public class SBMLDiff
extends de.unirostock.sems.bives.api.Diff
Modifier and Type | Field and Description |
---|---|
protected SBMLDocument |
doc1
The original document.
|
protected SBMLDocument |
doc2
The modified document.
|
protected SBMLGraphProducer |
graphProducer
The graph producer.
|
protected SBMLDiffInterpreter |
interpreter
The interpreter.
|
Constructor and Description |
---|
SBMLDiff(File a,
File b)
Instantiates a new SBML differ.
|
SBMLDiff(SBMLDocument a,
SBMLDocument b)
Instantiates a new sBML differ.
|
SBMLDiff(String a,
String b)
Instantiates a new SBML differ.
|
Modifier and Type | Method and Description |
---|---|
String |
getCRNDotGraph() |
Object |
getCRNGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) |
String |
getCRNGraphML() |
String |
getCRNJsonGraph() |
String |
getHierarchyDotGraph() |
Object |
getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) |
String |
getHierarchyGraphML() |
String |
getHierarchyJsonGraph() |
String |
getHTMLReport() |
String |
getMarkDownReport() |
String |
getReport(de.unirostock.sems.bives.markup.Typesetting ts) |
String |
getReStructuredTextReport() |
boolean |
mapTrees() |
protected SBMLDocument doc1
protected SBMLDocument doc2
protected SBMLGraphProducer graphProducer
protected SBMLDiffInterpreter interpreter
public SBMLDiff(File a, File b) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, FileNotFoundException, ParserConfigurationException, SAXException, IOException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, BivesSBMLParseException
a
- the file containing the original SBML modelb
- the file containing the modified SBML modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionFileNotFoundException
- the file not found exceptionParserConfigurationException
- the parser configuration exceptionSAXException
- the sAX exceptionIOException
- Signals that an I/O exception has occurred.de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionBivesSBMLParseException
- the bives sbml parse exceptionpublic SBMLDiff(String a, String b) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, FileNotFoundException, ParserConfigurationException, SAXException, IOException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, BivesSBMLParseException
a
- the XML code representing the original v modelb
- the XML code representing the modified SBML modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionFileNotFoundException
- the file not found exceptionParserConfigurationException
- the parser configuration exceptionSAXException
- the sAX exceptionIOException
- Signals that an I/O exception has occurred.de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionBivesSBMLParseException
- the bives sbml parse exceptionpublic SBMLDiff(SBMLDocument a, SBMLDocument b) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, FileNotFoundException, ParserConfigurationException, SAXException, IOException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
a
- the original SBML documentb
- the modified SBML documentde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionFileNotFoundException
- the file not found exceptionParserConfigurationException
- the parser configuration exceptionSAXException
- the sAX exceptionIOException
- Signals that an I/O exception has occurred.de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionpublic boolean mapTrees() throws BivesSBMLParseException, de.unirostock.sems.bives.exception.BivesConnectionException
mapTrees
in class de.unirostock.sems.bives.api.Diff
BivesSBMLParseException
de.unirostock.sems.bives.exception.BivesConnectionException
public String getCRNGraphML() throws ParserConfigurationException
getCRNGraphML
in class de.unirostock.sems.bives.api.Diff
ParserConfigurationException
public String getReport(de.unirostock.sems.bives.markup.Typesetting ts)
getReport
in class de.unirostock.sems.bives.api.Diff
public String getMarkDownReport()
getMarkDownReport
in class de.unirostock.sems.bives.api.Diff
public String getReStructuredTextReport()
getReStructuredTextReport
in class de.unirostock.sems.bives.api.Diff
public String getHTMLReport()
getHTMLReport
in class de.unirostock.sems.bives.api.Diff
public Object getCRNGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws Exception
getCRNGraph
in class de.unirostock.sems.bives.api.Diff
Exception
public String getCRNDotGraph()
getCRNDotGraph
in class de.unirostock.sems.bives.api.Diff
public String getCRNJsonGraph()
getCRNJsonGraph
in class de.unirostock.sems.bives.api.Diff
public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
getHierarchyGraph
in class de.unirostock.sems.bives.api.Diff
public String getHierarchyGraphML() throws ParserConfigurationException
getHierarchyGraphML
in class de.unirostock.sems.bives.api.Diff
ParserConfigurationException
public String getHierarchyDotGraph()
getHierarchyDotGraph
in class de.unirostock.sems.bives.api.Diff
public String getHierarchyJsonGraph()
getHierarchyJsonGraph
in class de.unirostock.sems.bives.api.Diff
Copyright © 2014 SEMS project @ University of Rostock. All rights reserved.