Uses of Class
org.biojava.bio.seq.db.IllegalIDException
Packages that use IllegalIDException
Package
Description
GFF manipulation.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Classes and interfaces to load Amino Acid Index database files.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
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Uses of IllegalIDException in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that throw IllegalIDExceptionModifier and TypeMethodDescriptionstatic 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 IllegalIDExceptionModifier and TypeMethodDescriptionSimilarityPairBuilder.getAnnotatedQuerySeq
(String queryID) SimilarityPairBuilder.getAnnotatedSubjectSeq
(String subjectID) -
Uses of IllegalIDException in org.biojava.bio.proteomics.aaindex
Methods in org.biojava.bio.proteomics.aaindex that throw IllegalIDExceptionModifier and TypeMethodDescriptionReturns the table with the specified name.Returns the table with the specified name. -
Uses of IllegalIDException in org.biojava.bio.seq
Methods in org.biojava.bio.seq that throw IllegalIDExceptionModifier and TypeMethodDescriptionRemoteFeature.Resolver.resolve
(RemoteFeature rFeat) Resolve rFeat. -
Uses of IllegalIDException in org.biojava.bio.seq.db
Methods in org.biojava.bio.seq.db that throw IllegalIDExceptionModifier and TypeMethodDescriptionvoid
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.Fetch an Index based upon an ID.DummySequenceDB.getSequence
(String id) HashSequenceDB.getSequence
(String id) IndexedSequenceDB.getSequence
(String id) 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
store
adds anIndex
to the store.void
Add the Index to the store.void
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Uses of IllegalIDException in org.biojava.bio.seq.db.biofetch
Methods in org.biojava.bio.seq.db.biofetch that throw IllegalIDException -
Uses of IllegalIDException in org.biojava.bio.seq.db.flat
Methods in org.biojava.bio.seq.db.flat that throw IllegalIDException -
Uses of IllegalIDException in org.biojava.bio.seq.distributed
Methods in org.biojava.bio.seq.distributed that throw IllegalIDException -
Uses of IllegalIDException in org.biojavax.bio.db
Methods in org.biojavax.bio.db that throw IllegalIDExceptionModifier and TypeMethodDescriptionvoid
AbstractBioEntryDB.addBioEntry
(BioEntry seq) void
AbstractRichSequenceDB.addBioEntry
(BioEntry seq) void
BioEntryDBLite.addBioEntry
(BioEntry seq) Adds a sequence to the database.protected void
HashBioEntryDB.addBioEntry
(String id, BioEntry seq) void
HashBioEntryDB.addBioEntry
(BioEntry seq) Add a BioEntry, the name of the BioEntry will be used as the IDvoid
AbstractRichSequenceDB.addRichSequence
(RichSequence seq) protected void
HashRichSequenceDB.addRichSequence
(String id, RichSequence seq) void
HashRichSequenceDB.addRichSequence
(RichSequence seq) Add a sequence.void
RichSequenceDBLite.addRichSequence
(RichSequence seq) Adds a sequence to the database.void
AbstractRichSequenceDB.addSequence
(Sequence seq) AbstractRichSequenceDB.getBioEntry
(String id) BioEntryDBLite.getBioEntry
(String id) Retrieve a single BioEntry by its id.HashBioEntryDB.getBioEntry
(String id) AbstractRichSequenceDB.getBioEntrys
(Set ids) AbstractRichSequenceDB.getBioEntrys
(Set ids, BioEntryDB db) BioEntryDBLite.getBioEntrys
(Set ids) Retrieve multiple BioEntry by their ids.BioEntryDBLite.getBioEntrys
(Set ids, BioEntryDB db) Retrieve multiple BioEntry into a specific sequence database.HashBioEntryDB.getBioEntrys
(Set ids) HashBioEntryDB.getBioEntrys
(Set ids, BioEntryDB db) HashRichSequenceDB.getRichSequence
(String id) RichSequenceDBLite.getRichSequence
(String id) Retrieve a single RichSequence by its id.HashRichSequenceDB.getRichSequences
(Set ids) HashRichSequenceDB.getRichSequences
(Set ids, RichSequenceDB db) RichSequenceDBLite.getRichSequences
(Set ids) Retrieve multiple RichSequence by its id.RichSequenceDBLite.getRichSequences
(Set ids, RichSequenceDB db) Retrieve multiple RichSequence into a specific sequence database.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
AbstractRichSequenceDB.removeRichSequence
(String id) void
RichSequenceDBLite.removeRichSequence
(String id) Remove the RichSequence associated with an ID from the database.void
AbstractRichSequenceDB.removeSequence
(String id) void
HashRichSequenceDB.removeSequence
(String id) -
Uses of IllegalIDException in org.biojavax.bio.db.biosql
Methods in org.biojavax.bio.db.biosql that throw IllegalIDExceptionModifier and TypeMethodDescriptionvoid
BioSQLBioEntryDB._addBioEntry
(BioEntry seq) void
BioSQLBioEntryDB.addBioEntry
(BioEntry seq) void
BioSQLRichSequenceDB.addRichSequence
(RichSequence seq) BioSQLRichSequenceDB.fullyLoadRichSequence
(RichSequence id) BioSQLBioEntryDB.getBioEntry
(String id) BioSQLBioEntryDB.getBioEntrys
(Set ids) BioSQLBioEntryDB.getBioEntrys
(Set ids, BioEntryDB db) BioSQLRichSequenceDB.getRichSequence
(String id) BioSQLRichSequenceDB.getRichSequences
(Set ids) 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 IllegalIDExceptionModifier and TypeMethodDescriptionGenbankRichSequenceDB.getRichSequence
(String id) Given the appropriate Genbank ID, return the matching RichSequence object.GenbankRichSequenceDB.getRichSequence
(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.GenpeptRichSequenceDB.getRichSequence
(String id) Given the appropriate Genbank ID, return the matching RichSequence object.GenpeptRichSequenceDB.getRichSequence
(String id, Namespace nsp) Given the appropriate Genbank ID, return the matching RichSequence object.GenbankRichSequenceDB.getRichSequences
(Set list) Retrieve rich sequences from a GenbankGenbankRichSequenceDB.getRichSequences
(Set list, RichSequenceDB database) Retrieve rich sequences from a GenbankGenpeptRichSequenceDB.getRichSequences
(Set list) Retrieve rich sequences from a GenbankGenpeptRichSequenceDB.getRichSequences
(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank