# 
# @file    multi_example3.cs
# @brief   multi create example
# @author  Sarah Keating
# @author  Frank Bergmann
# 
# <!--------------------------------------------------------------------------
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#     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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# Copyright (C) 2006-2008 by the California Institute of Technology,
#     Pasadena, CA, USA 
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# Copyright (C) 2002-2005 jointly by the following organizations:
#     1. California Institute of Technology, Pasadena, CA, USA
#     2. Japan Science and Technology Agency, Japan
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# This library is free software; you can redistribute it and/or modify it
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# in the file named "LICENSE.txt" included with this software distribution
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# 
from libsbml import * 

sbmlns = SBMLNamespaces(3,1,"multi",1)

# create the document

document = SBMLDocument(sbmlns)

# set the required attribute to True
docPlug = document.getPlugin("multi")
docPlug.setRequired(True)

# create the Model

model=document.createModel()

# create the compartments

c = model.createCompartment()
c.setId("membrane")
c.setConstant(True)

# set the multi attribute isType via the compartmentPlugin
compPlug = c.getPlugin("multi")
compPlug.setIsType(True)

# create the speciesTypes

modelPlug = model.getPlugin("multi")

st = modelPlug.createMultiSpeciesType()
st.setId("stX")
st.setCompartment("membrane")

# create species
s = model.createSpecies()
s.setId("s1")
s.setCompartment("membrane")
s.setBoundaryCondition(False)
s.setHasOnlySubstanceUnits(False)
s.setConstant(False)

# set the multi attribute speciesType via the compartmentPlugin
spPlug = s.getPlugin("multi")
spPlug.setSpeciesType("stX")

# create species feature
sf = spPlug.createSpeciesFeature()
sf.setSpeciesFeatureType("a")
sf.setOccur(1)
sf.setComponent("b")

sfv = sf.createSpeciesFeatureValue()
sfv.setValue("c")

# create a subListOfSpeciesFeatures
subloSF = spPlug.createSubListOfSpeciesFeatures()
subloSF.setRelation(Relation_fromString("and"))

# add speciesFeatures to the subList
sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a1")
sf1.setOccur(1)
sf1.setComponent("b1")

sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c1")

subloSF.appendAndOwn(sf1)

sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a2")
sf1.setOccur(1)
sf1.setComponent("b2")

sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c2")

subloSF.appendAndOwn(sf1)

# create a second subListOfSpeciesfeatures
subloSF = spPlug.createSubListOfSpeciesFeatures()
subloSF.setRelation(Relation_fromString("or"))

sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a3")
sf1.setOccur(1)
sf1.setComponent("b3")

sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c3")

subloSF.appendAndOwn(sf1)

sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a4")
sf1.setOccur(1)
sf1.setComponent("b4")

sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c4")

subloSF.appendAndOwn(sf1)

writeSBML(document,"multi_example3.xml")