COPASI API  4.16.103
Classes | Enumerations
CCellDesignerImporter.h File Reference
#include <vector>
#include <list>
#include <map>
#include <string>
#include <utility>
#include <limits>
#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"
Include dependency graph for CCellDesignerImporter.h:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

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

Enumerator
POLICY_UNDEFINED 
POLICY_DIRECT 
POLICY_SQUARE 

Definition at line 190 of file CCellDesignerImporter.h.

Enumerator
DIRECTION_UNDEFINED 
DIRECTION_UNKNOWN 
DIRECTION_HORIZONTAL 
DIRECTION_VERTICAL 

Definition at line 197 of file CCellDesignerImporter.h.

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 

Definition at line 139 of file CCellDesignerImporter.h.

140 {
159 };
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 

Definition at line 122 of file CCellDesignerImporter.h.

Enumerator
PAINT_UNDEFINED 
PAINT_COLOR 
PAINT_GRADIENT 

Definition at line 205 of file CCellDesignerImporter.h.

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 

Definition at line 169 of file CCellDesignerImporter.h.

Enumerator
UNDEFINED_POSITION 
OUTER_SURFACE 
TRANSMEMBRANE 
INNER_SURFACE 
INSIDE 
INSIDE_MEMBRANE 

Definition at line 90 of file CCellDesignerImporter.h.

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 

Definition at line 100 of file CCellDesignerImporter.h.

101 {
120 };
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 

Definition at line 38 of file CCellDesignerImporter.h.

39 {
42  , GENE_CLASS
43  , RNA_CLASS
46  , ION_CLASS
48  , DRUG_CLASS
51  , SQUARE_CLASS
52  , OVAL_CLASS
62  // the next three enums are actually not
63  // species classes but attributes on
64  // protein elements, but we will store them
65  // as a class enum
69 };
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 

Definition at line 71 of file CCellDesignerImporter.h.