Package de.unirostock.sems.bives.cellml.parser

Class CellMLUserUnit

java.lang.Object

de.unirostock.sems.bives.cellml.parser.CellMLEntity

de.unirostock.sems.bives.cellml.parser.CellMLUnit

de.unirostock.sems.bives.cellml.parser.CellMLUserUnit

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter, de.unirostock.sems.bives.markup.Markup

public class CellMLUserUnit
extends CellMLUnit
implements de.unirostock.sems.bives.algorithm.DiffReporter, de.unirostock.sems.bives.markup.Markup

The Class CellMLUserUnit representing a CellML unit defined by a user.

Author:

Martin Scharm

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	CellMLUserUnit.BaseQuantity	The Class BaseQuantity.

Field Summary

Fields inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

model

Constructor Summary

Constructors

Constructor	Description
CellMLUserUnit(CellMLModel model, CellMLUnitDictionary dict, CellMLComponent component, de.unirostock.sems.xmlutils.ds.DocumentNode node)	Instantiates a new CellML user unit.

Method Summary

Modifier and Type	Method	Description
void	getDependencies(Map<CellMLUserUnit,List<CellMLEntity>> list)	Add the units this unit depends on to a global list of dependencies.
String	markup()
void	renameUnit(String original, String newName)	Rename the corresponding unit.
de.unirostock.sems.bives.markup.MarkupElement	reportDelete()
de.unirostock.sems.bives.markup.MarkupElement	reportInsert()
de.unirostock.sems.bives.markup.MarkupElement	reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, de.unirostock.sems.bives.algorithm.DiffReporter docA, de.unirostock.sems.bives.algorithm.DiffReporter docB)
static int	scale(String s)	Get the scaling factor given a textual representation.

Methods inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

associateRdfDescription, flagMetaModifcations, getDocumentNode, getMetaId, getModel, getRdfBlocks, getRdfDescriptions, setMetaId, setModel

Methods inherited from class de.unirostock.sems.bives.cellml.parser.CellMLUnit

createStandardUnit, getName, isStandardUnits, setName, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

CellMLUserUnit

public CellMLUserUnit(CellMLModel model,
                      CellMLUnitDictionary dict,
                      CellMLComponent component,
                      de.unirostock.sems.xmlutils.ds.DocumentNode node)
               throws BivesCellMLParseException,
                      de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                      de.unirostock.sems.bives.exception.BivesLogicalException

Instantiates a new CellML user unit.

Parameters:

model - the model that defines the unit

dict - the unit dictionary

component - the corresponding component, if not defined globally

node - the corresponding node in the XML tree

Throws:

BivesCellMLParseException - the bives cell ml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.bives.exception.BivesLogicalException

Method Detail

scale

public static final int scale(String s)
                       throws BivesCellMLParseException

Get the scaling factor given a textual representation. E.g. kilo becomes 3, exa becomes 18, and femto becomes -15.

Parameters:

s - the scaling factor as a string

Returns:

the the scaling factor as a number

Throws:

BivesCellMLParseException - the bives cell ml parse exception

markup

public String markup()

Specified by:

markup in interface de.unirostock.sems.bives.markup.Markup

getDependencies

public void getDependencies(Map<CellMLUserUnit,List<CellMLEntity>> list)

Add the units this unit depends on to a global list of dependencies.

Parameters:

list - the global list of dependencies

reportModification

public de.unirostock.sems.bives.markup.MarkupElement reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                                                        de.unirostock.sems.bives.algorithm.DiffReporter docA,
                                                                        de.unirostock.sems.bives.algorithm.DiffReporter docB)

Specified by:

reportModification in interface de.unirostock.sems.bives.algorithm.DiffReporter

reportInsert

public de.unirostock.sems.bives.markup.MarkupElement reportInsert()

Specified by:

reportInsert in interface de.unirostock.sems.bives.algorithm.DiffReporter

reportDelete

public de.unirostock.sems.bives.markup.MarkupElement reportDelete()

Specified by:

reportDelete in interface de.unirostock.sems.bives.algorithm.DiffReporter

renameUnit

public void renameUnit(String original,
                       String newName)
                throws de.unirostock.sems.bives.exception.BivesLogicalException

Rename the corresponding unit. (Intended to be used for flattening)

Parameters:

original - the original name

newName - the new name

Throws:

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception