Class SBMLDiffAnnotator
- java.lang.Object
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- de.unirostock.sems.bives.algorithm.DiffAnnotator
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- de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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- de.unirostock.sems.bives.sbml.algorithm.SBMLDiffAnnotator
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public class SBMLDiffAnnotator extends de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
- Author:
- Martin Scharm
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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.
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Constructor Summary
Constructors Constructor Description SBMLDiffAnnotator()
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Field Detail
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functionPath
public static final Pattern functionPath
The XPATH to a function definition.
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eventPath
public static final Pattern eventPath
The XPATH to an event definition.
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rulePath
public static final Pattern rulePath
The XPATH to a rule.
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annotationPath
public static final Pattern annotationPath
The XPATH to a machine readable annotation.
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descriptionPath
public static final Pattern descriptionPath
The XPATH to a human readable annotation.
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speciesPath
public static final Pattern speciesPath
The XPATH to a species.
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reactionsPath
public static final Pattern reactionsPath
The XPATH to a reaction.
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kineticsPath
public static final Pattern kineticsPath
The XPATH to a kinetic law.
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unitsPath
public static final Pattern unitsPath
The XPATH to a reaction.
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parameterPath
public static final Pattern parameterPath
The XPATH to a parameter.
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creationDatePath
public static final Pattern creationDatePath
The XPATH to a machine readable annotation.
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modificationDatePath
public static final Pattern modificationDatePath
The XPATH to a machine readable annotation.
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contributorPath
public static final Pattern contributorPath
The XPATH to a machine readable annotation.
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creatorPath
public static final Pattern creatorPath
The XPATH to a machine readable annotation.
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reactionsSpeciesReference
public static final Pattern reactionsSpeciesReference
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reactionsModifierSpeciesReference
public static final Pattern reactionsModifierSpeciesReference
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ontologyLink
public static final Pattern ontologyLink
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Method Detail
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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 classde.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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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 classde.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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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 classde.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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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 classde.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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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 classde.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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annotatePatch
public void annotatePatch(String rootId, de.unirostock.sems.comodi.ChangeFactory changeFac)
- Overrides:
annotatePatch
in classde.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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