public class SBMLDiffAnnotator
extends de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
Modifier and Type | Field and 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 and Description |
---|
SBMLDiffAnnotator() |
Modifier and Type | Method and 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) |
public static final Pattern functionPath
public static final Pattern eventPath
public static final Pattern rulePath
public static final Pattern annotationPath
public static final Pattern descriptionPath
public static final Pattern speciesPath
public static final Pattern reactionsPath
public static final Pattern kineticsPath
public static final Pattern unitsPath
public static final Pattern parameterPath
public static final Pattern creationDatePath
public static final Pattern modificationDatePath
public static final Pattern contributorPath
public static final Pattern creatorPath
public static final Pattern reactionsSpeciesReference
public static final Pattern reactionsModifierSpeciesReference
public static final Pattern ontologyLink
public de.unirostock.sems.comodi.Change annotateDeletion(de.unirostock.sems.xmlutils.ds.TreeNode node, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac)
annotateDeletion
in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
public de.unirostock.sems.comodi.Change annotateInsertion(de.unirostock.sems.xmlutils.ds.TreeNode node, org.jdom2.Element diffNode, de.unirostock.sems.comodi.ChangeFactory changeFac)
annotateInsertion
in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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)
annotateMove
in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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)
annotateUpdateAttribute
in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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)
annotateUpdateText
in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
public void annotatePatch(String rootId, de.unirostock.sems.comodi.ChangeFactory changeFac)
annotatePatch
in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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