MATLAB_SBML_STRUCTURE_FUNCTIONS\COMPARTMENT

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

Function are:

Compartment = Compartment_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 Compartment 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

compartmentType = Compartment_getCompartmentType(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the compartmentType attribute

constant = Compartment_getConstant(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the constant attribute

id = Compartment_getId(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the id attribute

metaid = Compartment_getMetaid(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the metaid attribute

name = Compartment_getName(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the name attribute

outside = Compartment_getOutside(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the outside attribute

sboTerm = Compartment_getSBOTerm(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the sboTerm attribute

size = Compartment_getSize(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the size attribute

spatialDimensions = Compartment_getSpatialDimensions(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the spatialDimensions attribute

units = Compartment_getUnits(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the units attribute

volume = Compartment_getVolume(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the value of the volume attribute

y = Compartment_isAssignedByRateRule(SBMLCompartment, SBMLRules)

Takes

1. SBMLCompartment, an SBML Compartment 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 Compartment - 0 if the Compartment 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 = Compartment_isAssignedByRule(SBMLCompartment, SBMLRules)

Takes

1. SBMLCompartment, an SBML Compartment 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 Compartment - 0 if the Compartment 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 = Compartment_isInAlgebraicRule(SBMLCompartment, SBMLRules)

Takes

1. SBMLCompartment, an SBML Compartment 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 Compartment appears in - 0 if the Compartment 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 = Compartment_isSetCompartmentType(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetId(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetMetaid(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetName(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetOutside(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetSBOTerm(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetSize(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetSpatialDimensions(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetUnits(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

value = Compartment_isSetVolume(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

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

SBMLCompartment = Compartment_setCompartmentType(SBMLCompartment, compartmentType)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. compartmentType; a string representing the compartmentType to be set

Returns

1. the SBML Compartment structure with the new value for the compartmentType attribute

SBMLCompartment = Compartment_setConstant(SBMLCompartment, constant)

Takes

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

Returns

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

SBMLCompartment = Compartment_setId(SBMLCompartment, id)

Takes

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

Returns

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

SBMLCompartment = Compartment_setMetaid(SBMLCompartment, metaid)

Takes

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

Returns

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

SBMLCompartment = Compartment_setName(SBMLCompartment, name)

Takes

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

Returns

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

SBMLCompartment = Compartment_setOutside(SBMLCompartment, outside)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. outside; a string representing the outside to be set

Returns

1. the SBML Compartment structure with the new value for the outside attribute

SBMLCompartment = Compartment_setSBOTerm(SBMLCompartment, sboTerm)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. sboTerm, an integer representing the sboTerm to be set

Returns

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

SBMLCompartment = Compartment_setSize(SBMLCompartment, size)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. size; number representing the value of size to be set

Returns

1. the SBML Compartment structure with the new value for the size attribute

SBMLCompartment = Compartment_setSpatialDimensions(SBMLCompartment, spatialDimensions)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. spatialDimensions; number representing the value of spatialDimensions to be set

Returns

1. the SBML Compartment structure with the new value for the spatialDimensions attribute

SBMLCompartment = Compartment_setUnits(SBMLCompartment, units)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. units; a string representing the units to be set

Returns

1. the SBML Compartment structure with the new value for the units attribute

SBMLCompartment = Compartment_setVolume(SBMLCompartment, volume)

Takes

1. SBMLCompartment, an SBML Compartment structure
2. volume; number representing the value of volume to be set

Returns

1. the SBML Compartment structure with the new value for the volume attribute

SBMLCompartment = Compartment_unsetCompartmentType(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the compartmentType attribute unset

SBMLCompartment = Compartment_unsetId(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the id attribute unset

SBMLCompartment = Compartment_unsetMetaid(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the metaid attribute unset

SBMLCompartment = Compartment_unsetName(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the name attribute unset

SBMLCompartment = Compartment_unsetOutside(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the outside attribute unset

SBMLCompartment = Compartment_unsetSBOTerm(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the sboTerm attribute unset

SBMLCompartment = Compartment_unsetSize(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the size attribute unset

SBMLCompartment = Compartment_unsetSpatialDimensions(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the spatialDimensions attribute unset

SBMLCompartment = Compartment_unsetUnits(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the units attribute unset

SBMLCompartment = Compartment_unsetVolume(SBMLCompartment)

Takes

1. SBMLCompartment, an SBML Compartment structure

Returns

1. the SBML Compartment structure with the volume attribute unset