Package | Description |
---|---|
org.biojava.bio.program.phred |
Parser for Phred output
|
org.biojava.bio.program.ssaha |
SSAHA sequence searching API.
|
org.biojava.bio.program.xff |
Event-driven parsing system for the Extensible Feature Format (XFF).
|
org.biojava.bio.seq.io |
Classes and interfaces for processing and producing flat-file representations
of sequences.
|
org.biojava.bio.seq.io.agave |
Classes for converting between AGAVE XML and BioJava objects.
|
org.biojava.bio.seq.io.game |
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
|
org.biojava.bio.seq.io.game12 |
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
|
org.biojava.bio.symbol |
Representation of the Symbols that make up a sequence, and locations within
them.
|
org.biojavax.bio.seq.io |
Classes to support the I/O of RichSequence and
Bioentry objects.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PhredFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol) |
Modifier and Type | Method and Description |
---|---|
void |
SequenceStreamer.streamNext(SeqIOListener listener) |
void |
SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener) |
void |
SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener) |
Modifier and Type | Method and Description |
---|---|
SeqIOListener |
XFFFeatureSetHandler.getFeatureListener()
Return the object which receives startFeature/endFeature notifications.
|
Modifier and Type | Method and Description |
---|---|
void |
XFFFeatureSetHandler.setFeatureListener(SeqIOListener siol)
Set the object which receives startFeature/endFeature notifications.
|
Modifier and Type | Interface and Description |
---|---|
interface |
SeqFileFormer
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
interface |
SequenceBuilder
Interface for objects which accumulate state via SeqIOListener,
then construct a Sequence object.
|
Modifier and Type | Class and Description |
---|---|
class |
EmblFileFormer
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
EmblProcessor
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
FastaDescriptionLineParser
Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
|
class |
GenbankFileFormer
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
GenbankProcessor
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
OrganismParser
Deprecated.
Use org.biojavax.bio.taxa framework instead
|
class |
ProteinRefSeqFileFormer
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
ProteinRefSeqProcessor
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
SeqIOAdapter
Adapter class for SeqIOListener that has empty methods.
|
class |
SeqIOFilter
Base-class for listeners that pass filtered events onto another listener.
|
class |
SequenceBuilderBase
Basic SequenceBuilder implementation which accumulates all
notified information.
|
class |
SequenceBuilderFilter
Base-class for builders that pass filtered events onto another builder.
|
class |
SequenceDBSequenceBuilder
This SequenceBuilder has a variety of modes of operation.
|
class |
SimpleAssemblyBuilder
Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleAssembly.
|
class |
SimpleSequenceBuilder
Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleSequence.
|
class |
SmartSequenceBuilder
Basic SequenceBuilder implementation which accumulates all
notified information and chooses a sequence implementation
suited to the size of the sequence.
|
class |
SwissprotFileFormer
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
SwissprotProcessor
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
Modifier and Type | Method and Description |
---|---|
SeqIOListener |
SeqIOFilter.getDelegate()
Retrieve the delegate that is wrapped.
|
Modifier and Type | Method and Description |
---|---|
void |
SeqIOEventEmitter.getSeqIOEvents(Sequence seq,
SeqIOListener listener)
Deprecated.
getSeqIOEvents scans a Sequence
object and sends events describing its data to the
SeqIOListener . |
StreamParser |
WordTokenization.parseStream(SeqIOListener siol) |
StreamParser |
SymbolTokenization.parseStream(SeqIOListener listener)
Return an object which can parse an arbitrary character stream into
symbols.
|
StreamParser |
CharacterTokenization.parseStream(SeqIOListener listener) |
StreamParser |
AlternateTokenization.parseStream(SeqIOListener listener)
Will throw an exception.
|
boolean |
SequenceFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
GenbankXmlFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated.
|
boolean |
GenbankFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated.
Reads a sequence from the specified reader using the Symbol
parser and Sequence Factory provided.
|
boolean |
GAMEFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
this version only reads annotations (no symbols)
|
boolean |
FastaFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
Deprecated.
Reads information from a flatfile to a
SeqIOListener
using a SymbolTokenizer to convert sequence strings
to Symbol objects. |
boolean |
EmblLikeFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated.
|
Constructor and Description |
---|
SeqIOFilter(SeqIOListener delegate)
Create a new SeqIOFilter that will forward events on to another listener.
|
Modifier and Type | Field and Description |
---|---|
protected SeqIOListener |
StAXPropertyHandler.featureListener |
protected SeqIOListener |
StAXFeatureHandler.featureListener |
Modifier and Type | Method and Description |
---|---|
SeqIOListener |
StAXFeatureHandler.getFeatureListener()
Return current feature listener
|
Modifier and Type | Method and Description |
---|---|
void |
StAXFeatureHandler.setFeatureListener(SeqIOListener siol) |
Modifier and Type | Field and Description |
---|---|
protected SeqIOListener |
StAXPropertyHandler.featureListener |
protected SeqIOListener |
StAXFeatureHandler.featureListener |
Modifier and Type | Method and Description |
---|---|
SeqIOListener |
StAXFeatureHandler.getFeatureListener()
Return current feature listener
|
Modifier and Type | Method and Description |
---|---|
void |
StAXFeatureHandler.setFeatureListener(SeqIOListener siol) |
Constructor and Description |
---|
GAMEHandler(SeqIOListener listener)
Constructor for the GAMEHandler object
|
Modifier and Type | Method and Description |
---|---|
StreamParser |
SoftMaskedAlphabet.CaseSensitiveTokenization.parseStream(SeqIOListener l)
The current implementation only supports character parsing.
|
Modifier and Type | Interface and Description |
---|---|
interface |
RichSeqIOListener
An interface for classes that listen to BioEntry or
RichSequence I/O streams.
|
interface |
RichSequenceBuilder
An interface for objects that can build RichSequences.
|
Modifier and Type | Class and Description |
---|---|
class |
DebuggingRichSeqIOListener
This is purely for debugging purposes.
|
class |
RichSeqIOAdapter
This class implements all methods of RichSeqIOListener and takes no action.
|
class |
SimpleRichSequenceBuilder
Constructs BioEntry objects by listening to events.
|
Modifier and Type | Method and Description |
---|---|
boolean |
UniProtXMLFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
UniProtFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
INSDseqFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
GenbankFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
FastaFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
EMBLxmlFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
boolean |
EMBLFormat.readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
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