java.lang.Object

org.biojava.bio.seq.io.SeqIOFilter

All Implemented Interfaces:: SeqIOListener

public class SeqIOFilter extends Object implements SeqIOListener

Base-class for listeners that pass filtered events onto another listener.

Since:

1.1

Author:

Matthew Pocock

See Also:

RichSeqIOAdapter

Constructor Summary

Constructors

Constructor

Description

SeqIOFilter(SeqIOListener delegate)

Create a new SeqIOFilter that will forward events on to another listener.
Method Summary

Modifier and Type

Method

Description

void

addFeatureProperty(Object key, Object value)

Notify the listener of a feature property.

void

addSequenceProperty(Object key, Object value)

Notify the listener of a sequence-wide property.

void

addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)

Notify the listener of symbol data.

void

endFeature()

Mark the end of data associated with one specific feature.

void

endSequence()

Notify the listener that processing of the sequence is complete.

SeqIOListener

getDelegate()

Retrieve the delegate that is wrapped.

void

setName(String name)

Notify the listener that the current sequence is generally known by a particular name.

void

setURI(String uri)

Notify the listener of a URI identifying the current sequence.

void

startFeature(Feature.Template templ)

Notify the listener that a new feature object is starting.

void

startSequence()

Start the processing of a sequence.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SeqIOFilter
  
  public SeqIOFilter(SeqIOListener delegate)
  
  Create a new SeqIOFilter that will forward events on to another listener.
  
  Parameters:
  
  delegate - the SeqIOListener to wrap
Method Details
- getDelegate
  
  public SeqIOListener getDelegate()
  
  Retrieve the delegate that is wrapped.
  
  Returns:
  
  the SeqIOListener delegate
- startSequence
  
  public void startSequence() throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.
  
  Specified by:
  
  startSequence in interface SeqIOListener
  
  Throws:
  
  ParseException
- endSequence
  
  public void endSequence() throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener that processing of the sequence is complete.
  
  Specified by:
  
  endSequence in interface SeqIOListener
  
  Throws:
  
  ParseException
- setName
  
  public void setName(String name) throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener that the current sequence is generally known by a particular name.
  
  Specified by:
  
  setName in interface SeqIOListener
  
  Parameters:
  
  name - the String that should be returned by getName for the sequence being parsed
  
  Throws:
  
  ParseException
- setURI
  
  public void setURI(String uri) throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener of a URI identifying the current sequence.
  
  Specified by:
  
  setURI in interface SeqIOListener
  
  Throws:
  
  ParseException
- addSymbols
  
  public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception
  
  Specified by:
  
  addSymbols in interface SeqIOListener
  
  Parameters:
  
  alpha - The alphabet of the symbol data
  
  syms - An array containing symbols
  
  start - The start offset of valid data within the array
  
  length - The number of valid symbols in the array
  
  Throws:
  
  IllegalAlphabetException - if we can't cope with this alphabet.
- addSequenceProperty
  
  public void addSequenceProperty(Object key, Object value) throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.
  
  Specified by:
  
  addSequenceProperty in interface SeqIOListener
  
  Throws:
  
  ParseException
- startFeature
  
  public void startFeature(Feature.Template templ) throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.
  
  Specified by:
  
  startFeature in interface SeqIOListener
  
  Throws:
  
  ParseException
- endFeature
  
  public void endFeature() throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Mark the end of data associated with one specific feature.
  
  Specified by:
  
  endFeature in interface SeqIOListener
  
  Throws:
  
  ParseException
- addFeatureProperty
  
  public void addFeatureProperty(Object key, Object value) throws ParseException
  
  Description copied from interface: SeqIOListener
  
  Notify the listener of a feature property.
  
  Specified by:
  
  addFeatureProperty in interface SeqIOListener
  
  Throws:
  
  ParseException

Class SeqIOFilter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SeqIOFilter

Method Details

getDelegate

startSequence

endSequence

setName

setURI

addSymbols

addSequenceProperty

startFeature

endFeature

addFeatureProperty