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

Packages that use IllegalIDException
org.biojava.bio.program.das: Development client for the Distributed Annotation System.
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.das

Methods in org.biojava.bio.program.das that throw IllegalIDException
`Sequence` `DASSequenceDB.getSequence(String id)`

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

Methods in org.biojava.bio.program.gff that throw IllegalIDException
`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
`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
`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
`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
`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
`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
`Sequence` `FlatSequenceDB.getSequence(String id)`

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

Methods in org.biojava.bio.seq.distributed that throw IllegalIDException
`Sequence` `DistributedSequenceDB.getSequence(String id)`

Uses of IllegalIDException in org.biojavax.bio.db

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