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Packages that use IllegalIDException | |
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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 |
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Methods in org.biojava.bio.program.das that throw IllegalIDException | |
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Sequence |
DASSequenceDB.getSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojava.bio.program.gff |
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Methods in org.biojava.bio.program.gff that throw IllegalIDException | |
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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 |
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Methods in org.biojava.bio.program.ssbind that throw IllegalIDException | |
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Sequence |
SimilarityPairBuilder.getAnnotatedQuerySeq(java.lang.String queryID)
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Sequence |
SimilarityPairBuilder.getAnnotatedSubjectSeq(java.lang.String subjectID)
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Uses of IllegalIDException in org.biojava.bio.proteomics.aaindex |
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Methods in org.biojava.bio.proteomics.aaindex that throw IllegalIDException | |
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SymbolPropertyTable |
SimpleSymbolPropertyTableDB.table(java.lang.String name)
Returns the table with the specified name. |
SymbolPropertyTable |
SymbolPropertyTableDB.table(java.lang.String name)
Returns the table with the specified name. |
Uses of IllegalIDException in org.biojava.bio.seq |
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Methods in org.biojava.bio.seq that throw IllegalIDException | |
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Feature |
RemoteFeature.Resolver.resolve(RemoteFeature rFeat)
Resolve rFeat. |
Uses of IllegalIDException in org.biojava.bio.seq.db |
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Methods in org.biojava.bio.seq.db that throw IllegalIDException | |
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void |
IndexedSequenceDB.addFile(java.io.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)
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Index |
BioIndex.fetch(java.lang.String id)
|
Index |
EmblCDROMIndexStore.fetch(java.lang.String id)
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Index |
IndexStore.fetch(java.lang.String id)
Fetch an Index based upon an ID. |
Index |
TabIndexStore.fetch(java.lang.String id)
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Sequence |
HashSequenceDB.getSequence(java.lang.String id)
|
Sequence |
IndexedSequenceDB.getSequence(java.lang.String id)
|
Sequence |
SequenceDBLite.getSequence(java.lang.String id)
Retrieve a single sequence by its id. |
Sequence |
DummySequenceDB.getSequence(java.lang.String id)
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void |
SequenceDBLite.removeSequence(java.lang.String id)
Remove the sequence associated with an ID from the database. |
void |
DummySequenceDB.removeSequence(java.lang.String id)
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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 |
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Methods in org.biojava.bio.seq.db.biofetch that throw IllegalIDException | |
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Sequence |
BioFetchSequenceDB.getSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojava.bio.seq.db.flat |
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Methods in org.biojava.bio.seq.db.flat that throw IllegalIDException | |
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Sequence |
FlatSequenceDB.getSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojava.bio.seq.distributed |
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Methods in org.biojava.bio.seq.distributed that throw IllegalIDException | |
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Sequence |
DistributedSequenceDB.getSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojavax.bio.db |
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Methods in org.biojavax.bio.db that throw IllegalIDException | |
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void |
AbstractBioEntryDB.addBioEntry(BioEntry seq)
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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(java.lang.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(java.lang.String id,
RichSequence seq)
|
void |
AbstractRichSequenceDB.addSequence(Sequence seq)
|
BioEntry |
AbstractRichSequenceDB.getBioEntry(java.lang.String id)
|
BioEntry |
BioEntryDBLite.getBioEntry(java.lang.String id)
Retrieve a single BioEntry by its id. |
BioEntry |
HashBioEntryDB.getBioEntry(java.lang.String id)
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BioEntryDB |
AbstractRichSequenceDB.getBioEntrys(java.util.Set ids)
|
BioEntryDB |
BioEntryDBLite.getBioEntrys(java.util.Set ids)
Retrieve multiple BioEntry by their ids. |
BioEntryDB |
HashBioEntryDB.getBioEntrys(java.util.Set ids)
|
BioEntryDB |
AbstractRichSequenceDB.getBioEntrys(java.util.Set ids,
BioEntryDB db)
|
BioEntryDB |
BioEntryDBLite.getBioEntrys(java.util.Set ids,
BioEntryDB db)
Retrieve multiple BioEntry into a specific sequence database. |
BioEntryDB |
HashBioEntryDB.getBioEntrys(java.util.Set ids,
BioEntryDB db)
|
RichSequence |
RichSequenceDBLite.getRichSequence(java.lang.String id)
Retrieve a single RichSequence by its id. |
RichSequence |
HashRichSequenceDB.getRichSequence(java.lang.String id)
|
RichSequenceDB |
RichSequenceDBLite.getRichSequences(java.util.Set ids)
Retrieve multiple RichSequence by its id. |
RichSequenceDB |
HashRichSequenceDB.getRichSequences(java.util.Set ids)
|
RichSequenceDB |
RichSequenceDBLite.getRichSequences(java.util.Set ids,
RichSequenceDB db)
Retrieve multiple RichSequence into a specific sequence database. |
RichSequenceDB |
HashRichSequenceDB.getRichSequences(java.util.Set ids,
RichSequenceDB db)
|
Sequence |
AbstractRichSequenceDB.getSequence(java.lang.String id)
|
void |
AbstractBioEntryDB.removeBioEntry(java.lang.String id)
|
void |
AbstractRichSequenceDB.removeBioEntry(java.lang.String id)
|
void |
BioEntryDBLite.removeBioEntry(java.lang.String id)
Remove the BioEntry associated with an ID from the database. |
void |
HashBioEntryDB.removeBioEntry(java.lang.String id)
|
void |
RichSequenceDBLite.removeRichSequence(java.lang.String id)
Remove the RichSequence associated with an ID from the database. |
void |
AbstractRichSequenceDB.removeRichSequence(java.lang.String id)
|
void |
HashRichSequenceDB.removeSequence(java.lang.String id)
|
void |
AbstractRichSequenceDB.removeSequence(java.lang.String id)
|
Uses of IllegalIDException in org.biojavax.bio.db.biosql |
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Methods in org.biojavax.bio.db.biosql that throw IllegalIDException | |
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void |
BioSQLBioEntryDB._addBioEntry(BioEntry seq)
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void |
BioSQLBioEntryDB.addBioEntry(BioEntry seq)
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void |
BioSQLRichSequenceDB.addRichSequence(RichSequence seq)
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RichSequence |
BioSQLRichSequenceDB.fullyLoadRichSequence(RichSequence id)
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BioEntry |
BioSQLBioEntryDB.getBioEntry(java.lang.String id)
|
BioEntryDB |
BioSQLBioEntryDB.getBioEntrys(java.util.Set ids)
|
BioEntryDB |
BioSQLBioEntryDB.getBioEntrys(java.util.Set ids,
BioEntryDB db)
|
RichSequence |
BioSQLRichSequenceDB.getRichSequence(java.lang.String id)
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RichSequenceDB |
BioSQLRichSequenceDB.getRichSequences(java.util.Set ids)
|
RichSequenceDB |
BioSQLRichSequenceDB.getRichSequences(java.util.Set ids,
RichSequenceDB db)
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void |
BioSQLBioEntryDB.removeBioEntry(java.lang.String id)
|
void |
BioSQLRichSequenceDB.removeRichSequence(java.lang.String id)
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Uses of IllegalIDException in org.biojavax.bio.db.ncbi |
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Methods in org.biojavax.bio.db.ncbi that throw IllegalIDException | |
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RichSequence |
GenbankRichSequenceDB.getRichSequence(java.lang.String id)
Given the appropriate Genbank ID, return the matching RichSequence object. |
RichSequence |
GenbankRichSequenceDB.getRichSequence(java.lang.String id,
Namespace nsp)
Given the appropriate Genbank ID, return the matching RichSequence object. |
RichSequenceDB |
GenbankRichSequenceDB.getRichSequences(java.util.Set list)
Retrieve rich sequences from a Genbank |
RichSequenceDB |
GenbankRichSequenceDB.getRichSequences(java.util.Set list,
RichSequenceDB database)
Retrieve rich sequences from a Genbank |
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