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Packages that use SeqIOListener | |
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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. |
Uses of SeqIOListener in org.biojava.bio.program.phred |
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Methods in org.biojava.bio.program.phred with parameters of type SeqIOListener | |
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boolean |
PhredFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
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Uses of SeqIOListener in org.biojava.bio.program.ssaha |
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Methods in org.biojava.bio.program.ssaha with parameters of type SeqIOListener | |
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void |
SequenceStreamer.streamNext(SeqIOListener listener)
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void |
SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)
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void |
SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)
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Uses of SeqIOListener in org.biojava.bio.program.xff |
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Methods in org.biojava.bio.program.xff that return SeqIOListener | |
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SeqIOListener |
XFFFeatureSetHandler.getFeatureListener()
Return the object which receives startFeature/endFeature notifications. |
Methods in org.biojava.bio.program.xff with parameters of type SeqIOListener | |
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void |
XFFFeatureSetHandler.setFeatureListener(SeqIOListener siol)
Set the object which receives startFeature/endFeature notifications. |
Uses of SeqIOListener in org.biojava.bio.seq.io |
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Subinterfaces of SeqIOListener in org.biojava.bio.seq.io | |
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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. |
Classes in org.biojava.bio.seq.io that implement SeqIOListener | |
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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 |
Methods in org.biojava.bio.seq.io that return SeqIOListener | |
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SeqIOListener |
SeqIOFilter.getDelegate()
Retrieve the delegate that is wrapped. |
Methods in org.biojava.bio.seq.io with parameters of type SeqIOListener | |
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void |
SeqIOEventEmitter.getSeqIOEvents(Sequence seq,
SeqIOListener listener)
Deprecated. getSeqIOEvents scans a Sequence
object and sends events describing its data to the
SeqIOListener . |
StreamParser |
CharacterTokenization.parseStream(SeqIOListener listener)
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StreamParser |
WordTokenization.parseStream(SeqIOListener siol)
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StreamParser |
SymbolTokenization.parseStream(SeqIOListener listener)
Return an object which can parse an arbitrary character stream into symbols. |
StreamParser |
AlternateTokenization.parseStream(SeqIOListener listener)
Will throw an exception. |
boolean |
FastaFormat.readSequence(java.io.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 |
SequenceFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
GenbankXmlFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated. |
boolean |
GenbankFormat.readSequence(java.io.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(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
this version only reads annotations (no symbols) |
boolean |
EmblLikeFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated. |
Constructors in org.biojava.bio.seq.io with parameters of type SeqIOListener | |
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SeqIOFilter(SeqIOListener delegate)
Create a new SeqIOFilter that will forward events on to another listener. |
Uses of SeqIOListener in org.biojava.bio.seq.io.agave |
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Fields in org.biojava.bio.seq.io.agave declared as SeqIOListener | |
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protected SeqIOListener |
StAXPropertyHandler.featureListener
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protected SeqIOListener |
StAXFeatureHandler.featureListener
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Methods in org.biojava.bio.seq.io.agave that return SeqIOListener | |
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SeqIOListener |
StAXFeatureHandler.getFeatureListener()
Return current feature listener |
Methods in org.biojava.bio.seq.io.agave with parameters of type SeqIOListener | |
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void |
StAXFeatureHandler.setFeatureListener(SeqIOListener siol)
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Uses of SeqIOListener in org.biojava.bio.seq.io.game |
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Fields in org.biojava.bio.seq.io.game declared as SeqIOListener | |
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protected SeqIOListener |
StAXPropertyHandler.featureListener
|
protected SeqIOListener |
StAXFeatureHandler.featureListener
|
Methods in org.biojava.bio.seq.io.game that return SeqIOListener | |
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SeqIOListener |
StAXFeatureHandler.getFeatureListener()
Return current feature listener |
Methods in org.biojava.bio.seq.io.game with parameters of type SeqIOListener | |
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void |
StAXFeatureHandler.setFeatureListener(SeqIOListener siol)
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Uses of SeqIOListener in org.biojava.bio.seq.io.game12 |
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Constructors in org.biojava.bio.seq.io.game12 with parameters of type SeqIOListener | |
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GAMEHandler(SeqIOListener listener)
Constructor for the GAMEHandler object |
Uses of SeqIOListener in org.biojava.bio.symbol |
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Methods in org.biojava.bio.symbol with parameters of type SeqIOListener | |
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StreamParser |
SoftMaskedAlphabet.CaseSensitiveTokenization.parseStream(SeqIOListener l)
The current implementation only supports character parsing. |
Uses of SeqIOListener in org.biojavax.bio.seq.io |
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Subinterfaces of SeqIOListener in org.biojavax.bio.seq.io | |
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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. |
Classes in org.biojavax.bio.seq.io that implement SeqIOListener | |
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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. |
Methods in org.biojavax.bio.seq.io with parameters of type SeqIOListener | |
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boolean |
EMBLxmlFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
FastaFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
UniProtXMLFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
EMBLFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
UniProtFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
GenbankFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
INSDseqFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
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