Class SBMLDiff
- java.lang.Object
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- de.unirostock.sems.bives.api.Diff
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- de.unirostock.sems.bives.sbml.api.SBMLDiff
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public class SBMLDiff extends de.unirostock.sems.bives.api.Diff
The Class SBMLDiff to compare two SBML models.- Author:
- Martin Scharm
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Field Summary
Fields Modifier and Type Field Description protected SBMLDocument
doc1
The original document.protected SBMLDocument
doc2
The modified document.protected SBMLGraphProducer
graphProducer
The graph producer.protected SBMLDiffInterpreter
interpreter
The interpreter.
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Constructor Summary
Constructors Constructor Description SBMLDiff(SBMLDocument a, SBMLDocument b)
Instantiates a new SBML differ.SBMLDiff(SBMLDocument a, SBMLDocument b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
Instantiates a new SBML differ.SBMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a, de.unirostock.sems.xmlutils.ds.TreeDocument b)
Instantiates a new SBML differ.SBMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a, de.unirostock.sems.xmlutils.ds.TreeDocument b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
Instantiates a new SBML differ.SBMLDiff(File a, File b)
Instantiates a new SBML differ.SBMLDiff(File a, File b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
Instantiates a new SBML differ.SBMLDiff(String a, String b)
Instantiates a new SBML differ.SBMLDiff(String a, String b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
Instantiates a new SBML differ.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getHierarchyDotGraph()
Object
getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
String
getHierarchyGraphML()
String
getHierarchyJsonGraph()
String
getHTMLReport()
String
getMarkDownReport()
String
getReactionsDotGraph()
Object
getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
String
getReactionsGraphML()
String
getReactionsJsonGraph()
String
getReactionsSbgnJsonGraph()
String
getReport(de.unirostock.sems.bives.markup.Typesetting ts)
String
getReStructuredTextReport()
boolean
mapTrees(boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames)
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Field Detail
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doc1
protected SBMLDocument doc1
The original document.
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doc2
protected SBMLDocument doc2
The modified document.
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graphProducer
protected SBMLGraphProducer graphProducer
The graph producer.
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interpreter
protected SBMLDiffInterpreter interpreter
The interpreter.
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Constructor Detail
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SBMLDiff
public SBMLDiff(File a, File b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator) throws BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException
Instantiates a new SBML differ.- Parameters:
a
- the file containing the original SBML modelb
- the file containing the modified SBML modeldiffAnnotator
- the diff annotator- Throws:
BivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exception
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SBMLDiff
public SBMLDiff(String a, String b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new SBML differ.- Parameters:
a
- the XML code representing the original SBML modelb
- the XML code representing the modified SBML modeldiffAnnotator
- the diff annotator- Throws:
de.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exception
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SBMLDiff
public SBMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a, de.unirostock.sems.xmlutils.ds.TreeDocument b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator) throws BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new SBML differ.- Parameters:
a
- the tree document representing the original modelb
- the tree document representing the modified modeldiffAnnotator
- the diff annotator- Throws:
BivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exception
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SBMLDiff
public SBMLDiff(SBMLDocument a, SBMLDocument b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
Instantiates a new SBML differ.- Parameters:
a
- the original documentb
- the modified documentdiffAnnotator
- the diff annotator
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SBMLDiff
public SBMLDiff(File a, File b) throws BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException
Instantiates a new SBML differ.- Parameters:
a
- the file containing the original SBML modelb
- the file containing the modified SBML model- Throws:
BivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exception
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SBMLDiff
public SBMLDiff(String a, String b) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new SBML differ.- Parameters:
a
- the XML code representing the original SBML modelb
- the XML code representing the modified SBML model- Throws:
de.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exception
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SBMLDiff
public SBMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a, de.unirostock.sems.xmlutils.ds.TreeDocument b) throws BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new SBML differ.- Parameters:
a
- the tree document representing the original modelb
- the tree document representing the modified model- Throws:
BivesSBMLParseException
- the bives sbml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exception
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SBMLDiff
public SBMLDiff(SBMLDocument a, SBMLDocument b)
Instantiates a new SBML differ.- Parameters:
a
- the original documentb
- the modified document
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Method Detail
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mapTrees
public boolean mapTrees(boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames) throws de.unirostock.sems.bives.exception.BivesConnectionException
- Specified by:
mapTrees
in classde.unirostock.sems.bives.api.Diff
- Throws:
de.unirostock.sems.bives.exception.BivesConnectionException
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getReactionsGraphML
public String getReactionsGraphML()
- Specified by:
getReactionsGraphML
in classde.unirostock.sems.bives.api.Diff
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getReport
public String getReport(de.unirostock.sems.bives.markup.Typesetting ts)
- Specified by:
getReport
in classde.unirostock.sems.bives.api.Diff
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getMarkDownReport
public String getMarkDownReport()
- Specified by:
getMarkDownReport
in classde.unirostock.sems.bives.api.Diff
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getReStructuredTextReport
public String getReStructuredTextReport()
- Specified by:
getReStructuredTextReport
in classde.unirostock.sems.bives.api.Diff
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getHTMLReport
public String getHTMLReport()
- Specified by:
getHTMLReport
in classde.unirostock.sems.bives.api.Diff
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getReactionsGraph
public Object getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws Exception
- Specified by:
getReactionsGraph
in classde.unirostock.sems.bives.api.Diff
- Throws:
Exception
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getReactionsDotGraph
public String getReactionsDotGraph()
- Specified by:
getReactionsDotGraph
in classde.unirostock.sems.bives.api.Diff
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getReactionsJsonGraph
public String getReactionsJsonGraph()
- Specified by:
getReactionsJsonGraph
in classde.unirostock.sems.bives.api.Diff
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getHierarchyGraph
public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
- Specified by:
getHierarchyGraph
in classde.unirostock.sems.bives.api.Diff
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getHierarchyGraphML
public String getHierarchyGraphML()
- Specified by:
getHierarchyGraphML
in classde.unirostock.sems.bives.api.Diff
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getHierarchyDotGraph
public String getHierarchyDotGraph()
- Specified by:
getHierarchyDotGraph
in classde.unirostock.sems.bives.api.Diff
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getHierarchyJsonGraph
public String getHierarchyJsonGraph()
- Specified by:
getHierarchyJsonGraph
in classde.unirostock.sems.bives.api.Diff
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