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

enum CONNECTION_POLICY
Enumerator
POLICY_UNDEFINED 
POLICY_DIRECT 
POLICY_SQUARE 

Definition at line 190 of file CCellDesignerImporter.h.

191 {
192  POLICY_UNDEFINED
193  , POLICY_DIRECT
194  , POLICY_SQUARE
195 };
enum DIRECTION_VALUE
Enumerator
DIRECTION_UNDEFINED 
DIRECTION_UNKNOWN 
DIRECTION_HORIZONTAL 
DIRECTION_VERTICAL 

Definition at line 197 of file CCellDesignerImporter.h.

198 {
199  DIRECTION_UNDEFINED
200  , DIRECTION_UNKNOWN
201  , DIRECTION_HORIZONTAL
202  , DIRECTION_VERTICAL
203 };
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 

Definition at line 139 of file CCellDesignerImporter.h.

140 {
141  UNDEFINED_ML_TYPE
142  , CATALYSIS_ML_TYPE
143  , UNKNOWN_CATALYSIS_ML_TYPE
144  , INHIBITION_ML_TYPE
145  , UNKNOWN_INHIBITION_ML_TYPE
146  , TRANSPORT_ML_TYPE
147  , HETERODIMER_ASSOCIATION_ML_TYPE
148  , TRANSCRIPTIONAL_ACTIVATION_ML_TYPE
149  , TRANSCRIPTIONAL_INHIBITION_ML_TYPE
150  , TRANSLATIONAL_ACTIVATION_ML_TYPE
151  , TRANSLATIONAL_INHIBITION_ML_TYPE
152  , PHYSICAL_STIMULATION_ML_TYPE
153  , MODULATION_ML_TYPE
154  , TRIGGER_ML_TYPE
155  , BOOLEAN_LOGIC_GATE_AND_ML_TYPE
156  , BOOLEAN_LOGIC_GATE_OR_ML_TYPE
157  , BOOLEAN_LOGIC_GATE_NOT_ML_TYPE
158  , BOOLEAN_LOGIC_GATE_UNKNOWN_ML_TYPE
159 };
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 

Definition at line 122 of file CCellDesignerImporter.h.

123 {
124  UNDEFINED_MTYPE
125  , CATALYSIS_MTYPE
126  , UNKNOWN_CATALYSIS_MTYPE
127  , INHIBITION_MTYPE
128  , UNKNOWN_INHIBITION_MTYPE
129  , TRANSPORT_MTYPE
130  , HETERODIMER_ASSOCIATION_MTYPE
131  , TRANSCRIPTIONAL_ACTIVATION_MTYPE
132  , TRANSCRIPTIONAL_INHIBITION_MTYPE
133  , TRANSLATIONAL_ACTIVATION_MTYPE
134  , TRANSLATIONAL_INHIBITION_MTYPE
135  , PHYSICAL_STIMULATION_MTYPE
136  , MODULATION_MTYPE
137 };
enum PAINT_SCHEME
Enumerator
PAINT_UNDEFINED 
PAINT_COLOR 
PAINT_GRADIENT 

Definition at line 205 of file CCellDesignerImporter.h.

206 {
207  PAINT_UNDEFINED
208  , PAINT_COLOR
209  , PAINT_GRADIENT
210 };
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.

170 {
171  POSITION_UNDEFINED
172  , POSITION_N
173  , POSITION_E
174  , POSITION_S
175  , POSITION_W
176  , POSITION_NE
177  , POSITION_NW
178  , POSITION_SE
179  , POSITION_SW
180  , POSITION_NNE
181  , POSITION_ENE
182  , POSITION_ESE
183  , POSITION_SSE
184  , POSITION_SSW
185  , POSITION_WSW
186  , POSITION_WNW
187  , POSITION_NNW
188 };
enum POSITION_TO_COMPARTMENT
Enumerator
UNDEFINED_POSITION 
OUTER_SURFACE 
TRANSMEMBRANE 
INNER_SURFACE 
INSIDE 
INSIDE_MEMBRANE 

Definition at line 90 of file CCellDesignerImporter.h.

91 {
92  UNDEFINED_POSITION
93  , OUTER_SURFACE
94  , TRANSMEMBRANE
95  , INNER_SURFACE
96  , INSIDE
97  , INSIDE_MEMBRANE
98 };
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 

Definition at line 100 of file CCellDesignerImporter.h.

101 {
102  UNDEFINED_RTYPE
103  , STATE_TRANSITION_RTYPE
104  , KNOWN_TRANSITION_OMITTED_RTYPE
105  , UNKNOWN_TRANSITION_RTYPE
106  , CATALYSIS_RTYPE
107  , UNKNOWN_CATALYSIS_RTYPE
108  , INHIBITION_RTYPE
109  , UNKNOWN_INHIBITION_RTYPE
110  , TRANSPORT_RTYPE
111  , HETERODIMER_ASSOCIATION_RTYPE
112  , DISSOCIATION_RTYPE
113  , TRUNCATION_RTYPE
114  , TRANSCRIPTIONAL_ACTIVATION_RTYPE
115  , TRANSCRIPTIONAL_INHIBITION_RTYPE
116  , TRANSLATIONAL_ACTIVATION_RTYPE
117  , TRANSLATIONAL_INHIBITION_RTYPE
118  , TRANSCRIPTION_RTYPE
119  , TRANSLATION_RTYPE
120 };
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 

Definition at line 38 of file CCellDesignerImporter.h.

39 {
40  UNDEFINED_CLASS
41  , PROTEIN_CLASS
42  , GENE_CLASS
43  , RNA_CLASS
44  , ANTISENSE_RNA_CLASS
45  , PHENOTYPE_CLASS
46  , ION_CLASS
47  , SIMPLE_MOLECULE_CLASS
48  , DRUG_CLASS
49  , UNKNOWN_CLASS
50  , COMPLEX_CLASS
51  , SQUARE_CLASS
52  , OVAL_CLASS
53  , SQUARE_NW_CLASS
54  , SQUARE_NE_CLASS
55  , SQUARE_SW_CLASS
56  , SQUARE_SE_CLASS
57  , SQUARE_N_CLASS
58  , SQUARE_E_CLASS
59  , SQUARE_W_CLASS
60  , SQUARE_S_CLASS
61  , DEGRADED_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
66  , TRUNCATED_CLASS
67  , RECEPTOR_CLASS
68  , CHANNEL_CLASS
69 };
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 

Definition at line 71 of file CCellDesignerImporter.h.

72 {
73  UNDEFINED_MOD_TYPE
74  , PHOSPHORYLATED_MOD_TYPE
75  , ACETYLATED_MOD_TYPE
76  , UBIQUITINATED_MOD_TYPE
77  , METHYLATED_MOD_TYPE
78  , HYDROXYLATED_MOD_TYPE
79  , DONTCARE_MOD_TYPE
80  , UNKNOWN_MOD_TYPE
81  , GLYCOSYLATED_MOD_TYPE
82  , MYRISTOYLATED_MOD_TYPE
83  , PALMYTOYLATED_MOD_TYPE
84  , PRENYLATED_MOD_TYPE
85  , PROTONATED_MOD_TYPE
86  , SUFLATED_MOD_TYPE
87  , EMPTY_MOD_TYPE
88 };
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