libSBML C++ API
libSBML 5.18.0 C++ API
|
A version of example2.cpp
for SBML Level 3.
#if (!defined LIBSBML_HAS_PACKAGE_LAYOUT)
#error "This example requires libSBML to be built with the layout extension."
#endif
Species* createSpecies(
const char*
id,
const char* name,
const char* compartmentId,
Model* model)
{
return species;
}
int main(int argc, char** argv)
{
model->
setId(
"Glycolysis");
compartment->
setId(
"Yeast");
Species* species_Gluc = createSpecies(
"Glucose",
"Glucose",
compartment->
getId().c_str(), model);
Species* species_G6P = createSpecies(
"Glucose_hyphen_6_hyphen_phosphate",
"Glucose-6-phosphate",
compartment->
getId().c_str(), model);
Species* species_F6P = createSpecies(
"Fructose_hyphen_6_hyphen_phosphate",
"Fructose-6-phosphate",
compartment->
getId().c_str(), model);
Species* species_F16BP = createSpecies(
"Fructose_hyphen_1_6_hyphen_bisphosphate",
"Fructose-1, 6-bisphosphate",
compartment->
getId().c_str(), model);
Species* species_DHAP = createSpecies(
"Dihydroxyacetonephosphate",
"Dihydroxyacetonephosphate",
compartment->
getId().c_str(), model);
Species* species_GAP = createSpecies(
"Glyceraldehyd_hyphen_3_hyphen_phosphate",
"Glyceraldehyd-3-phosphate",
compartment->
getId().c_str(), model);
Species* species_BPG = createSpecies(
"_1_3_hyphen_Bisphosphoglycerate",
"1, 3-Bisphosphoglycerate",
compartment->
getId().c_str(), model);
Species* species_3PG = createSpecies(
"_3_hyphen_Phosphoglycerate",
"3-Phosphoglycerate",
compartment->
getId().c_str(), model);
Species* species_2PG = createSpecies(
"_2_hyphen_Phosphoglycerate",
"2-Phosphoglycerate",
compartment->
getId().c_str(), model);
Species* species_PEP = createSpecies(
"Phosphoenolpyruvate",
"Phosphoenolpyruvate",
compartment->
getId().c_str(), model);
Species* species_Pyr = createSpecies(
"Pyruvate",
"Pyruvate",
compartment->
getId().c_str(), model);
Species* species_ATP = createSpecies(
"ATP",
"ATP",
compartment->
getId().c_str(), model);
Species* species_ADP = createSpecies(
"ADP",
"ADP",
compartment->
getId().c_str(), model);
Species* species_H = createSpecies(
"H_plus_",
"H+",
compartment->
getId().c_str(), model);
Species* species_NAD = createSpecies(
"NAD_plus_",
"NAD+",
compartment->
getId().c_str(), model);
Species* species_NADH = createSpecies(
"NADH",
"NADH",
compartment->
getId().c_str(), model);
Species* species_H2O = createSpecies(
"H2O",
"H2O",
compartment->
getId().c_str(), model);
Species* species_PI = createSpecies(
"Pi",
"Pi",
compartment->
getId().c_str(), model);
reaction_Hexokinase->
setId(
"Hexokinase");
reaction_Hexokinase->
setFast(
false);
reference_Gluc->
setId(
"ref_Gluc");
reference_G6P_1->
setId(
"ref_G6P_1");
reference_ATP_1->
setId(
"ref_ATP_1");
reference_ADP_1->
setId(
"ref_ADP_1");
reference_H_1->
setId(
"ref_H_1");
reaction_PGIsomerase->
setId(
"Phosphoglucoseisomerase");
reaction_PGIsomerase->
setFast(
false);
reference_G6P_2->
setId(
"ref_G6P_2");
reference_F6P_1->
setId(
"ref_F6P_1");
reaction_PFK->
setId(
"Phosphofructokinase");
reference_F6P_2->
setId(
"ref_F6P_2");
reference_F16BP_1->
setId(
"ref_F16BP_1");
reference_ATP_2->
setId(
"ref_ATP_2");
reference_ADP_2->
setId(
"ref_ADP_2");
reference_H_2->
setId(
"ref_H_2");
reaction_Aldolase->
setId(
"Aldolase");
reference_F16BP_2->
setId(
"ref_F16BP_2");
reference_DHAP_1->
setId(
"ref_DHAP_1");
reference_GAP_1->
setId(
"ref_GAP_1");
reaction_TPI->
setId(
"triose_phosphate_isomerase");
reference_DHAP_2->
setId(
"ref_DHAP_2");
reference_GAP_2->
setId(
"ref_GAP_2");
reaction_GAPDeh->
setId(
"GAP_Dehydrogenase");
reference_GAP_3->
setId(
"ref_GAP_3");
reference_BPG_1->
setId(
"ref_BPG_1");
reference_NAD_1->
setId(
"ref_NAD_1");
reference_NADH_1->
setId(
"ref_NADH_1");
reference_H_5->
setId(
"ref_H_5");
reference_PI_1->
setId(
"ref_PI_1");
reaction_PGK->
setId(
"Phosphoglyceratekinase");
reference_BPG_2->
setId(
"ref_BPG_2");
reference_3PG_1->
setId(
"ref_3PG_1");
reference_ATP_3->
setId(
"ref_ATP_3");
reference_ADP_3->
setId(
"ref_ADP_3");
reference_H_3->
setId(
"ref_H_3");
reaction_PGM->
setId(
"Phosphoglyceratemutase");
reference_3PG_2->
setId(
"ref_3PG_2");
reference_2PG_1->
setId(
"ref_2PG_1");
reaction_Enolase->
setId(
"Enolase");
reference_2PG_2->
setId(
"ref_2PG_2");
reference_PEP_1->
setId(
"ref_PEP_1");
reference_H2O_1->
setId(
"ref_H2O_1");
reaction_PK->
setId(
"Pyruvatekinase");
reference_PEP_2->
setId(
"ref_PEP_2");
reference_Pyr_1->
setId(
"ref_Pyr_1");
reference_ATP_4->
setId(
"ref_ATP_4");
reference_ADP_4->
setId(
"ref_ADP_4");
reference_H_4->
setId(
"ref_H_4");
layout->
setId(
"Glycolysis_Layout");
glyph_Gluc->
setId(
"glyph_Gluc");
tGlyph->
setId(
"TextGlyph_01");
bb =
BoundingBox(&layoutns,
"bbT_01", 115, 20, 110, 20);
glyph_ATP_1->
setId(
"glyph_ATP_1");
tGlyph->
setId(
"TextGlyph_02");
bb =
BoundingBox(&layoutns,
"bbT_02", 280, 70, 60, 20);
glyph_ADP_1->
setId(
"glyph_ADP_1");
bb =
BoundingBox(&layoutns,
"bb_03", 270, 140, 80, 20);
tGlyph->
setId(
"TextGlyph_03");
bb =
BoundingBox(&layoutns,
"bbT_03", 280, 140, 60, 20);
tGlyph->
setId(
"TextGlyph_plus_01");
bb =
BoundingBox(&layoutns,
"bb_plus_01", 350, 140, 20, 20);
glyph_H_1->
setId(
"glyph_H_1");
bb =
BoundingBox(&layoutns,
"bb_04", 380, 140, 60, 20);
tGlyph->
setId(
"TextGlyph_04");
bb =
BoundingBox(&layoutns,
"bbT_04", 390, 140, 40, 20);
glyph_G6P->
setId(
"glyph_G6P");
bb =
BoundingBox(&layoutns,
"bb_05", 50, 190, 270, 20);
tGlyph->
setId(
"TextGlyph_05");
bb =
BoundingBox(&layoutns,
"bbT_05", 60, 190, 250, 20);
glyph_F6P->
setId(
"glyph_F6P");
bb =
BoundingBox(&layoutns,
"bb_06", 50, 360, 270, 20);
tGlyph->
setId(
"TextGlyph_06");
bb =
BoundingBox(&layoutns,
"bbT_06", 60, 360, 250, 20);
glyph_ATP_2->
setId(
"glyph_ATP_2");
bb =
BoundingBox(&layoutns,
"bb_07", 270, 410, 80, 20);
tGlyph->
setId(
"TextGlyph_07");
bb =
BoundingBox(&layoutns,
"bbT_07", 280, 410, 60, 20);
glyph_ADP_2->
setId(
"glyph_ADP_2");
bb =
BoundingBox(&layoutns,
"bb_08", 270, 480, 80, 20);
tGlyph->
setId(
"TextGlyph_08");
bb =
BoundingBox(&layoutns,
"bbT_08", 280, 480, 60, 20);
tGlyph->
setId(
"TextGlyph_plus_02");
bb =
BoundingBox(&layoutns,
"bb_plus_02", 350, 480, 20, 20);
glyph_H_2->
setId(
"glyph_H_2");
bb =
BoundingBox(&layoutns,
"bb_09", 380, 480, 60, 20);
tGlyph->
setId(
"TextGlyph_09");
bb =
BoundingBox(&layoutns,
"bbT_09", 390, 480, 40, 20);
glyph_F16BP->
setId(
"glyph_F16BP");
bb =
BoundingBox(&layoutns,
"bb_10", 20, 530, 340, 20);
tGlyph->
setId(
"TextGlyph_10");
bb =
BoundingBox(&layoutns,
"bbT_10", 30, 530, 320, 20);
glyph_DHAP->
setId(
"glyph_DHAP");
bb =
BoundingBox(&layoutns,
"bb_11", 380, 595, 340, 20);
tGlyph->
setId(
"TextGlyph_11");
bb =
BoundingBox(&layoutns,
"bbT_11", 390, 595, 320, 20);
glyph_GAP->
setId(
"glyph_GAP");
bb =
BoundingBox(&layoutns,
"bb_12", 20, 700, 340, 20);
tGlyph->
setId(
"TextGlyph_12");
bb =
BoundingBox(&layoutns,
"bbT_12", 30, 700, 320, 20);
glyph_NAD_1->
setId(
"glyph_NAD_1");
bb =
BoundingBox(&layoutns,
"bb_13", 270, 750, 80, 20);
tGlyph->
setId(
"TextGlyph_13");
bb =
BoundingBox(&layoutns,
"bbT_13", 280, 750, 60, 20);
tGlyph->
setId(
"TextGlyph_plus_06");
bb =
BoundingBox(&layoutns,
"bb_plus_06", 350, 750, 20, 20);
glyph_PI_1->
setId(
"glyph_PI_1");
bb =
BoundingBox(&layoutns,
"bb_14", 380, 750, 60, 20);
tGlyph->
setId(
"TextGlyph_14");
bb =
BoundingBox(&layoutns,
"bbT_14", 390, 750, 40, 20);
glyph_NADH_1->
setId(
"glyph_NADH_1");
bb =
BoundingBox(&layoutns,
"bb_15", 270, 820, 100, 20);
tGlyph->
setId(
"TextGlyph_15");
bb =
BoundingBox(&layoutns,
"bbT_15", 280, 820, 80, 20);
tGlyph->
setId(
"TextGlyph_plus_06");
bb =
BoundingBox(&layoutns,
"bb_plus_06", 365, 820, 20, 20);
glyph_H_5->
setId(
"glyph_H_5");
bb =
BoundingBox(&layoutns,
"bb_16", 390, 820, 60, 20);
tGlyph->
setId(
"TextGlyph_16");
bb =
BoundingBox(&layoutns,
"bbT_16", 400, 820, 40, 20);
glyph_BPG->
setId(
"glyph_BPG");
bb =
BoundingBox(&layoutns,
"bb_17", 30, 870, 310, 20);
tGlyph->
setId(
"TextGlyph_17");
bb =
BoundingBox(&layoutns,
"bbT_17", 40, 870, 290, 20);
glyph_ADP_3->
setId(
"glyph_ADP_3");
bb =
BoundingBox(&layoutns,
"bb_18", 270, 920, 80, 20);
tGlyph->
setId(
"TextGlyph_18");
bb =
BoundingBox(&layoutns,
"bbT_18", 280, 920, 60, 20);
tGlyph->
setId(
"TextGlyph_plus_03");
bb =
BoundingBox(&layoutns,
"bb_plus_03", 350, 920, 20, 20);
glyph_H_3->
setId(
"glyph_H_3");
bb =
BoundingBox(&layoutns,
"bb_19", 380, 920, 60, 20);
tGlyph->
setId(
"TextGlyph_19");
bb =
BoundingBox(&layoutns,
"bbT_19", 390, 920, 40, 20);
glyph_ATP_3->
setId(
"glyph_ATP_3");
bb =
BoundingBox(&layoutns,
"bb_20", 270, 990, 80, 20);
tGlyph->
setId(
"TextGlyph_20");
bb =
BoundingBox(&layoutns,
"bbT_20", 280, 990, 60, 20);
glyph_3PG->
setId(
"glyph_3PG");
bb =
BoundingBox(&layoutns,
"bb_21", 50, 1040, 250, 20);
tGlyph->
setId(
"TextGlyph_21");
bb =
BoundingBox(&layoutns,
"bbT_21", 60, 1040, 230, 20);
glyph_2PG->
setId(
"glyph_2PG");
bb =
BoundingBox(&layoutns,
"bb_22", 50, 1210, 250, 20);
tGlyph->
setId(
"TextGlyph_22");
bb =
BoundingBox(&layoutns,
"bbT_22", 60, 1210, 230, 20);
glyph_H2O_1->
setId(
"glyph_H2O_1");
bb =
BoundingBox(&layoutns,
"bb_23", 270, 1350, 80, 20);
tGlyph->
setId(
"TextGlyph_23");
bb =
BoundingBox(&layoutns,
"bbT_23", 280, 1350, 60, 20);
glyph_PEP->
setId(
"glyph_PEP");
bb =
BoundingBox(&layoutns,
"bb_24", 40, 1380, 265, 20);
tGlyph->
setId(
"TextGlyph_24");
bb =
BoundingBox(&layoutns,
"bbT_24", 50, 1380, 245, 20);
glyph_ADP_4->
setId(
"glyph_ADP_4");
bb =
BoundingBox(&layoutns,
"bb_25", 270, 1430, 80, 20);
tGlyph->
setId(
"TextGlyph_25");
bb =
BoundingBox(&layoutns,
"bbT_25", 280, 1430, 60, 20);
tGlyph->
setId(
"TextGlyph_plus_04");
bb =
BoundingBox(&layoutns,
"bb_plus_04", 345, 1430, 20, 20);
glyph_H_4->
setId(
"glyph_H_4");
bb =
BoundingBox(&layoutns,
"bb_26", 370, 1430, 60, 20);
tGlyph->
setId(
"TextGlyph_26");
bb =
BoundingBox(&layoutns,
"bbT_26", 380, 1430, 40, 20);
glyph_ATP_4->
setId(
"glyph_ATP_4");
bb =
BoundingBox(&layoutns,
"bb_27", 270, 1520, 80, 20);
tGlyph->
setId(
"TextGlyph_27");
bb =
BoundingBox(&layoutns,
"bbT_27", 280, 1520, 60, 20);
glyph_Pyr->
setId(
"glyph_Pyr");
bb =
BoundingBox(&layoutns,
"bb_28", 100, 1550, 140, 20);
tGlyph->
setId(
"TextGlyph_28");
bb =
BoundingBox(&layoutns,
"bbT_28", 110, 1550, 120, 20);
glyph_Hexokinase->
setId(
"glyph_Hexokinase");
Point p(&layoutns, 170, 100);
p =
Point(&layoutns, 170, 130);
glyph_PGIsomerase->
setId(
"glyph_PGIsomerase");
p =
Point(&layoutns, 170, 270);
p =
Point(&layoutns, 170, 300);
glyph_PFK->
setId(
"glyph_PFK");
p =
Point(&layoutns, 170, 440);
p =
Point(&layoutns, 170, 470);
glyph_Aldolase->
setId(
"glyph_Aldolase");
p =
Point(&layoutns, 170, 610);
p =
Point(&layoutns, 170, 640);
glyph_TPI->
setId(
"glyph_TPI");
p =
Point(&layoutns, 515, 700);
p =
Point(&layoutns, 515, 700);
glyph_GAPDeh->
setId(
"glyph_GAPDeh");
p =
Point(&layoutns, 170, 780);
p =
Point(&layoutns, 170, 810);
glyph_PGK->
setId(
"glyph_PGK");
p =
Point(&layoutns, 170, 950);
p =
Point(&layoutns, 170, 980);
glyph_PGM->
setId(
"glyph_PGM");
p =
Point(&layoutns, 170, 1120);
p =
Point(&layoutns, 170, 1150);
glyph_Enolase->
setId(
"glyph_Enolase");
p =
Point(&layoutns, 170, 1290);
p =
Point(&layoutns, 170, 1320);
glyph_PK->
setId(
"glyph_PK");
p =
Point(&layoutns, 170, 1460);
p =
Point(&layoutns, 170, 1490);
speciesReferenceGlyph1->
setId(
"SpeciesReferenceGlyph_01");
p =
Point(&layoutns, 170, 100);
p =
Point(&layoutns, 170, 50);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_02");
p =
Point(&layoutns, 170, 270);
p =
Point(&layoutns, 170, 220);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_03");
p =
Point(&layoutns, 170, 440);
p =
Point(&layoutns, 170, 390);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_04");
p =
Point(&layoutns, 170, 610);
p =
Point(&layoutns, 170, 560);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_05");
p =
Point(&layoutns, 170, 780);
p =
Point(&layoutns, 170, 730);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_06");
p =
Point(&layoutns, 170, 950);
p =
Point(&layoutns, 170, 900);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_07");
p =
Point(&layoutns, 170, 1120);
p =
Point(&layoutns, 170, 1070);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_08");
p =
Point(&layoutns, 170, 1290);
p =
Point(&layoutns, 170, 1240);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_09");
p =
Point(&layoutns, 170, 1460);
p =
Point(&layoutns, 170, 1410);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_10");
p =
Point(&layoutns, 515, 700);
p =
Point(&layoutns, 535, 680);
p =
Point(&layoutns, 535, 680);
p =
Point(&layoutns, 535, 625);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_11");
p =
Point(&layoutns, 170, 130);
p =
Point(&layoutns, 170, 180);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_12");
p =
Point(&layoutns, 170, 300);
p =
Point(&layoutns, 170, 350);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_13");
p =
Point(&layoutns, 170, 470);
p =
Point(&layoutns, 170, 520);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_14");
p =
Point(&layoutns, 170, 640);
p =
Point(&layoutns, 170, 690);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_15");
p =
Point(&layoutns, 170, 640);
p =
Point(&layoutns, 270, 700);
p =
Point(&layoutns, 270, 605);
p =
Point(&layoutns, 370, 605);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_16");
p =
Point(&layoutns, 170, 810);
p =
Point(&layoutns, 170, 860);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_17");
p =
Point(&layoutns, 170, 980);
p =
Point(&layoutns, 170, 1030);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_18");
p =
Point(&layoutns, 170, 1150);
p =
Point(&layoutns, 170, 1200);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_19");
p =
Point(&layoutns, 170, 1320);
p =
Point(&layoutns, 170, 1370);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_20");
p =
Point(&layoutns, 170, 1490);
p =
Point(&layoutns, 170, 1540);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_21");
p =
Point(&layoutns, 515, 700);
p =
Point(&layoutns, 505, 710);
p =
Point(&layoutns, 505, 710);
p =
Point(&layoutns, 370, 710);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_22");
p =
Point(&layoutns, 170, 100);
p =
Point(&layoutns, 170, 80);
p =
Point(&layoutns, 170, 80);
p =
Point(&layoutns, 260, 80);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_23");
p =
Point(&layoutns, 170, 130);
p =
Point(&layoutns, 170, 150);
p =
Point(&layoutns, 170, 150);
p =
Point(&layoutns, 260, 150);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_24");
p =
Point(&layoutns, 170, 440);
p =
Point(&layoutns, 170, 420);
p =
Point(&layoutns, 170, 420);
p =
Point(&layoutns, 260, 420);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_24");
p =
Point(&layoutns, 170, 470);
p =
Point(&layoutns, 170, 490);
p =
Point(&layoutns, 170, 490);
p =
Point(&layoutns, 260, 490);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_25");
p =
Point(&layoutns, 170, 780);
p =
Point(&layoutns, 170, 760);
p =
Point(&layoutns, 170, 760);
p =
Point(&layoutns, 260, 760);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_26");
p =
Point(&layoutns, 170, 810);
p =
Point(&layoutns, 170, 830);
p =
Point(&layoutns, 170, 830);
p =
Point(&layoutns, 260, 830);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_27");
p =
Point(&layoutns, 170, 950);
p =
Point(&layoutns, 170, 930);
p =
Point(&layoutns, 170, 930);
p =
Point(&layoutns, 260, 930);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_28");
p =
Point(&layoutns, 170, 980);
p =
Point(&layoutns, 170, 1000);
p =
Point(&layoutns, 170, 1000);
p =
Point(&layoutns, 260, 1000);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_29");
p =
Point(&layoutns, 170, 1320);
p =
Point(&layoutns, 170, 1360);
p =
Point(&layoutns, 170, 1360);
p =
Point(&layoutns, 260, 1360);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_30");
p =
Point(&layoutns, 170, 1460);
p =
Point(&layoutns, 170, 1440);
p =
Point(&layoutns, 170, 1440);
p =
Point(&layoutns, 260, 1440);
speciesReferenceGlyph->
setId(
"SpeciesReferenceGlyph_31");
p =
Point(&layoutns, 170, 1490);
p =
Point(&layoutns, 170, 1530);
p =
Point(&layoutns, 170, 1530);
p =
Point(&layoutns, 260, 1530);
writeSBML(document,
"layout_example2_L3.xml");
delete document;
}
@sbmlpackage{core}
Definition: SpeciesReference.h:276
int setModel(const Model *m)
Sets the Model for this SBMLDocument to a copy of the given Model.
Definition: SBMLDocument.cpp:599
int setConstant(bool value)
Sets the value of the "constant" attribute of this Compartment object.
Definition: Compartment.cpp:681
void setRole(const std::string &role)
Sets the role based on a string.
Definition: SpeciesReferenceGlyph.cpp:338
@sbmlpackage{layout}
Definition: Dimensions.h:66
@sbmlpackage{core}
Definition: Reaction.h:219
virtual int setName(const std::string &name)
Sets the value of the "name" attribute of this Species.
Definition: Species.cpp:613
Definition of Layout for SBML Layout.
void setBasePoint1(const Point *p)
Initializes first base point with a copy of the given point.
Definition: CubicBezier.cpp:403
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this GraphicalObject.
Definition: GraphicalObject.cpp:385
@sbmlpackage{layout}
Definition: CubicBezier.h:66
@sbmlpackage{layout}
Definition: Point.h:60
@sbmlpackage{layout}
Definition: Curve.h:212
virtual const std::string & getId() const
Returns the value of the "id" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:128
Definition of LayoutModelPlugin, the plugin class of layout package for Model element.
SpeciesReferenceGlyph * createSpeciesReferenceGlyph()
Creates a new SpeciesReferenceGlyph object, adds it to the end of the list of species reference objec...
Definition: ReactionGlyph.cpp:496
LineSegment * createLineSegment()
Creates a new LineSegment and adds it to the end of the list.
Definition: Curve.cpp:359
Definition of Point for SBML Layout.
Reaction * createReaction()
Creates a new Reaction inside this Model and returns it.
Definition: Model.cpp:1779
LineSegment * createLineSegment()
Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curv...
Definition: SpeciesReferenceGlyph.cpp:457
@sbmlpackage{layout}
Definition: LayoutModelPlugin.h:63
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:375
int setReversible(bool value)
Sets the value of the "reversible" attribute of this Reaction.
Definition: Reaction.cpp:607
@sbmlpackage{layout}
Definition: ReactionGlyph.h:250
CubicBezier * createCubicBezier()
Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curv...
Definition: SpeciesReferenceGlyph.cpp:469
@ SPECIES_ROLE_SUBSTRATE
Definition: SpeciesReferenceRole.h:56
Definition of SpeciesGlyph for SBML Layout.
void setSpeciesId(const std::string &id)
Sets the id of the associated species object.
Definition: SpeciesGlyph.cpp:201
Definition of SpeciesReferenceGlyph for SBML Layout.
Model * createModel(const std::string sid="")
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
Definition: SBMLDocument.cpp:643
Layout * createLayout()
Creates a new layout object and adds it to the list of layout objects and returns it.
Definition: LayoutModelPlugin.cpp:475
void setEnd(const Point *end)
Initializes the end point with a copy of the given Point object.
Definition: LineSegment.cpp:369
int setFast(bool value)
Sets the value of the "fast" attribute of this Reaction.
Definition: Reaction.cpp:620
Species * createSpecies()
Creates a new Species inside this Model and returns it.
Definition: Model.cpp:1590
Definition of CubicBezier for SBML Layout.
void setSpeciesGlyphId(const std::string &speciesGlyphId)
Sets the id of the associated species glyph.
Definition: SpeciesReferenceGlyph.cpp:284
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:210
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Compartment object.
Definition: Compartment.cpp:474
Definition of BoundingBox for SBML Layout.
TextGlyph * createTextGlyph()
Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer t...
Definition: Layout.cpp:1443
SpeciesReference * createReactant()
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
Definition: Reaction.cpp:955
const Curve * getCurve() const
Returns the curve object for the reaction glyph.
Definition: ReactionGlyph.cpp:447
Definitions of SpeciesReference and ListOfSpeciesReferences.
void setSpeciesReferenceId(const std::string &id)
Sets the id of the associated species reference.
Definition: SpeciesReferenceGlyph.cpp:304
int setConstant(bool value)
Sets the "constant" attribute of this Species object.
Definition: Species.cpp:824
Definition of ReactionGlyph for SBML Layout.
void setBasePoint2(const Point *p)
Initializes second base point with a copy of the given point.
Definition: CubicBezier.cpp:452
@sbmlpackage{core}
Definition: Compartment.h:485
@sbmlpackage{layout}
Definition: SpeciesGlyph.h:60
ReactionGlyph * createReactionGlyph()
Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a p...
Definition: Layout.cpp:1412
Definition of LayoutExtension, the core module of layout package.
Definition of Curve for SBML Layout.
int setSpecies(const std::string &sid)
Sets the "species" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:192
Definitions of Species and ListOfSpecies.
@sbmlpackage{layout}
Definition: Layout.h:784
@sbmlpackage{core}
Definition: Model.h:480
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Species.
Definition: Species.cpp:586
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Layout.
Definition: Layout.cpp:449
int setGraphicalObjectId(const std::string &id)
Sets the id of the associated graphical object.
Definition: TextGlyph.cpp:241
Definition of LineSegment for SBML Layout.
virtual const std::string & getId() const
Returns the value of the "id" attribute of this GraphicalObject.
Definition: GraphicalObject.cpp:367
Writes an SBML Document to file or in-memory string.
Definitions of Reaction and ListOfReactions.
@sbmlpackage{layout}
Definition: BoundingBox.h:59
@sbmlpackage{layout}
Definition: LineSegment.h:64
SpeciesReference * createProduct()
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
Definition: Reaction.cpp:983
int setReactionId(const std::string &id)
Sets the id of the associated reaction.
Definition: ReactionGlyph.cpp:319
Top-level container for an SBML Model and associated data.
void setStart(const Point *start)
Initializes the start point with a copy of the given Point object.
Definition: LineSegment.cpp:322
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:516
int enableDefaultNS(const std::string &package, bool flag)
Set/unset default namespace to each top-level element defined in the given package extension.
Definition: SBMLDocument.cpp:1382
int setOriginOfTextId(const std::string &orig)
Sets the id of the origin of text.
Definition: TextGlyph.cpp:261
void setDimensions(const Dimensions *dimensions)
Sets the dimensions of the layout.
Definition: Layout.cpp:515
Definition of CompartmentGlyph for SBML Layout.
int setConstant(bool flag)
Sets the "constant" attribute of this SpeciesReference to the given boolean flag.
Definition: SpeciesReference.cpp:395
@sbmlpackage{core}
Definition: SBMLNamespaces.h:140
SpeciesGlyph * createSpeciesGlyph()
Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a poi...
Definition: Layout.cpp:1396
int setCompartment(const std::string &sid)
Sets the "compartment" attribute of this Species object.
Definition: Species.cpp:665
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Compartment.
Definition: Compartment.cpp:238
Definition of Dimensions for SBML Layout.
Definitions of Compartment and ListOfCompartments.
@sbmlpackage{layout}
Definition: TextGlyph.h:60
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Model.
Definition: Model.cpp:717
Compartment * createCompartment()
Creates a new Compartment inside this Model and returns it.
Definition: Model.cpp:1563
@sbmlpackage{layout}
Definition: SpeciesReferenceGlyph.h:66
void setBoundingBox(const BoundingBox *bb)
Sets the boundingbox for the GraphicalObject.
Definition: GraphicalObject.cpp:470
@ SPECIES_ROLE_SIDESUBSTRATE
Definition: SpeciesReferenceRole.h:58
@ SPECIES_ROLE_PRODUCT
Definition: SpeciesReferenceRole.h:57
@sbmlpackage{core}
Definition: Species.h:424
@ SPECIES_ROLE_SIDEPRODUCT
Definition: SpeciesReferenceRole.h:59
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Species.
Definition: Species.cpp:273
void setText(const std::string &text)
Sets the text to be displayed by the text glyph.
Definition: TextGlyph.cpp:221
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
@sbmlpackage{core}
Definition: SBMLDocument.h:343
SBasePlugin * getPlugin(const std::string &package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given p...
Definition: SBase.cpp:3460
int setBoundaryCondition(bool value)
Sets the "boundaryCondition" attribute of this Species object.
Definition: Species.cpp:791
int setHasOnlySubstanceUnits(bool value)
Sets the "hasOnlySubstanceUnits" attribute of this Species object.
Definition: Species.cpp:771
int writeSBML(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file named by filename.