org.sbml.jsbml.ext.arrays.flattening

Class ArraysFlattening

java.lang.Object

org.sbml.jsbml.ext.arrays.flattening.ArraysFlattening

public class ArraysFlattening
extends java.lang.Object

Since:

1.0

Version:

$Rev: 1963 $

Author:

Leandro Watanabe

Field Summary

Fields

Modifier and Type	Field and Description
private static ASTNode	unknown

Constructor Summary

Constructors

Constructor and Description
ArraysFlattening()

Method Summary

Methods

Modifier and Type	Method and Description
private static void	addToParent(Model model, SBase parent, SBase child) Add the new SBase to the corresponding ListOf object.
private static void	convert(Model model, javax.swing.tree.TreeNode node, java.util.List<SBase> sbases, java.util.Map<java.lang.String,ASTNode> idToVector) This is recursively getting each TreeNode of a certain SBMLDocument.
static SBMLDocument	convert(SBMLDocument document) This method flattens out arrays objects of a given SBMLDocument.
private static void	convert(SBMLDocument doc, Model model, java.util.List<SBase> itemsToDelete, java.util.Map<java.lang.String,ASTNode> idToVector)
private static void	convertArraysMath(Model model, javax.swing.tree.TreeNode child, java.util.Map<java.lang.String,ASTNode> idToVector)
private static void	convertEvent(Model model, Event event, java.util.List<SBase> itemsToDelete, java.util.Map<java.lang.String,ASTNode> idToVector) When an event is converted, the MathContainer objects (trigger, delay, and priority) are expanded.
private static void	convertEvents(Model model, java.util.List<SBase> itemsToDelete, java.util.Map<java.lang.String,ASTNode> idToVector) Iterate through the events in the model and convert the events using the arrays package.
private static void	convertIndex(Model model, ArraysSBasePlugin arraysPlugin, SBase sbase, ArraysCompiler compiler, java.util.Map<java.lang.String,ASTNode> idToVector) This is flattening index objects by replacing the dimension ids with the corresponding index value and updating the referenced attribute.
private static void	convertMath(Model model, javax.swing.tree.TreeNode node, java.util.Map<java.lang.String,ASTNode> idToVector) This is recursively getting each TreeNode of a certain SBMLDocument and flattening vector/selector MathML objects.
private static void	convertMath(SBMLDocument doc, Model model, java.util.Map<java.lang.String,ASTNode> idToVector)
private static void	convertReaction(Model model, Reaction reaction, java.util.List<SBase> itemsToDelete, java.util.Map<java.lang.String,ASTNode> idToVector)
private static void	convertReactions(Model model, java.util.List<SBase> itemsToDelete, java.util.Map<java.lang.String,ASTNode> idToVector)
private static void	expandDim(Model model, SBase sbase, SBase parent, ArraysSBasePlugin arraysPlugin, ArraysCompiler compiler, ASTNode vector, int dim, java.util.Map<java.lang.String,ASTNode> idToVector) This method is transforming the attributes of a certain SBase object associated with the arrays package so that the SBase no longer uses the package.
private static void	expandDim(Model model, SBase sbase, SBase parent, ArraysSBasePlugin arraysPlugin, ArraysCompiler compiler, int dim, java.util.Map<java.lang.String,ASTNode> idToVector) This method is transforming the attributes of a certain SBase object associated with the arrays package so that the SBase no longer uses the package.
private static void	expandDim(Model model, javax.swing.tree.TreeNode child, java.util.List<SBase> sbases, java.util.Map<java.lang.String,ASTNode> idToVector) This expands an SBase that has a list of Dimension objects.
private static void	expandEvent(Model model, ArraysSBasePlugin arraysPlugin, SBase parent, Event event, ASTNode vector, int dim) This method is inlining the event objects present in an array.
private static void	expandReaction(Model model, ArraysSBasePlugin arraysPlugin, SBase parent, Reaction reaction, java.util.Map<java.lang.String,ASTNode> idToVector, ASTNode vector, int dim)
private static void	getVectors(SBase sbase, java.util.Map<java.lang.String,ASTNode> ids)
private static void	recursiveReplaceDimensionId(ASTNode math, java.lang.String id, int index)
private static void	removeSBases(java.util.List<SBase> itemsToDelete) This method removes a list of SBase from the respective parent.
private static ASTNode	replaceDimensionId(ASTNode math, java.lang.String id, int index)
private static void	updateEventAssignmentIndex(Model model, Event event, Dimension dimension, int index) This updates the index math of the EventAssignments of a certain Event object that utlizes the Dimension id of the parent Event.
private static void	updateEventChildrenMetaId(Model model, ArraysSBasePlugin arraysPlugin, Event event, int index)
private static void	updateIndexMath(SBase sbase, Dimension dimension, int index)
private static void	updateMathContainer(Model model, ArraysSBasePlugin arraysPlugin, MathContainer sbase, java.lang.String dimId, int index, java.util.Map<java.lang.String,ASTNode> idToVector) This updates the dimension id that appears in the math.
private static void	updateReactionChildrenMetaId(Model model, ArraysSBasePlugin arraysPlugin, Reaction reaction, int index)
private static void	updateSBase(SBMLDocument doc, ArraysSBasePlugin arraysPlugin, SBase sbase, int index) This updates the metaid of an SBase.
private static void	updateSpecRefId(Model model, ArraysSBasePlugin arraysPlugin, Reaction reaction, java.util.Map<java.lang.String,ASTNode> idToVector, int index)
private static void	updateSpecRefIndex(Model model, Reaction reaction, Dimension dimension, int index)

Methods inherited from class java.lang.Object

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

Field Detail

unknown

private static final ASTNode unknown

Constructor Detail

ArraysFlattening

public ArraysFlattening()

Method Detail

convert

public static SBMLDocument convert(SBMLDocument document)

This method flattens out arrays objects of a given SBMLDocument.

Parameters:

document - - the document you want to convert.

Returns:

new Document that is not associated with the arrays package.

removeSBases

private static void removeSBases(java.util.List<SBase> itemsToDelete)

This method removes a list of SBase from the respective parent.

Parameters:

itemsToDelete -

getVectors

private static void getVectors(SBase sbase,
              java.util.Map<java.lang.String,ASTNode> ids)

convertEvents

private static void convertEvents(Model model,
                 java.util.List<SBase> itemsToDelete,
                 java.util.Map<java.lang.String,ASTNode> idToVector)

Iterate through the events in the model and convert the events using the arrays package.

Parameters:

model -

idToIndices -

itemsToDelete -

convertEvent

private static void convertEvent(Model model,
                Event event,
                java.util.List<SBase> itemsToDelete,
                java.util.Map<java.lang.String,ASTNode> idToVector)
                          throws SBMLException

When an event is converted, the MathContainer objects (trigger, delay, and priority) are expanded. The event is expanded afterwards in case it is an array.

Parameters:

model -

event -

itemsToDelete -

Throws:

SBMLException

expandEvent

private static void expandEvent(Model model,
               ArraysSBasePlugin arraysPlugin,
               SBase parent,
               Event event,
               ASTNode vector,
               int dim)

This method is inlining the event objects present in an array.

Parameters:

model -

arraysPlugin -

parent -

event -

dim -

updateEventAssignmentIndex

private static void updateEventAssignmentIndex(Model model,
                              Event event,
                              Dimension dimension,
                              int index)

This updates the index math of the EventAssignments of a certain Event object that utlizes the Dimension id of the parent Event.

Parameters:

model -

event -

dimension -

index -

convertReactions

private static void convertReactions(Model model,
                    java.util.List<SBase> itemsToDelete,
                    java.util.Map<java.lang.String,ASTNode> idToVector)

Parameters:

model -

idToIndices -

itemsToDelete -

convertReaction

private static void convertReaction(Model model,
                   Reaction reaction,
                   java.util.List<SBase> itemsToDelete,
                   java.util.Map<java.lang.String,ASTNode> idToVector)
                             throws SBMLException

Parameters:

model -

reaction -

itemsToDelete -

Throws:

SBMLException

updateSpecRefId

private static void updateSpecRefId(Model model,
                   ArraysSBasePlugin arraysPlugin,
                   Reaction reaction,
                   java.util.Map<java.lang.String,ASTNode> idToVector,
                   int index)

Parameters:

arraysPlugin -

reaction -

index -

updateReactionChildrenMetaId

private static void updateReactionChildrenMetaId(Model model,
                                ArraysSBasePlugin arraysPlugin,
                                Reaction reaction,
                                int index)

Parameters:

arraysPlugin -

reaction -

index -

updateEventChildrenMetaId

private static void updateEventChildrenMetaId(Model model,
                             ArraysSBasePlugin arraysPlugin,
                             Event event,
                             int index)

Parameters:

arraysPlugin -

reaction -

index -

expandReaction

private static void expandReaction(Model model,
                  ArraysSBasePlugin arraysPlugin,
                  SBase parent,
                  Reaction reaction,
                  java.util.Map<java.lang.String,ASTNode> idToVector,
                  ASTNode vector,
                  int dim)

Parameters:

model -

arraysPlugin -

parent -

reaction -

dim -

updateSpecRefIndex

private static void updateSpecRefIndex(Model model,
                      Reaction reaction,
                      Dimension dimension,
                      int index)

Parameters:

model -

reaction -

dimension -

index -

updateIndexMath

private static void updateIndexMath(SBase sbase,
                   Dimension dimension,
                   int index)

Parameters:

sbase -

dimension -

index -

convert

private static void convert(SBMLDocument doc,
           Model model,
           java.util.List<SBase> itemsToDelete,
           java.util.Map<java.lang.String,ASTNode> idToVector)

Parameters:

model -

idToIndices -

itemsToDelete -

convert

private static void convert(Model model,
           javax.swing.tree.TreeNode node,
           java.util.List<SBase> sbases,
           java.util.Map<java.lang.String,ASTNode> idToVector)

This is recursively getting each TreeNode of a certain SBMLDocument.

Parameters:

model -

node -

sbases -

convertMath

private static void convertMath(SBMLDocument doc,
               Model model,
               java.util.Map<java.lang.String,ASTNode> idToVector)

Parameters:

model -

idToIndices -

itemsToDelete -

convertMath

private static void convertMath(Model model,
               javax.swing.tree.TreeNode node,
               java.util.Map<java.lang.String,ASTNode> idToVector)

This is recursively getting each TreeNode of a certain SBMLDocument and flattening vector/selector MathML objects.

Parameters:

model -

node -

sbases -

convertArraysMath

private static void convertArraysMath(Model model,
                     javax.swing.tree.TreeNode child,
                     java.util.Map<java.lang.String,ASTNode> idToVector)

Parameters:

model -

child -

sbases -

expandDim

private static void expandDim(Model model,
             javax.swing.tree.TreeNode child,
             java.util.List<SBase> sbases,
             java.util.Map<java.lang.String,ASTNode> idToVector)

This expands an SBase that has a list of Dimension objects.

Parameters:

model -

child -

sbases -

expandDim

private static void expandDim(Model model,
             SBase sbase,
             SBase parent,
             ArraysSBasePlugin arraysPlugin,
             ArraysCompiler compiler,
             ASTNode vector,
             int dim,
             java.util.Map<java.lang.String,ASTNode> idToVector)

This method is transforming the attributes of a certain SBase object associated with the arrays package so that the SBase no longer uses the package.

Parameters:

model -

sbase -

parent -

arraysPlugin -

compiler -

dim -

expandDim

private static void expandDim(Model model,
             SBase sbase,
             SBase parent,
             ArraysSBasePlugin arraysPlugin,
             ArraysCompiler compiler,
             int dim,
             java.util.Map<java.lang.String,ASTNode> idToVector)

This method is transforming the attributes of a certain SBase object associated with the arrays package so that the SBase no longer uses the package.

Parameters:

model -

sbase -

parent -

arraysPlugin -

compiler -

dim -

addToParent

private static void addToParent(Model model,
               SBase parent,
               SBase child)

Add the new SBase to the corresponding ListOf object.

Parameters:

parent -

child -

convertIndex

private static void convertIndex(Model model,
                ArraysSBasePlugin arraysPlugin,
                SBase sbase,
                ArraysCompiler compiler,
                java.util.Map<java.lang.String,ASTNode> idToVector)

This is flattening index objects by replacing the dimension ids with the corresponding index value and updating the referenced attribute.

Parameters:

model -

arraysPlugin -

sbase -

compiler -

updateMathContainer

private static void updateMathContainer(Model model,
                       ArraysSBasePlugin arraysPlugin,
                       MathContainer sbase,
                       java.lang.String dimId,
                       int index,
                       java.util.Map<java.lang.String,ASTNode> idToVector)

This updates the dimension id that appears in the math.

Parameters:

model -

arraysPlugin -

sbase -

dimId -

index -

Throws:

ParseException

updateSBase

private static void updateSBase(SBMLDocument doc,
               ArraysSBasePlugin arraysPlugin,
               SBase sbase,
               int index)

This updates the metaid of an SBase.

Parameters:

arraysPlugin -

sbase -

index -

replaceDimensionId

private static ASTNode replaceDimensionId(ASTNode math,
                         java.lang.String id,
                         int index)

recursiveReplaceDimensionId

private static void recursiveReplaceDimensionId(ASTNode math,
                               java.lang.String id,
                               int index)