fern.network
Interface AnnotationManager

All Known Implementing Classes:
AnnotationManagerImpl, CytoscapeAnnotationManager, 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

Author:
Florian Erhard

Method Summary
 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