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Packages that use BioException | |
org.biojava.bio.alignment |
Implementation of the Alignment interface. |
org.biojava.bio.chromatogram | Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment. |
org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.gui | Graphical interfaces for biojava objects. |
org.biojava.bio.molbio | The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. |
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.program.gff | GFF manipulation. |
org.biojava.bio.program.indexdb | A flat-file ascii index of ascii flat files as per the OBDA specification. |
org.biojava.bio.program.phred | Parser for Phred output |
org.biojava.bio.program.ssaha | SSAHA sequence searching API. |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.program.unigene | Objects for representing Unigene clusters. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
org.biojava.bio.search | Interfaces and classes for representing sequence similarity search results. |
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. |
org.biojava.bio.seq.homol | The classes and interfaces for defining sequence similarity and honology. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.bio.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.seq.projection | Code for projecting Feature objects into alternate coordinate systems. |
org.biojava.bio.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
org.biojava.bio.taxa | Taxonomy object for representing species information. |
org.biojava.directory | Open Bio Sequence Database Access (OBDA) registry support. |
org.biojava.utils.math | Mathematical utility classes. |
Uses of BioException in org.biojava.bio.alignment |
Methods in org.biojava.bio.alignment that throw BioException | |
void |
ARAlignment.addSequence(AlignmentElement ae)
|
void |
FlexibleAlignment.addSequence(AlignmentElement ae)
add a new a alignment usings a location to the reference sequence. |
Constructors in org.biojava.bio.alignment that throw BioException | |
SimpleAlignmentElement(java.lang.Object label,
SymbolList seq,
Location loc)
|
|
FlexibleAlignment(java.util.List seqList)
construct this object with the reference sequence which can either be a gappedSymbolList or not label in all cases refers to an object that holds the display name (generally just a String). |
Uses of BioException in org.biojava.bio.chromatogram |
Subclasses of BioException in org.biojava.bio.chromatogram | |
class |
UnsupportedChromatogramFormatException
Exception indicating that some provided data does not represent a supported chromatogram format. |
Uses of BioException in org.biojava.bio.dist |
Methods in org.biojava.bio.dist that throw BioException | |
static boolean |
DistributionTools.areEmissionSpectraEqual(Distribution a,
Distribution b)
Compares the emission spectra of two distributions |
static boolean |
DistributionTools.areEmissionSpectraEqual(Distribution[] a,
Distribution[] b)
Compares the emission spectra of two distribution arrays |
Uses of BioException in org.biojava.bio.dp |
Subclasses of BioException in org.biojava.bio.dp | |
class |
IllegalTransitionException
This exception indicates that there is no transition between two states. |
Methods in org.biojava.bio.dp that throw BioException | |
void |
AbstractTrainer.train(SequenceDB db,
double nullModelWeight,
StoppingCriteria stopper)
Trains the sequences in db until stopper says to finnish. |
void |
TrainingAlgorithm.train(SequenceDB db,
double nullWeight,
StoppingCriteria stopper)
Trains the sequences in db untill stopper says to finnish. |
Sequence |
WeightMatrixAnnotator.annotate(Sequence seq)
|
void |
WMAsMM.registerWithTrainer(ModelTrainer modelTrainer)
|
DP |
DPFactory.createDP(MarkovModel model)
|
DP |
DPFactory.DefaultFactory.createDP(MarkovModel model)
|
static State[] |
DP.stateList(MarkovModel mm)
|
DPMatrix |
DP.forwardsBackwards(SymbolList[] symList,
ScoreType scoreType)
|
StatePath |
DP.generate(int length)
Generates an alignment from a model. |
static WeightMatrix |
XmlMarkovModel.readMatrix(org.w3c.dom.Element root)
|
static MarkovModel |
XmlMarkovModel.readModel(org.w3c.dom.Element root)
|
void |
Trainable.registerWithTrainer(ModelTrainer mt)
Perform any registration that is necessary with mt. |
Constructors in org.biojava.bio.dp that throw BioException | |
DP(MarkovModel model)
|
Uses of BioException in org.biojava.bio.dp.onehead |
Constructors in org.biojava.bio.dp.onehead that throw BioException | |
SingleDP(MarkovModel model)
|
Uses of BioException in org.biojava.bio.dp.twohead |
Methods in org.biojava.bio.dp.twohead that throw BioException | |
CellCalculatorFactory |
CellCalculatorFactoryMaker.make(DP dp)
|
Constructors in org.biojava.bio.dp.twohead that throw BioException | |
PairwiseDP(MarkovModel mm,
CellCalculatorFactoryMaker ccfm)
|
Uses of BioException in org.biojava.bio.gui |
Methods in org.biojava.bio.gui that throw BioException | |
void |
FeatureTree.setSequenceDB(SequenceDB db)
Use this method to provide the sequences for the tree to work with. |
Uses of BioException in org.biojava.bio.molbio |
Methods in org.biojava.bio.molbio that throw BioException | |
int[] |
RestrictionEnzyme.getUpstreamCut()
getUpstreamCut returns the cut site upstream of
the recognition site. |
int |
RestrictionEnzyme.getUpstreamEndType()
getUpstreamEndType returns the double-stranded end
type produced by the secondary (upstream) cut. |
Uses of BioException in org.biojava.bio.program.das |
Methods in org.biojava.bio.program.das that throw BioException | |
Sequence |
DASSequenceDB.getSequence(java.lang.String id)
|
void |
DASSequence.addAnnotationSource(java.net.URL dataSourceURL)
|
void |
DASSequence.removeAnnotationSource(java.net.URL dataSourceURL)
|
protected SymbolList |
DASSequence.getSymbols()
|
Feature |
DASSequence.realizeFeature(FeatureHolder dest,
Feature.Template temp)
|
SequenceDBLite |
DASSequenceDBProvider.getSequenceDB(java.util.Map config)
|
SequenceDB |
ReferenceServer.getDB()
|
DistDataSource |
ReferenceServer.getDistDataSource()
|
DistDataSource |
DataSource.getDistDataSource()
|
static java.util.Set |
DAS.getTypes(java.net.URL dasURL)
|
void |
DAS.addDasURL(java.net.URL dasURL)
|
Constructors in org.biojava.bio.program.das that throw BioException | |
DASSequenceDB(java.net.URL dataSourceURL)
|
Uses of BioException in org.biojava.bio.program.gff |
Methods in org.biojava.bio.program.gff that throw BioException | |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler)
Informs handler of each line of gff read from bReader. |
void |
GFFParser.parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler,
java.lang.String locator)
Informs handler of each line of GFF read from bReader |
protected GFFRecord |
GFFParser.createRecord(GFFDocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment)
Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler. |
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName)
Reads a GFFEntrySet from a file with no filtering |
static GFFEntrySet |
GFFTools.readGFF(java.lang.String fileName,
GFFRecordFilter recFilt)
Reads a GFFEntrySet from a file with the specified filter |
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn)
|
static GFFEntrySet |
GFFTools.readGFF(java.io.BufferedReader gffIn,
GFFRecordFilter recFilt)
|
static SequenceDB |
GFFTools.annotateSequences(SequenceDB seqs,
GFFEntrySet ents)
Annotates all sequences in a sequence DB with features from a GFF entry set. |
static GFFEntrySet |
GFFTools.gffFromSequence(Sequence seq)
Creates a GFFEntrySet containing one entry for each feature on a sequence. |
void |
GFFWriter.invalidStart(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
GFFWriter.invalidEnd(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
GFFWriter.invalidScore(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
GFFWriter.invalidStrand(java.lang.String token)
|
void |
GFFWriter.invalidFrame(java.lang.String token,
java.lang.NumberFormatException nfe)
|
protected void |
SequencesAsGFF.doProcessSequence(Sequence seq,
GFFDocumentHandler handler,
java.lang.String id)
Internal method to process an individual Sequence. |
protected void |
SequencesAsGFF.doProcessSequence(Sequence seq,
GFFDocumentHandler handler,
java.lang.String id)
Internal method to process an individual Sequence. |
void |
SequencesAsGFF.processSequence(Sequence seq,
GFFDocumentHandler handler)
Process an individual Sequence, informing handler of any suitable features. |
void |
SequencesAsGFF.processSequence(Sequence seq,
GFFDocumentHandler handler)
Process an individual Sequence, informing handler of any suitable features. |
void |
SequencesAsGFF.processDB(SequenceDB seqDB,
GFFDocumentHandler handler)
Process all Sequences within a SequenceDB, informing handler of any suitable features. |
void |
SequencesAsGFF.processDB(SequenceDB seqDB,
GFFDocumentHandler handler)
Process all Sequences within a SequenceDB, informing handler of any suitable features. |
Uses of BioException in org.biojava.bio.program.indexdb |
Methods in org.biojava.bio.program.indexdb that throw BioException | |
static void |
IndexTools.indexFasta(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexFasta indexes DNA, RNA or protein Fasta
format sequence files on primary identifier. |
static void |
IndexTools.indexEmbl(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexEmbl indexes DNA, RNA or protein EMBL format
sequence files on ID as primary identifier and AC as secondary. |
static void |
IndexTools.indexGenbank(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexGenbank indexes DNA, RNA or protein Genbank
format sequence files on LOCUS as primary identifier and
ACCESSION as secondary. |
static void |
IndexTools.indexSwissprot(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles)
indexSwissprot indexes Swissprot format protein
sequence files on ID as primary identifier. |
java.util.List |
BioStore.get(java.lang.String id,
java.lang.String namespace)
|
Record |
IndexStore.get(java.lang.String id)
get returns a record specified by a primary
identifier. |
java.util.List |
IndexStore.get(java.lang.String id,
java.lang.String namespace)
get returns a list of Record s by
searching against the primary identifiers if the namespace
argument is equal to the primary namespace or otherwise by
searching the secondary namespaces. |
BioStore |
BioStoreFactory.createBioStore()
createBioStore creates a BioStore
reflecting the current state of the factory and returns a
reference to it. |
Constructors in org.biojava.bio.program.indexdb that throw BioException | |
BioStore(java.io.File location,
boolean cache)
Creates a new BioStore flatfile index at the
specified location with the specified caching behaviour. |
Uses of BioException in org.biojava.bio.program.phred |
Methods in org.biojava.bio.program.phred that throw BioException | |
static void |
PhredTools.writePhredQuality(java.io.OutputStream qual,
java.io.OutputStream seq,
SequenceDB db)
Writes Phred quality data in a Fasta type format. |
Uses of BioException in org.biojava.bio.program.ssaha |
Methods in org.biojava.bio.program.ssaha that throw BioException | |
DataStore |
CompactedDataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
|
DataStore |
CompactedDataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceStreamer streamer,
Packing packing,
int wordLength,
int stepSize,
int threshold)
|
void |
SequenceStreamer.streamNext(SeqIOListener listener)
|
void |
SequenceStreamer.reset()
|
void |
SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)
|
void |
SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)
|
DataStore |
DataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
Build a new DataStore. |
DataStore |
NIODataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
|
DataStore |
MappedDataStoreFactory.buildDataStore(java.io.File storeFile,
SequenceDB seqDB,
Packing packing,
int wordLength,
int threshold)
|
Uses of BioException in org.biojava.bio.program.ssbind |
Methods in org.biojava.bio.program.ssbind that throw BioException | |
protected Sequence |
ViewSequenceFactory.makeQueryViewSequence(java.lang.String queryID)
|
protected Sequence |
ViewSequenceFactory.makeSubjectViewSequence(java.lang.String subjectID)
|
SeqSimilaritySearchResult |
BlastLikeSearchBuilder.makeSearchResult()
|
static FiniteAlphabet |
AlphabetResolver.resolveAlphabet(java.lang.String identifier)
resolveAlphabet returns an appropriate
Alphabet for an arbitrary identifier. |
Uses of BioException in org.biojava.bio.program.unigene |
Methods in org.biojava.bio.program.unigene that throw BioException | |
static UnigeneDB |
UnigeneTools.loadUnigene(java.net.URL dbURL)
Load a UnigeneDB instance referred to by a URL. |
static UnigeneDB |
UnigeneTools.createUnigene(java.net.URL dbURL)
Create a new UnigeneDB instance referred to by a URL. |
static UnigeneFactory |
UnigeneTools.findFactory(java.net.URL dbURL)
Find the UnigeneFactory that can accept a URL. |
UnigeneDB |
FlatFileUnigeneFactory.loadUnigene(java.net.URL unigeneLoc)
|
UnigeneDB |
FlatFileUnigeneFactory.createUnigene(java.net.URL unigeneLoc)
|
UnigeneDB |
SQLUnigeneFactory.loadUnigene(java.net.URL dbURL)
|
UnigeneDB |
SQLUnigeneFactory.createUnigene(java.net.URL dbURL)
|
UnigeneCluster |
UnigeneDB.getCluster(java.lang.String clusterID)
Fetch a cluster by its cluster id. |
UnigeneCluster |
UnigeneDB.addCluster(UnigeneCluster cluster)
Add a cluster to a database. |
UnigeneDB |
UnigeneFactory.loadUnigene(java.net.URL unigeneURL)
|
UnigeneDB |
UnigeneFactory.createUnigene(java.net.URL unigeneURL)
|
Uses of BioException in org.biojava.bio.program.xff |
Methods in org.biojava.bio.program.xff that throw BioException | |
static void |
XFFTools.annotateXFF(java.io.File xffFile,
Sequence sequence)
|
static Sequence |
XFFTools.readXFF(java.io.File xffFile,
java.lang.String seqID,
FiniteAlphabet alpha)
|
Uses of BioException in org.biojava.bio.proteomics |
Methods in org.biojava.bio.proteomics that throw BioException | |
double |
IsoelectricPointCalc.getPI(SymbolList peptide,
boolean hasFreeNTerm,
boolean hasFreeCTerm)
Computes isoelectric point of specified peptide. |
void |
Digest.addDigestFeatures()
Adds peptides as features to the Sequence in this class. |
static Protease |
Protease.getProteaseByName(java.lang.String proteaseName)
Retrieves a reference to the named Protease. |
static Protease |
ProteaseManager.createProtease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes,
java.lang.String name)
Creates and registers a new Protease. |
static Protease |
ProteaseManager.createProtease(SymbolList cleaveRes,
boolean endoProtease,
java.lang.String name)
|
static Protease |
ProteaseManager.createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes,
java.lang.String name)
|
static Protease |
ProteaseManager.createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String name)
|
static void |
ProteaseManager.registerProtease(Protease prot)
Registers a protease and ensures its flyweight status |
static Protease |
ProteaseManager.getProteaseByName(java.lang.String proteaseName)
Gets a Protease instance by name. |
Constructors in org.biojava.bio.proteomics that throw BioException | |
Protease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
|
Protease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
|
Protease(java.lang.String cleavageRes,
boolean endoProtease)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
Uses of BioException in org.biojava.bio.search |
Methods in org.biojava.bio.search that throw BioException | |
SeqSimilaritySearchResult |
SearchBuilder.makeSearchResult()
The makeSearchResult method returns a
SeqSimilaritySearchResult instance created from
accumulated data. |
SeqSimilaritySearchResult |
SeqSimilaritySearcher.search(SymbolList querySeq,
SequenceDB db,
java.util.Map searchParameters)
Using this sequence similarity searcher, search with the given sequence against the given sequence database. |
Uses of BioException in org.biojava.bio.seq |
Methods in org.biojava.bio.seq that throw BioException | |
Feature |
FeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template template)
Install a feature on the specified sequence. |
void |
Feature.Template.populate(Feature feat)
This attempts to populate the fields of this template using the publically accessible information in a feature. |
Sequence |
SequenceIterator.nextSequence()
Returns the next sequence in the iterator. |
Sequence |
SequenceAnnotator.annotate(Sequence seq)
Return an annotated version of a sequence. |
Feature |
ViewSequence.realizeFeature(FeatureHolder parent,
Feature.Template template)
|
Feature |
ViewSequence.createFeature(Feature.Template template)
|
Feature |
CircularView.createFeature(Feature.Template template)
Over rides ViewSequence to allow the use of locations that have coordinates outside of the sequence length (which are needed to describe locations that overlap the origin of a circular sequence). |
Feature |
SimpleAssembly.createFeature(Feature.Template temp)
|
Feature |
SimpleAssembly.realizeFeature(FeatureHolder fh,
Feature.Template temp)
|
Feature |
FeatureHolder.createFeature(Feature.Template ft)
Create a new Feature, and add it to this FeatureHolder. |
Feature |
SimpleGappedSequence.createFeature(Feature.Template templ)
|
void |
SimpleFeatureRealizer.addImplementation(java.lang.Class template,
java.lang.Class impl)
Install a new mapping from a class of Feature.Template to a class of Feature implementations. |
Feature |
SimpleFeatureRealizer.realizeFeature(Sequence seq,
FeatureHolder parent,
Feature.Template temp)
|
Feature |
ProjectedFeatureHolder.createFeature(Feature.Template templ)
|
Feature |
ProjectedFeatureHolder.createFeature(Feature f,
Feature.Template templ)
|
Feature |
RealizingFeatureHolder.realizeFeature(FeatureHolder parent,
Feature.Template template)
Realize a feature template. |
Feature |
RemoteFeature.getRemoteFeature()
Retrieve the Feature on some assembly Sequence that can represent this RemoteFeature properly. |
Feature |
RemoteFeature.Resolver.resolve(RemoteFeature rFeat)
Resolve rFeat. |
Feature |
AbstractFeatureHolder.createFeature(Feature.Template temp)
|
Feature |
SubSequence.createFeature(Feature.Template templ)
|
static void |
SequenceTools.addAllFeatures(Sequence seq,
FeatureHolder fh)
Add features to a sequence that contain the same information as all those in a feature holder. |
Feature |
DummySequence.createFeature(Feature.Template template)
|
Feature |
LazyFeatureHolder.createFeature(Feature.Template template)
|
Uses of BioException in org.biojava.bio.seq.db |
Subclasses of BioException in org.biojava.bio.seq.db | |
class |
IllegalIDException
|
Methods in org.biojava.bio.seq.db that throw BioException | |
void |
EmblCDROMIndexStore.store(Index index)
store adds an Index to the store. |
void |
EmblCDROMIndexStore.commit()
commit commits changes. |
Index |
EmblCDROMIndexStore.fetch(java.lang.String id)
|
Sequence |
AnnotatedSequenceDB.getSequence(java.lang.String id)
|
protected Sequence |
AnnotatedSequenceDB.doAnnotation(Sequence seq)
Apply the annotation to a sequence. |
Sequence |
DummySequenceDB.getSequence(java.lang.String id)
|
void |
DummySequenceDB.addSequence(Sequence seq)
|
void |
DummySequenceDB.removeSequence(java.lang.String id)
|
void |
TabIndexStore.store(Index indx)
|
Index |
TabIndexStore.fetch(java.lang.String id)
|
void |
TabIndexStore.commit()
|
void |
IndexedSequenceDB.addFile(java.io.File seqFile)
Add sequences from a file to the sequence database. |
Sequence |
IndexedSequenceDB.getSequence(java.lang.String id)
|
Sequence |
GenpeptSequenceDB.getSequence(java.lang.String id)
|
void |
AbstractSequenceDB.addSequence(Sequence seq)
|
void |
AbstractSequenceDB.removeSequence(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. |
void |
IndexStore.commit()
Commit the stored indices to permanent storage. |
Index |
IndexStore.fetch(java.lang.String id)
Fetch an Index based upon an ID. |
void |
NCBISequenceDB.setDatabase(java.lang.String dataBase)
|
void |
NCBISequenceDB.setSequenceFormat(SequenceFormat format)
|
Sequence |
SwissprotSequenceDB.getSequence(java.lang.String id)
|
Sequence |
WebSequenceDB.getSequence(java.lang.String id)
Gets a sequence using its unique ID (eg for GenBank this would be the GI number) |
Index |
BioIndex.fetch(java.lang.String id)
|
void |
BioIndex.commit()
|
void |
HashSequenceDB.removeSequence(java.lang.String id)
|
Sequence |
CachingSequenceDB.getSequence(java.lang.String id)
|
SequenceDB |
GenbankSequenceDB.getSequences(java.util.Set list)
Retrieve sequences from a Genbank |
SequenceDB |
GenbankSequenceDB.getSequences(java.util.Set list,
SequenceDB database)
Retrieve sequences from a Genbank |
Sequence |
ViewingSequenceDB.getSequence(java.lang.String id)
|
Sequence |
SubSequenceDB.getSequence(java.lang.String id)
|
Constructors in org.biojava.bio.seq.db that throw BioException | |
TabIndexStore(java.io.File storeFile,
java.io.File indexFile,
java.lang.String name,
SequenceFormat format,
SequenceBuilderFactory sbFactory,
SymbolTokenization symbolParser)
|
|
BioIndex(java.io.File indexDirectory,
java.lang.String namespace,
int idLength)
|
|
BioIndex(java.io.File indexDirectory)
Load an existing index file. |
|
SubSequenceDB(SequenceDB parent,
java.util.Set ids)
|
Uses of BioException in org.biojava.bio.seq.db.biofetch |
Methods in org.biojava.bio.seq.db.biofetch that throw BioException | |
Sequence |
BioFetchSequenceDB.getSequence(java.lang.String id)
|
SequenceDBLite |
BioFetchSequenceDBProvider.getSequenceDB(java.util.Map config)
|
Uses of BioException in org.biojava.bio.seq.db.biosql |
Methods in org.biojava.bio.seq.db.biosql that throw BioException | |
void |
BioSQLSequenceDB.createDummySequence(java.lang.String id,
Alphabet alphabet,
int length)
|
void |
BioSQLSequenceDB.addSequence(Sequence seq)
|
Sequence |
BioSQLSequenceDB.getSequence(java.lang.String id)
|
void |
BioSQLSequenceDB.removeSequence(java.lang.String id)
|
SequenceDBLite |
BioSQLSequenceDBProvider.getSequenceDB(java.util.Map config)
|
Constructors in org.biojava.bio.seq.db.biosql that throw BioException | |
BioSQLSequenceDB(java.lang.String dbURL,
java.lang.String dbUser,
java.lang.String dbPass,
java.lang.String biodatabase,
boolean create)
Connect to a BioSQL database. |
Uses of BioException in org.biojava.bio.seq.db.flat |
Methods in org.biojava.bio.seq.db.flat that throw BioException | |
Sequence |
FlatSequenceDB.getSequence(java.lang.String id)
|
SequenceDBLite |
FlatSequenceDBProvider.getSequenceDB(java.util.Map config)
|
Constructors in org.biojava.bio.seq.db.flat that throw BioException | |
FlatSequenceDB(java.lang.String location,
java.lang.String dbName)
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Uses of BioException in org.biojava.bio.seq.distributed |
Methods in org.biojava.bio.seq.distributed that throw BioException | |
boolean |
GFFDataSource.hasSequence(java.lang.String id)
|
boolean |
GFFDataSource.hasFeatures(java.lang.String id)
|
FeatureHolder |
GFFDataSource.getFeatures(FeatureFilter ff)
|
FeatureHolder |
GFFDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
|
Sequence |
GFFDataSource.getSequence(java.lang.String id)
|
java.util.Set |
GFFDataSource.ids(boolean topLevel)
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boolean |
SequenceDBDataSource.hasSequence(java.lang.String id)
|
boolean |
SequenceDBDataSource.hasFeatures(java.lang.String id)
|
FeatureHolder |
SequenceDBDataSource.getFeatures(FeatureFilter ff)
|
FeatureHolder |
SequenceDBDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
|
Sequence |
SequenceDBDataSource.getSequence(java.lang.String id)
|
java.util.Set |
SequenceDBDataSource.ids(boolean topLevel)
|
boolean |
DistDataSource.hasSequence(java.lang.String id)
Find out if this DistDataSource provides the sequence information for a sequence ID. |
boolean |
DistDataSource.hasFeatures(java.lang.String id)
Find out if this DistDataSource can provide features on a sequence with a particular ID. |
FeatureHolder |
DistDataSource.getFeatures(FeatureFilter ff)
Get all features matching a FeatureFilter provided by this DistDataSource. |
FeatureHolder |
DistDataSource.getFeatures(java.lang.String id,
FeatureFilter ff,
boolean recurse)
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats. |
Sequence |
DistDataSource.getSequence(java.lang.String id)
Get a Sequence object for an ID. |
java.util.Set |
DistDataSource.ids(boolean topLevel)
Get the complete set of sequence IDs provided by this DistDataSource. |
Sequence |
DistributedSequenceDB.getSequence(java.lang.String id)
|
Uses of BioException in org.biojava.bio.seq.homol |
Methods in org.biojava.bio.seq.homol that throw BioException | |
void |
SimpleHomology.setAlignment(Alignment alignment)
setAlignment sets the alignment which describes
the homology. |
Uses of BioException in org.biojava.bio.seq.impl |
Methods in org.biojava.bio.seq.impl that throw BioException | |
Feature |
SimpleRemoteFeature.getRemoteFeature()
|
Feature |
SimpleRemoteFeature.DBResolver.resolve(RemoteFeature rFeat)
|
Feature |
SimpleSequence.realizeFeature(FeatureHolder parent,
Feature.Template template)
|
Feature |
SimpleSequence.createFeature(Feature.Template template)
|
Feature |
SimpleSequence.createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated. Please use new 1-arg createFeature instead. |
Feature |
SimpleFeature.realizeFeature(FeatureHolder fh,
Feature.Template templ)
|
Feature |
SimpleFeature.createFeature(Feature.Template temp)
|
Feature |
RevCompSequence.createFeature(Feature.Template ft)
createFeature() will call createFeature() on the underlying Sequence. |
Uses of BioException in org.biojava.bio.seq.io |
Subclasses of BioException in org.biojava.bio.seq.io | |
class |
ParseException
ParseException should be thrown to indicate that there was a problem with parsing sequence information. |
Methods in org.biojava.bio.seq.io that throw BioException | |
Sequence |
SequenceBuilder.makeSequence()
Return the Sequence object which has been constructed by this builder. |
Sequence |
StreamReader.nextSequence()
Pull the next sequence out of the stream. |
Sequence |
SequenceBuilderFilter.makeSequence()
|
void |
FastaAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
Writes out the alignment to an FASTA file. |
void |
FastaAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align)
|
void |
FastaAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align)
|
void |
FeatureTableParser.startFeature(java.lang.String type)
|
void |
FeatureTableParser.featureData(java.lang.String line)
|
void |
FeatureTableParser.endFeature()
|
SymbolList |
ChunkedSymbolListFactory.make(SymbolReader sr)
Method to create a Sequence with a SymbolReader. |
boolean |
SequenceFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
void |
MSFAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
|
void |
MSFAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align)
|
void |
MSFAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align)
|
ComponentFeature |
SimpleAssemblyBuilder.addComponentSequence(ComponentFeature.Template cft)
|
Feature.Template |
EmblLikeLocationParser.parseLocation(java.lang.String location,
Feature.Template theTemplate)
parseLocation creates a Location from
the String and returns a stranded location. |
static SequenceDB |
SeqIOTools.readFasta(java.io.InputStream seqFile,
Alphabet alpha)
Create a sequence database from a fasta file provided as an input stream. |
static void |
SeqIOTools.writeSwissprot(java.io.OutputStream os,
SequenceIterator in)
Writes a stream of Sequences to an OutputStream in SwissProt format. |
static void |
SeqIOTools.writeSwissprot(java.io.OutputStream os,
Sequence seq)
Writes a single Sequence to an OutputStream in SwissProt format. |
static void |
SeqIOTools.writeGenpept(java.io.OutputStream os,
SequenceIterator in)
Writes a stream of Sequences to an OutputStream in Genpept format. |
static void |
SeqIOTools.writeGenpept(java.io.OutputStream os,
Sequence seq)
Writes a single Sequence to an OutputStream in Genpept format. |
static SequenceFormat |
SeqIOTools.getSequenceFormat(int identifier)
getSequenceFormat accepts a value which represents
a sequence format and returns the relevant
SequenceFormat object. |
static SequenceBuilderFactory |
SeqIOTools.getBuilderFactory(int identifier)
getBuilderFactory accepts a value which represents
a sequence format and returns the relevant
SequenceBuilderFactory object. |
static FiniteAlphabet |
SeqIOTools.getAlphabet(int identifier)
getAlphabet accepts a value which represents a
sequence format and returns the relevant
FiniteAlphabet object. |
static SequenceBuilderFactory |
SeqIOTools.formatToFactory(SequenceFormat format,
Alphabet alpha)
Deprecated. as this essentially duplicates the operation available in the method identifyBuilderFactory . |
static java.lang.Object |
SeqIOTools.fileToBiojava(java.lang.String formatName,
java.lang.String alphabetName,
java.io.BufferedReader br)
Reads a file with the specified format and alphabet |
static java.lang.Object |
SeqIOTools.fileToBiojava(int fileType,
java.io.BufferedReader br)
Reads a file and returns the corresponding Biojava object. |
static void |
SeqIOTools.biojavaToFile(java.lang.String formatName,
java.lang.String alphabetName,
java.io.OutputStream os,
java.lang.Object biojava)
Writes a Biojava SequenceIterator ,
SequenceDB , Sequence or Aligment
to an OutputStream |
static void |
SeqIOTools.biojavaToFile(int fileType,
java.io.OutputStream os,
java.lang.Object biojava)
Converts a Biojava object to the given filetype. |
Constructors in org.biojava.bio.seq.io that throw BioException | |
CrossProductTokenization(Alphabet alpha)
|
Uses of BioException in org.biojava.bio.seq.projection |
Methods in org.biojava.bio.seq.projection that throw BioException | |
Feature |
ProjectedFeature.createFeature(Feature.Template temp)
|
Feature |
ProjectionContext.createFeature(Feature f,
Feature.Template templ)
Delegate for createFeature |
Uses of BioException in org.biojava.bio.seq.ragbag |
Methods in org.biojava.bio.seq.ragbag that throw BioException | |
org.biojava.bio.seq.ragbag.RagbagFileParser |
RagbagFileParserFactory.getParser(java.io.File inputFile)
Return a RagbagFileParser for given file |
Constructors in org.biojava.bio.seq.ragbag that throw BioException | |
RagbagAssembly(java.lang.String name,
java.lang.String urn,
java.io.File thisDir,
RagbagSequenceFactory seqFactory,
RagbagComponentDirectory compDir)
|
Uses of BioException in org.biojava.bio.symbol |
Subclasses of BioException in org.biojava.bio.symbol | |
class |
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
class |
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
Methods in org.biojava.bio.symbol that throw BioException | |
SymbolTokenization |
AbstractAlphabet.getTokenization(java.lang.String name)
|
static void |
AlphabetManager.loadAlphabets(org.xml.sax.InputSource is)
Load additional Alphabets, defined in XML format, into the AlphabetManager's registry. |
static AlphabetIndex |
AlphabetManager.getAlphabetIndex(Symbol[] syms)
Get an indexer for an array of symbols. |
static MergeLocation |
MergeLocation.mergeLocations(java.util.List componentLocations)
Static Factory method for getting an instance of a MergeLocation |
static MergeLocation |
MergeLocation.mergeLocations(Location locA,
Location locB)
|
SymbolTokenization |
Alphabet.getTokenization(java.lang.String name)
Get a SymbolTokenization by name. |
SymbolTokenization |
DoubleAlphabet.SubDoubleAlphabet.getTokenization(java.lang.String name)
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Constructors in org.biojava.bio.symbol that throw BioException | |
PackedDnaSymbolList(SymbolList symList)
constructor taking another symbol list. |
|
PackedDnaSymbolList(int length,
byte[] byteArray)
constructor taking a byte array previously created by another PackedDnaSymbolList object. |
Uses of BioException in org.biojava.bio.taxa |
Subclasses of BioException in org.biojava.bio.taxa | |
class |
CircularReferenceException
|
Uses of BioException in org.biojava.directory |
Methods in org.biojava.directory that throw BioException | |
SequenceDBLite |
SequenceDBProvider.getSequenceDB(java.util.Map config)
Get a sequence database. |
SequenceDBLite |
Registry.getDatabase(java.lang.String dbName)
getDatabase retrieves a database instance known by
a name String . |
Uses of BioException in org.biojava.utils.math |
Methods in org.biojava.utils.math that throw BioException | |
static double |
BinarySearch.solve(double min,
double max,
double tolerance,
ComputeObject obj)
method that will attempt solving the equation. |
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