## Uses of Class
org.biojava.bio.seq.io.ParseException

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)`