Package de.unirostock.sems.bives.cellml.api

Class CellMLDiff

java.lang.Object

de.unirostock.sems.bives.api.Diff

de.unirostock.sems.bives.cellml.api.CellMLDiff

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

The Class CellMLDiff to compare two CellML models.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
protected CellMLGraphProducer	graphProducer	The graph producer.
protected CellMLDiffInterpreter	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
CellMLDiff(CellMLDocument a, CellMLDocument b)	Instantiates a new CellML differ.
CellMLDiff(CellMLDocument a, CellMLDocument b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)	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.
CellMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a, de.unirostock.sems.xmlutils.ds.TreeDocument b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)	Instantiates a new CellML differ.
CellMLDiff(File a, File b)	Instantiates a new CellML differ.
CellMLDiff(File a, File b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)	Instantiates a new CellML differ.
CellMLDiff(String a, String b)	Instantiates a new CellML differ.
CellMLDiff(String a, String b, de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)	Instantiates a new CellML 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

graphProducer

protected CellMLGraphProducer graphProducer

The graph producer.

interpreter

protected CellMLDiffInterpreter interpreter

The interpreter.

Constructor Detail

CellMLDiff

public CellMLDiff(File a,
                  File b,
                  de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
           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

Instantiates a new CellML differ.

Parameters:

a - the file containing the original CellML model

b - the file containing the modified CellML model

diffAnnotator - the annotator for identified changes

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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLDiff

public CellMLDiff(String a,
                  String b,
                  de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
           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

Instantiates a new CellML differ.

Parameters:

a - the XML code representing the original CellML model

b - the XML code representing the modified CellML model

diffAnnotator - the annotator for identified changes

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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLDiff

public CellMLDiff(de.unirostock.sems.xmlutils.ds.TreeDocument a,
                  de.unirostock.sems.xmlutils.ds.TreeDocument b,
                  de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)
           throws BivesCellMLParseException,
                  de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                  de.unirostock.sems.bives.exception.BivesLogicalException,
                  de.unirostock.sems.bives.exception.BivesImportException,
                  IOException,
                  URISyntaxException

Instantiates a new CellML differ.

Parameters:

a - the tree document representing the original CellML model

b - the tree document representing the modified CellML model

diffAnnotator - the annotator for identified changes

Throws:

URISyntaxException

IOException

de.unirostock.sems.bives.exception.BivesImportException

de.unirostock.sems.bives.exception.BivesLogicalException

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

BivesCellMLParseException

CellMLDiff

public CellMLDiff(CellMLDocument a,
                  CellMLDocument b,
                  de.unirostock.sems.bives.algorithm.DiffAnnotator diffAnnotator)

Instantiates a new CellML differ.

Parameters:

a - the original CellML document

b - the modified CellML document

diffAnnotator - the annotator for identified changes

CellMLDiff

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

Instantiates a new CellML differ. This CellML differ uses a CellMLDiffAnnotator to annotate the differences.

Parameters:

a - the file containing the original CellML model

b - the file containing the modified CellML 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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLDiff

public 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

Instantiates a new CellML differ.

Parameters:

a - the XML code representing the original CellML model

b - the XML code representing the modified CellML 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

BivesCellMLParseException - the bives cell ml parse exception

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

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

URISyntaxException - the uRI syntax exception

CellMLDiff

public 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

Instantiates a new CellML differ.

Parameters:

a - the tree document representing the original CellML model

b - the tree document representing the modified CellML model

Throws:

URISyntaxException

IOException

de.unirostock.sems.bives.exception.BivesImportException

de.unirostock.sems.bives.exception.BivesLogicalException

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

BivesCellMLParseException

CellMLDiff

public CellMLDiff(CellMLDocument a,
                  CellMLDocument b)

Instantiates a new CellML differ.

Parameters:

a - the original CellML document

b - the modified CellML 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

getHierarchyGraph

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

Specified by:

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

Throws:

Exception

getHierarchyGraphML

public String getHierarchyGraphML()

Specified by:

getHierarchyGraphML 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

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

getReport

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

Specified by:

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

getReactionsSbgnJsonGraph

public String getReactionsSbgnJsonGraph()

Specified by:

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