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Packages that use ParseException | |
org.biojava.bio.program.phred | Parser for Phred output |
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.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 ParseException in org.biojava.bio.program.phred |
Methods in org.biojava.bio.program.phred that throw ParseException | |
boolean |
PhredFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
|
Uses of ParseException in org.biojava.bio.program.xff |
Methods in org.biojava.bio.program.xff that throw ParseException | |
protected void |
FeatureHandler.fireStartFeature()
Fire the startFeature event. |
protected void |
FeatureHandler.fireEndFeature()
Fire the endFeature event. |
protected void |
FeatureHandler.setFeatureProperty(java.lang.Object key,
java.lang.Object value)
Set a property. |
Uses of ParseException in org.biojava.bio.seq.io |
Methods in org.biojava.bio.seq.io that throw ParseException | |
void |
SequenceBuilderBase.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
Add an annotation-bundle entry to the feature. |
void |
ProteinRefSeqFileFormer.startFeature(Feature.Template templ)
|
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. |
void |
SequenceBuilderFilter.startSequence()
|
void |
SequenceBuilderFilter.endSequence()
|
void |
SequenceBuilderFilter.setName(java.lang.String name)
|
void |
SequenceBuilderFilter.setURI(java.lang.String uri)
|
void |
SequenceBuilderFilter.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SequenceBuilderFilter.startFeature(Feature.Template templ)
|
void |
SequenceBuilderFilter.endFeature()
|
void |
SequenceBuilderFilter.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
|
void |
FastaDescriptionLineParser.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SeqIOListener.startSequence()
Start the processing of a sequence. |
void |
SeqIOListener.endSequence()
Notify the listener that processing of the sequence is complete. |
void |
SeqIOListener.setName(java.lang.String name)
Notify the listener that the current sequence is generally known by a particular name. |
void |
SeqIOListener.setURI(java.lang.String uri)
Notify the listener of a URI identifying the current sequence. |
void |
SeqIOListener.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
Notify the listener of a sequence-wide property. |
void |
SeqIOListener.startFeature(Feature.Template templ)
Notify the listener that a new feature object is starting. |
void |
SeqIOListener.endFeature()
Mark the end of data associated with one specific feature. |
void |
SeqIOListener.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
Notify the listener of a feature property. |
void |
EmblProcessor.endSequence()
|
void |
EmblProcessor.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SwissprotFileFormer.startSequence()
Start the processing of a sequence. |
void |
SwissprotFileFormer.endSequence()
Notify the listener that processing of the sequence is complete. |
void |
SwissprotFileFormer.setName(java.lang.String theName)
The name is printed out as part of the identifier line. |
void |
SwissprotFileFormer.setURI(java.lang.String theURI)
Null implementation. |
void |
SwissprotFileFormer.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
Notify the listener of a sequence-wide property. |
void |
SwissprotFileFormer.startFeature(Feature.Template templ)
Null implementation. |
void |
SwissprotFileFormer.endFeature()
Null implementation. |
void |
SwissprotFileFormer.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
Null implementation |
void |
SeqIOAdapter.startSequence()
|
void |
SeqIOAdapter.endSequence()
|
void |
SeqIOAdapter.setName(java.lang.String name)
|
void |
SeqIOAdapter.setURI(java.lang.String uri)
|
void |
SeqIOAdapter.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SeqIOAdapter.startFeature(Feature.Template templ)
|
void |
SeqIOAdapter.endFeature()
|
void |
SeqIOAdapter.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SwissprotProcessor.endSequence()
|
void |
SwissprotProcessor.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SeqIOFilter.startSequence()
|
void |
SeqIOFilter.endSequence()
|
void |
SeqIOFilter.setName(java.lang.String name)
|
void |
SeqIOFilter.setURI(java.lang.String uri)
|
void |
SeqIOFilter.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
SeqIOFilter.startFeature(Feature.Template templ)
|
void |
SeqIOFilter.endFeature()
|
void |
SeqIOFilter.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
|
void |
GenbankProcessor.endSequence()
|
void |
GenbankProcessor.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
OrganismParser.addSequenceProperty(java.lang.Object sciNameKey,
java.lang.Object value)
|
void |
OrganismParser.endSequence()
|
boolean |
FastaFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
|
void |
EmblFileFormer.setName(java.lang.String id)
|
void |
EmblFileFormer.startSequence()
|
void |
EmblFileFormer.endSequence()
|
void |
EmblFileFormer.setURI(java.lang.String uri)
|
void |
EmblFileFormer.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
EmblFileFormer.startFeature(Feature.Template templ)
|
void |
EmblFileFormer.endFeature()
|
void |
EmblFileFormer.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
|
boolean |
EmblLikeFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
|
protected void |
EmblLikeFormat.processSequenceLine(java.lang.String line,
StreamParser parser)
Dispatch symbol data from SQ-block line of an EMBL-like file. |
void |
GenbankFileFormer.setName(java.lang.String id)
|
void |
GenbankFileFormer.startSequence()
|
void |
GenbankFileFormer.endSequence()
|
void |
GenbankFileFormer.setURI(java.lang.String uri)
|
void |
GenbankFileFormer.addSequenceProperty(java.lang.Object key,
java.lang.Object value)
|
void |
GenbankFileFormer.startFeature(Feature.Template templ)
|
void |
GenbankFileFormer.endFeature()
|
void |
GenbankFileFormer.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
|
Uses of ParseException in org.biojava.bio.seq.io.agave |
Methods in org.biojava.bio.seq.io.agave that throw ParseException | |
protected java.util.ListIterator |
StAXPropertyHandler.getHandlerStackIterator()
get iterator for current stack starting at the position below mine. |
Uses of ParseException in org.biojava.bio.seq.io.game |
Methods in org.biojava.bio.seq.io.game that throw ParseException | |
protected java.util.ListIterator |
StAXPropertyHandler.getHandlerStackIterator()
get iterator for current stack starting at the position below mine. |
Uses of ParseException in org.biojava.bio.seq.ragbag |
Methods in org.biojava.bio.seq.ragbag that throw ParseException | |
void |
RagbagIdleSequenceBuilder.addFeatureProperty(java.lang.Object key,
java.lang.Object value)
|
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