Package de.unirostock.sems.bives.sbml.algorithm

Class SBMLDiffAnnotator

java.lang.Object

de.unirostock.sems.bives.algorithm.DiffAnnotator

de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator

public class SBMLDiffAnnotator
extends de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
static Pattern	annotationPath	The XPATH to a machine readable annotation.
static Pattern	contributorPath	The XPATH to a machine readable annotation.
static Pattern	creationDatePath	The XPATH to a machine readable annotation.
static Pattern	creatorPath	The XPATH to a machine readable annotation.
static Pattern	descriptionPath	The XPATH to a human readable annotation.
static Pattern	eventPath	The XPATH to an event definition.
static Pattern	functionPath	The XPATH to a function definition.
static Pattern	kineticsPath	The XPATH to a kinetic law.
static Pattern	modificationDatePath	The XPATH to a machine readable annotation.
static Pattern	ontologyLink
static Pattern	parameterPath	The XPATH to a parameter.
static Pattern	reactionsModifierSpeciesReference
static Pattern	reactionsPath	The XPATH to a reaction.
static Pattern	reactionsSpeciesReference
static Pattern	rulePath	The XPATH to a rule.
static Pattern	speciesPath	The XPATH to a species.
static Pattern	unitsPath	The XPATH to a reaction.

Constructor Summary

Constructors

Constructor	Description
SBMLDiffAnnotator()

Method Summary

Modifier and Type	Method	Description
de.unirostock.sems.comodi.Change	annotateDeletion(de.unirostock.sems.xmlutils.ds.TreeNode node, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac)
de.unirostock.sems.comodi.Change	annotateInsertion(de.unirostock.sems.xmlutils.ds.TreeNode node, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac)
de.unirostock.sems.comodi.Change	annotateMove(de.unirostock.sems.xmlutils.ds.TreeNode nodeA, de.unirostock.sems.xmlutils.ds.TreeNode nodeB, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac, boolean permutation)
void	annotatePatch(String rootId, de.unirostock.sems.comodi.ChangeFactory changeFac)
de.unirostock.sems.comodi.Change	annotateUpdateAttribute(de.unirostock.sems.xmlutils.ds.TreeNode nodeA, de.unirostock.sems.xmlutils.ds.TreeNode nodeB, String attributeName, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac)
de.unirostock.sems.comodi.Change	annotateUpdateText(de.unirostock.sems.xmlutils.ds.TextNode nodeA, de.unirostock.sems.xmlutils.ds.TextNode nodeB, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac)

Methods inherited from class java.lang.Object

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

Field Detail

functionPath

public static final Pattern functionPath

The XPATH to a function definition.

eventPath

public static final Pattern eventPath

The XPATH to an event definition.

rulePath

public static final Pattern rulePath

The XPATH to a rule.

annotationPath

public static final Pattern annotationPath

The XPATH to a machine readable annotation.

descriptionPath

public static final Pattern descriptionPath

The XPATH to a human readable annotation.

speciesPath

public static final Pattern speciesPath

The XPATH to a species.

reactionsPath

public static final Pattern reactionsPath

The XPATH to a reaction.

kineticsPath

public static final Pattern kineticsPath

The XPATH to a kinetic law.

unitsPath

public static final Pattern unitsPath

The XPATH to a reaction.

parameterPath

public static final Pattern parameterPath

The XPATH to a parameter.

creationDatePath

public static final Pattern creationDatePath

The XPATH to a machine readable annotation.

modificationDatePath

public static final Pattern modificationDatePath

The XPATH to a machine readable annotation.

contributorPath

public static final Pattern contributorPath

The XPATH to a machine readable annotation.

creatorPath

public static final Pattern creatorPath

The XPATH to a machine readable annotation.

reactionsSpeciesReference

public static final Pattern reactionsSpeciesReference

reactionsModifierSpeciesReference

public static final Pattern reactionsModifierSpeciesReference

ontologyLink

public static final Pattern ontologyLink

Constructor Detail

SBMLDiffAnnotator

public SBMLDiffAnnotator()

Method Detail

annotateDeletion

public de.unirostock.sems.comodi.Change annotateDeletion(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                                         org.jdom2.Element diffNode,
                                                         de.unirostock.sems.comodi.ChangeFactory changeFac)

Overrides:

annotateDeletion in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

annotateInsertion

public de.unirostock.sems.comodi.Change annotateInsertion(de.unirostock.sems.xmlutils.ds.TreeNode node,
                                                          org.jdom2.Element diffNode,
                                                          de.unirostock.sems.comodi.ChangeFactory changeFac)

Overrides:

annotateInsertion in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

annotateMove

public de.unirostock.sems.comodi.Change annotateMove(de.unirostock.sems.xmlutils.ds.TreeNode nodeA,
                                                     de.unirostock.sems.xmlutils.ds.TreeNode nodeB,
                                                     org.jdom2.Element diffNode,
                                                     de.unirostock.sems.comodi.ChangeFactory changeFac,
                                                     boolean permutation)

Overrides:

annotateMove in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

annotateUpdateAttribute

public de.unirostock.sems.comodi.Change annotateUpdateAttribute(de.unirostock.sems.xmlutils.ds.TreeNode nodeA,
                                                                de.unirostock.sems.xmlutils.ds.TreeNode nodeB,
                                                                String attributeName,
                                                                org.jdom2.Element diffNode,
                                                                de.unirostock.sems.comodi.ChangeFactory changeFac)

Overrides:

annotateUpdateAttribute in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

annotateUpdateText

public de.unirostock.sems.comodi.Change annotateUpdateText(de.unirostock.sems.xmlutils.ds.TextNode nodeA,
                                                           de.unirostock.sems.xmlutils.ds.TextNode nodeB,
                                                           org.jdom2.Element diffNode,
                                                           de.unirostock.sems.comodi.ChangeFactory changeFac)

Overrides:

annotateUpdateText in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator

annotatePatch

public void annotatePatch(String rootId,
                          de.unirostock.sems.comodi.ChangeFactory changeFac)

Overrides:

annotatePatch in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator