fern.network

Interface AnnotationManager

All Known Implementing Classes:

AnnotationManagerImpl, FernMLAnnotationManager

public interface AnnotationManager

AnnotationManager objects are the places, where static (or quasi-static) properties of a network are stored. At this time, all the annotations and the initial amounts of the species belong to the static properties. Annotations are only supposed to hold data which

• almost never changes
• is read very infrequently

Author:

Florian Erhard

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.

Method Detail

containsSpeciesAnnotation

boolean containsSpeciesAnnotation(int species,
                                  String typ)

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

Parameters:

species - index of the species

typ - field name of the annotation

Returns:

true iff such an annotation is present

getSpeciesAnnotationTypes

Collection<String> getSpeciesAnnotationTypes(int species)

Gets the names of the species annotations.

Parameters:

species - index of the species

Returns:

names of the fields

getSpeciesAnnotation

String getSpeciesAnnotation(int species,
                            String typ)

Gets the species annotation of the specified field.

Parameters:

species - index of the species

typ - name of the field

Returns:

species annotation

setSpeciesAnnotation

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

Sets the species annotation of the specified field.

Parameters:

species - index of the species

typ - name of the field

annotation - species annotation

containsReactionAnnotation

boolean containsReactionAnnotation(int reaction,
                                   String typ)

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

Parameters:

reaction - index of the reaction

typ - field name of the annotation

Returns:

true iff such an annotation is present

getReactionAnnotationTypes

Collection<String> getReactionAnnotationTypes(int reaction)

Gets the names of the species reaction.

Parameters:

reaction - index of the reaction

Returns:

names of the fields

getReactionAnnotation

String getReactionAnnotation(int reaction,
                             String typ)

Gets the reaction annotation of the specified field.

Parameters:

reaction - index of the reaction

typ - name of the field

Returns:

reaction annotation

setReactionAnnotation

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

Sets the reaction annotation of the specified field.

Parameters:

reaction - index of the reaction

typ - name of the field

annotation - reaction annotation

containsNetworkAnnotation

boolean containsNetworkAnnotation(String typ)

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

Parameters:

typ - field name of the annotation

Returns:

true iff such an annotation is present

getNetworkAnnotationTypes

Collection<String> getNetworkAnnotationTypes()

Gets the names of the network reaction.

Returns:

names of the fields

getNetworkAnnotation

String getNetworkAnnotation(String typ)

Gets the network annotation of the specified field.

Parameters:

typ - name of the field

Returns:

network annotation

setNetworkAnnotation

void setNetworkAnnotation(String typ,
                          String annotation)

Sets the network annotation of the specified field.

Parameters:

typ - name of the field

annotation - network annotation