MATLABSBMLSTRUCTURE_FUNCTIONS\SPECIESREFERENCE

The functions allow users to create and work with the SBML SpeciesReference structure.

Function are:

SpeciesReference = SpeciesReference_create(level(optional), version(optional) )

Takes

1. level, an integer representing an SBML level (optional)
2. version, an integer representing an SBML version (optional)

Returns

1. a MATLAB_SBML SpeciesReference structure of the appropriate level and version

NOTE: the optional level and version preserve backwards compatibility a missing version argument will default to L1V2; L2V4 or L3V1 missing both arguments will default to L3V1

SBMLSpeciesReference = SpeciesReference_createStoichiometryMath(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with a new SBML StoichiometryMath structure added

constant = SpeciesReference_getConstant(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the constant attribute

denominator = SpeciesReference_getDenominator(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the denominator attribute

id = SpeciesReference_getId(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the id attribute

metaid = SpeciesReference_getMetaid(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the metaid attribute

name = SpeciesReference_getName(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the name attribute

sboTerm = SpeciesReference_getSBOTerm(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the sboTerm attribute

species = SpeciesReference_getSpecies(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the species attribute

stoichiometry = SpeciesReference_getStoichiometry(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the value of the stoichiometry attribute

stoichiometryMath = SpeciesReference_getStoichiometryMath(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML StoichiometryMath structure

y = SpeciesReference_isAssignedByRateRule(SBMLSpeciesReference, SBMLRules)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. SBMLRules; the array of rules from an SBML Model structure

Returns

y = - the index of the rateRule used to assigned value to the SpeciesReference - 0 if the SpeciesReference is not assigned by rateRule

!--------------------------------------------------------------------------- This file is part of SBMLToolbox. Please visit http://sbml.org for more information about SBML, and the latest version of SBMLToolbox.

Copyright (C) 2009-2016 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK

Copyright (C) 2006-2008 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. University of Hertfordshire, Hatfield, UK

Copyright (C) 2003-2005 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. Japan Science and Technology Agency, Japan 3. University of Hertfordshire, Hatfield, UK

SBMLToolbox is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution. ---------------------------------------------------------------------- -->

y = SpeciesReference_isAssignedByRule(SBMLSpeciesReference, SBMLRules)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. SBMLRules; the array of rules from an SBML Model structure

Returns

y = - the index of the assignmentRule used to assigned value to the SpeciesReference - 0 if the SpeciesReference is not assigned by assignmentRule

!--------------------------------------------------------------------------- This file is part of SBMLToolbox. Please visit http://sbml.org for more information about SBML, and the latest version of SBMLToolbox.

Copyright (C) 2009-2016 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK

Copyright (C) 2006-2008 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. University of Hertfordshire, Hatfield, UK

Copyright (C) 2003-2005 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. Japan Science and Technology Agency, Japan 3. University of Hertfordshire, Hatfield, UK

SBMLToolbox is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution. ---------------------------------------------------------------------- -->

y = SpeciesReference_isInAlgebraicRule(SBMLSpeciesReference, SBMLRules)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. SBMLRules; the array of rules from an SBML Model structure

Returns

y = - an array of the indices of any algebraicRules the id of the SpeciesReference appears in - 0 if the SpeciesReference appears in no algebraicRules

!--------------------------------------------------------------------------- This file is part of SBMLToolbox. Please visit http://sbml.org for more information about SBML, and the latest version of SBMLToolbox.

Copyright (C) 2009-2016 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK

Copyright (C) 2006-2008 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. University of Hertfordshire, Hatfield, UK

Copyright (C) 2003-2005 jointly by the following organizations: 1. California Institute of Technology, Pasadena, CA, USA 2. Japan Science and Technology Agency, Japan 3. University of Hertfordshire, Hatfield, UK

SBMLToolbox is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. A copy of the license agreement is provided in the file named "LICENSE.txt" included with this software distribution. ---------------------------------------------------------------------- -->

value = SpeciesReference_isSetDenominator(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the denominator attribute is set
   • 0 otherwise

value = SpeciesReference_isSetId(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the id attribute is set
   • 0 otherwise

value = SpeciesReference_isSetMetaid(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the metaid attribute is set
   • 0 otherwise

value = SpeciesReference_isSetName(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the name attribute is set
   • 0 otherwise

value = SpeciesReference_isSetSBOTerm(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the sboTerm attribute is set
   • 0 otherwise

value = SpeciesReference_isSetSpecies(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the species attribute is set
   • 0 otherwise

value = SpeciesReference_isSetStoichiometry(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the stoichiometry attribute is set
   • 0 otherwise

value = SpeciesReference_isSetStoichiometryMath(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. value =
   • 1 if the stoichiometryMath structure is set
   • 0 otherwise

SBMLSpeciesReference = SpeciesReference_setConstant(SBMLSpeciesReference, constant)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. constant, an integer (0/1) representing the value of constant to be set

Returns

1. the SBML SpeciesReference structure with the new value for the constant attribute

SBMLSpeciesReference = SpeciesReference_setDenominator(SBMLSpeciesReference, denominator)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. denominator, an integer representing the denominator to be set

Returns

1. the SBML SpeciesReference structure with the new value for the denominator attribute

SBMLSpeciesReference = SpeciesReference_setId(SBMLSpeciesReference, id)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. id; a string representing the id to be set

Returns

1. the SBML SpeciesReference structure with the new value for the id attribute

SBMLSpeciesReference = SpeciesReference_setMetaid(SBMLSpeciesReference, metaid)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. metaid; a string representing the metaid to be set

Returns

1. the SBML SpeciesReference structure with the new value for the metaid attribute

SBMLSpeciesReference = SpeciesReference_setName(SBMLSpeciesReference, name)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. name; a string representing the name to be set

Returns

1. the SBML SpeciesReference structure with the new value for the name attribute

SBMLSpeciesReference = SpeciesReference_setSBOTerm(SBMLSpeciesReference, sboTerm)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. sboTerm, an integer representing the sboTerm to be set

Returns

1. the SBML SpeciesReference structure with the new value for the sboTerm attribute

SBMLSpeciesReference = SpeciesReference_setSpecies(SBMLSpeciesReference, species)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. species; a string representing the species to be set

Returns

1. the SBML SpeciesReference structure with the new value for the species attribute

SBMLSpeciesReference = SpeciesReference_setStoichiometry(SBMLSpeciesReference, stoichiometry)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. stoichiometry; number representing the value of stoichiometry to be set

Returns

1. the SBML SpeciesReference structure with the new value for the stoichiometry attribute

SBMLSpeciesReference = SpeciesReference_setStoichiometryMath(SBMLSpeciesReference, SBMLStoichiometryMath)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure
2. SBMLStoichiometryMath, an SBML StoichiometryMath structure

Returns

1. the SBML SpeciesReference structure with the new value for the stoichiometryMath field

SBMLSpeciesReference = SpeciesReference_unsetDenominator(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the denominator attribute unset

SBMLSpeciesReference = SpeciesReference_unsetId(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the id attribute unset

SBMLSpeciesReference = SpeciesReference_unsetMetaid(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the metaid attribute unset

SBMLSpeciesReference = SpeciesReference_unsetName(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the name attribute unset

SBMLSpeciesReference = SpeciesReference_unsetSBOTerm(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the sboTerm attribute unset

SBMLSpeciesReference = SpeciesReference_unsetSpecies(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the species attribute unset

SBMLSpeciesReference = SpeciesReference_unsetStoichiometry(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the stoichiometry attribute unset

SBMLSpeciesReference = SpeciesReference_unsetStoichiometryMath(SBMLSpeciesReference)

Takes

1. SBMLSpeciesReference, an SBML SpeciesReference structure

Returns

1. the SBML SpeciesReference structure with the stoichiometryMath field unset