerator
POLICY_UNDEFINED
POLICY_DIRECT
POLICY_SQUARE

DIRECTION_VALUE

enum DIRECTION_VALUE

Enumerator
DIRECTION_UNDEFINED
DIRECTION_UNKNOWN
DIRECTION_HORIZONTAL
DIRECTION_VERTICAL

MODIFICATION_LINK_TYPE

enum MODIFICATION_LINK_TYPE

Enumerator
UNDEFINED_ML_TYPE
CATALYSIS_ML_TYPE
UNKNOWN_CATALYSIS_ML_TYPE
INHIBITION_ML_TYPE
UNKNOWN_INHIBITION_ML_TYPE
TRANSPORT_ML_TYPE
HETERODIMER_ASSOCIATION_ML_TYPE
TRANSCRIPTIONAL_ACTIVATION_ML_TYPE
TRANSCRIPTIONAL_INHIBITION_ML_TYPE
TRANSLATIONAL_ACTIVATION_ML_TYPE
TRANSLATIONAL_INHIBITION_ML_TYPE
PHYSICAL_STIMULATION_ML_TYPE
MODULATION_ML_TYPE
TRIGGER_ML_TYPE
BOOLEAN_LOGIC_GATE_AND_ML_TYPE
BOOLEAN_LOGIC_GATE_OR_ML_TYPE
BOOLEAN_LOGIC_GATE_NOT_ML_TYPE
BOOLEAN_LOGIC_GATE_UNKNOWN_ML_TYPE

MODIFICATION_TYPE

enum MODIFICATION_TYPE

Enumerator
UNDEFINED_MTYPE
CATALYSIS_MTYPE
UNKNOWN_CATALYSIS_MTYPE
INHIBITION_MTYPE
UNKNOWN_INHIBITION_MTYPE
TRANSPORT_MTYPE
HETERODIMER_ASSOCIATION_MTYPE
TRANSCRIPTIONAL_ACTIVATION_MTYPE
TRANSCRIPTIONAL_INHIBITION_MTYPE
TRANSLATIONAL_ACTIVATION_MTYPE
TRANSLATIONAL_INHIBITION_MTYPE
PHYSICAL_STIMULATION_MTYPE
MODULATION_MTYPE

PAINT_SCHEME

enum PAINT_SCHEME

Enumerator
PAINT_UNDEFINED
PAINT_COLOR
PAINT_GRADIENT

POSITION

enum POSITION

The positions are ordered so that the mid points of the edges come before corners and those come before the rest. This way the connection finding algorithm will favor connections to side midpoints before connections to other anchor points.

Enumerator
POSITION_UNDEFINED
POSITION_N
POSITION_E
POSITION_S
POSITION_W
POSITION_NE
POSITION_NW
POSITION_SE
POSITION_SW
POSITION_NNE
POSITION_ENE
POSITION_ESE
POSITION_SSE
POSITION_SSW
POSITION_WSW
POSITION_WNW
POSITION_NNW

POSITION_TO_COMPARTMENT

enum POSITION_TO_COMPARTMENT

Enumerator
UNDEFINED_POSITION
OUTER_SURFACE
TRANSMEMBRANE
INNER_SURFACE
INSIDE
INSIDE_MEMBRANE

REACTION_TYPE

enum REACTION_TYPE

Enumerator
UNDEFINED_RTYPE
STATE_TRANSITION_RTYPE
KNOWN_TRANSITION_OMITTED_RTYPE
UNKNOWN_TRANSITION_RTYPE
CATALYSIS_RTYPE
UNKNOWN_CATALYSIS_RTYPE
INHIBITION_RTYPE
UNKNOWN_INHIBITION_RTYPE
TRANSPORT_RTYPE
HETERODIMER_ASSOCIATION_RTYPE
DISSOCIATION_RTYPE
TRUNCATION_RTYPE
TRANSCRIPTIONAL_ACTIVATION_RTYPE
TRANSCRIPTIONAL_INHIBITION_RTYPE
TRANSLATIONAL_ACTIVATION_RTYPE
TRANSLATIONAL_INHIBITION_RTYPE
TRANSCRIPTION_RTYPE
TRANSLATION_RTYPE

SPECIES_CLASS

enum SPECIES_CLASS

Enumerator
UNDEFINED_CLASS
PROTEIN_CLASS
GENE_CLASS
RNA_CLASS
ANTISENSE_RNA_CLASS
PHENOTYPE_CLASS
ION_CLASS
SIMPLE_MOLECULE_CLASS
DRUG_CLASS
UNKNOWN_CLASS
COMPLEX_CLASS
SQUARE_CLASS
OVAL_CLASS
SQUARE_NW_CLASS
SQUARE_NE_CLASS
SQUARE_SW_CLASS
SQUARE_SE_CLASS
SQUARE_N_CLASS
SQUARE_E_CLASS
SQUARE_W_CLASS
SQUARE_S_CLASS
DEGRADED_CLASS
TRUNCATED_CLASS
RECEPTOR_CLASS
CHANNEL_CLASS

SPECIES_MODIFICATION_TYPE

enum SPECIES_MODIFICATION_TYPE

Enumerator
UNDEFINED_MOD_TYPE
PHOSPHORYLATED_MOD_TYPE
ACETYLATED_MOD_TYPE
UBIQUITINATED_MOD_TYPE
METHYLATED_MOD_TYPE
HYDROXYLATED_MOD_TYPE
DONTCARE_MOD_TYPE
UNKNOWN_MOD_TYPE
GLYCOSYLATED_MOD_TYPE
MYRISTOYLATED_MOD_TYPE
PALMYTOYLATED_MOD_TYPE
PRENYLATED_MOD_TYPE
PROTONATED_MOD_TYPE
SUFLATED_MOD_TYPE
EMPTY_MOD_TYPE