org.jbei.ice.lib.entry.sequence.annotation

Class Annotations

java.lang.Object

org.jbei.ice.lib.entry.sequence.annotation.Annotations

public class Annotations
extends Object

ICE Annotations with support for generating potential annotations for a specified entry

Author:

Hector Plahar

Constructor Summary

Constructors

Constructor and Description
Annotations(String userId)

Method Summary

Modifier and Type	Method and Description
void	curate(List<DNAFeature> features) Curates a specified set of annotations.
Results<DNAFeature>	filter(int offset, int limit, String filter)
FeaturedDNASequence	generate(FeaturedDNASequence sequence) Using existing and potentially curated annotations on this ICE instance, this generates matching features for the passed sequence
FeaturedDNASequence	generate(long entryId, boolean ownerFeatures) Auto generate annotations for specified entry
Results<DNAFeatures>	get(int offset, int limit, String sort) Retrieves list of annotations that are available
protected boolean	isAdministrator()
void	rebuild() Rebuild the annotations blast database

Methods inherited from class java.lang.Object

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

Constructor Detail

Annotations

public Annotations(String userId)

Method Detail

get

public Results<DNAFeatures> get(int offset,
                                int limit,
                                String sort)

Retrieves list of annotations that are available

Parameters:

offset - paging start

limit - maximum number of annotations to return

sort - paging sort

Returns:

available annotations that conform to parameters along with the total number that are available

Throws:

PermissionException - if the requesting user's account does not have administrative privileges

filter

public Results<DNAFeature> filter(int offset,
                                  int limit,
                                  String filter)

generate

public FeaturedDNASequence generate(long entryId,
                                    boolean ownerFeatures)

Auto generate annotations for specified entry

Parameters:

entryId - unique (local) identifier for entry

ownerFeatures - whether to only include the features created by the requesting user

Returns:

wrapper around generated annotations, if any are found

generate

public FeaturedDNASequence generate(FeaturedDNASequence sequence)

Using existing and potentially curated annotations on this ICE instance, this generates matching features for the passed sequence

Parameters:

sequence - wrapper around dna sequence

Returns:

wrapper around passed sequence and now with list if annotations for that sequence

rebuild

public void rebuild()

Rebuild the annotations blast database

Throws:

PermissionException - if the specified user does not have administrator privileges

isAdministrator

protected boolean isAdministrator()

curate

public void curate(List<DNAFeature> features)

Curates a specified set of annotations. The curation properties are contained in each annotation (feature) object

Parameters:

features - set of features to be curated