Uses of Class org.biojava.bio.seq.db.IllegalIDException (BioJava-1.5-beta API)

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## 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 |
org.biojavax.bio.db.ncbi |

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` | `SimpleSymbolPropertyTableDB.table(String name)` Returns the table with the specified name.
`SymbolPropertyTable` | `SymbolPropertyTableDB.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` | `BioIndex.fetch(String id)`
`Index` | `EmblCDROMIndexStore.fetch(String id)`
`Index` | `IndexStore.fetch(String id)` Fetch an Index based upon an ID.
`Index` | `TabIndexStore.fetch(String id)`
`Sequence` | `HashSequenceDB.getSequence(String id)`
`Sequence` | `IndexedSequenceDB.getSequence(String id)`
`Sequence` | `SequenceDBLite.getSequence(String id)` Retrieve a single sequence by its 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` | `EmblCDROMIndexStore.store(Index index)` `store` adds an `Index` to the store.
`void` | `IndexStore.store(Index indx)` Add the Index to the store.
`void` | `TabIndexStore.store(Index indx)`

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` | `AbstractBioEntryDB.addBioEntry(BioEntry seq)`
`void` | `AbstractRichSequenceDB.addBioEntry(BioEntry seq)`
`void` | `BioEntryDBLite.addBioEntry(BioEntry seq)` Adds a sequence to the database.
`void` | `HashBioEntryDB.addBioEntry(BioEntry seq)` Add a BioEntry, the name of the BioEntry will be used as the ID
`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` | `AbstractRichSequenceDB.getBioEntry(String id)`
`BioEntry` | `BioEntryDBLite.getBioEntry(String id)` Retrieve a single BioEntry by its id.
`BioEntry` | `HashBioEntryDB.getBioEntry(String id)`
`BioEntryDB` | `AbstractRichSequenceDB.getBioEntrys(Set ids)`
`BioEntryDB` | `BioEntryDBLite.getBioEntrys(Set ids)` Retrieve multiple BioEntry by their ids.
`BioEntryDB` | `HashBioEntryDB.getBioEntrys(Set ids)`
`BioEntryDB` | `AbstractRichSequenceDB.getBioEntrys(Set ids, BioEntryDB db)`
`BioEntryDB` | `BioEntryDBLite.getBioEntrys(Set ids, BioEntryDB db)` Retrieve multiple BioEntry into a specific sequence database.
`BioEntryDB` | `HashBioEntryDB.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` | `AbstractBioEntryDB.removeBioEntry(String id)`
`void` | `AbstractRichSequenceDB.removeBioEntry(String id)`
`void` | `BioEntryDBLite.removeBioEntry(String id)` Remove the BioEntry associated with an ID from the database.
`void` | `HashBioEntryDB.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` | `GenbankRichSequenceDB.getRichSequence(String id)` 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` | `GenbankRichSequenceDB.getRichSequences(Set list)` Retrieve rich sequences from a Genbank
`RichSequenceDB` | `GenbankRichSequenceDB.getRichSequences(Set list, RichSequenceDB database)` Retrieve rich sequences from a Genbank

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