Uses of Class
org.biojava.bio.seq.db.IllegalIDException

Packages that use IllegalIDException

Package	Description
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.proteomics.aaindex	Classes and interfaces to load Amino Acid Index database files.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.

Uses of IllegalIDException in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that throw IllegalIDException

Modifier and Type	Method and Description
static SequenceDB	GFFTools.annotateSequences(SequenceDB seqs, GFFEntrySet ents) Annotates all sequences in a sequence DB with features from a GFF entry set.

Uses of IllegalIDException in org.biojava.bio.program.ssbind

Methods in org.biojava.bio.program.ssbind that throw IllegalIDException

Modifier and Type	Method and Description
Sequence	SimilarityPairBuilder.getAnnotatedQuerySeq(String queryID)
Sequence	SimilarityPairBuilder.getAnnotatedSubjectSeq(String subjectID)

Uses of IllegalIDException in org.biojava.bio.proteomics.aaindex

Methods in org.biojava.bio.proteomics.aaindex that throw IllegalIDException

Modifier and Type	Method and Description
SymbolPropertyTable	SymbolPropertyTableDB.table(String name) Returns the table with the specified name.
SymbolPropertyTable	SimpleSymbolPropertyTableDB.table(String name) Returns the table with the specified name.

Uses of IllegalIDException in org.biojava.bio.seq

Methods in org.biojava.bio.seq that throw IllegalIDException

Modifier and Type	Method and Description
Feature	RemoteFeature.Resolver.resolve(RemoteFeature rFeat) Resolve rFeat.

Uses of IllegalIDException in org.biojava.bio.seq.db

Methods in org.biojava.bio.seq.db that throw IllegalIDException

Modifier and Type	Method and Description
void	IndexedSequenceDB.addFile(File seqFile) Add sequences from a file to the sequence database.
void	SequenceDBLite.addSequence(Sequence seq) Adds a sequence to the database.
void	DummySequenceDB.addSequence(Sequence seq)
Index	TabIndexStore.fetch(String id)
Index	IndexStore.fetch(String id) Fetch an Index based upon an ID.
Index	EmblCDROMIndexStore.fetch(String id)
Index	BioIndex.fetch(String id)
Sequence	SequenceDBLite.getSequence(String id) Retrieve a single sequence by its id.
Sequence	IndexedSequenceDB.getSequence(String id)
Sequence	HashSequenceDB.getSequence(String id)
Sequence	DummySequenceDB.getSequence(String id)
void	SequenceDBLite.removeSequence(String id) Remove the sequence associated with an ID from the database.
void	DummySequenceDB.removeSequence(String id)
void	TabIndexStore.store(Index indx)
void	IndexStore.store(Index indx) Add the Index to the store.
void	EmblCDROMIndexStore.store(Index index) store adds an Index to the store.

Uses of IllegalIDException in org.biojava.bio.seq.db.biofetch

Methods in org.biojava.bio.seq.db.biofetch that throw IllegalIDException

Modifier and Type	Method and Description
Sequence	BioFetchSequenceDB.getSequence(String id)

Uses of IllegalIDException in org.biojava.bio.seq.db.flat

Methods in org.biojava.bio.seq.db.flat that throw IllegalIDException

Modifier and Type	Method and Description
Sequence	FlatSequenceDB.getSequence(String id)

Uses of IllegalIDException in org.biojava.bio.seq.distributed

Methods in org.biojava.bio.seq.distributed that throw IllegalIDException

Modifier and Type	Method and Description
Sequence	DistributedSequenceDB.getSequence(String id)

Uses of IllegalIDException in org.biojavax.bio.db

Methods in org.biojavax.bio.db that throw IllegalIDException

Modifier and Type	Method and Description
void	HashBioEntryDB.addBioEntry(BioEntry seq) Add a BioEntry, the name of the BioEntry will be used as the ID
void	BioEntryDBLite.addBioEntry(BioEntry seq) Adds a sequence to the database.
void	AbstractRichSequenceDB.addBioEntry(BioEntry seq)
void	AbstractBioEntryDB.addBioEntry(BioEntry seq)
protected void	HashBioEntryDB.addBioEntry(String id, BioEntry seq)
void	RichSequenceDBLite.addRichSequence(RichSequence seq) Adds a sequence to the database.
void	HashRichSequenceDB.addRichSequence(RichSequence seq) Add a sequence.
void	AbstractRichSequenceDB.addRichSequence(RichSequence seq)
protected void	HashRichSequenceDB.addRichSequence(String id, RichSequence seq)
void	AbstractRichSequenceDB.addSequence(Sequence seq)
BioEntry	HashBioEntryDB.getBioEntry(String id)
BioEntry	BioEntryDBLite.getBioEntry(String id) Retrieve a single BioEntry by its id.
BioEntry	AbstractRichSequenceDB.getBioEntry(String id)
BioEntryDB	HashBioEntryDB.getBioEntrys(Set ids)
BioEntryDB	BioEntryDBLite.getBioEntrys(Set ids) Retrieve multiple BioEntry by their ids.
BioEntryDB	AbstractRichSequenceDB.getBioEntrys(Set ids)
BioEntryDB	HashBioEntryDB.getBioEntrys(Set ids, BioEntryDB db)
BioEntryDB	BioEntryDBLite.getBioEntrys(Set ids, BioEntryDB db) Retrieve multiple BioEntry into a specific sequence database.
BioEntryDB	AbstractRichSequenceDB.getBioEntrys(Set ids, BioEntryDB db)
RichSequence	RichSequenceDBLite.getRichSequence(String id) Retrieve a single RichSequence by its id.
RichSequence	HashRichSequenceDB.getRichSequence(String id)
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids) Retrieve multiple RichSequence by its id.
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids)
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids, RichSequenceDB db) Retrieve multiple RichSequence into a specific sequence database.
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)
Sequence	AbstractRichSequenceDB.getSequence(String id)
void	HashBioEntryDB.removeBioEntry(String id)
void	BioEntryDBLite.removeBioEntry(String id) Remove the BioEntry associated with an ID from the database.
void	AbstractRichSequenceDB.removeBioEntry(String id)
void	AbstractBioEntryDB.removeBioEntry(String id)
void	RichSequenceDBLite.removeRichSequence(String id) Remove the RichSequence associated with an ID from the database.
void	AbstractRichSequenceDB.removeRichSequence(String id)
void	HashRichSequenceDB.removeSequence(String id)
void	AbstractRichSequenceDB.removeSequence(String id)

Uses of IllegalIDException in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that throw IllegalIDException

Modifier and Type	Method and Description
void	BioSQLBioEntryDB._addBioEntry(BioEntry seq)
void	BioSQLBioEntryDB.addBioEntry(BioEntry seq)
void	BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
RichSequence	BioSQLRichSequenceDB.fullyLoadRichSequence(RichSequence id)
BioEntry	BioSQLBioEntryDB.getBioEntry(String id)
BioEntryDB	BioSQLBioEntryDB.getBioEntrys(Set ids)
BioEntryDB	BioSQLBioEntryDB.getBioEntrys(Set ids, BioEntryDB db)
RichSequence	BioSQLRichSequenceDB.getRichSequence(String id)
RichSequenceDB	BioSQLRichSequenceDB.getRichSequences(Set ids)
RichSequenceDB	BioSQLRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)
void	BioSQLBioEntryDB.removeBioEntry(String id)
void	BioSQLRichSequenceDB.removeRichSequence(String id)

Uses of IllegalIDException in org.biojavax.bio.db.ncbi

Methods in org.biojavax.bio.db.ncbi that throw IllegalIDException

Modifier and Type	Method and Description
RichSequence	GenpeptRichSequenceDB.getRichSequence(String id) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenbankRichSequenceDB.getRichSequence(String id) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenpeptRichSequenceDB.getRichSequence(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequence	GenbankRichSequenceDB.getRichSequence(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.
RichSequenceDB	GenpeptRichSequenceDB.getRichSequences(Set list) Retrieve rich sequences from a Genbank
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list) Retrieve rich sequences from a Genbank
RichSequenceDB	GenpeptRichSequenceDB.getRichSequences(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank