de.unirostock.sems.bives.api

Class Diff

java.lang.Object

de.unirostock.sems.bives.api.Diff

Direct Known Subclasses:

RegularDiff

public abstract class Diff
extends Object

The Class Diff, the central object if it comes to the comparison of XML documents. All methods might return null if not available in a certain case.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	ALLOW_DIFFERENT_IDS Are mappings of nodes with different ids allowed? At the first glimpse that might sound stupid, but ids are generally arbitrary and say nothing valuable about the entities.
static boolean	CARE_ABOUT_NAMES Do we care about names? Should we treat names differently? They often provide more information than other attributes.
protected SimpleConnectionManager	connections The connections.
static boolean	STRICTER_NAMES Should we handle names very strictly? Go for this option if you're sure that you're names are very similar.
protected de.unirostock.sems.xmlutils.ds.TreeDocument	treeA The tree corresponding to the former version.
protected de.unirostock.sems.xmlutils.ds.TreeDocument	treeB The tree corresponding to the later version.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
String	getCRNDotGraph() Deprecated. As of 1.3.3 replaced by getReactionsDotGraph()
Object	getCRNGraph(GraphTranslator gt) Deprecated. As of 1.3.3 replaced by getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator)
String	getCRNGraphML() Deprecated. As of 1.3.3 replaced by getReactionsGraphML()
String	getCRNJsonGraph() Deprecated. As of 1.3.3 replaced by getReactionsJsonGraph()
String	getDiff() Gets the diff as a string, encoded in XML.
String	getDiff(boolean inclAnnotations) Gets the differences encoded in an XML string
abstract String	getHierarchyDotGraph() Returns the component's hierarchy graph encoded in DOT language.
abstract Object	getHierarchyGraph(GraphTranslator gt) Returns the component's hierarchy graph providing an own graph translator.
abstract String	getHierarchyGraphML() Returns the component's hierarchy graph encoded in GraphML.
abstract String	getHierarchyJsonGraph() Returns the component's hierarchy graph encoded in JSON.
abstract String	getHTMLReport() Returns the report encoded in HTML.
abstract String	getMarkDownReport() Returns the report encoded MarkDown.
Patch	getPatch() Gets the patch object.
abstract String	getReactionsDotGraph() Returns the graph of the reaction network encoded in DOT language.
abstract Object	getReactionsGraph(GraphTranslator gt) Returns the graph of the reaction network providing an own graph translator.
abstract String	getReactionsGraphML() Returns the graph of the reaction network encoded in GraphML.
abstract String	getReactionsJsonGraph() Returns the graph of the reaction network encoded in JSON.
abstract String	getReactionsSbgnJsonGraph() Returns the graph of the reaction network encoded in an SBGN-JSON format.
abstract String	getReport(Typesetting ts) Returns the report providing an on markup processor.
abstract String	getReStructuredTextReport() Returns the report encoded in ReStructured text.
boolean	mapTrees() Map both trees.
abstract boolean	mapTrees(boolean allowDifferentIds, boolean careAboutNames, boolean stricterNames) Map both trees.

Methods inherited from class java.lang.Object

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

Field Detail

ALLOW_DIFFERENT_IDS

public static final boolean ALLOW_DIFFERENT_IDS

Are mappings of nodes with different ids allowed? At the first glimpse that might sound stupid, but ids are generally arbitrary and say nothing valuable about the entities. they just need to be unique.. Look at the following two species:

 <species id="s1" name="glucose" initial_concentration="0.1" compartment="cell" initialAmount="1" hasOnlySubstanceUnits="true" boundaryCondition="true" />
 <species id="species1" name="glucose" initial_concentration="0.1" compartment="cell" initialAmount="1" hasOnlySubstanceUnits="true" boundaryCondition="true" />
 

The id attribute might just be assigned by two different tools, everything else is the same. Should we map these entities? By default this is true.

See Also:

DocumentNode.getAttributeDistance(DocumentNode, boolean, boolean, boolean), Constant Field Values

CARE_ABOUT_NAMES

public static final boolean CARE_ABOUT_NAMES

Do we care about names? Should we treat names differently? They often provide more information than other attributes.

See Also:

DocumentNode.getAttributeDistance(DocumentNode, boolean, boolean, boolean), Constant Field Values

STRICTER_NAMES

public static final boolean STRICTER_NAMES

Should we handle names very strictly? Go for this option if you're sure that you're names are very similar.

See Also:

DocumentNode.getAttributeDistance(DocumentNode, boolean, boolean, boolean), Constant Field Values

treeA

protected de.unirostock.sems.xmlutils.ds.TreeDocument treeA

The tree corresponding to the former version.

treeB

protected de.unirostock.sems.xmlutils.ds.TreeDocument treeB

The tree corresponding to the later version.

connections

protected SimpleConnectionManager connections

The connections.

Constructor Detail

Diff

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

Instantiates a new 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

Diff

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

Instantiates a new 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

Diff

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

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

Parameters:

treeA - the former version of the tree

treeB - the later version of the tree

Diff

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

Instantiates a new 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

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

Diff

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

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

Parameters:

docA - the former version

docB - the later version

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

Diff

public Diff(de.unirostock.sems.xmlutils.ds.TreeDocument treeA,
            de.unirostock.sems.xmlutils.ds.TreeDocument treeB,
            DiffAnnotator diffAnnotator)

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

Parameters:

treeA - the former version of the tree

treeB - the later version of the tree

diffAnnotator - the annotator for identified changes

Method Detail

getDiff

public String getDiff()

Gets the diff as a string, encoded in XML.

Returns:

the diff

getDiff

public String getDiff(boolean inclAnnotations)

Gets the differences encoded in an XML string

Parameters:

inclAnnotations - include annotations in the XML patch

Returns:

the diff

getPatch

public Patch getPatch()

Gets the patch object.

Returns:

the patch

mapTrees

public abstract boolean mapTrees(boolean allowDifferentIds,
                                 boolean careAboutNames,
                                 boolean stricterNames)
                          throws Exception

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 ALLOW_DIFFERENT_IDS, CARE_ABOUT_NAMES, and STRICTER_NAMES.

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:

Exception - the exception

mapTrees

public boolean mapTrees()
                 throws Exception

Map both trees. This method by default allows different ids, better cares about names (that means, different names are worse than different concentrations) but doesn't handle the names too strict. Compare DocumentNode.getAttributeDistance(DocumentNode, boolean, boolean, boolean).

Returns:

true, if successful

Throws:

Exception - the exception

getCRNGraph

@Deprecated
public Object getCRNGraph(GraphTranslator gt)
                               throws Exception

Deprecated. As of 1.3.3 replaced by getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator)

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

Parameters:

gt - the graph translator

Returns:

the chemical reaction network or null if not available

Throws:

Exception - the exception

getReactionsGraph

public abstract Object getReactionsGraph(GraphTranslator gt)
                                  throws Exception

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

Parameters:

gt - the graph translator

Returns:

the reaction network or null if not available

Throws:

Exception - the exception

getHierarchyGraph

public abstract Object getHierarchyGraph(GraphTranslator gt)
                                  throws Exception

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

Parameters:

gt - the graph translator

Returns:

the hierarchy graph or null if not available

Throws:

Exception - the exception

getCRNGraphML

@Deprecated
public String getCRNGraphML()
                                 throws Exception

Deprecated. As of 1.3.3 replaced by getReactionsGraphML()

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

Returns:

the chemical reaction network or null if not available

Throws:

Exception - the exception

getReactionsGraphML

public abstract String getReactionsGraphML()
                                    throws Exception

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

Returns:

the reaction network or null if not available

Throws:

Exception - the exception

getHierarchyGraphML

public abstract String getHierarchyGraphML()
                                    throws Exception

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

Returns:

the hierarchy graph or null if not available

Throws:

Exception - the exception

getCRNDotGraph

@Deprecated
public String getCRNDotGraph()
                                  throws Exception

Deprecated. As of 1.3.3 replaced by getReactionsDotGraph()

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

Returns:

the chemical reaction network or null if not available

Throws:

Exception - the exception

getReactionsDotGraph

public abstract String getReactionsDotGraph()
                                     throws Exception

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

Returns:

the reaction network or null if not available

Throws:

Exception - the exception

getHierarchyDotGraph

public abstract String getHierarchyDotGraph()
                                     throws Exception

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

Returns:

the hierarchy graph or null if not available

Throws:

Exception - the exception

getCRNJsonGraph

@Deprecated
public String getCRNJsonGraph()
                                   throws Exception

Deprecated. As of 1.3.3 replaced by getReactionsJsonGraph()

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

Returns:

the chemical reaction network or null if not available

Throws:

Exception - the exception

getReactionsJsonGraph

public abstract String getReactionsJsonGraph()
                                      throws Exception

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

Returns:

the reaction network or null if not available

Throws:

Exception - the exception

getHierarchyJsonGraph

public abstract String getHierarchyJsonGraph()
                                      throws Exception

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

Returns:

the hierarchy graph or null if not available

Throws:

Exception - the exception

getReactionsSbgnJsonGraph

public abstract String getReactionsSbgnJsonGraph()
                                          throws Exception

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

Returns:

the reaction network or null if not available

Throws:

Exception - the exception

getReport

public abstract String getReport(Typesetting ts)
                          throws Exception

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

Parameters:

ts - the ts

Returns:

the report or null if not available

Throws:

Exception - the exception

getHTMLReport

public abstract String getHTMLReport()
                              throws Exception

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

Returns:

the hTML report or null if not available

Throws:

Exception - the exception

getMarkDownReport

public abstract String getMarkDownReport()
                                  throws Exception

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

Returns:

the mark down report or null if not available

Throws:

Exception - the exception

getReStructuredTextReport

public abstract String getReStructuredTextReport()
                                          throws Exception

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

Returns:

the ReStructured text report or null if not available

Throws:

Exception - the exception