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 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 DummySequenceDB.addSequence(Sequence seq)
           
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 Index IndexStore.fetch(String id)
          Fetch an Index based upon an ID.
 Index BioIndex.fetch(String id)
           
 Index TabIndexStore.fetch(String id)
           
 Index EmblCDROMIndexStore.fetch(String id)
           
 Sequence IndexedSequenceDB.getSequence(String id)
           
 Sequence HashSequenceDB.getSequence(String id)
           
 Sequence DummySequenceDB.getSequence(String id)
           
 Sequence SequenceDBLite.getSequence(String id)
          Retrieve a single sequence by its id.
 void DummySequenceDB.removeSequence(String id)
           
 void SequenceDBLite.removeSequence(String id)
          Remove the sequence associated with an ID from the database.
 void IndexStore.store(Index indx)
          Add the Index to the store.
 void TabIndexStore.store(Index indx)
           
 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 HashRichSequenceDB.addRichSequence(RichSequence seq)
          Add a sequence.
 void RichSequenceDBLite.addRichSequence(RichSequence seq)
          Adds a sequence to the database.
 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 HashRichSequenceDB.getRichSequence(String id)
           
 RichSequence RichSequenceDBLite.getRichSequence(String id)
          Retrieve a single RichSequence by its id.
 RichSequenceDB HashRichSequenceDB.getRichSequences(Set ids)
           
 RichSequenceDB RichSequenceDBLite.getRichSequences(Set ids)
          Retrieve multiple RichSequence by its id.
 RichSequenceDB HashRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)
           
 RichSequenceDB RichSequenceDBLite.getRichSequences(Set ids, RichSequenceDB db)
          Retrieve multiple RichSequence into a specific sequence database.
 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 GenbankRichSequenceDB.getRichSequence(String id)
          Given the appropriate Genbank ID, return the matching RichSequence object.
 RichSequence GenpeptRichSequenceDB.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.
 RichSequence GenpeptRichSequenceDB.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 GenpeptRichSequenceDB.getRichSequences(Set list)
          Retrieve rich sequences from a Genbank
 RichSequenceDB GenbankRichSequenceDB.getRichSequences(Set list, RichSequenceDB database)
          Retrieve rich sequences from a Genbank
 RichSequenceDB GenpeptRichSequenceDB.getRichSequences(Set list, RichSequenceDB database)
          Retrieve rich sequences from a Genbank