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Packages that use SeqIOListener | |
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.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
Uses of SeqIOListener in org.biojava.bio.program.phred |
Methods in org.biojava.bio.program.phred with parameters of type SeqIOListener | |
boolean |
PhredFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
|
Uses of SeqIOListener in org.biojava.bio.program.ssaha |
Methods in org.biojava.bio.program.ssaha with parameters of type SeqIOListener | |
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 |
Methods in org.biojava.bio.program.xff that return SeqIOListener | |
SeqIOListener |
XFFFeatureSetHandler.getFeatureListener()
Return the object which receives startFeature/endFeature notifications. |
Methods in org.biojava.bio.program.xff with parameters of type SeqIOListener | |
void |
XFFFeatureSetHandler.setFeatureListener(SeqIOListener siol)
Set the object which receives startFeature/endFeature notifications. |
Uses of SeqIOListener in org.biojava.bio.seq.io |
Subinterfaces of SeqIOListener in org.biojava.bio.seq.io | |
interface |
SeqFileFormer
Objects implementing the SeqFileFormer interface are
responsible for the detailed formatting of sequence data prior to
writing to a PrintStream . |
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 | |
class |
EmblFileFormer
EmblFileFormer performs the detailed formatting of
EMBL entries for writing to a PrintStream . |
class |
EmblProcessor
Simple filter which handles attribute lines from an EMBL file. |
class |
FastaDescriptionLineParser
Simple filter which performs a default extraction of data from the description lines of FASTA files. |
class |
GenbankFileFormer
GenbankFileFormer performs the detailed formatting of
Genbank entries for writing to a PrintStream . |
class |
GenbankProcessor
Simple filter which handles attribute lines from a Genbank file |
class |
OrganismParser
A parser that is able to generate Taxon entries for sequence builder event streams. |
class |
ProteinRefSeqFileFormer
This class performs the detailed formatting of refseq protein entries. |
class |
ProteinRefSeqProcessor
Class description |
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
Formats a sequence into Swissprot/TrEMBL format. |
class |
SwissprotProcessor
Simple filter which handles attribute lines from an Swissprot entry. |
Methods in org.biojava.bio.seq.io that return SeqIOListener | |
SeqIOListener |
SeqIOFilter.getDelegate()
Retrieve the delegate that is wrapped. |
Methods in org.biojava.bio.seq.io with parameters of type SeqIOListener | |
boolean |
GenbankFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. |
StreamParser |
CharacterTokenization.parseStream(SeqIOListener listener)
|
StreamParser |
SymbolTokenization.parseStream(SeqIOListener listener)
Return an object which can parse an arbitrary character stream into symbols. |
StreamParser |
WordTokenization.parseStream(SeqIOListener siol)
|
boolean |
SequenceFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
GAMEFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
this version only reads annotations (no symbols) |
boolean |
FastaFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
|
boolean |
EmblLikeFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
|
Constructors in org.biojava.bio.seq.io with parameters of type SeqIOListener | |
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 |
Fields in org.biojava.bio.seq.io.agave declared as SeqIOListener | |
protected SeqIOListener |
StAXPropertyHandler.featureListener
|
protected SeqIOListener |
StAXFeatureHandler.featureListener
|
Methods in org.biojava.bio.seq.io.agave that return SeqIOListener | |
SeqIOListener |
StAXFeatureHandler.getFeatureListener()
Return current feature listener |
Methods in org.biojava.bio.seq.io.agave with parameters of type SeqIOListener | |
void |
StAXFeatureHandler.setFeatureListener(SeqIOListener siol)
|
Uses of SeqIOListener in org.biojava.bio.seq.io.game |
Fields in org.biojava.bio.seq.io.game declared as SeqIOListener | |
protected SeqIOListener |
StAXPropertyHandler.featureListener
|
protected SeqIOListener |
StAXFeatureHandler.featureListener
|
Methods in org.biojava.bio.seq.io.game that return SeqIOListener | |
SeqIOListener |
StAXFeatureHandler.getFeatureListener()
Return current feature listener |
Methods in org.biojava.bio.seq.io.game with parameters of type SeqIOListener | |
void |
StAXFeatureHandler.setFeatureListener(SeqIOListener siol)
|
Uses of SeqIOListener in org.biojava.bio.seq.io.game12 |
Constructors in org.biojava.bio.seq.io.game12 with parameters of type SeqIOListener | |
GAMEHandler(SeqIOListener listener)
Constructor for the GAMEHandler object |
Uses of SeqIOListener in org.biojava.bio.seq.ragbag |
Classes in org.biojava.bio.seq.ragbag that implement SeqIOListener | |
class |
RagbagIdleSequenceBuilder
A breakfast cereal of a SequenceBuilder, jes' sits there soakin' up all those events and doin' absolutely nuffin'. |
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