fern.network.fernml

Class FernMLAnnotationManager

java.lang.Object

fern.network.fernml.FernMLAnnotationManager

All Implemented Interfaces:

AnnotationManager

public class FernMLAnnotationManager
extends Object
implements AnnotationManager

AnnotationManager for FernMLNetworks. The data is not copied but maintained within the tree (which should not be an efficiency issue except you want to use the annotations to store user data of reactions / species and do this very excessive - so don't do that). This avoids problems when saving the FernMLNetwork again.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
FernMLAnnotationManager(org.jdom.Element rootElement) Create the AnnotationManager from the root element of the jdom tree.

Method Summary

Modifier and Type	Method and Description
boolean	containsNetworkAnnotation(String typ) Returns true iff the network contains an annotation of the specified type.
boolean	containsReactionAnnotation(int reaction, String typ) Returns true iff the reaction contains an annotation of the specified type.
boolean	containsSpeciesAnnotation(int species, String typ) Returns true iff the species contains an annotation of the specified type.
String	getNetworkAnnotation(String typ) Gets the network annotation of the specified field.
Collection<String>	getNetworkAnnotationTypes() Gets the names of the network reaction.
String	getReactionAnnotation(int reaction, String typ) Gets the reaction annotation of the specified field.
Collection<String>	getReactionAnnotationTypes(int reaction) Gets the names of the species reaction.
String	getSpeciesAnnotation(int species, String typ) Gets the species annotation of the specified field.
Collection<String>	getSpeciesAnnotationTypes(int species) Gets the names of the species annotations.
void	setNetworkAnnotation(String typ, String annotation) Sets the network annotation of the specified field.
void	setReactionAnnotation(int reaction, String typ, String annotation) Sets the reaction annotation of the specified field.
void	setSpeciesAnnotation(int species, String typ, String annotation) Sets the species annotation of the specified field.

Methods inherited from class java.lang.Object

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

Constructor Detail

FernMLAnnotationManager

public FernMLAnnotationManager(org.jdom.Element rootElement)

Create the AnnotationManager from the root element of the jdom tree.

Parameters:

rootElement - the root element of the jdom tree

Method Detail

containsNetworkAnnotation

public boolean containsNetworkAnnotation(String typ)

Description copied from interface: AnnotationManager

Returns true iff the network contains an annotation of the specified type.

Specified by:

containsNetworkAnnotation in interface AnnotationManager

Parameters:

typ - field name of the annotation

Returns:

true iff such an annotation is present

getNetworkAnnotation

public String getNetworkAnnotation(String typ)

Description copied from interface: AnnotationManager

Gets the network annotation of the specified field.

Specified by:

getNetworkAnnotation in interface AnnotationManager

Parameters:

typ - name of the field

Returns:

network annotation

getNetworkAnnotationTypes

public Collection<String> getNetworkAnnotationTypes()

Description copied from interface: AnnotationManager

Gets the names of the network reaction.

Specified by:

getNetworkAnnotationTypes in interface AnnotationManager

Returns:

names of the fields

setNetworkAnnotation

public void setNetworkAnnotation(String typ,
                                 String annotation)

Description copied from interface: AnnotationManager

Sets the network annotation of the specified field.

Specified by:

setNetworkAnnotation in interface AnnotationManager

Parameters:

typ - name of the field

annotation - network annotation

containsReactionAnnotation

public boolean containsReactionAnnotation(int reaction,
                                          String typ)

Description copied from interface: AnnotationManager

Returns true iff the reaction contains an annotation of the specified type.

Specified by:

containsReactionAnnotation in interface AnnotationManager

Parameters:

reaction - index of the reaction

typ - field name of the annotation

Returns:

true iff such an annotation is present

getReactionAnnotation

public String getReactionAnnotation(int reaction,
                                    String typ)

Description copied from interface: AnnotationManager

Gets the reaction annotation of the specified field.

Specified by:

getReactionAnnotation in interface AnnotationManager

Parameters:

reaction - index of the reaction

typ - name of the field

Returns:

reaction annotation

getReactionAnnotationTypes

public Collection<String> getReactionAnnotationTypes(int reaction)

Description copied from interface: AnnotationManager

Gets the names of the species reaction.

Specified by:

getReactionAnnotationTypes in interface AnnotationManager

Parameters:

reaction - index of the reaction

Returns:

names of the fields

setReactionAnnotation

public void setReactionAnnotation(int reaction,
                                  String typ,
                                  String annotation)

Description copied from interface: AnnotationManager

Sets the reaction annotation of the specified field.

Specified by:

setReactionAnnotation in interface AnnotationManager

Parameters:

reaction - index of the reaction

typ - name of the field

annotation - reaction annotation

containsSpeciesAnnotation

public boolean containsSpeciesAnnotation(int species,
                                         String typ)

Description copied from interface: AnnotationManager

Returns true iff the species contains an annotation of the specified type.

Specified by:

containsSpeciesAnnotation in interface AnnotationManager

Parameters:

species - index of the species

typ - field name of the annotation

Returns:

true iff such an annotation is present

getSpeciesAnnotation

public String getSpeciesAnnotation(int species,
                                   String typ)

Description copied from interface: AnnotationManager

Gets the species annotation of the specified field.

Specified by:

getSpeciesAnnotation in interface AnnotationManager

Parameters:

species - index of the species

typ - name of the field

Returns:

species annotation

getSpeciesAnnotationTypes

public Collection<String> getSpeciesAnnotationTypes(int species)

Description copied from interface: AnnotationManager

Gets the names of the species annotations.

Specified by:

getSpeciesAnnotationTypes in interface AnnotationManager

Parameters:

species - index of the species

Returns:

names of the fields

setSpeciesAnnotation

public void setSpeciesAnnotation(int species,
                                 String typ,
                                 String annotation)

Description copied from interface: AnnotationManager

Sets the species annotation of the specified field.

Specified by:

setSpeciesAnnotation in interface AnnotationManager

Parameters:

species - index of the species

typ - name of the field

annotation - species annotation