Package de.unirostock.sems.bives.sbml.api

Class SBMLDiff

java.lang.Object

de.unirostock.sems.bives.api.Diff

de.unirostock.sems.bives.sbml.api.SBMLDiff

public class SBMLDiff
extends de.unirostock.sems.bives.api.Diff

The Class SBMLDiff to compare two SBML models.

Author:

Martin Scharm

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.

Fields inherited from class de.unirostock.sems.bives.api.Diff

ALLOW_DIFFERENT_IDS, CARE_ABOUT_NAMES, connections, STRICTER_NAMES, treeA, treeB

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.

Method Summary

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)

Methods inherited from class de.unirostock.sems.bives.api.Diff

getCRNDotGraph, getCRNGraph, getCRNGraphML, getCRNJsonGraph, getDiff, getDiff, getPatch, mapTrees

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

doc1

protected SBMLDocument doc1

The original document.

doc2

protected SBMLDocument doc2

The modified document.

graphProducer

protected SBMLGraphProducer graphProducer

The graph producer.

interpreter

protected SBMLDiffInterpreter interpreter

The interpreter.

Constructor Detail

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 model

b - the file containing the modified SBML model

diffAnnotator - the diff annotator

Throws:

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

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 model

b - the XML code representing the modified SBML model

diffAnnotator - the diff annotator

Throws:

de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

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 model

b - the tree document representing the modified model

diffAnnotator - the diff annotator

Throws:

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

SBMLDiff

public SBMLDiff(SBMLDocument a,
                SBMLDocument b,
                de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)

Instantiates a new SBML differ.

Parameters:

a - the original document

b - the modified document

diffAnnotator - the diff annotator

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 model

b - the file containing the modified SBML model

Throws:

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

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 model

b - the XML code representing the modified SBML model

Throws:

de.unirostock.sems.xmlutils.exception.XmlDocumentParseException - the xml document parse exception

IOException - Signals that an I/O exception has occurred.

org.jdom2.JDOMException - the jDOM exception

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

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 model

b - the tree document representing the modified model

Throws:

BivesSBMLParseException - the bives sbml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

SBMLDiff

public SBMLDiff(SBMLDocument a,
                SBMLDocument b)

Instantiates a new SBML differ.

Parameters:

a - the original document

b - the modified document

Method Detail

mapTrees

public boolean mapTrees(boolean allowDifferentIds,
                        boolean careAboutNames,
                        boolean stricterNames)
                 throws de.unirostock.sems.bives.exception.BivesConnectionException

Specified by:

mapTrees in class de.unirostock.sems.bives.api.Diff

Throws:

de.unirostock.sems.bives.exception.BivesConnectionException

getReactionsGraphML

public String getReactionsGraphML()

Specified by:

getReactionsGraphML in class de.unirostock.sems.bives.api.Diff

getReport

public String getReport(de.unirostock.sems.bives.markup.Typesetting ts)

Specified by:

getReport in class de.unirostock.sems.bives.api.Diff

getMarkDownReport

public String getMarkDownReport()

Specified by:

getMarkDownReport in class de.unirostock.sems.bives.api.Diff

getReStructuredTextReport

public String getReStructuredTextReport()

Specified by:

getReStructuredTextReport in class de.unirostock.sems.bives.api.Diff

getHTMLReport

public String getHTMLReport()

Specified by:

getHTMLReport in class de.unirostock.sems.bives.api.Diff

getReactionsGraph

public Object getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)
                         throws Exception

Specified by:

getReactionsGraph in class de.unirostock.sems.bives.api.Diff

Throws:

Exception

getReactionsDotGraph

public String getReactionsDotGraph()

Specified by:

getReactionsDotGraph in class de.unirostock.sems.bives.api.Diff

getReactionsJsonGraph

public String getReactionsJsonGraph()

Specified by:

getReactionsJsonGraph in class de.unirostock.sems.bives.api.Diff

getHierarchyGraph

public Object getHierarchyGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator gt)

Specified by:

getHierarchyGraph in class de.unirostock.sems.bives.api.Diff

getHierarchyGraphML

public String getHierarchyGraphML()

Specified by:

getHierarchyGraphML in class de.unirostock.sems.bives.api.Diff

getHierarchyDotGraph

public String getHierarchyDotGraph()

Specified by:

getHierarchyDotGraph in class de.unirostock.sems.bives.api.Diff

getHierarchyJsonGraph

public String getHierarchyJsonGraph()

Specified by:

getHierarchyJsonGraph in class de.unirostock.sems.bives.api.Diff

getReactionsSbgnJsonGraph

public String getReactionsSbgnJsonGraph()
                                 throws Exception

Specified by:

getReactionsSbgnJsonGraph in class de.unirostock.sems.bives.api.Diff

Throws:

Exception