de.unirostock.sems.bives.api

Class Single

java.lang.Object

de.unirostock.sems.bives.api.Single

public abstract class Single
extends Object

The Class Single, providing an API to extract some information about single XML files. All methods might return null if not available in a certain case.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field and Description
protected de.unirostock.sems.xmlutils.ds.TreeDocument	tree The tree.

Constructor Summary

Constructors

Constructor and Description
Single(File file) Instantiates a new single object reading the document from a file.
Single(String str) Instantiates a new single object reading the document from a string.
Single(de.unirostock.sems.xmlutils.ds.TreeDocument tree) Instantiates a new single object.

Method Summary

Modifier and Type	Method and Description
abstract String	flatten() Flatten the document.
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()
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	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.

Methods inherited from class java.lang.Object

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

Field Detail

tree

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

The tree.

Constructor Detail

Single

public Single(File file)
       throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
              IOException,
              org.jdom2.JDOMException

Instantiates a new single object reading the document from a file.

Parameters:

file - the file containing the document

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

Single

public Single(String str)
       throws de.unirostock.sems.xmlutils.exception.XmlDocumentParseException,
              IOException,
              org.jdom2.JDOMException

Instantiates a new single object reading the document from a string.

Parameters:

str - the string containing the document

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

Single

public Single(de.unirostock.sems.xmlutils.ds.TreeDocument tree)

Instantiates a new single object.

Parameters:

tree - the tree

Method Detail

flatten

public abstract String flatten()
                        throws Exception

Flatten the document.

Returns:

the flattened document

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