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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.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.biosql | General purpose Sequence storage in a relational database. |
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. |
Uses of IllegalIDException in org.biojava.bio.program.das |
Methods in org.biojava.bio.program.das that throw IllegalIDException | |
Sequence |
DASSequenceDB.getSequence(java.lang.String id)
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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(java.lang.String queryID)
|
Sequence |
SimilarityPairBuilder.getAnnotatedSubjectSeq(java.lang.String subjectID)
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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 |
EmblCDROMIndexStore.store(Index index)
store adds an Index to the store. |
Index |
EmblCDROMIndexStore.fetch(java.lang.String id)
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Sequence |
DummySequenceDB.getSequence(java.lang.String id)
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void |
DummySequenceDB.addSequence(Sequence seq)
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void |
DummySequenceDB.removeSequence(java.lang.String id)
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void |
TabIndexStore.store(Index indx)
|
Index |
TabIndexStore.fetch(java.lang.String id)
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void |
IndexedSequenceDB.addFile(java.io.File seqFile)
Add sequences from a file to the sequence database. |
Sequence |
IndexedSequenceDB.getSequence(java.lang.String id)
|
Sequence |
SequenceDBLite.getSequence(java.lang.String id)
Retrieve a single sequence by its id. |
void |
SequenceDBLite.addSequence(Sequence seq)
Adds a sequence to the database. |
void |
SequenceDBLite.removeSequence(java.lang.String id)
Remove the sequence associated with an ID from the database. |
void |
IndexStore.store(Index indx)
Add the Index to the store. |
Index |
IndexStore.fetch(java.lang.String id)
Fetch an Index based upon an ID. |
Index |
BioIndex.fetch(java.lang.String id)
|
Sequence |
HashSequenceDB.getSequence(java.lang.String id)
|
Uses of IllegalIDException in org.biojava.bio.seq.db.biofetch |
Methods in org.biojava.bio.seq.db.biofetch that throw IllegalIDException | |
Sequence |
BioFetchSequenceDB.getSequence(java.lang.String id)
|
Uses of IllegalIDException in org.biojava.bio.seq.db.biosql |
Methods in org.biojava.bio.seq.db.biosql that throw IllegalIDException | |
void |
BioSQLSequenceDB.createDummySequence(java.lang.String id,
Alphabet alphabet,
int length)
|
void |
BioSQLSequenceDB.addSequence(Sequence seq)
|
Sequence |
BioSQLSequenceDB.getSequence(java.lang.String id)
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void |
BioSQLSequenceDB.removeSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojava.bio.seq.db.flat |
Methods in org.biojava.bio.seq.db.flat that throw IllegalIDException | |
Sequence |
FlatSequenceDB.getSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojava.bio.seq.distributed |
Methods in org.biojava.bio.seq.distributed that throw IllegalIDException | |
Sequence |
DistributedSequenceDB.getSequence(java.lang.String id)
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