de.unirostock.sems.bives.api

Class RegularDiff

java.lang.Object

de.unirostock.sems.bives.api.Diff

de.unirostock.sems.bives.api.RegularDiff

public class RegularDiff
extends Diff

The Class RegularDiff to compare two regular XML documents.

Author:

Martin Scharm

Field Summary

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 and Description
RegularDiff(File fileA, File fileB) Instantiates a new regular diff object in order to compare two documents stored in files fileA and fileB.
RegularDiff(String docA, String docB) Instantiates a new regular diff object in order to compare two documents stored in strings docA and docB.
RegularDiff(de.unirostock.sems.xmlutils.ds.TreeDocument treeA, de.unirostock.sems.xmlutils.ds.TreeDocument treeB) Instantiates a new regular diff object in order to compare two tree documents.

Method Summary

Modifier and Type	Method and Description
String	getHierarchyDotGraph() Returns the component's hierarchy graph encoded in DOT language.
String	getHierarchyGraph(GraphTranslator gt) Returns the component's hierarchy graph providing an own graph translator.
String	getHierarchyGraphML() Returns the component's hierarchy graph encoded in GraphML.
String	getHierarchyJsonGraph() Returns the component's hierarchy graph encoded in JSON.
String	getHTMLReport() Returns the report encoded in HTML.
String	getMarkDownReport() Returns the report encoded MarkDown.
String	getReactionsDotGraph() Returns the graph of the reaction network encoded in DOT language.
Object	getReactionsGraph(GraphTranslator gt) Returns the graph of the reaction network providing an own graph translator.
String	getReactionsGraphML() Returns the graph of the reaction network encoded in GraphML.
String	getReactionsJsonGraph() Returns the graph of the reaction network encoded in JSON.
String	getReactionsSbgnJsonGraph() Returns the graph of the reaction network encoded in an SBGN-JSON format.
String	getReport(Typesetting ts) Returns the report providing an on markup processor.
String	getReStructuredTextReport() Returns the report encoded in ReStructured text.
boolean	mapTrees(boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames) Map both trees.

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

Constructor Detail

RegularDiff

public RegularDiff(File fileA,
                   File fileB)
            throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                   IOException,
                   org.jdom2.JDOMException

Instantiates a new regular diff object in order to compare two documents stored in files fileA and fileB.

Parameters:

fileA - the file containing the former version

fileB - the file containing the later version

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

RegularDiff

public RegularDiff(String docA,
                   String docB)
            throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
                   IOException,
                   org.jdom2.JDOMException

Instantiates a new regular diff object in order to compare two documents stored in strings docA and docB.

Parameters:

docA - the former version

docB - the later version

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

RegularDiff

public RegularDiff(de.unirostock.sems.xmlutils.ds.TreeDocument treeA,
                   de.unirostock.sems.xmlutils.ds.TreeDocument treeB)

Instantiates a new regular diff object in order to compare two tree documents.

Parameters:

treeA - the former version of the tree

treeB - the later version of the tree

Method Detail

mapTrees

public boolean mapTrees(boolean allowDifferentIds,
                        boolean careAboutNames,
                        boolean stricterNames)
                 throws BivesConnectionException

Description copied from class: Diff

Map both trees. This method let's you decide whether

• mapped entities may have different ids,
• we specially treat name attributes,
• we handle names very strictly.

For default values see Diff.ALLOW_DIFFERENT_IDS, Diff.CARE_ABOUT_NAMES, and Diff.STRICTER_NAMES.

Specified by:

mapTrees in class Diff

Parameters:

allowDifferentIds - are mapped entities allowed to have different ids?

careAboutNames - should we care about names?

stricterNames - should we handle names very strictly?

Returns:

true, if successful mapped

Throws:

BivesConnectionException

getReactionsGraph

public Object getReactionsGraph(GraphTranslator gt)
                         throws Exception

Description copied from class: Diff

Returns the graph of the reaction network providing an own graph translator. Might return null if not available.

Specified by:

getReactionsGraph in class Diff

Parameters:

gt - the graph translator

Returns:

the reaction network or null if not available

Throws:

Exception - the exception

getReactionsGraphML

public String getReactionsGraphML()

Description copied from class: Diff

Returns the graph of the reaction network encoded in GraphML. Might return null if not available.

Specified by:

getReactionsGraphML in class Diff

Returns:

the reaction network or null if not available

getReactionsDotGraph

public String getReactionsDotGraph()

Description copied from class: Diff

Returns the graph of the reaction network encoded in DOT language. Might return null if not available.

Specified by:

getReactionsDotGraph in class Diff

Returns:

the reaction network or null if not available

getHTMLReport

public String getHTMLReport()

Description copied from class: Diff

Returns the report encoded in HTML. Might return null if not available.

Specified by:

getHTMLReport in class Diff

Returns:

the hTML report or null if not available

getMarkDownReport

public String getMarkDownReport()

Description copied from class: Diff

Returns the report encoded MarkDown. Might return null if not available.

Specified by:

getMarkDownReport in class Diff

Returns:

the mark down report or null if not available

getReStructuredTextReport

public String getReStructuredTextReport()

Description copied from class: Diff

Returns the report encoded in ReStructured text. Might return null if not available.

Specified by:

getReStructuredTextReport in class Diff

Returns:

the ReStructured text report or null if not available

getHierarchyGraph

public String getHierarchyGraph(GraphTranslator gt)

Description copied from class: Diff

Returns the component's hierarchy graph providing an own graph translator. Might return null if not available.

Specified by:

getHierarchyGraph in class Diff

Parameters:

gt - the graph translator

Returns:

the hierarchy graph or null if not available

getHierarchyGraphML

public String getHierarchyGraphML()

Description copied from class: Diff

Returns the component's hierarchy graph encoded in GraphML. Might return null if not available.

Specified by:

getHierarchyGraphML in class Diff

Returns:

the hierarchy graph or null if not available

getHierarchyDotGraph

public String getHierarchyDotGraph()

Description copied from class: Diff

Returns the component's hierarchy graph encoded in DOT language. Might return null if not available.

Specified by:

getHierarchyDotGraph in class Diff

Returns:

the hierarchy graph or null if not available

getReactionsJsonGraph

public String getReactionsJsonGraph()

Description copied from class: Diff

Returns the graph of the reaction network encoded in JSON. Might return null if not available.

Specified by:

getReactionsJsonGraph in class Diff

Returns:

the reaction network or null if not available

getHierarchyJsonGraph

public String getHierarchyJsonGraph()

Description copied from class: Diff

Returns the component's hierarchy graph encoded in JSON. Might return null if not available.

Specified by:

getHierarchyJsonGraph in class Diff

Returns:

the hierarchy graph or null if not available

getReport

public String getReport(Typesetting ts)

Description copied from class: Diff

Returns the report providing an on markup processor. Might return null if not available.

Specified by:

getReport in class Diff

Parameters:

ts - the ts

Returns:

the report or null if not available

getReactionsSbgnJsonGraph

public String getReactionsSbgnJsonGraph()
                                 throws Exception

Description copied from class: Diff

Returns the graph of the reaction network encoded in an SBGN-JSON format. Might return null if not available.

Specified by:

getReactionsSbgnJsonGraph in class Diff

Returns:

the reaction network or null if not available

Throws:

Exception - the exception