public class CellMLDiff
extends de.unirostock.sems.bives.api.Diff
Modifier and Type | Field and Description |
---|---|
protected CellMLGraphProducer |
graphProducer
The graph producer.
|
protected CellMLDiffInterpreter |
interpreter
The interpreter.
|
Constructor and Description |
---|
CellMLDiff(CellMLDocument a,
CellMLDocument b)
Instantiates a new CellML differ.
|
CellMLDiff(File a,
File b)
Instantiates a new CellML differ.
|
CellMLDiff(String a,
String b)
Instantiates a new CellML differ.
|
CellMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a,
de.unirostock.sems.xmlutils.ds.TreeDocument b)
Instantiates a new CellML differ.
|
Modifier and Type | Method and 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 |
getReport(de.unirostock.sems.bives.markup.Typesetting ts) |
String |
getReStructuredTextReport() |
boolean |
mapTrees() |
protected CellMLGraphProducer graphProducer
protected CellMLDiffInterpreter interpreter
public CellMLDiff(File a, File b) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesCellMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, de.unirostock.sems.bives.exception.BivesLogicalException, de.unirostock.sems.bives.exception.BivesImportException, URISyntaxException
a
- the file containing the original CellML modelb
- the file containing the modified CellML modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesCellMLParseException
- the bives cell ml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionde.unirostock.sems.bives.exception.BivesLogicalException
- the bives logical exceptionde.unirostock.sems.bives.exception.BivesImportException
- the bives import exceptionURISyntaxException
- the uRI syntax exceptionpublic CellMLDiff(String a, String b) throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException, IOException, org.jdom2.JDOMException, BivesCellMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, de.unirostock.sems.bives.exception.BivesLogicalException, de.unirostock.sems.bives.exception.BivesImportException, URISyntaxException
a
- the XML code representing the original CellML modelb
- the XML code representing the modified CellML modelde.unirostock.sems.xmlutils.exception.XmlDocumentParseException
- the xml document parse exceptionIOException
- Signals that an I/O exception has occurred.org.jdom2.JDOMException
- the jDOM exceptionBivesCellMLParseException
- the bives cell ml parse exceptionde.unirostock.sems.bives.exception.BivesDocumentConsistencyException
- the bives document consistency exceptionde.unirostock.sems.bives.exception.BivesLogicalException
- the bives logical exceptionde.unirostock.sems.bives.exception.BivesImportException
- the bives import exceptionURISyntaxException
- the uRI syntax exceptionpublic CellMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a, de.unirostock.sems.xmlutils.ds.TreeDocument b) throws BivesCellMLParseException, de.unirostock.sems.bives.exception.BivesDocumentConsistencyException, de.unirostock.sems.bives.exception.BivesLogicalException, de.unirostock.sems.bives.exception.BivesImportException, IOException, URISyntaxException
a
- the tree document representing the original CellML modelb
- the tree document representing the modified CellML modelURISyntaxException
IOException
de.unirostock.sems.bives.exception.BivesImportException
de.unirostock.sems.bives.exception.BivesLogicalException
de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
BivesCellMLParseException
public CellMLDiff(CellMLDocument a, CellMLDocument b)
a
- the original CellML documentb
- the modified CellML documentpublic boolean mapTrees() throws de.unirostock.sems.bives.exception.BivesConnectionException
mapTrees
in class de.unirostock.sems.bives.api.Diff
de.unirostock.sems.bives.exception.BivesConnectionException
public String getReactionsGraphML()
getReactionsGraphML
in class de.unirostock.sems.bives.api.Diff
public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws Exception
getHierarchyGraph
in class de.unirostock.sems.bives.api.Diff
Exception
public String getHierarchyGraphML()
getHierarchyGraphML
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 getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt) throws Exception
getReactionsGraph
in class de.unirostock.sems.bives.api.Diff
Exception
public String getReactionsDotGraph()
getReactionsDotGraph
in class de.unirostock.sems.bives.api.Diff
public String getReactionsJsonGraph()
getReactionsJsonGraph
in class de.unirostock.sems.bives.api.Diff
public String getHierarchyDotGraph()
getHierarchyDotGraph
in class de.unirostock.sems.bives.api.Diff
public String getHierarchyJsonGraph()
getHierarchyJsonGraph
in class de.unirostock.sems.bives.api.Diff
public String getReport(de.unirostock.sems.bives.markup.Typesetting ts)
getReport
in class de.unirostock.sems.bives.api.Diff
Copyright © 2015 SEMS project @ University of Rostock. All rights reserved.