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 EmblProcessor.endSequence()
           
 void EmblProcessor.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)
           
 boolean FastaFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)
           
 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 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 GenbankProcessor.endSequence()
           
 void GenbankProcessor.addSequenceProperty(java.lang.Object key, java.lang.Object value)
           
 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)
           
 void SequenceBuilderBase.addFeatureProperty(java.lang.Object key, java.lang.Object value)
          Add an annotation-bundle entry to the feature.
 void SwissprotProcessor.endSequence()
           
 void SwissprotProcessor.addSequenceProperty(java.lang.Object key, java.lang.Object value)
           
 void OrganismParser.addSequenceProperty(java.lang.Object sciNameKey, java.lang.Object value)
           
 void OrganismParser.endSequence()
           
 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
 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 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)
           
 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 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.
 

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)