jp.ac.keio.bio.fun.xitosbml.pane

Class SBMLProcessUtil

java.lang.Object

jp.ac.keio.bio.fun.xitosbml.pane.SBMLProcessUtil

public class SBMLProcessUtil
extends Object

The class SBMLProcessUtil, which contains several useful static methods to manipulate SBML objects. Date Created: Jan 20, 2016

Author:

Kaito Ii <ii@fun.bio.keio.ac.jp>, Akira Funahashi <funa@bio.keio.ac.jp>

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	bounds The Constant bounds.
static String[]	boundType The Constant boundType.
static String[]	diffType The Constant diffType.
static String[]	lcoord The Constant lcoord.

Constructor Summary

Constructors

Constructor and Description
SBMLProcessUtil()

Method Summary

Modifier and Type	Method and Description
static org.sbml.jsbml.Parameter	copyAdvectionCoefficientContents(org.sbml.jsbml.Parameter src, org.sbml.jsbml.Parameter dst) Copy contents of AdvectionCoefficient from src to dst and returns dst object.
static org.sbml.jsbml.Parameter	copyBoundaryConditionContents(org.sbml.jsbml.Parameter src, org.sbml.jsbml.Parameter dst) Copy contents of BoundaryCondition from src to dst and returns dst object.
static org.sbml.jsbml.Parameter	copyDiffusionCoefficientContents(org.sbml.jsbml.Parameter src, org.sbml.jsbml.Parameter dst) Copy contents of DiffusionCoefficient from src to dst and returns dst object.
static org.sbml.jsbml.Parameter	copyParameterContents(org.sbml.jsbml.Parameter src, org.sbml.jsbml.Parameter dst) Copy contents of Parameter from src to dst and returns dst object.
static org.sbml.jsbml.Reaction	copyReactionContents(org.sbml.jsbml.Reaction src, org.sbml.jsbml.Reaction dst) Copy contents of Reaction from src to dst and returns dst object.
static org.sbml.jsbml.Species	copySpeciesContents(org.sbml.jsbml.Species src, org.sbml.jsbml.Species dst) Copy contents of Species from src to dst and returns dst object.
static String[]	listIdToStringArray(org.sbml.jsbml.ListOf<?> lo) Converts list of SBase to a String.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

lcoord

public static final String[] lcoord

The Constant lcoord.

bounds

public static final String[] bounds

The Constant bounds.

boundType

public static final String[] boundType

The Constant boundType.

diffType

public static final String[] diffType

The Constant diffType.

Constructor Detail

SBMLProcessUtil

public SBMLProcessUtil()

Method Detail

listIdToStringArray

public static String[] listIdToStringArray(org.sbml.jsbml.ListOf<?> lo)

Converts list of SBase to a String. The converted array of string will contain the id of all SBase included in the list.

Parameters:

lo - the list of Objects (SBase)

Returns:

the converted array of string (string[])

copySpeciesContents

public static org.sbml.jsbml.Species copySpeciesContents(org.sbml.jsbml.Species src,
                                                         org.sbml.jsbml.Species dst)

Copy contents of Species from src to dst and returns dst object.

Parameters:

src - source Species

dst - destination Species

Returns:

destination Species

copyParameterContents

public static org.sbml.jsbml.Parameter copyParameterContents(org.sbml.jsbml.Parameter src,
                                                             org.sbml.jsbml.Parameter dst)

Copy contents of Parameter from src to dst and returns dst object.

Parameters:

src - source Parameter

dst - destination Parameter

Returns:

destination Parameter

copyReactionContents

public static org.sbml.jsbml.Reaction copyReactionContents(org.sbml.jsbml.Reaction src,
                                                           org.sbml.jsbml.Reaction dst)

Copy contents of Reaction from src to dst and returns dst object. KineticLaw is replaced by deep-copied src.kineticLaw.

Parameters:

src - source Reaction

dst - destination Reaction

Returns:

destination Reaction

copyAdvectionCoefficientContents

public static org.sbml.jsbml.Parameter copyAdvectionCoefficientContents(org.sbml.jsbml.Parameter src,
                                                                        org.sbml.jsbml.Parameter dst)

Copy contents of AdvectionCoefficient from src to dst and returns dst object.

Parameters:

src - source AdvectionCoefficient

dst - destination AdvectionCoefficient

Returns:

destination AdvectionCoefficient

copyBoundaryConditionContents

public static org.sbml.jsbml.Parameter copyBoundaryConditionContents(org.sbml.jsbml.Parameter src,
                                                                     org.sbml.jsbml.Parameter dst)

Copy contents of BoundaryCondition from src to dst and returns dst object.

Parameters:

src - source BoundaryCondition

dst - destination BoundaryCondition

Returns:

destination BoundaryCondition

copyDiffusionCoefficientContents

public static org.sbml.jsbml.Parameter copyDiffusionCoefficientContents(org.sbml.jsbml.Parameter src,
                                                                        org.sbml.jsbml.Parameter dst)

Copy contents of DiffusionCoefficient from src to dst and returns dst object.

Parameters:

src - source DiffusionCoefficient

dst - destination DiffusionCoefficient

Returns:

destination DiffusionCoefficient